From ee13d63234571c1505d2f054045c2b8a7c6f3b7f Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Wed, 29 Oct 2025 11:33:41 -0600 Subject: [PATCH 01/81] adding USDA yaml schemas to test LinkML --- schemas/common/geography.yaml | 61 +++++++++++ schemas/common/locations_address.yml | 65 ++++++++++++ schemas/usda/census_survey.yaml | 153 +++++++++++++++++++++++++++ 3 files changed, 279 insertions(+) create mode 100644 schemas/common/geography.yaml create mode 100644 schemas/common/locations_address.yml create mode 100644 schemas/usda/census_survey.yaml diff --git a/schemas/common/geography.yaml b/schemas/common/geography.yaml new file mode 100644 index 00000000..41c9cf1c --- /dev/null +++ b/schemas/common/geography.yaml @@ -0,0 +1,61 @@ +id: geography +name: Geography +description: > + Common geographic identifiers used across multiple datasets. Includes states, + counties, FIPS codes, and optional regions. + +prefixes: + linkml: https://w3id.org/linkml/ + usda: https://schema.myorg.org/usda/ + agrovoc: https://agrovoc.fao.org/agrontology/en/page/ + +default_prefix: usda +imports: + - linkml:types + +classes: + Geography: + description: Reference table for U.S. geographic identifiers. + slots: + - state_name + - state_fips + - county_name + - county_fips + - geoid + - region_name + - agg_level_desc + +slots: + state_name: + range: string + description: U.S. state name. + exact_mappings: [] # TODO: map to AGROVOC/state concept + + state_fips: + range: string + pattern: "^[0-9]{2}$" + description: Two-digit FIPS code for the state. + + county_name: + range: string + description: U.S. county name. + exact_mappings: [] # TODO: map to AGROVOC/county concept + + county_fips: + range: string + pattern: "^[0-9]{3}$" + description: Three-digit county FIPS code. + + geoid: + range: string + pattern: "^[0-9]{5}$" + description: Combined state + county FIPS (e.g., 06019). + + region_name: + range: string + description: + Optional higher-level region grouping (e.g., San Joaquin Valley). + + agg_level_desc: + range: string + description: Aggregation level (e.g., COUNTY, STATE, NATIONAL). diff --git a/schemas/common/locations_address.yml b/schemas/common/locations_address.yml new file mode 100644 index 00000000..d36b769c --- /dev/null +++ b/schemas/common/locations_address.yml @@ -0,0 +1,65 @@ +id: location +name: Location +description: > + Specific address or farm location. Can be linked to a Geography row + (county-level). + +prefixes: + linkml: https://w3id.org/linkml/ + usda: https://schema.myorg.org/usda/ + agrovoc: https://agrovoc.fao.org/agrontology/en/page/ + +default_prefix: usda + +imports: + - ../common/geography.yaml + - linkml:types + +classes: + Location: + description: > + Represents a specific address or field location. References a parent + Geography (county-level). + slots: + - location_id + - geography # FK to Geography + - address_line1 + - address_line2 + - city + - zip + - lat + - lon + +slots: + location_id: + range: integer + description: Primary key for Location. + + geography: + range: Geography + description: Link to parent geography (county-level). + + address_line1: + range: string + description: Street address line 1. + + address_line2: + range: string + description: Street address line 2 (optional). + + city: + range: string + description: City name. + + zip: + range: string + pattern: "^[0-9]{5}$" + description: 5-digit ZIP code. + + lat: + range: float + description: Latitude in decimal degrees. + + lon: + range: float + description: Longitude in decimal degrees. diff --git a/schemas/usda/census_survey.yaml b/schemas/usda/census_survey.yaml new file mode 100644 index 00000000..9d91585a --- /dev/null +++ b/schemas/usda/census_survey.yaml @@ -0,0 +1,153 @@ +id: usda_data +name: USDA_Data +description: > + Schema for USDA Census and Survey data records accessed via the NASS Quick + Stats API, focusing on county-level data for key California crops. + +prefixes: + linkml: https://w3id.org/linkml/ + usda: https://schema.myorg.org/usda/ + agrovoc: https://agrovoc.fao.org/agrontology/en/page/ + ucum: http://unitsofmeasure.org/ucum.html + +default_prefix: usda +imports: + - linkml:types + - ../common/geography.yaml + +classes: + USDARecord: + description: Base class for USDA agricultural data records. + slots: + - year + - geography + - crop + - variable + - unit + - value + - bearing_status + - class_desc + - domain_desc + - source + - notes + slot_usage: + geography: + range: Geography + crop: + range: CropEnum + variable: + range: VariableEnum + unit: + range: UnitEnum + bearing_status: + range: BearingStatusEnum + + CensusRecord: + is_a: USDARecord + description: A USDA Census of Agriculture record (every 5 years). + + SurveyRecord: + is_a: USDARecord + description: A USDA Survey record (annual, seasonal, or periodic). + slots: + - period_desc + - freq_desc + - program_desc + +slots: + year: + range: integer + required: true + description: Census or survey year. + + geography: + range: Geography + description: Geographic information (state, county, FIPS). + + agg_level_desc: + range: string + description: Aggregation level (e.g., COUNTY, STATE, NATIONAL). + + crop: + description: Commodity or crop name. + exact_mappings: [] # TODO: map to AGROVOC crop concepts + + variable: + description: + Census or survey variable measured (e.g., Acreage, Yield, Production). + exact_mappings: [] # TODO: map to AGROVOC variable concepts + + unit: + description: Unit of measure (e.g., acres, tons, tons per acre). + exact_mappings: [] # TODO: map to UCUM or AGROVOC unit concepts + + value: + range: float + description: Reported numeric value. + + bearing_status: + description: Bearing or nonbearing acreage (if applicable). + + class_desc: + range: string + description: Class description (e.g., BEARING, NONBEARING). + + domain_desc: + range: string + description: Domain category (e.g., TOTAL, CHEMICAL, AREA HARVESTED). + + period_desc: + range: string + description: + For surveys, the time period of data collection (e.g., ANNUAL, MARCH). + + freq_desc: + range: string + description: + For surveys, the frequency of data collection (e.g., ANNUAL, MONTHLY). + + program_desc: + range: string + description: Survey program name (e.g., FRUIT & TREE NUTS, VEGETABLES). + + source: + range: string + description: Data source citation (e.g., USDA NASS Quick Stats API). + + notes: + range: string + description: Supplemental notes or flags (e.g., (D) data suppressed). + +enums: + CropEnum: + permissible_values: + Almond: + exact_mappings: [] # TODO: AGROVOC c_330 + Pistachio: + exact_mappings: [] # TODO: AGROVOC c_5733 + Tomato: + exact_mappings: [] # TODO: AGROVOC c_7824 + Olive: + exact_mappings: [] # TODO: AGROVOC c_5681 + + VariableEnum: + permissible_values: + ACREAGE_TOTAL: [] # TODO: AGROVOC mapping + ACREAGE_BEARING: [] # TODO: AGROVOC mapping + ACREAGE_NONBEARING: [] # TODO: AGROVOC mapping + YIELD: [] # TODO: AGROVOC mapping + PRODUCTION: [] # TODO: AGROVOC mapping + OPERATIONS: [] # TODO: AGROVOC mapping + + UnitEnum: + permissible_values: + ACRES: [] # TODO: UCUM mapping + TONS: [] # TODO: UCUM mapping + TONS_PER_ACRE: [] # TODO: UCUM mapping + OPERATIONS: [] # TODO: AGROVOC or UCUM mapping + + BearingStatusEnum: + permissible_values: + BEARING: [] # TODO: AGROVOC mapping + NONBEARING: [] # TODO: AGROVOC mapping + NA: [] # TODO: not applicable From fe0312b6cac54f48d0f5a4ac2b429635e1b0731e Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Thu, 30 Oct 2025 11:16:15 -0600 Subject: [PATCH 02/81] feat:Adding linkml and modifying alembic .env to ensure compatiblity. Everything works I think. --- alembic/env.py | 26 ++ ...9_testing_linkml_created_python_object_.py | 32 ++ ...490235da5633_use_snake_case_table_names.py | 158 +++++++++ ...4_testing_linkml_created_python_object_.py | 96 ++++++ pixi.toml | 19 +- schemas/common/geography.yaml | 2 + schemas/generated/census_survey.py | 132 ++++++++ schemas/generated/geography.py | 29 ++ schemas/linkml_sqla_generation.md | 108 +++++++ schemas/pydantic/census_survey.py | 304 ++++++++++++++++++ schemas/pydantic/geography.py | 153 +++++++++ schemas/template.yaml | 45 +++ schemas/usda/census_survey.yaml | 65 ++-- .../pipeline/utils/test_lookup_utils.ipynb | 203 ++++++++++++ 14 files changed, 1342 insertions(+), 30 deletions(-) create mode 100644 alembic/versions/38398b232319_testing_linkml_created_python_object_.py create mode 100644 alembic/versions/490235da5633_use_snake_case_table_names.py create mode 100644 alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py create mode 100644 schemas/generated/census_survey.py create mode 100644 schemas/generated/geography.py create mode 100644 schemas/linkml_sqla_generation.md create mode 100644 schemas/pydantic/census_survey.py create mode 100644 schemas/pydantic/geography.py create mode 100644 schemas/template.yaml create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/test_lookup_utils.ipynb diff --git a/alembic/env.py b/alembic/env.py index 2d1671a0..8f072a32 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -25,6 +25,27 @@ from ca_biositing.datamodels.specific_aalysis_results import * from ca_biositing.datamodels.user import * from sqlmodel import SQLModel +import importlib.util +from pathlib import Path + +# --- Import generated models --- +# You can explicitly import your generated models here, or uncomment the +# code below to dynamically import them. +from schemas.generated.census_survey import * +from schemas.generated.geography import * + +# # --- Dynamically import generated models --- +# # This code will dynamically import all Python files from the +# # schemas/generated directory. This is a convenience so that you don't have +# # to add a new import statement every time you generate a new model from a +# # LinkML schema. +# generated_path = Path(__file__).resolve().parents[1] / "schemas" / "generated" +# for file in os.listdir(generated_path): +# if file.endswith(".py") and file != "__init__.py": +# module_name = file[:-3] +# spec = importlib.util.spec_from_file_location(module_name, generated_path / file) +# module = importlib.util.module_from_spec(spec) +# spec.loader.exec_module(module) # --- Alembic Config object, provides access to alembic.ini values --- config = context.config @@ -41,6 +62,11 @@ fileConfig(config.config_file_name) # --- Metadata from your models for autogenerate --- +# Combine metadata from all models +# See: https://alembic.sqlalchemy.org/en/latest/autogenerate.html#affecting-the-autogenerate-process +for table in SQLModel.metadata.tables.values(): + table.tometadata(SQLModel.metadata) + target_metadata = SQLModel.metadata diff --git a/alembic/versions/38398b232319_testing_linkml_created_python_object_.py b/alembic/versions/38398b232319_testing_linkml_created_python_object_.py new file mode 100644 index 00000000..fd2da614 --- /dev/null +++ b/alembic/versions/38398b232319_testing_linkml_created_python_object_.py @@ -0,0 +1,32 @@ +"""testing linkml created python object creation + +Revision ID: 38398b232319 +Revises: 8de419051d03 +Create Date: 2025-10-30 16:23:52.506268 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '38398b232319' +down_revision: Union[str, Sequence[str], None] = '8de419051d03' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/alembic/versions/490235da5633_use_snake_case_table_names.py b/alembic/versions/490235da5633_use_snake_case_table_names.py new file mode 100644 index 00000000..0a51c6d2 --- /dev/null +++ b/alembic/versions/490235da5633_use_snake_case_table_names.py @@ -0,0 +1,158 @@ +"""use snake_case table names + +Revision ID: 490235da5633 +Revises: 99af25a3b574 +Create Date: 2025-10-30 16:42:11.402363 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '490235da5633' +down_revision: Union[str, Sequence[str], None] = '99af25a3b574' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + op.drop_table('USDARecord') + op.drop_table('SurveyRecord') + op.drop_table('CensusRecord') + op.drop_table('Geography') + op.create_table('geography', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('state_name', sa.Text(), nullable=True), + sa.Column('state_fips', sa.Text(), nullable=True), + sa.Column('county_name', sa.Text(), nullable=True), + sa.Column('county_fips', sa.Text(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('region_name', sa.Text(), nullable=True), + sa.Column('agg_level_desc', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_record', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('census_record', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('survey_record', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('period_desc', sa.Text(), nullable=True), + sa.Column('freq_desc', sa.Text(), nullable=True), + sa.Column('program_desc', sa.Text(), nullable=True), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + + +def downgrade() -> None: + """Downgrade schema.""" + op.drop_table('survey_record') + op.drop_table('census_record') + op.drop_table('usda_record') + op.drop_table('geography') + op.create_table('USDARecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('SurveyRecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('period_desc', sa.Text(), nullable=True), + sa.Column('freq_desc', sa.Text(), nullable=True), + sa.Column('program_desc', sa.Text(), nullable=True), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('CensusRecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Geography', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('state_name', sa.Text(), nullable=True), + sa.Column('state_fips', sa.Text(), nullable=True), + sa.Column('county_name', sa.Text(), nullable=True), + sa.Column('county_fips', sa.Text(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('region_name', sa.Text(), nullable=True), + sa.Column('agg_level_desc', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) diff --git a/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py b/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py new file mode 100644 index 00000000..0d1fba2e --- /dev/null +++ b/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py @@ -0,0 +1,96 @@ +"""testing linkml created python object creation + +Revision ID: 99af25a3b574 +Revises: 38398b232319 +Create Date: 2025-10-30 16:38:00.752859 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '99af25a3b574' +down_revision: Union[str, Sequence[str], None] = '38398b232319' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('Geography', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('state_name', sa.Text(), nullable=True), + sa.Column('state_fips', sa.Text(), nullable=True), + sa.Column('county_name', sa.Text(), nullable=True), + sa.Column('county_fips', sa.Text(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('region_name', sa.Text(), nullable=True), + sa.Column('agg_level_desc', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('CensusRecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('SurveyRecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('period_desc', sa.Text(), nullable=True), + sa.Column('freq_desc', sa.Text(), nullable=True), + sa.Column('program_desc', sa.Text(), nullable=True), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('USDARecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('USDARecord') + op.drop_table('SurveyRecord') + op.drop_table('CensusRecord') + op.drop_table('Geography') + # ### end Alembic commands ### diff --git a/pixi.toml b/pixi.toml index 10ce33b6..a088e880 100644 --- a/pixi.toml +++ b/pixi.toml @@ -25,11 +25,20 @@ python = "~=3.12" pre-commit = ">=4.2.0,<5" pytest = ">=8.4.2,<9" pytest-cov = ">=7.0.0,<8" -pip = ">=25.2,<26" -docker-compose = ">=2.39.2,<3" -docker-cli = ">=28.3.1,<29" -testcontainers = ">=4.13.2,<5" -python-dotenv = ">=1.2.1,<2" +sqlmodel = ">=0.0.19,<0.1" +alembic = ">=1.13.2,<2" +psycopg2 = ">=2.9.9,<3" +python-dotenv = ">=1.0.1,<2" +pandas = ">=2.2.0,<3" +pyjanitor = "*" +gspread = "*" +gspread-dataframe = "*" +pydantic-settings = "*" +google-auth-oauthlib = "*" +prefect = "*" +uvicorn = ">=0.30.0,<1" +fastapi = ">=0.115.0,<1" +linkml = "*" [tasks] pre-commit-all = "pre-commit run --all-files" diff --git a/schemas/common/geography.yaml b/schemas/common/geography.yaml index 41c9cf1c..d5d6fda2 100644 --- a/schemas/common/geography.yaml +++ b/schemas/common/geography.yaml @@ -16,6 +16,8 @@ imports: classes: Geography: description: Reference table for U.S. geographic identifiers. + annotations: + __tablename__: geography slots: - state_name - state_fips diff --git a/schemas/generated/census_survey.py b/schemas/generated/census_survey.py new file mode 100644 index 00000000..158c32a4 --- /dev/null +++ b/schemas/generated/census_survey.py @@ -0,0 +1,132 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class USDARecord(Base): + """ + Base class for USDA agricultural data records. + """ + __tablename__ = 'USDARecord' + + id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) + year = Column(Integer(), nullable=False ) + crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) + variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) + unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) + value = Column(Float()) + bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) + class_desc = Column(Text()) + domain_desc = Column(Text()) + source = Column(Text()) + notes = Column(Text()) + geography_id = Column(Integer(), ForeignKey('Geography.id')) + geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) + + + def __repr__(self): + return f"USDARecord(id={self.id},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" + + + + + + +class Geography(Base): + """ + Reference table for U.S. geographic identifiers. + """ + __tablename__ = 'Geography' + + id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + geoid = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(id={self.id},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},geoid={self.geoid},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class CensusRecord(USDARecord): + """ + A USDA Census of Agriculture record (every 5 years). + """ + __tablename__ = 'CensusRecord' + + id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) + year = Column(Integer(), nullable=False ) + crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) + variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) + unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) + value = Column(Float()) + bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) + class_desc = Column(Text()) + domain_desc = Column(Text()) + source = Column(Text()) + notes = Column(Text()) + geography_id = Column(Integer(), ForeignKey('Geography.id')) + geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) + + + def __repr__(self): + return f"CensusRecord(id={self.id},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SurveyRecord(USDARecord): + """ + A USDA Survey record (annual, seasonal, or periodic). + """ + __tablename__ = 'SurveyRecord' + + id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) + period_desc = Column(Text()) + freq_desc = Column(Text()) + program_desc = Column(Text()) + year = Column(Integer(), nullable=False ) + crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) + variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) + unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) + value = Column(Float()) + bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) + class_desc = Column(Text()) + domain_desc = Column(Text()) + source = Column(Text()) + notes = Column(Text()) + geography_id = Column(Integer(), ForeignKey('Geography.id')) + geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) + + + def __repr__(self): + return f"SurveyRecord(id={self.id},period_desc={self.period_desc},freq_desc={self.freq_desc},program_desc={self.program_desc},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/schemas/generated/geography.py b/schemas/generated/geography.py new file mode 100644 index 00000000..dcc8a564 --- /dev/null +++ b/schemas/generated/geography.py @@ -0,0 +1,29 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Geography(Base): + """ + Reference table for U.S. geographic identifiers. + """ + __tablename__ = 'Geography' + + id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + geoid = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(id={self.id},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},geoid={self.geoid},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" diff --git a/schemas/linkml_sqla_generation.md b/schemas/linkml_sqla_generation.md new file mode 100644 index 00000000..7c3692cf --- /dev/null +++ b/schemas/linkml_sqla_generation.md @@ -0,0 +1,108 @@ +# Generating SQLAlchemy Models from LinkML Schemas + +This document outlines the process of generating SQLAlchemy (SQLA) models from +LinkML schemas and integrating them with Alembic for database migrations. + +## 1. Create a LinkML Schema + +Create a YAML file (e.g., `my_schema.yaml`) to define your data model. The +schema should include: + +- **`id`**: A unique identifier for the schema. +- **`name`**: A human-readable name for the schema. +- **`description`**: A brief description of the schema's purpose. +- **`prefixes`**: A mapping of prefixes to URIs for linked data. +- **`imports`**: A list of other LinkML schemas to import. +- **`classes`**: The main data structures of your model. +- **`slots`**: The properties of your classes. +- **`enums`**: Controlled vocabularies for your slots. + +## 2. Define Classes and Slots + +Define your classes and their corresponding slots. For SQLAlchemy model +generation, it's important to specify the table name using the `__tablename__` +annotation to ensure snake_case naming conventions. + +```yaml +classes: + MyClassName: + description: "A description of my class." + annotations: + __tablename__: my_snake_case_name + slots: + - my_slot_name +``` + +## 3. Generate SQLAlchemy Models + +Use the `linkml-sqla` generator to create SQLAlchemy models from your schema. +The following command will generate a Python file containing your models: + +```bash +linkml generate sqla my_schema.yaml > schemas/generated/my_model.py +``` + +If your schema imports other schemas, you may want to use the +`--no-mergeimports` flag to avoid including the imported models in the generated +file: + +```bash +linkml generate sqla --no-mergeimports my_schema.yaml > schemas/generated/my_model.py +``` + +## 4. Integrate with Alembic + +Once you have your generated models, you can use Alembic to create and apply +database migrations. + +### a. Configure Alembic + +Ensure your `alembic/env.py` is configured to use your generated models. You +will need to explicitly import your generated models and then merge their +metadata with your main `SQLModel` metadata. + +```python +# alembic/env.py +import os +import sys +from sqlmodel import SQLModel + +# Add the project root to the Python path +sys.path.append(str(Path(__file__).resolve().parents[1])) + +# Import your main models +from src.pipeline.etl.models import * + +# Import your generated models +from schemas.generated.my_model import * + +# Merge metadata +for table in SQLModel.metadata.tables.values(): + table.tometadata(SQLModel.metadata) + +target_metadata = SQLModel.metadata +``` + +Alternatively, you can uncomment the dynamic import code in `alembic/env.py` to +automatically import all generated models from the `schemas/generated` +directory. + +### b. Create a Migration + +Generate a new migration file using the `alembic revision` command: + +```bash +alembic revision --autogenerate -m "Add my_snake_case_name table" +``` + +### c. Apply the Migration + +Apply the migration to your database using the `alembic upgrade` command: + +```bash +alembic upgrade head +``` + +By following these steps, you can effectively use LinkML to define your data +models and generate SQLAlchemy models for your database, while maintaining a +clean and organized migration history with Alembic. diff --git a/schemas/pydantic/census_survey.py b/schemas/pydantic/census_survey.py new file mode 100644 index 00000000..c858fbaa --- /dev/null +++ b/schemas/pydantic/census_survey.py @@ -0,0 +1,304 @@ +from __future__ import annotations + +import re +import sys +from datetime import ( + date, + datetime, + time +) +from decimal import Decimal +from enum import Enum +from typing import ( + Any, + ClassVar, + Literal, + Optional, + Union +) + +from pydantic import ( + BaseModel, + ConfigDict, + Field, + RootModel, + SerializationInfo, + SerializerFunctionWrapHandler, + field_validator, + model_serializer +) + + +metamodel_version = "None" +version = "None" + + +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + serialize_by_alias = True, + validate_by_name = True, + validate_assignment = True, + validate_default = True, + extra = "forbid", + arbitrary_types_allowed = True, + use_enum_values = True, + strict = False, + ) + + @model_serializer(mode='wrap', when_used='unless-none') + def treat_empty_lists_as_none( + self, handler: SerializerFunctionWrapHandler, + info: SerializationInfo) -> dict[str, Any]: + if info.exclude_none: + _instance = self.model_copy() + for field, field_info in type(_instance).model_fields.items(): + if getattr(_instance, field) == [] and not( + field_info.is_required()): + setattr(_instance, field, None) + else: + _instance = self + return handler(_instance, info) + + + +class LinkMLMeta(RootModel): + root: dict[str, Any] = {} + model_config = ConfigDict(frozen=True) + + def __getattr__(self, key:str): + return getattr(self.root, key) + + def __getitem__(self, key:str): + return self.root[key] + + def __setitem__(self, key:str, value): + self.root[key] = value + + def __contains__(self, key:str) -> bool: + return key in self.root + + +linkml_meta = LinkMLMeta({'default_prefix': 'usda', + 'description': 'Schema for USDA Census and Survey data records accessed via ' + 'the NASS Quick Stats API, focusing on county-level data for ' + 'key California crops.\n', + 'id': 'usda_data', + 'imports': ['linkml:types', '../common/geography'], + 'name': 'USDA_Data', + 'prefixes': {'agrovoc': {'prefix_prefix': 'agrovoc', + 'prefix_reference': 'https://agrovoc.fao.org/agrontology/en/page/'}, + 'linkml': {'prefix_prefix': 'linkml', + 'prefix_reference': 'https://w3id.org/linkml/'}, + 'ucum': {'prefix_prefix': 'ucum', + 'prefix_reference': 'http://unitsofmeasure.org/ucum.html'}, + 'usda': {'prefix_prefix': 'usda', + 'prefix_reference': 'https://schema.myorg.org/usda/'}}, + 'source_file': 'schemas/usda/census_survey.yaml'} ) + +class CropEnum(str, Enum): + Almond = "Almond" + """ + TODO: AGROVOC c_330 + """ + Pistachio = "Pistachio" + """ + TODO: AGROVOC c_5733 + """ + Tomato = "Tomato" + """ + TODO: AGROVOC c_7824 + """ + Olive = "Olive" + """ + TODO: AGROVOC c_5681 + """ + + +class VariableEnum(str, Enum): + ACREAGE_TOTAL = "ACREAGE_TOTAL" + """ + TODO: AGROVOC mapping + """ + ACREAGE_BEARING = "ACREAGE_BEARING" + """ + TODO: AGROVOC mapping + """ + ACREAGE_NONBEARING = "ACREAGE_NONBEARING" + """ + TODO: AGROVOC mapping + """ + YIELD = "YIELD" + """ + TODO: AGROVOC mapping + """ + PRODUCTION = "PRODUCTION" + """ + TODO: AGROVOC mapping + """ + OPERATIONS = "OPERATIONS" + """ + TODO: AGROVOC mapping + """ + + +class UnitEnum(str, Enum): + ACRES = "ACRES" + """ + TODO: UCUM mapping + """ + TONS = "TONS" + """ + TODO: UCUM mapping + """ + TONS_PER_ACRE = "TONS_PER_ACRE" + """ + TODO: UCUM mapping + """ + OPERATIONS = "OPERATIONS" + """ + TODO: AGROVOC or UCUM mapping + """ + + +class BearingStatusEnum(str, Enum): + BEARING = "BEARING" + """ + TODO: AGROVOC mapping + """ + NONBEARING = "NONBEARING" + """ + TODO: AGROVOC mapping + """ + NA = "NA" + """ + TODO: not applicable + """ + + + +class Geography(ConfiguredBaseModel): + """ + Reference table for U.S. geographic identifiers. + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'geography'}) + + state_name: Optional[str] = Field(default=None, description="""U.S. state name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + state_fips: Optional[str] = Field(default=None, description="""Two-digit FIPS code for the state.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + county_name: Optional[str] = Field(default=None, description="""U.S. county name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + county_fips: Optional[str] = Field(default=None, description="""Three-digit county FIPS code.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + geoid: Optional[str] = Field(default=None, description="""Combined state + county FIPS (e.g., 06019).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + region_name: Optional[str] = Field(default=None, description="""Optional higher-level region grouping (e.g., San Joaquin Valley).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + agg_level_desc: Optional[str] = Field(default=None, description="""Aggregation level (e.g., COUNTY, STATE, NATIONAL).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + + @field_validator('state_fips') + def pattern_state_fips(cls, v): + pattern=re.compile(r"^[0-9]{2}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid state_fips format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid state_fips format: {v}" + raise ValueError(err_msg) + return v + + @field_validator('county_fips') + def pattern_county_fips(cls, v): + pattern=re.compile(r"^[0-9]{3}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid county_fips format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid county_fips format: {v}" + raise ValueError(err_msg) + return v + + @field_validator('geoid') + def pattern_geoid(cls, v): + pattern=re.compile(r"^[0-9]{5}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid geoid format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid geoid format: {v}" + raise ValueError(err_msg) + return v + + +class USDARecord(ConfiguredBaseModel): + """ + Base class for USDA agricultural data records. + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'usda_data', + 'slot_usage': {'bearing_status': {'name': 'bearing_status', + 'range': 'BearingStatusEnum'}, + 'crop': {'name': 'crop', 'range': 'CropEnum'}, + 'geography': {'name': 'geography', 'range': 'Geography'}, + 'unit': {'name': 'unit', 'range': 'UnitEnum'}, + 'variable': {'name': 'variable', 'range': 'VariableEnum'}}}) + + year: int = Field(default=..., description="""Census or survey year.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + geography: Optional[Geography] = Field(default=None, description="""Geographic information (state, county, FIPS).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + crop: Optional[CropEnum] = Field(default=None, description="""Commodity or crop name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + variable: Optional[VariableEnum] = Field(default=None, description="""Census or survey variable measured (e.g., Acreage, Yield, Production).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + unit: Optional[UnitEnum] = Field(default=None, description="""Unit of measure (e.g., acres, tons, tons per acre).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + value: Optional[float] = Field(default=None, description="""Reported numeric value.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + bearing_status: Optional[BearingStatusEnum] = Field(default=None, description="""Bearing or nonbearing acreage (if applicable).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + class_desc: Optional[str] = Field(default=None, description="""Class description (e.g., BEARING, NONBEARING).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + domain_desc: Optional[str] = Field(default=None, description="""Domain category (e.g., TOTAL, CHEMICAL, AREA HARVESTED).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + source: Optional[str] = Field(default=None, description="""Data source citation (e.g., USDA NASS Quick Stats API).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + notes: Optional[str] = Field(default=None, description="""Supplemental notes or flags (e.g., (D) data suppressed).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + + +class CensusRecord(USDARecord): + """ + A USDA Census of Agriculture record (every 5 years). + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'usda_data'}) + + year: int = Field(default=..., description="""Census or survey year.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + geography: Optional[Geography] = Field(default=None, description="""Geographic information (state, county, FIPS).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + crop: Optional[CropEnum] = Field(default=None, description="""Commodity or crop name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + variable: Optional[VariableEnum] = Field(default=None, description="""Census or survey variable measured (e.g., Acreage, Yield, Production).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + unit: Optional[UnitEnum] = Field(default=None, description="""Unit of measure (e.g., acres, tons, tons per acre).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + value: Optional[float] = Field(default=None, description="""Reported numeric value.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + bearing_status: Optional[BearingStatusEnum] = Field(default=None, description="""Bearing or nonbearing acreage (if applicable).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + class_desc: Optional[str] = Field(default=None, description="""Class description (e.g., BEARING, NONBEARING).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + domain_desc: Optional[str] = Field(default=None, description="""Domain category (e.g., TOTAL, CHEMICAL, AREA HARVESTED).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + source: Optional[str] = Field(default=None, description="""Data source citation (e.g., USDA NASS Quick Stats API).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + notes: Optional[str] = Field(default=None, description="""Supplemental notes or flags (e.g., (D) data suppressed).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + + +class SurveyRecord(USDARecord): + """ + A USDA Survey record (annual, seasonal, or periodic). + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'usda_data'}) + + period_desc: Optional[str] = Field(default=None, description="""For surveys, the time period of data collection (e.g., ANNUAL, MARCH).""", json_schema_extra = { "linkml_meta": {'domain_of': ['SurveyRecord']} }) + freq_desc: Optional[str] = Field(default=None, description="""For surveys, the frequency of data collection (e.g., ANNUAL, MONTHLY).""", json_schema_extra = { "linkml_meta": {'domain_of': ['SurveyRecord']} }) + program_desc: Optional[str] = Field(default=None, description="""Survey program name (e.g., FRUIT & TREE NUTS, VEGETABLES).""", json_schema_extra = { "linkml_meta": {'domain_of': ['SurveyRecord']} }) + year: int = Field(default=..., description="""Census or survey year.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + geography: Optional[Geography] = Field(default=None, description="""Geographic information (state, county, FIPS).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + crop: Optional[CropEnum] = Field(default=None, description="""Commodity or crop name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + variable: Optional[VariableEnum] = Field(default=None, description="""Census or survey variable measured (e.g., Acreage, Yield, Production).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + unit: Optional[UnitEnum] = Field(default=None, description="""Unit of measure (e.g., acres, tons, tons per acre).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + value: Optional[float] = Field(default=None, description="""Reported numeric value.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + bearing_status: Optional[BearingStatusEnum] = Field(default=None, description="""Bearing or nonbearing acreage (if applicable).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + class_desc: Optional[str] = Field(default=None, description="""Class description (e.g., BEARING, NONBEARING).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + domain_desc: Optional[str] = Field(default=None, description="""Domain category (e.g., TOTAL, CHEMICAL, AREA HARVESTED).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + source: Optional[str] = Field(default=None, description="""Data source citation (e.g., USDA NASS Quick Stats API).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + notes: Optional[str] = Field(default=None, description="""Supplemental notes or flags (e.g., (D) data suppressed).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + + +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +Geography.model_rebuild() +USDARecord.model_rebuild() +CensusRecord.model_rebuild() +SurveyRecord.model_rebuild() diff --git a/schemas/pydantic/geography.py b/schemas/pydantic/geography.py new file mode 100644 index 00000000..7e0cdb4b --- /dev/null +++ b/schemas/pydantic/geography.py @@ -0,0 +1,153 @@ +from __future__ import annotations + +import re +import sys +from datetime import ( + date, + datetime, + time +) +from decimal import Decimal +from enum import Enum +from typing import ( + Any, + ClassVar, + Literal, + Optional, + Union +) + +from pydantic import ( + BaseModel, + ConfigDict, + Field, + RootModel, + SerializationInfo, + SerializerFunctionWrapHandler, + field_validator, + model_serializer +) + + +metamodel_version = "None" +version = "None" + + +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + serialize_by_alias = True, + validate_by_name = True, + validate_assignment = True, + validate_default = True, + extra = "forbid", + arbitrary_types_allowed = True, + use_enum_values = True, + strict = False, + ) + + @model_serializer(mode='wrap', when_used='unless-none') + def treat_empty_lists_as_none( + self, handler: SerializerFunctionWrapHandler, + info: SerializationInfo) -> dict[str, Any]: + if info.exclude_none: + _instance = self.model_copy() + for field, field_info in type(_instance).model_fields.items(): + if getattr(_instance, field) == [] and not( + field_info.is_required()): + setattr(_instance, field, None) + else: + _instance = self + return handler(_instance, info) + + + +class LinkMLMeta(RootModel): + root: dict[str, Any] = {} + model_config = ConfigDict(frozen=True) + + def __getattr__(self, key:str): + return getattr(self.root, key) + + def __getitem__(self, key:str): + return self.root[key] + + def __setitem__(self, key:str, value): + self.root[key] = value + + def __contains__(self, key:str) -> bool: + return key in self.root + + +linkml_meta = LinkMLMeta({'default_prefix': 'usda', + 'description': 'Common geographic identifiers used across multiple datasets. ' + 'Includes states, counties, FIPS codes, and optional ' + 'regions.\n', + 'id': 'geography', + 'imports': ['linkml:types'], + 'name': 'Geography', + 'prefixes': {'agrovoc': {'prefix_prefix': 'agrovoc', + 'prefix_reference': 'https://agrovoc.fao.org/agrontology/en/page/'}, + 'linkml': {'prefix_prefix': 'linkml', + 'prefix_reference': 'https://w3id.org/linkml/'}, + 'usda': {'prefix_prefix': 'usda', + 'prefix_reference': 'https://schema.myorg.org/usda/'}}, + 'source_file': 'schemas/common/geography.yaml'} ) + + +class Geography(ConfiguredBaseModel): + """ + Reference table for U.S. geographic identifiers. + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'geography'}) + + state_name: Optional[str] = Field(default=None, description="""U.S. state name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + state_fips: Optional[str] = Field(default=None, description="""Two-digit FIPS code for the state.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + county_name: Optional[str] = Field(default=None, description="""U.S. county name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + county_fips: Optional[str] = Field(default=None, description="""Three-digit county FIPS code.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + geoid: Optional[str] = Field(default=None, description="""Combined state + county FIPS (e.g., 06019).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + region_name: Optional[str] = Field(default=None, description="""Optional higher-level region grouping (e.g., San Joaquin Valley).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + agg_level_desc: Optional[str] = Field(default=None, description="""Aggregation level (e.g., COUNTY, STATE, NATIONAL).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + + @field_validator('state_fips') + def pattern_state_fips(cls, v): + pattern=re.compile(r"^[0-9]{2}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid state_fips format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid state_fips format: {v}" + raise ValueError(err_msg) + return v + + @field_validator('county_fips') + def pattern_county_fips(cls, v): + pattern=re.compile(r"^[0-9]{3}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid county_fips format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid county_fips format: {v}" + raise ValueError(err_msg) + return v + + @field_validator('geoid') + def pattern_geoid(cls, v): + pattern=re.compile(r"^[0-9]{5}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid geoid format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid geoid format: {v}" + raise ValueError(err_msg) + return v + + +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +Geography.model_rebuild() diff --git a/schemas/template.yaml b/schemas/template.yaml new file mode 100644 index 00000000..c1de51ef --- /dev/null +++ b/schemas/template.yaml @@ -0,0 +1,45 @@ +id: new_schema +name: NewSchema +description: > + A template for creating new LinkML schemas. + +prefixes: + linkml: https://w3id.org/linkml/ + schema: https://schema.org/ + skos: http://www.w3.org/2004/02/skos/core# + +default_prefix: schema +imports: + - linkml:types + +classes: + MyClass: + description: "A description of my class." + annotations: + __tablename__: my_class + slots: + - id + - name + - description + +slots: + id: + identifier: true + range: string + description: "A unique identifier for the instance." + + name: + range: string + description: "A human-readable name for the instance." + + description: + range: string + description: "A description of the instance." + +enums: + MyEnum: + permissible_values: + VALUE_1: + description: "The first value." + VALUE_2: + description: "The second value." diff --git a/schemas/usda/census_survey.yaml b/schemas/usda/census_survey.yaml index 9d91585a..6ab40f7f 100644 --- a/schemas/usda/census_survey.yaml +++ b/schemas/usda/census_survey.yaml @@ -13,11 +13,13 @@ prefixes: default_prefix: usda imports: - linkml:types - - ../common/geography.yaml + - ../common/geography classes: USDARecord: description: Base class for USDA agricultural data records. + annotations: + __tablename__: usda_record slots: - year - geography @@ -45,10 +47,14 @@ classes: CensusRecord: is_a: USDARecord description: A USDA Census of Agriculture record (every 5 years). + annotations: + __tablename__: census_record SurveyRecord: is_a: USDARecord description: A USDA Survey record (annual, seasonal, or periodic). + annotations: + __tablename__: survey_record slots: - period_desc - freq_desc @@ -64,22 +70,18 @@ slots: range: Geography description: Geographic information (state, county, FIPS). - agg_level_desc: - range: string - description: Aggregation level (e.g., COUNTY, STATE, NATIONAL). - crop: description: Commodity or crop name. - exact_mappings: [] # TODO: map to AGROVOC crop concepts + exact_mappings: # TODO: map to AGROVOC crop concepts variable: description: Census or survey variable measured (e.g., Acreage, Yield, Production). - exact_mappings: [] # TODO: map to AGROVOC variable concepts + exact_mappings: # TODO: map to AGROVOC variable concepts unit: description: Unit of measure (e.g., acres, tons, tons per acre). - exact_mappings: [] # TODO: map to UCUM or AGROVOC unit concepts + exact_mappings: # TODO: map to AGROVOC unit concepts value: range: float @@ -122,32 +124,45 @@ enums: CropEnum: permissible_values: Almond: - exact_mappings: [] # TODO: AGROVOC c_330 + description: "TODO: AGROVOC c_330" Pistachio: - exact_mappings: [] # TODO: AGROVOC c_5733 + description: "TODO: AGROVOC c_5733" Tomato: - exact_mappings: [] # TODO: AGROVOC c_7824 + description: "TODO: AGROVOC c_7824" Olive: - exact_mappings: [] # TODO: AGROVOC c_5681 + description: "TODO: AGROVOC c_5681" VariableEnum: permissible_values: - ACREAGE_TOTAL: [] # TODO: AGROVOC mapping - ACREAGE_BEARING: [] # TODO: AGROVOC mapping - ACREAGE_NONBEARING: [] # TODO: AGROVOC mapping - YIELD: [] # TODO: AGROVOC mapping - PRODUCTION: [] # TODO: AGROVOC mapping - OPERATIONS: [] # TODO: AGROVOC mapping + ACREAGE_TOTAL: + description: "TODO: AGROVOC mapping" + ACREAGE_BEARING: + description: "TODO: AGROVOC mapping" + ACREAGE_NONBEARING: + description: "TODO: AGROVOC mapping" + YIELD: + description: "TODO: AGROVOC mapping" + PRODUCTION: + description: "TODO: AGROVOC mapping" + OPERATIONS: + description: "TODO: AGROVOC mapping" UnitEnum: permissible_values: - ACRES: [] # TODO: UCUM mapping - TONS: [] # TODO: UCUM mapping - TONS_PER_ACRE: [] # TODO: UCUM mapping - OPERATIONS: [] # TODO: AGROVOC or UCUM mapping + ACRES: + description: "TODO: UCUM mapping" + TONS: + description: "TODO: UCUM mapping" + TONS_PER_ACRE: + description: "TODO: UCUM mapping" + OPERATIONS: + description: "TODO: AGROVOC or UCUM mapping" BearingStatusEnum: permissible_values: - BEARING: [] # TODO: AGROVOC mapping - NONBEARING: [] # TODO: AGROVOC mapping - NA: [] # TODO: not applicable + BEARING: + description: "TODO: AGROVOC mapping" + NONBEARING: + description: "TODO: AGROVOC mapping" + NA: + description: "TODO: not applicable" diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/test_lookup_utils.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/test_lookup_utils.ipynb new file mode 100644 index 00000000..5f7c94e0 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/test_lookup_utils.ipynb @@ -0,0 +1,203 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Test Notebook for Lookup Utils\n", + "\n", + "This notebook demonstrates how to use the utility functions in `lookup_utils.py` to swap foreign key IDs with names and vice-versa." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "from sqlmodel import Session, select\n", + "import sys\n", + "import os\n", + "\n", + "# Add the project root to the Python path to allow for module imports\n", + "project_root = os.path.abspath(os.path.join(os.getcwd(), '..'))\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + "\n", + "from src.database import engine\n", + "from src.models.biomass import Biomass, BiomassType\n", + "from src.utils.lookup_utils import replace_id_with_name_df, replace_name_with_id_df" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Create a Database Session\n", + "\n", + "First, we create a database session using the engine from our `database.py` module. This session is used to communicate with the database." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "db = Session(engine)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 2. Load Tables into Pandas DataFrames\n", + "\n", + "Next, we query the `Biomass` and `BiomassType` tables and load their contents into pandas DataFrames. This simulates the data you would be working with in a transformation script." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Load Biomass table\n", + "biomass_statement = select(Biomass)\n", + "biomass_records = db.exec(biomass_statement).all()\n", + "biomass_df = pd.DataFrame([record.dict() for record in biomass_records])\n", + "\n", + "print(\"Original Biomass DataFrame:\")\n", + "display(biomass_df.head())" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Load BiomassType table\n", + "biomass_type_statement = select(BiomassType)\n", + "biomass_type_records = db.exec(biomass_type_statement).all()\n", + "biomass_type_df = pd.DataFrame([record.dict() for record in biomass_type_records])\n", + "\n", + "print(\"Biomass Type Reference DataFrame:\")\n", + "display(biomass_type_df.head())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 3. Example Usage\n", + "\n", + "Now you can use the utility functions to transform the DataFrames. The cells below provide examples that you can run and modify." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Example 1: Replace `biomass_type_id` with `biomass_type` Name" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# To run this, uncomment the following lines:\n", + "# df_with_names = replace_id_with_name_df(\n", + "# db=db,\n", + "# df=biomass_df,\n", + "# ref_model=BiomassType,\n", + "# id_column_name=\"biomass_type_id\",\n", + "# name_column_name=\"biomass_type\"\n", + "# )\n", + "#\n", + "# print(\"DataFrame with Biomass Type Names:\")\n", + "# display(df_with_names.head())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Example 2: Replace `biomass_type` Name with `biomass_type_id`\n", + "\n", + "This example also demonstrates the 'get or create' functionality. Let's first add a new, non-existent biomass type to our DataFrame to see if the function correctly adds it to the database." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Create a dummy DataFrame for this example\n", + "data = {'biomass_name': ['Test Biomass 1', 'Test Biomass 2'], 'biomass_type': ['ag_residue', 'new_test_type']}\n", + "name_df = pd.DataFrame(data)\n", + "\n", + "# To run this, uncomment the following lines:\n", + "# df_with_ids = replace_name_with_id_df(\n", + "# db=db,\n", + "# df=name_df,\n", + "# ref_model=BiomassType,\n", + "# name_column_name=\"biomass_type\",\n", + "# id_column_name=\"biomass_type_id\"\n", + "# )\n", + "#\n", + "# print(\"DataFrame with Biomass Type IDs:\")\n", + "# display(df_with_ids.head())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Verify New Type was Added\n", + "\n", + "If you ran the cell above, you can run this cell to query the `BiomassType` table again and see the new `new_test_type` entry." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# To run this, uncomment the following lines:\n", + "# updated_biomass_type_statement = select(BiomassType)\n", + "# updated_biomass_type_records = db.exec(updated_biomass_type_statement).all()\n", + "# updated_biomass_type_df = pd.DataFrame([record.dict() for record in updated_biomass_type_records])\n", + "#\n", + "# print(\"Updated Biomass Type Table:\")\n", + "# display(updated_biomass_type_df)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "default", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.11" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} From f5eed118eb34f6974eb10dade740d5a39356176a Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Thu, 30 Oct 2025 12:54:10 -0600 Subject: [PATCH 03/81] adding win-64 to platforms in pixi toml --- pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.toml b/pixi.toml index a088e880..1d81689f 100644 --- a/pixi.toml +++ b/pixi.toml @@ -6,7 +6,7 @@ requires-pixi = ">=0.55,<1.0" authors = ["SSEC Team"] channels = ["conda-forge"] name = "ca-biositing" -platforms = ["osx-arm64", "osx-64", "linux-64", "linux-aarch64"] +platforms = ["osx-arm64", "osx-64", "linux-64", "linux-aarch64", "win-64"] version = "0.1.0" [environments] From 584b1f78da6b1174cb9475d67eb8724a5f87383a Mon Sep 17 00:00:00 2001 From: mglbleta Date: Thu, 30 Oct 2025 14:38:13 -0700 Subject: [PATCH 04/81] total test --- test.txt | 1 + 1 file changed, 1 insertion(+) create mode 100644 test.txt diff --git a/test.txt b/test.txt new file mode 100644 index 00000000..b33c5606 --- /dev/null +++ b/test.txt @@ -0,0 +1 @@ +test test From a000cae056c09db828697fa8a290cd23319d8fd1 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Thu, 30 Oct 2025 14:45:39 -0700 Subject: [PATCH 05/81] test is our commit message --- test.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test.txt b/test.txt index b33c5606..d49aab15 100644 --- a/test.txt +++ b/test.txt @@ -1 +1 @@ -test test +test test test From d0373aadcd7ebcb1679dcc43a088b208796907c4 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Sun, 2 Nov 2025 15:30:23 -0800 Subject: [PATCH 06/81] Removing test file and revising docker setup instructions in README.md --- src/pipeline/README.md | 6 ++---- test.txt | 1 - 2 files changed, 2 insertions(+), 5 deletions(-) delete mode 100644 test.txt diff --git a/src/pipeline/README.md b/src/pipeline/README.md index fc01d1f0..f2db60b9 100644 --- a/src/pipeline/README.md +++ b/src/pipeline/README.md @@ -119,9 +119,7 @@ Follow these steps to set up and run the project for the first time. **3. Build the Docker Image:** -- From the project root directory, build the Docker image. You do not need to - activate the `pixi shell` for this, as the container manages its own - environment. +- From the project root directory, build the Docker image. ```bash docker-compose build @@ -143,7 +141,7 @@ Follow these steps to set up and run the project for the first time. migrations. ```bash - docker-compose exec app alembic upgrade head + docker-compose exec app pixi run alembic upgrade head ``` The environment is now fully set up and running. diff --git a/test.txt b/test.txt deleted file mode 100644 index d49aab15..00000000 --- a/test.txt +++ /dev/null @@ -1 +0,0 @@ -test test test From d53ade3c1000e400726ab520a08117a88f045f5a Mon Sep 17 00:00:00 2001 From: mglbleta Date: Sun, 2 Nov 2025 15:51:51 -0800 Subject: [PATCH 07/81] Adding notes to env.example which would've explained points I got confused on. --- src/ca_biositing/pipeline/.env.example | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/ca_biositing/pipeline/.env.example b/src/ca_biositing/pipeline/.env.example index 818cbf5a..1f839159 100644 --- a/src/ca_biositing/pipeline/.env.example +++ b/src/ca_biositing/pipeline/.env.example @@ -2,6 +2,8 @@ # --- # This file serves as an example. Copy it to a new file named .env # and replace the placeholder values with your actual development settings. +# These development settings are NOT found elsewhere and input here. You generate them in +# this document. # 1. Individual Connection Parameters # These are used by docker-compose to initialize the PostgreSQL container. @@ -17,7 +19,9 @@ POSTGRES_PORT=5432 # 3. Application Database URL # This is the full connection string used by the Python application (e.g., SQLAlchemy, Alembic) -# to connect to the database container. +# to connect to the database container. Make sure to replace the placeholders with the actual values. +# Do NOT use POSTGRES_USER, POSTGRES_PASSWORD, and POSTGRES_DB as variables here, type the +#actual username, password and database name from above in the DATABASE_URL string. # Note: # - It uses the service name 'db' as the host, which is how containers talk to each other. # - It uses the internal port '5432', not the host port. From 04743bc8c51d40bdd7db22292b99532328dd58de Mon Sep 17 00:00:00 2001 From: mglbleta Date: Sun, 2 Nov 2025 15:53:28 -0800 Subject: [PATCH 08/81] potentially fixed whitespace --- src/ca_biositing/pipeline/.env.example | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ca_biositing/pipeline/.env.example b/src/ca_biositing/pipeline/.env.example index 1f839159..7c5efee0 100644 --- a/src/ca_biositing/pipeline/.env.example +++ b/src/ca_biositing/pipeline/.env.example @@ -21,7 +21,7 @@ POSTGRES_PORT=5432 # This is the full connection string used by the Python application (e.g., SQLAlchemy, Alembic) # to connect to the database container. Make sure to replace the placeholders with the actual values. # Do NOT use POSTGRES_USER, POSTGRES_PASSWORD, and POSTGRES_DB as variables here, type the -#actual username, password and database name from above in the DATABASE_URL string. +# actual username, password and database name from above in the DATABASE_URL string. # Note: # - It uses the service name 'db' as the host, which is how containers talk to each other. # - It uses the internal port '5432', not the host port. From cbccecd1e8ca24f24d4cc024a15f83ab52797669 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Sun, 2 Nov 2025 16:16:12 -0800 Subject: [PATCH 09/81] Added explation for @task instruction --- docs/pipeline/ETL_WORKFLOW.md | 30 ++++++++++-------------------- 1 file changed, 10 insertions(+), 20 deletions(-) diff --git a/docs/pipeline/ETL_WORKFLOW.md b/docs/pipeline/ETL_WORKFLOW.md index b5279625..b6a13ff3 100644 --- a/docs/pipeline/ETL_WORKFLOW.md +++ b/docs/pipeline/ETL_WORKFLOW.md @@ -9,33 +9,16 @@ and how to use Prefect to execute it. The ETL pipeline is designed to extract data from Google Sheets, transform it into a structured format, and load it into the PostgreSQL database. The system -is built to be modular and extensible. The ETL pipeline is designed to extract -data from Google Sheets, transform it into a structured format, and load it into -the PostgreSQL database. The system is built to be modular and extensible. +is built to be modular and extensible. - **Structure:** The core logic is organized into three main packages within - `src/etl/`: + `src/pipeline/etl/`: - `extract`: Contains functions to pull raw data from sources (e.g., Google Sheets). - `transform`: Contains functions to clean, process, and structure the raw data. - `load`: Contains functions to insert the transformed data into the database. -- **Structure:** The core logic is organized into three main packages within - `src/etl/`: - - `extract`: Contains functions to pull raw data from sources (e.g., Google - Sheets). - - `transform`: Contains functions to clean, process, and structure the raw - data. - - `load`: Contains functions to insert the transformed data into the database. - -- **Hierarchical Pipelines:** To keep the project organized, individual - pipelines are nested within subdirectories that reflect the data they handle - (e.g., `products`, `analysis`). A complete pipeline for a single data type, - like `primary_product`, consists of three corresponding files: - - `src/etl/extract/products/primary_product.py` - - `src/etl/transform/products/primary_product.py` - - `src/etl/load/products/primary_product.py` - **Hierarchical Pipelines:** To keep the project organized, individual pipelines are nested within subdirectories that reflect the data they handle (e.g., `products`, `analysis`). A complete pipeline for a single data type, @@ -69,7 +52,14 @@ in the main `run_prefect_flow.py` script. **Step 1: Create the Task Files** Create the three Python files for your extract, transform, and load logic in the -appropriate subdirectories. Decorate each function with `@task`. +appropriate subdirectories. Decorate each function with `@task`, which is a +Prefect decorator that transforms a normal Python function into a managed Task. +Applying `@task` enables Prefect to: + +- Schedule and orchestrate the function as an individual Task within a flow. +- Track the Task’s execution state (pending, running, succeeded, failed). +- Automatically handle retries, timeouts, and result caching when configured. +- Collect logs and metrics for observability and debugging. - `src/etl/extract/samples/new_sample_type.py` - `src/etl/transform/samples/new_sample_type.py` From 603e0718eee285135d282da9fdcdf675bcddc2c9 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Fri, 14 Nov 2025 12:33:31 -0700 Subject: [PATCH 10/81] trying to commit again --- .../pipeline/utils/database_interaction.ipynb | 204 ++++++++++++++++++ 1 file changed, 204 insertions(+) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb new file mode 100644 index 00000000..41d5e443 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb @@ -0,0 +1,204 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Interactive Database Querying\n", + "\n", + "This notebook demonstrates how to connect to the project's PostgreSQL database from a local Jupyter environment to perform interactive queries and data analysis. It is intended as an educational tool and a template for data exploration." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Step 1: Import Necessary Libraries\n", + "\n", + "We begin by importing the required libraries:\n", + "- `pandas` for data manipulation.\n", + "- `create_engine`, `Session`, and `select` from `sqlmodel` for database interaction.\n", + "- The specific SQLModel data models (`FieldSample`, `GeographicLocation`) we want to query." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "from sqlmodel import create_engine, Session, select\n", + "\n", + "try:\n", + " from ca_biositing.datamodels.biomass import FieldSample\n", + " from ca_biositing.datamodels.biomass import PrimaryProduct\n", + " from ca_biositing.datamodels.geographic_locations import GeographicLocation\n", + " print(\"Libraries and models imported successfully.\")\n", + "except ImportError as e:\n", + " print(f\"Error importing models: {e}\")\n", + " print(\"Please ensure the project is installed correctly by running 'pixi install' in your terminal.\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Step 2: Create the Database Engine\n", + "\n", + "Next, we create a SQLAlchemy engine to manage connections to the database. \n", + "\n", + "**Note:** We are hardcoding the database URL here to ensure the notebook runs reliably. It connects to `localhost:5432`, which is the default port mapped to the project's Dockerized database." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "DATABASE_URL = \"postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db\"\n", + "\n", + "try:\n", + " engine = create_engine(DATABASE_URL, echo=False)\n", + " print(f\"Database engine created. Ready to connect to: {DATABASE_URL.replace('biocirv_dev_password', '')}\")\n", + "except Exception as e:\n", + " print(f\"Error creating database engine: {e}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Step 3: Query the Tables\n", + "\n", + "Now we can use the engine to open a session and query our tables. We will query the `field_samples` and `geographic_locations` tables and load them into separate pandas DataFrames." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "field_samples_df = None\n", + "locations_df = None\n", + "primary_product_df = None\n", + "\n", + "try:\n", + " with Session(engine) as session:\n", + " # Query the field_samples table\n", + " statement_samples = select(FieldSample)\n", + " results_samples = session.exec(statement_samples).all()\n", + " field_samples_df = pd.DataFrame([sample.model_dump() for sample in results_samples])\n", + " print(f\"- Loaded {len(field_samples_df)} records from 'field_samples'.\")\n", + " \n", + " # Query the geographic_locations table\n", + " statement_locations = select(GeographicLocation)\n", + " results_locations = session.exec(statement_locations).all()\n", + " locations_df = pd.DataFrame([location.model_dump() for location in results_locations])\n", + " print(f\"- Loaded {len(locations_df)} records from 'geographic_locations'.\")\n", + "\n", + " # Query the primary_product table\n", + " statement_products = select(PrimaryProduct)\n", + " results_products = session.exec(statement_products).all()\n", + " primary_product_df = pd.DataFrame([product.model_dump() for product in results_products])\n", + " print(f\"- Loaded {len(primary_product_df)} records from 'primary_product'.\")\n", + "\n", + "except Exception as e:\n", + " print(f\"Error during database query: {e}\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "df2 = pd.read_sql(\"SELECT * FROM analysis_types\", engine)\n", + "df2 = df2.set_index(\"analysis_type_id\")\n", + "\n", + "df2.head()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Step 4: Join the DataFrames\n", + "\n", + "With our data loaded into DataFrames, we can now perform a standard `left` join using pandas to combine them on the `location_id` key. \n", + "\n", + "We include error handling to manage the case where the database is empty. If the DataFrames are empty, the join key might not exist, and the merge will fail. Our code will catch this and print a helpful message." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "merged_df = None\n", + "\n", + "try:\n", + " # Ensure dataframes are not None and not empty before merging\n", + " if field_samples_df is not None and not field_samples_df.empty:\n", + " merged_df = pd.merge(\n", + " left=field_samples_df, \n", + " right=locations_df, \n", + " how='left', \n", + " on='location_id'\n", + " )\n", + " print(\"Join complete.\")\n", + " else:\n", + " print(\"Skipping join because 'field_samples' table is empty.\")\n", + "except KeyError as e:\n", + " print(f\"Error during join: Could not find join key {e}. This can happen if the tables are empty.\")\n", + "except Exception as e:\n", + " print(f\"An unexpected error occurred during the join: {e}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Step 5: Display Results\n", + "\n", + "Finally, we can display the head of the merged DataFrame to inspect the result." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "if merged_df is not None:\n", + " display(merged_df.head())\n", + "else:\n", + " print(\"No data to display.\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "default", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.14.0" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} From 8bd307d9da4e87445724bb719d93a870753d94d9 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Fri, 14 Nov 2025 14:02:33 -0700 Subject: [PATCH 11/81] feat: attempting to add schemas folder to datamodels module and import sqlalchemy via alembic --- alembic/env.py | 19 +- ...9_testing_linkml_created_python_object_.py | 32 - ...490235da5633_use_snake_case_table_names.py | 158 ---- .../523eedbcaf6e_initial_migration.py | 877 ++++++++++++++++++ ...4_testing_linkml_created_python_object_.py | 96 -- .../datamodels/schemas/__init__.py | 1 + .../datamodels/schemas}/common/geography.yaml | 0 .../schemas}/common/locations_address.yml | 0 .../datamodels/schemas/generated/__init__.py | 1 + .../schemas}/generated/census_survey.py | 0 .../schemas}/generated/geography.py | 0 .../schemas}/linkml_sqla_generation.md | 0 .../schemas}/pydantic/census_survey.py | 0 .../datamodels/schemas}/pydantic/geography.py | 0 .../datamodels/schemas}/template.yaml | 0 .../schemas}/usda/census_survey.yaml | 0 16 files changed, 881 insertions(+), 303 deletions(-) delete mode 100644 alembic/versions/38398b232319_testing_linkml_created_python_object_.py delete mode 100644 alembic/versions/490235da5633_use_snake_case_table_names.py create mode 100644 alembic/versions/523eedbcaf6e_initial_migration.py delete mode 100644 alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/common/geography.yaml (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/common/locations_address.yml (100%) create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/generated/census_survey.py (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/generated/geography.py (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/linkml_sqla_generation.md (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/pydantic/census_survey.py (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/pydantic/geography.py (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/template.yaml (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/usda/census_survey.yaml (100%) diff --git a/alembic/env.py b/alembic/env.py index 8f072a32..4b372e23 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -29,23 +29,8 @@ from pathlib import Path # --- Import generated models --- -# You can explicitly import your generated models here, or uncomment the -# code below to dynamically import them. -from schemas.generated.census_survey import * -from schemas.generated.geography import * - -# # --- Dynamically import generated models --- -# # This code will dynamically import all Python files from the -# # schemas/generated directory. This is a convenience so that you don't have -# # to add a new import statement every time you generate a new model from a -# # LinkML schema. -# generated_path = Path(__file__).resolve().parents[1] / "schemas" / "generated" -# for file in os.listdir(generated_path): -# if file.endswith(".py") and file != "__init__.py": -# module_name = file[:-3] -# spec = importlib.util.spec_from_file_location(module_name, generated_path / file) -# module = importlib.util.module_from_spec(spec) -# spec.loader.exec_module(module) +from ca_biositing.datamodels.schemas.generated.census_survey import * +from ca_biositing.datamodels.schemas.generated.geography import * # --- Alembic Config object, provides access to alembic.ini values --- config = context.config diff --git a/alembic/versions/38398b232319_testing_linkml_created_python_object_.py b/alembic/versions/38398b232319_testing_linkml_created_python_object_.py deleted file mode 100644 index fd2da614..00000000 --- a/alembic/versions/38398b232319_testing_linkml_created_python_object_.py +++ /dev/null @@ -1,32 +0,0 @@ -"""testing linkml created python object creation - -Revision ID: 38398b232319 -Revises: 8de419051d03 -Create Date: 2025-10-30 16:23:52.506268 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '38398b232319' -down_revision: Union[str, Sequence[str], None] = '8de419051d03' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### diff --git a/alembic/versions/490235da5633_use_snake_case_table_names.py b/alembic/versions/490235da5633_use_snake_case_table_names.py deleted file mode 100644 index 0a51c6d2..00000000 --- a/alembic/versions/490235da5633_use_snake_case_table_names.py +++ /dev/null @@ -1,158 +0,0 @@ -"""use snake_case table names - -Revision ID: 490235da5633 -Revises: 99af25a3b574 -Create Date: 2025-10-30 16:42:11.402363 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '490235da5633' -down_revision: Union[str, Sequence[str], None] = '99af25a3b574' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - op.drop_table('USDARecord') - op.drop_table('SurveyRecord') - op.drop_table('CensusRecord') - op.drop_table('Geography') - op.create_table('geography', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('state_name', sa.Text(), nullable=True), - sa.Column('state_fips', sa.Text(), nullable=True), - sa.Column('county_name', sa.Text(), nullable=True), - sa.Column('county_fips', sa.Text(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('region_name', sa.Text(), nullable=True), - sa.Column('agg_level_desc', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_record', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('census_record', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('survey_record', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('period_desc', sa.Text(), nullable=True), - sa.Column('freq_desc', sa.Text(), nullable=True), - sa.Column('program_desc', sa.Text(), nullable=True), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - - -def downgrade() -> None: - """Downgrade schema.""" - op.drop_table('survey_record') - op.drop_table('census_record') - op.drop_table('usda_record') - op.drop_table('geography') - op.create_table('USDARecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('SurveyRecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('period_desc', sa.Text(), nullable=True), - sa.Column('freq_desc', sa.Text(), nullable=True), - sa.Column('program_desc', sa.Text(), nullable=True), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('CensusRecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('Geography', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('state_name', sa.Text(), nullable=True), - sa.Column('state_fips', sa.Text(), nullable=True), - sa.Column('county_name', sa.Text(), nullable=True), - sa.Column('county_fips', sa.Text(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('region_name', sa.Text(), nullable=True), - sa.Column('agg_level_desc', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) diff --git a/alembic/versions/523eedbcaf6e_initial_migration.py b/alembic/versions/523eedbcaf6e_initial_migration.py new file mode 100644 index 00000000..402bc49d --- /dev/null +++ b/alembic/versions/523eedbcaf6e_initial_migration.py @@ -0,0 +1,877 @@ +"""Initial migration + +Revision ID: 523eedbcaf6e +Revises: +Create Date: 2025-11-14 20:44:50.143083 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa +import sqlmodel + +# revision identifiers, used by Alembic. +revision: str = '523eedbcaf6e' +down_revision: Union[str, Sequence[str], None] = None +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('affiliations', + sa.Column('affiliation_id', sa.Integer(), nullable=False), + sa.Column('affiliation_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('affiliation_id'), + sa.UniqueConstraint('affiliation_name') + ) + op.create_table('ag_treatments', + sa.Column('ag_treatment_id', sa.Integer(), nullable=False), + sa.Column('ag_treatment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('ag_treatment_id') + ) + op.create_table('analysis_abbreviations', + sa.Column('analysis_abbreviations_id', sa.Integer(), nullable=False), + sa.Column('analysis_abbreviation', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_abbreviations_id'), + sa.UniqueConstraint('analysis_abbreviation') + ) + op.create_table('analysis_replicate_id', + sa.Column('analysis_replicate_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('analysis_types_id', sa.Integer(), nullable=True), + sa.Column('analysis_replicate_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_replicate_id') + ) + op.create_table('analysis_results', + sa.Column('result_id', sa.Integer(), nullable=False), + sa.Column('anlaysis_sample', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('analysis_timestamp', sa.DateTime(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('qc_result_id', sa.Integer(), nullable=True), + sa.Column('measurement_equipment_id', sa.Integer(), nullable=True), + sa.Column('raw_data_url_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('analysis_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('result_id') + ) + op.create_index('idx_analysis_results_parameter_id', 'analysis_results', ['parameter_id'], unique=False) + op.create_index('uq_analysis_results_experiment_parameter_replicate', 'analysis_results', ['experiment_id', 'parameter_id', 'replicate_no'], unique=True) + op.create_table('analysis_types', + sa.Column('analysis_type_id', sa.Integer(), nullable=False), + sa.Column('analysis_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_type_id'), + sa.UniqueConstraint('analysis_name') + ) + op.create_table('analyst_contact', + sa.Column('analyst_id', sa.Integer(), nullable=False), + sa.Column('analyst_first_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_last_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_email', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_affiliation', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('analyst_id') + ) + op.create_table('autoclave_profile', + sa.Column('autoclave_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('autoclave_id') + ) + op.create_table('biomass', + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('biomass_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('primary_product_id', sa.Integer(), nullable=True), + sa.Column('taxonomy_id', sa.Integer(), nullable=True), + sa.Column('biomass_type_id', sa.Integer(), nullable=True), + sa.Column('biomass_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('biomass_id') + ) + op.create_index(op.f('ix_biomass_biomass_name'), 'biomass', ['biomass_name'], unique=False) + op.create_index(op.f('ix_biomass_biomass_type_id'), 'biomass', ['biomass_type_id'], unique=False) + op.create_table('biomass_availability', + sa.Column('availability_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('primary_product_id', sa.Integer(), nullable=True), + sa.Column('from_month', sa.Numeric(), nullable=True), + sa.Column('to_month', sa.Numeric(), nullable=True), + sa.Column('kg_low', sa.Numeric(), nullable=True), + sa.Column('kg_avg', sa.Numeric(), nullable=True), + sa.Column('kg_high', sa.Numeric(), nullable=True), + sa.Column('bdt_low', sa.Numeric(), nullable=True), + sa.Column('bdt_avg', sa.Numeric(), nullable=True), + sa.Column('bdt_high', sa.Numeric(), nullable=True), + sa.Column('data_source', sa.Integer(), nullable=True), + sa.Column('availability_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('availability_id') + ) + op.create_index(op.f('ix_biomass_availability_biomass_id'), 'biomass_availability', ['biomass_id'], unique=False) + op.create_table('biomass_price', + sa.Column('price_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('price_per_kg_low', sa.Numeric(), nullable=True), + sa.Column('price_per_kg_avg', sa.Numeric(), nullable=True), + sa.Column('price_per_kg_high', sa.Numeric(), nullable=True), + sa.Column('price_data_sources', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('price_id') + ) + op.create_index(op.f('ix_biomass_price_biomass_id'), 'biomass_price', ['biomass_id'], unique=False) + op.create_table('biomass_quality', + sa.Column('quality_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('expected_quality', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('output_feedstocks', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('convertibility', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('disposal_challenges', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('existing_markets', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('substitute_materials', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('regulatory_issues', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('quality_data_sources', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('quality_id') + ) + op.create_index(op.f('ix_biomass_quality_biomass_id'), 'biomass_quality', ['biomass_id'], unique=False) + op.create_table('biomass_test', + sa.Column('biomass_test_id', sa.Integer(), nullable=False), + sa.Column('biomass_test_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('biomass_test_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('biomass_test_id') + ) + op.create_index(op.f('ix_biomass_test_biomass_test_name'), 'biomass_test', ['biomass_test_name'], unique=False) + op.create_table('biomass_type', + sa.Column('biomass_type_id', sa.Integer(), nullable=False), + sa.Column('biomass_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('biomass_type_id'), + sa.UniqueConstraint('biomass_type') + ) + op.create_table('buildings', + sa.Column('building_id', sa.Integer(), nullable=False), + sa.Column('building_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('affiliation_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('building_id'), + sa.UniqueConstraint('building_name') + ) + op.create_table('cities', + sa.Column('city_id', sa.Integer(), nullable=False), + sa.Column('city_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('city_id'), + sa.UniqueConstraint('city_name') + ) + op.create_table('collection_methods', + sa.Column('collection_method_id', sa.Integer(), nullable=False), + sa.Column('collection_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('collection_method_id'), + sa.UniqueConstraint('collection_method_name') + ) + op.create_table('collectors', + sa.Column('collector_id', sa.Integer(), nullable=False), + sa.Column('collector_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('collector_affiliation', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('collector_id'), + sa.UniqueConstraint('collector_name') + ) + op.create_table('compositional_analysis', + sa.Column('cmp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('calculated_parameter_id', sa.Integer(), nullable=True), + sa.Column('calculated_parameter_value', sa.Numeric(), nullable=True), + sa.Column('calculated_parameter_unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('cmp_id') + ) + op.create_table('counties', + sa.Column('county_id', sa.Integer(), nullable=False), + sa.Column('county_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('county_id'), + sa.UniqueConstraint('county_name') + ) + op.create_table('data_sources', + sa.Column('source_id', sa.Integer(), nullable=False), + sa.Column('source_name_id', sa.Integer(), nullable=True), + sa.Column('source_type_id', sa.Integer(), nullable=True), + sa.Column('data_resolution_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('url_id', sa.Integer(), nullable=True), + sa.Column('import_timestamp', sa.DateTime(), nullable=True), + sa.PrimaryKeyConstraint('source_id') + ) + op.create_index('idx_data_sources_source_name_id', 'data_sources', ['source_name_id'], unique=False) + op.create_table('doi', + sa.Column('doi_id', sa.Integer(), nullable=False), + sa.Column('doi', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('doi_id') + ) + op.create_table('equipment', + sa.Column('equipment_id', sa.Integer(), nullable=False), + sa.Column('equipment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('equipment_room_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('equipment_id'), + sa.UniqueConstraint('equipment_name') + ) + op.create_table('experiment_methods', + sa.Column('experiment_method_id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('experiment_method_id') + ) + op.create_index('idx_experiment_methods_experiment_id', 'experiment_methods', ['experiment_id'], unique=False) + op.create_index('idx_experiment_methods_method_id', 'experiment_methods', ['method_id'], unique=False) + op.create_table('experiments', + sa.Column('experiment_id', sa.Integer(), nullable=False), + sa.Column('exper_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('gsheet_exper_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('analysis_abbrev_id', sa.Integer(), nullable=True), + sa.Column('exper_start_date', sa.Date(), nullable=True), + sa.Column('exper_duration', sa.Numeric(), nullable=True), + sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('exper_location_id', sa.Integer(), nullable=True), + sa.Column('exper_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('experiment_id'), + sa.UniqueConstraint('exper_uuid'), + sa.UniqueConstraint('gsheet_exper_id') + ) + op.create_index('idx_experiments_analysis_type_id', 'experiments', ['analysis_type_id'], unique=False) + op.create_table('external_atip', + sa.Column('atip_ID', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('atip_ID') + ) + op.create_table('external_dairy_one', + sa.Column('dairy_one_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('samples_count', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('accumulated_years_from', sa.Date(), nullable=True), + sa.Column('accumulated_years_to', sa.Date(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('dairy_one_id') + ) + op.create_index('idx_external_dairy_one_biomass_id', 'external_dairy_one', ['biomass_id'], unique=False) + op.create_index('idx_external_dairy_one_parameter_id', 'external_dairy_one', ['parameter_id'], unique=False) + op.create_table('external_ebmud', + sa.Column('ebmud_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('ebmud_id') + ) + op.create_table('external_inl_biofeedstock_library', + sa.Column('bfl_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('state_id', sa.Integer(), nullable=True), + sa.Column('affiliations_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('accumulated_years_from', sa.Date(), nullable=True), + sa.Column('accumulated_years_to', sa.Date(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('bfl_id') + ) + op.create_index('idx_external_inl_biofeedstock_library_biomass_id', 'external_inl_biofeedstock_library', ['biomass_id'], unique=False) + op.create_table('external_land_id', + sa.Column('land_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('land_id') + ) + op.create_table('external_phyllis2', + sa.Column('phyllis_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('phyllis_id') + ) + op.create_index('idx_external_phyllis2_analysis_type_id', 'external_phyllis2', ['analysis_type_id'], unique=False) + op.create_index('idx_external_phyllis2_biomass_id', 'external_phyllis2', ['biomass_id'], unique=False) + op.create_table('external_usda', + sa.Column('usda_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('usda_id') + ) + op.create_table('fermentation_profile', + sa.Column('fp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('organism_id', sa.Integer(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('fp_id') + ) + op.create_table('field_samples', + sa.Column('sample_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('sample_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('source_codename_id', sa.Integer(), nullable=True), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('field_storage_id', sa.Integer(), nullable=True), + sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), + sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('collection_timestamp', sa.DateTime(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_date', sa.Date(), nullable=True), + sa.Column('amount_collected_kg', sa.Numeric(), nullable=True), + sa.Column('provider_id', sa.Integer(), nullable=True), + sa.Column('collector_id', sa.Integer(), nullable=True), + sa.Column('basic_sample_info_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.PrimaryKeyConstraint('sample_id') + ) + op.create_index(op.f('ix_field_samples_biomass_id'), 'field_samples', ['biomass_id'], unique=False) + op.create_index(op.f('ix_field_samples_source_codename_id'), 'field_samples', ['source_codename_id'], unique=False) + op.create_table('field_storage', + sa.Column('field_storage_id', sa.Integer(), nullable=False), + sa.Column('storage_method', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('field_storage_id'), + sa.UniqueConstraint('storage_method') + ) + op.create_table('fips', + sa.Column('fips_id', sa.Integer(), nullable=False), + sa.Column('fips_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('fips_id') + ) + op.create_table('gasification_profile', + sa.Column('gasification_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('gasification_id') + ) + op.create_table('geographic_locations', + sa.Column('location_id', sa.Integer(), nullable=False), + sa.Column('street_address_id', sa.Integer(), nullable=True), + sa.Column('city_id', sa.Integer(), nullable=True), + sa.Column('zip_id', sa.Integer(), nullable=True), + sa.Column('county_id', sa.Integer(), nullable=True), + sa.Column('state_id', sa.Integer(), nullable=True), + sa.Column('region_id', sa.Integer(), nullable=True), + sa.Column('fips_id', sa.Integer(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('location_resolution_id', sa.Integer(), nullable=True), + sa.Column('is_anonymous', sa.Boolean(), nullable=True), + sa.PrimaryKeyConstraint('location_id') + ) + op.create_table('harvest_methods', + sa.Column('harvest_method_id', sa.Integer(), nullable=False), + sa.Column('harvest_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('harvest_method_id'), + sa.UniqueConstraint('harvest_method_name') + ) + op.create_table('icp_analysis', + sa.Column('icp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('concentration_calculation_url_id', sa.Integer(), nullable=True), + sa.Column('result_wavelength', sa.Numeric(), nullable=True), + sa.Column('raw_url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('icp_id') + ) + op.create_table('import_log', + sa.Column('import_id', sa.Integer(), nullable=False), + sa.Column('import_timestamp', sa.DateTime(), nullable=True), + sa.Column('destination', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('source_file', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('records_imported', sa.Integer(), nullable=True), + sa.Column('import_status', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('error_log', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_user', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('import_id') + ) + op.create_table('location_resolutions', + sa.Column('location_resolution_id', sa.Integer(), nullable=False), + sa.Column('resolution_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('location_resolution_id'), + sa.UniqueConstraint('resolution_type') + ) + op.create_table('metadata', + sa.Column('metadata_id', sa.Integer(), nullable=False), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('ag_treatment_id', sa.Integer(), nullable=True), + sa.Column('last_application_date', sa.Date(), nullable=True), + sa.Column('treatment_amount_per_acre', sa.Numeric(), nullable=True), + sa.Column('soil_type', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('metadata_id') + ) + op.create_table('method_abbrevs', + sa.Column('method_abbrev_id', sa.Integer(), nullable=False), + sa.Column('method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_abbrev_id'), + sa.UniqueConstraint('method_abbrev') + ) + op.create_table('method_categories', + sa.Column('method_category_id', sa.Integer(), nullable=False), + sa.Column('method_category', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_category_id'), + sa.UniqueConstraint('method_category') + ) + op.create_table('method_equipment', + sa.Column('method_equipment_id', sa.Integer(), nullable=False), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('equipment_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('method_equipment_id') + ) + op.create_index('idx_method_equipment_equipment_id', 'method_equipment', ['equipment_id'], unique=False) + op.create_index('idx_method_equipment_method_id', 'method_equipment', ['method_id'], unique=False) + op.create_table('method_standards', + sa.Column('method_standard_id', sa.Integer(), nullable=False), + sa.Column('method_standard', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_standard_id'), + sa.UniqueConstraint('method_standard') + ) + op.create_table('methods', + sa.Column('method_id', sa.Integer(), nullable=False), + sa.Column('method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('method_category_id', sa.Integer(), nullable=True), + sa.Column('method_standard_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('detection_limits', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('procedure_reference_id', sa.Integer(), nullable=True), + sa.Column('method_url_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('method_id'), + sa.UniqueConstraint('method_name') + ) + op.create_index('idx_methods_method_name', 'methods', ['method_name'], unique=False) + op.create_table('organisms', + sa.Column('organism_id', sa.Integer(), nullable=False), + sa.Column('organism_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('organism_strain_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('organism_id') + ) + op.create_table('parameter_catagories', + sa.Column('parameter_catagory_id', sa.Integer(), nullable=False), + sa.Column('parameter_catagory', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('parameter_catagory_id') + ) + op.create_table('parameter_methods', + sa.Column('param_method_id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('param_method_id') + ) + op.create_table('parameter_units', + sa.Column('parameter_unit_id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('parameter_unit_id') + ) + op.create_index('idx_parameter_units_parameter_id', 'parameter_units', ['parameter_id'], unique=False) + op.create_index('idx_parameter_units_unit_id', 'parameter_units', ['unit_id'], unique=False) + op.create_table('parameters', + sa.Column('parameter_id', sa.Integer(), nullable=False), + sa.Column('parameter_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('parameter_category_id', sa.Integer(), nullable=True), + sa.Column('standard_unit_id', sa.Integer(), nullable=True), + sa.Column('calculated', sa.Boolean(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('typical_range_min', sa.Numeric(), nullable=True), + sa.Column('typical_range_max', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('parameter_id'), + sa.UniqueConstraint('parameter_name') + ) + op.create_table('particle_size', + sa.Column('particle_size_id', sa.Integer(), nullable=False), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('particle_length', sa.Integer(), nullable=True), + sa.Column('particle_width', sa.Integer(), nullable=True), + sa.Column('particle_height', sa.Integer(), nullable=True), + sa.Column('particle_units', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('particle_size_id') + ) + op.create_table('preprocessed_samples', + sa.Column('prepro_material_id', sa.Integer(), nullable=False), + sa.Column('prepro_material_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('biomass_sample_id', sa.Integer(), nullable=True), + sa.Column('prepro_method_id', sa.Integer(), nullable=True), + sa.Column('amount_before_drying_g', sa.Numeric(), nullable=True), + sa.Column('amount_after_drying', sa.Numeric(), nullable=True), + sa.Column('processing_date', sa.Date(), nullable=True), + sa.Column('storage_building', sa.Integer(), nullable=True), + sa.Column('amount_remaining_g', sa.Numeric(), nullable=True), + sa.Column('amount_as_of_date', sa.Date(), nullable=True), + sa.Column('prepro_analyst_id', sa.Integer(), nullable=True), + sa.Column('prepro_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prepro_material_id') + ) + op.create_index('idx_preprocessed_samples_biomass_sample_id', 'preprocessed_samples', ['biomass_sample_id'], unique=False) + op.create_index('idx_preprocessed_samples_prepro_method_id', 'preprocessed_samples', ['prepro_method_id'], unique=False) + op.create_table('preprocessing_methods', + sa.Column('prepro_method_id', sa.Integer(), nullable=False), + sa.Column('prepro_method', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('prepro_method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('prepro_temp_c', sa.Numeric(), nullable=True), + sa.Column('drying_step', sa.Boolean(), nullable=True), + sa.Column('method_ref_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('prepro_method_id') + ) + op.create_table('preprocessing_methods_abbreviations', + sa.Column('prepro_methods_abbrev_id', sa.Integer(), nullable=False), + sa.Column('prepro_method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prepro_methods_abbrev_id'), + sa.UniqueConstraint('prepro_method_abbrev') + ) + op.create_table('primary_product', + sa.Column('primary_product_id', sa.Integer(), nullable=False), + sa.Column('primary_product_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('primary_product_id'), + sa.UniqueConstraint('primary_product_name') + ) + op.create_table('product_type', + sa.Column('product_type_id', sa.Integer(), nullable=False), + sa.Column('product', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('product_type_id') + ) + op.create_table('provider_types', + sa.Column('provider_type_id', sa.Integer(), nullable=False), + sa.Column('provider_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('provider_type_id') + ) + op.create_table('providers', + sa.Column('provider_id', sa.Integer(), nullable=False), + sa.Column('provider_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('provider_affiliation', sa.Integer(), nullable=True), + sa.Column('provider_type_id', sa.Integer(), nullable=True), + sa.Column('anonymous', sa.Boolean(), nullable=True), + sa.PrimaryKeyConstraint('provider_id'), + sa.UniqueConstraint('provider_name') + ) + op.create_table('proximate_analysis', + sa.Column('prox_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prox_id') + ) + op.create_table('qc_results', + sa.Column('qc_result_id', sa.Integer(), nullable=False), + sa.Column('qc_result', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('qc_result_id'), + sa.UniqueConstraint('qc_result') + ) + op.create_table('raster_metadata', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('resolution', sa.Float(), nullable=True), + sa.Column('srid', sa.Integer(), nullable=True), + sa.Column('acquisition_date', sa.Date(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('references', + sa.Column('reference_id', sa.Integer(), nullable=False), + sa.Column('reference_title', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_author', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_publication', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_date', sa.Date(), nullable=True), + sa.Column('reference_doi_id', sa.Integer(), nullable=True), + sa.Column('url_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('reference_id') + ) + op.create_table('regions', + sa.Column('region_id', sa.Integer(), nullable=False), + sa.Column('region_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('region_id'), + sa.UniqueConstraint('region_name') + ) + op.create_table('rooms', + sa.Column('room_id', sa.Integer(), nullable=False), + sa.Column('room_number', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('building_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('room_id'), + sa.UniqueConstraint('room_number') + ) + op.create_table('soil_type', + sa.Column('soil_type_id', sa.Integer(), nullable=False), + sa.Column('soil_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('soil_location', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('soil_type_id'), + sa.UniqueConstraint('soil_type') + ) + op.create_table('source_names', + sa.Column('source_name_id', sa.Integer(), nullable=False), + sa.Column('source_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('source_name_id'), + sa.UniqueConstraint('source_name') + ) + op.create_table('source_types', + sa.Column('source_type_id', sa.Integer(), nullable=False), + sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('source_type_id'), + sa.UniqueConstraint('source_type') + ) + op.create_table('states', + sa.Column('state_id', sa.Integer(), nullable=False), + sa.Column('state_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('state_id'), + sa.UniqueConstraint('state_name') + ) + op.create_table('street_addresses', + sa.Column('street_address_id', sa.Integer(), nullable=False), + sa.Column('street_address', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('street_address_id') + ) + op.create_table('taxonomy', + sa.Column('taxonomy_id', sa.Integer(), nullable=False), + sa.Column('kingdom', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('phylum', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('order', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('family', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('genus', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('species', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('variety_subspecies_cultivar', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('taxonomy_id') + ) + op.create_table('testusers2', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('fullname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('nickname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('units', + sa.Column('unit_id', sa.Integer(), nullable=False), + sa.Column('unit', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('unit_id'), + sa.UniqueConstraint('unit') + ) + op.create_table('url', + sa.Column('url_id', sa.Integer(), nullable=False), + sa.Column('url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('url_id'), + sa.UniqueConstraint('url') + ) + op.create_table('vectorized_raster_polygons', + sa.Column('vectorized_ID', sa.Integer(), nullable=False), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('raster_id', sa.Integer(), nullable=True), + sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('mean_value', sa.Float(), nullable=True), + sa.Column('std_dev', sa.Float(), nullable=True), + sa.Column('area_m2', sa.Float(), nullable=True), + sa.Column('date_acquired', sa.Date(), nullable=True), + sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('vectorized_ID') + ) + op.create_table('xrf_analysis', + sa.Column('xrf_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('xrf_id') + ) + op.create_table('zips', + sa.Column('zip_id', sa.Integer(), nullable=False), + sa.Column('zip_code', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('zip_id'), + sa.UniqueConstraint('zip_code') + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('zips') + op.drop_table('xrf_analysis') + op.drop_table('vectorized_raster_polygons') + op.drop_table('url') + op.drop_table('units') + op.drop_table('testusers2') + op.drop_table('taxonomy') + op.drop_table('street_addresses') + op.drop_table('states') + op.drop_table('source_types') + op.drop_table('source_names') + op.drop_table('soil_type') + op.drop_table('rooms') + op.drop_table('regions') + op.drop_table('references') + op.drop_table('raster_metadata') + op.drop_table('qc_results') + op.drop_table('proximate_analysis') + op.drop_table('providers') + op.drop_table('provider_types') + op.drop_table('product_type') + op.drop_table('primary_product') + op.drop_table('preprocessing_methods_abbreviations') + op.drop_table('preprocessing_methods') + op.drop_index('idx_preprocessed_samples_prepro_method_id', table_name='preprocessed_samples') + op.drop_index('idx_preprocessed_samples_biomass_sample_id', table_name='preprocessed_samples') + op.drop_table('preprocessed_samples') + op.drop_table('particle_size') + op.drop_table('parameters') + op.drop_index('idx_parameter_units_unit_id', table_name='parameter_units') + op.drop_index('idx_parameter_units_parameter_id', table_name='parameter_units') + op.drop_table('parameter_units') + op.drop_table('parameter_methods') + op.drop_table('parameter_catagories') + op.drop_table('organisms') + op.drop_index('idx_methods_method_name', table_name='methods') + op.drop_table('methods') + op.drop_table('method_standards') + op.drop_index('idx_method_equipment_method_id', table_name='method_equipment') + op.drop_index('idx_method_equipment_equipment_id', table_name='method_equipment') + op.drop_table('method_equipment') + op.drop_table('method_categories') + op.drop_table('method_abbrevs') + op.drop_table('metadata') + op.drop_table('location_resolutions') + op.drop_table('import_log') + op.drop_table('icp_analysis') + op.drop_table('harvest_methods') + op.drop_table('geographic_locations') + op.drop_table('gasification_profile') + op.drop_table('fips') + op.drop_table('field_storage') + op.drop_index(op.f('ix_field_samples_source_codename_id'), table_name='field_samples') + op.drop_index(op.f('ix_field_samples_biomass_id'), table_name='field_samples') + op.drop_table('field_samples') + op.drop_table('fermentation_profile') + op.drop_table('external_usda') + op.drop_index('idx_external_phyllis2_biomass_id', table_name='external_phyllis2') + op.drop_index('idx_external_phyllis2_analysis_type_id', table_name='external_phyllis2') + op.drop_table('external_phyllis2') + op.drop_table('external_land_id') + op.drop_index('idx_external_inl_biofeedstock_library_biomass_id', table_name='external_inl_biofeedstock_library') + op.drop_table('external_inl_biofeedstock_library') + op.drop_table('external_ebmud') + op.drop_index('idx_external_dairy_one_parameter_id', table_name='external_dairy_one') + op.drop_index('idx_external_dairy_one_biomass_id', table_name='external_dairy_one') + op.drop_table('external_dairy_one') + op.drop_table('external_atip') + op.drop_index('idx_experiments_analysis_type_id', table_name='experiments') + op.drop_table('experiments') + op.drop_index('idx_experiment_methods_method_id', table_name='experiment_methods') + op.drop_index('idx_experiment_methods_experiment_id', table_name='experiment_methods') + op.drop_table('experiment_methods') + op.drop_table('equipment') + op.drop_table('doi') + op.drop_index('idx_data_sources_source_name_id', table_name='data_sources') + op.drop_table('data_sources') + op.drop_table('counties') + op.drop_table('compositional_analysis') + op.drop_table('collectors') + op.drop_table('collection_methods') + op.drop_table('cities') + op.drop_table('buildings') + op.drop_table('biomass_type') + op.drop_index(op.f('ix_biomass_test_biomass_test_name'), table_name='biomass_test') + op.drop_table('biomass_test') + op.drop_index(op.f('ix_biomass_quality_biomass_id'), table_name='biomass_quality') + op.drop_table('biomass_quality') + op.drop_index(op.f('ix_biomass_price_biomass_id'), table_name='biomass_price') + op.drop_table('biomass_price') + op.drop_index(op.f('ix_biomass_availability_biomass_id'), table_name='biomass_availability') + op.drop_table('biomass_availability') + op.drop_index(op.f('ix_biomass_biomass_type_id'), table_name='biomass') + op.drop_index(op.f('ix_biomass_biomass_name'), table_name='biomass') + op.drop_table('biomass') + op.drop_table('autoclave_profile') + op.drop_table('analyst_contact') + op.drop_table('analysis_types') + op.drop_index('uq_analysis_results_experiment_parameter_replicate', table_name='analysis_results') + op.drop_index('idx_analysis_results_parameter_id', table_name='analysis_results') + op.drop_table('analysis_results') + op.drop_table('analysis_replicate_id') + op.drop_table('analysis_abbreviations') + op.drop_table('ag_treatments') + op.drop_table('affiliations') + # ### end Alembic commands ### diff --git a/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py b/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py deleted file mode 100644 index 0d1fba2e..00000000 --- a/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py +++ /dev/null @@ -1,96 +0,0 @@ -"""testing linkml created python object creation - -Revision ID: 99af25a3b574 -Revises: 38398b232319 -Create Date: 2025-10-30 16:38:00.752859 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '99af25a3b574' -down_revision: Union[str, Sequence[str], None] = '38398b232319' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.create_table('Geography', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('state_name', sa.Text(), nullable=True), - sa.Column('state_fips', sa.Text(), nullable=True), - sa.Column('county_name', sa.Text(), nullable=True), - sa.Column('county_fips', sa.Text(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('region_name', sa.Text(), nullable=True), - sa.Column('agg_level_desc', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('CensusRecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('SurveyRecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('period_desc', sa.Text(), nullable=True), - sa.Column('freq_desc', sa.Text(), nullable=True), - sa.Column('program_desc', sa.Text(), nullable=True), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('USDARecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.drop_table('USDARecord') - op.drop_table('SurveyRecord') - op.drop_table('CensusRecord') - op.drop_table('Geography') - # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py new file mode 100644 index 00000000..dbb70e85 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py @@ -0,0 +1 @@ +# This file makes this a Python package. diff --git a/schemas/common/geography.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/common/geography.yaml similarity index 100% rename from schemas/common/geography.yaml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/common/geography.yaml diff --git a/schemas/common/locations_address.yml b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/common/locations_address.yml similarity index 100% rename from schemas/common/locations_address.yml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/common/locations_address.yml diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py new file mode 100644 index 00000000..dbb70e85 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py @@ -0,0 +1 @@ +# This file makes this a Python package. diff --git a/schemas/generated/census_survey.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py similarity index 100% rename from schemas/generated/census_survey.py rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py diff --git a/schemas/generated/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py similarity index 100% rename from schemas/generated/geography.py rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py diff --git a/schemas/linkml_sqla_generation.md b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/linkml_sqla_generation.md similarity index 100% rename from schemas/linkml_sqla_generation.md rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/linkml_sqla_generation.md diff --git a/schemas/pydantic/census_survey.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/pydantic/census_survey.py similarity index 100% rename from schemas/pydantic/census_survey.py rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/pydantic/census_survey.py diff --git a/schemas/pydantic/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/pydantic/geography.py similarity index 100% rename from schemas/pydantic/geography.py rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/pydantic/geography.py diff --git a/schemas/template.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/template.yaml similarity index 100% rename from schemas/template.yaml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/template.yaml diff --git a/schemas/usda/census_survey.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/usda/census_survey.yaml similarity index 100% rename from schemas/usda/census_survey.yaml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/usda/census_survey.yaml From ade469461d9dbd719d70adc163064310c9ec0e7e Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Fri, 14 Nov 2025 11:54:16 -0700 Subject: [PATCH 12/81] added a jupyter notebook for playing around with connecting to db --- ERD_VIEW.md | 61 ++ .../301006b4795f_initial_migration.py | 32 + .../e15bda744fef_initial_migration.py | 877 ++++++++++++++++++ census.survey.mmd | 53 ++ review_summary.txt | 76 ++ 5 files changed, 1099 insertions(+) create mode 100644 ERD_VIEW.md create mode 100644 alembic/versions/301006b4795f_initial_migration.py create mode 100644 alembic/versions/e15bda744fef_initial_migration.py create mode 100644 census.survey.mmd create mode 100644 review_summary.txt diff --git a/ERD_VIEW.md b/ERD_VIEW.md new file mode 100644 index 00000000..05b1930f --- /dev/null +++ b/ERD_VIEW.md @@ -0,0 +1,61 @@ +# ERD for USDA Census and Survey Data + +To view this diagram, open the Command Palette (`Cmd+Shift+P` on Mac or +`Ctrl+Shift+P` on Windows/Linux) and run **"Markdown: Open Preview to the +Side"**. + +```mermaid +erDiagram +CensusRecord { + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} +Geography { + string state_name + string state_fips + string county_name + string county_fips + string geoid + string region_name + string agg_level_desc +} +SurveyRecord { + string period_desc + string freq_desc + string program_desc + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} +UsdaRecord { + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} + +CensusRecord ||--|o Geography : "geography" +SurveyRecord ||--|o Geography : "geography" +UsdaRecord ||--|o Geography : "geography" +``` diff --git a/alembic/versions/301006b4795f_initial_migration.py b/alembic/versions/301006b4795f_initial_migration.py new file mode 100644 index 00000000..8e4f7afd --- /dev/null +++ b/alembic/versions/301006b4795f_initial_migration.py @@ -0,0 +1,32 @@ +"""Initial migration + +Revision ID: 301006b4795f +Revises: e15bda744fef +Create Date: 2025-11-12 20:54:01.573577 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '301006b4795f' +down_revision: Union[str, Sequence[str], None] = 'e15bda744fef' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/alembic/versions/e15bda744fef_initial_migration.py b/alembic/versions/e15bda744fef_initial_migration.py new file mode 100644 index 00000000..18517bc2 --- /dev/null +++ b/alembic/versions/e15bda744fef_initial_migration.py @@ -0,0 +1,877 @@ +"""Initial migration + +Revision ID: e15bda744fef +Revises: +Create Date: 2025-11-04 20:03:41.870493 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa +import sqlmodel + +# revision identifiers, used by Alembic. +revision: str = 'e15bda744fef' +down_revision: Union[str, Sequence[str], None] = None +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('affiliations', + sa.Column('affiliation_id', sa.Integer(), nullable=False), + sa.Column('affiliation_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('affiliation_id'), + sa.UniqueConstraint('affiliation_name') + ) + op.create_table('ag_treatments', + sa.Column('ag_treatment_id', sa.Integer(), nullable=False), + sa.Column('ag_treatment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('ag_treatment_id') + ) + op.create_table('analysis_abbreviations', + sa.Column('analysis_abbreviations_id', sa.Integer(), nullable=False), + sa.Column('analysis_abbreviation', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_abbreviations_id'), + sa.UniqueConstraint('analysis_abbreviation') + ) + op.create_table('analysis_replicate_id', + sa.Column('analysis_replicate_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('analysis_types_id', sa.Integer(), nullable=True), + sa.Column('analysis_replicate_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_replicate_id') + ) + op.create_table('analysis_results', + sa.Column('result_id', sa.Integer(), nullable=False), + sa.Column('anlaysis_sample', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('analysis_timestamp', sa.DateTime(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('qc_result_id', sa.Integer(), nullable=True), + sa.Column('measurement_equipment_id', sa.Integer(), nullable=True), + sa.Column('raw_data_url_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('analysis_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('result_id') + ) + op.create_index('idx_analysis_results_parameter_id', 'analysis_results', ['parameter_id'], unique=False) + op.create_index('uq_analysis_results_experiment_parameter_replicate', 'analysis_results', ['experiment_id', 'parameter_id', 'replicate_no'], unique=True) + op.create_table('analysis_types', + sa.Column('analysis_type_id', sa.Integer(), nullable=False), + sa.Column('analysis_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_type_id'), + sa.UniqueConstraint('analysis_name') + ) + op.create_table('analyst_contact', + sa.Column('analyst_id', sa.Integer(), nullable=False), + sa.Column('analyst_first_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_last_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_email', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_affiliation', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('analyst_id') + ) + op.create_table('autoclave_profile', + sa.Column('autoclave_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('autoclave_id') + ) + op.create_table('biomass', + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('biomass_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('primary_product_id', sa.Integer(), nullable=True), + sa.Column('taxonomy_id', sa.Integer(), nullable=True), + sa.Column('biomass_type_id', sa.Integer(), nullable=True), + sa.Column('biomass_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('biomass_id') + ) + op.create_index(op.f('ix_biomass_biomass_name'), 'biomass', ['biomass_name'], unique=False) + op.create_index(op.f('ix_biomass_biomass_type_id'), 'biomass', ['biomass_type_id'], unique=False) + op.create_table('biomass_availability', + sa.Column('availability_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('primary_product_id', sa.Integer(), nullable=True), + sa.Column('from_month', sa.Numeric(), nullable=True), + sa.Column('to_month', sa.Numeric(), nullable=True), + sa.Column('kg_low', sa.Numeric(), nullable=True), + sa.Column('kg_avg', sa.Numeric(), nullable=True), + sa.Column('kg_high', sa.Numeric(), nullable=True), + sa.Column('bdt_low', sa.Numeric(), nullable=True), + sa.Column('bdt_avg', sa.Numeric(), nullable=True), + sa.Column('bdt_high', sa.Numeric(), nullable=True), + sa.Column('data_source', sa.Integer(), nullable=True), + sa.Column('availability_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('availability_id') + ) + op.create_index(op.f('ix_biomass_availability_biomass_id'), 'biomass_availability', ['biomass_id'], unique=False) + op.create_table('biomass_price', + sa.Column('price_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('price_per_kg_low', sa.Numeric(), nullable=True), + sa.Column('price_per_kg_avg', sa.Numeric(), nullable=True), + sa.Column('price_per_kg_high', sa.Numeric(), nullable=True), + sa.Column('price_data_sources', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('price_id') + ) + op.create_index(op.f('ix_biomass_price_biomass_id'), 'biomass_price', ['biomass_id'], unique=False) + op.create_table('biomass_quality', + sa.Column('quality_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('expected_quality', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('output_feedstocks', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('convertibility', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('disposal_challenges', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('existing_markets', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('substitute_materials', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('regulatory_issues', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('quality_data_sources', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('quality_id') + ) + op.create_index(op.f('ix_biomass_quality_biomass_id'), 'biomass_quality', ['biomass_id'], unique=False) + op.create_table('biomass_test', + sa.Column('biomass_test_id', sa.Integer(), nullable=False), + sa.Column('biomass_test_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('biomass_test_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('biomass_test_id') + ) + op.create_index(op.f('ix_biomass_test_biomass_test_name'), 'biomass_test', ['biomass_test_name'], unique=False) + op.create_table('biomass_type', + sa.Column('biomass_type_id', sa.Integer(), nullable=False), + sa.Column('biomass_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('biomass_type_id'), + sa.UniqueConstraint('biomass_type') + ) + op.create_table('buildings', + sa.Column('building_id', sa.Integer(), nullable=False), + sa.Column('building_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('affiliation_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('building_id'), + sa.UniqueConstraint('building_name') + ) + op.create_table('cities', + sa.Column('city_id', sa.Integer(), nullable=False), + sa.Column('city_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('city_id'), + sa.UniqueConstraint('city_name') + ) + op.create_table('collection_methods', + sa.Column('collection_method_id', sa.Integer(), nullable=False), + sa.Column('collection_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('collection_method_id'), + sa.UniqueConstraint('collection_method_name') + ) + op.create_table('collectors', + sa.Column('collector_id', sa.Integer(), nullable=False), + sa.Column('collector_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('collector_affiliation', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('collector_id'), + sa.UniqueConstraint('collector_name') + ) + op.create_table('compositional_analysis', + sa.Column('cmp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('calculated_parameter_id', sa.Integer(), nullable=True), + sa.Column('calculated_parameter_value', sa.Numeric(), nullable=True), + sa.Column('calculated_parameter_unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('cmp_id') + ) + op.create_table('counties', + sa.Column('county_id', sa.Integer(), nullable=False), + sa.Column('county_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('county_id'), + sa.UniqueConstraint('county_name') + ) + op.create_table('data_sources', + sa.Column('source_id', sa.Integer(), nullable=False), + sa.Column('source_name_id', sa.Integer(), nullable=True), + sa.Column('source_type_id', sa.Integer(), nullable=True), + sa.Column('data_resolution_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('url_id', sa.Integer(), nullable=True), + sa.Column('import_timestamp', sa.DateTime(), nullable=True), + sa.PrimaryKeyConstraint('source_id') + ) + op.create_index('idx_data_sources_source_name_id', 'data_sources', ['source_name_id'], unique=False) + op.create_table('doi', + sa.Column('doi_id', sa.Integer(), nullable=False), + sa.Column('doi', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('doi_id') + ) + op.create_table('equipment', + sa.Column('equipment_id', sa.Integer(), nullable=False), + sa.Column('equipment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('equipment_room_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('equipment_id'), + sa.UniqueConstraint('equipment_name') + ) + op.create_table('experiment_methods', + sa.Column('experiment_method_id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('experiment_method_id') + ) + op.create_index('idx_experiment_methods_experiment_id', 'experiment_methods', ['experiment_id'], unique=False) + op.create_index('idx_experiment_methods_method_id', 'experiment_methods', ['method_id'], unique=False) + op.create_table('experiments', + sa.Column('experiment_id', sa.Integer(), nullable=False), + sa.Column('exper_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('gsheet_exper_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('analysis_abbrev_id', sa.Integer(), nullable=True), + sa.Column('exper_start_date', sa.Date(), nullable=True), + sa.Column('exper_duration', sa.Numeric(), nullable=True), + sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('exper_location_id', sa.Integer(), nullable=True), + sa.Column('exper_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('experiment_id'), + sa.UniqueConstraint('exper_uuid'), + sa.UniqueConstraint('gsheet_exper_id') + ) + op.create_index('idx_experiments_analysis_type_id', 'experiments', ['analysis_type_id'], unique=False) + op.create_table('external_atip', + sa.Column('atip_ID', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('atip_ID') + ) + op.create_table('external_dairy_one', + sa.Column('dairy_one_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('samples_count', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('accumulated_years_from', sa.Date(), nullable=True), + sa.Column('accumulated_years_to', sa.Date(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('dairy_one_id') + ) + op.create_index('idx_external_dairy_one_biomass_id', 'external_dairy_one', ['biomass_id'], unique=False) + op.create_index('idx_external_dairy_one_parameter_id', 'external_dairy_one', ['parameter_id'], unique=False) + op.create_table('external_ebmud', + sa.Column('ebmud_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('ebmud_id') + ) + op.create_table('external_inl_biofeedstock_library', + sa.Column('bfl_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('state_id', sa.Integer(), nullable=True), + sa.Column('affiliations_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('accumulated_years_from', sa.Date(), nullable=True), + sa.Column('accumulated_years_to', sa.Date(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('bfl_id') + ) + op.create_index('idx_external_inl_biofeedstock_library_biomass_id', 'external_inl_biofeedstock_library', ['biomass_id'], unique=False) + op.create_table('external_land_id', + sa.Column('land_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('land_id') + ) + op.create_table('external_phyllis2', + sa.Column('phyllis_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('phyllis_id') + ) + op.create_index('idx_external_phyllis2_analysis_type_id', 'external_phyllis2', ['analysis_type_id'], unique=False) + op.create_index('idx_external_phyllis2_biomass_id', 'external_phyllis2', ['biomass_id'], unique=False) + op.create_table('external_usda', + sa.Column('usda_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('usda_id') + ) + op.create_table('fermentation_profile', + sa.Column('fp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('organism_id', sa.Integer(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('fp_id') + ) + op.create_table('field_samples', + sa.Column('sample_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('sample_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('source_codename_id', sa.Integer(), nullable=True), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('field_storage_id', sa.Integer(), nullable=True), + sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), + sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('collection_timestamp', sa.DateTime(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_date', sa.Date(), nullable=True), + sa.Column('amount_collected_kg', sa.Numeric(), nullable=True), + sa.Column('provider_id', sa.Integer(), nullable=True), + sa.Column('collector_id', sa.Integer(), nullable=True), + sa.Column('basic_sample_info_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.PrimaryKeyConstraint('sample_id') + ) + op.create_index(op.f('ix_field_samples_biomass_id'), 'field_samples', ['biomass_id'], unique=False) + op.create_index(op.f('ix_field_samples_source_codename_id'), 'field_samples', ['source_codename_id'], unique=False) + op.create_table('field_storage', + sa.Column('field_storage_id', sa.Integer(), nullable=False), + sa.Column('storage_method', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('field_storage_id'), + sa.UniqueConstraint('storage_method') + ) + op.create_table('fips', + sa.Column('fips_id', sa.Integer(), nullable=False), + sa.Column('fips_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('fips_id') + ) + op.create_table('gasification_profile', + sa.Column('gasification_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('gasification_id') + ) + op.create_table('geographic_locations', + sa.Column('location_id', sa.Integer(), nullable=False), + sa.Column('street_address_id', sa.Integer(), nullable=True), + sa.Column('city_id', sa.Integer(), nullable=True), + sa.Column('zip_id', sa.Integer(), nullable=True), + sa.Column('county_id', sa.Integer(), nullable=True), + sa.Column('state_id', sa.Integer(), nullable=True), + sa.Column('region_id', sa.Integer(), nullable=True), + sa.Column('fips_id', sa.Integer(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('location_resolution_id', sa.Integer(), nullable=True), + sa.Column('is_anonymous', sa.Boolean(), nullable=True), + sa.PrimaryKeyConstraint('location_id') + ) + op.create_table('harvest_methods', + sa.Column('harvest_method_id', sa.Integer(), nullable=False), + sa.Column('harvest_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('harvest_method_id'), + sa.UniqueConstraint('harvest_method_name') + ) + op.create_table('icp_analysis', + sa.Column('icp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('concentration_calculation_url_id', sa.Integer(), nullable=True), + sa.Column('result_wavelength', sa.Numeric(), nullable=True), + sa.Column('raw_url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('icp_id') + ) + op.create_table('import_log', + sa.Column('import_id', sa.Integer(), nullable=False), + sa.Column('import_timestamp', sa.DateTime(), nullable=True), + sa.Column('destination', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('source_file', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('records_imported', sa.Integer(), nullable=True), + sa.Column('import_status', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('error_log', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_user', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('import_id') + ) + op.create_table('location_resolutions', + sa.Column('location_resolution_id', sa.Integer(), nullable=False), + sa.Column('resolution_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('location_resolution_id'), + sa.UniqueConstraint('resolution_type') + ) + op.create_table('metadata', + sa.Column('metadata_id', sa.Integer(), nullable=False), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('ag_treatment_id', sa.Integer(), nullable=True), + sa.Column('last_application_date', sa.Date(), nullable=True), + sa.Column('treatment_amount_per_acre', sa.Numeric(), nullable=True), + sa.Column('soil_type', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('metadata_id') + ) + op.create_table('method_abbrevs', + sa.Column('method_abbrev_id', sa.Integer(), nullable=False), + sa.Column('method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_abbrev_id'), + sa.UniqueConstraint('method_abbrev') + ) + op.create_table('method_categories', + sa.Column('method_category_id', sa.Integer(), nullable=False), + sa.Column('method_category', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_category_id'), + sa.UniqueConstraint('method_category') + ) + op.create_table('method_equipment', + sa.Column('method_equipment_id', sa.Integer(), nullable=False), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('equipment_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('method_equipment_id') + ) + op.create_index('idx_method_equipment_equipment_id', 'method_equipment', ['equipment_id'], unique=False) + op.create_index('idx_method_equipment_method_id', 'method_equipment', ['method_id'], unique=False) + op.create_table('method_standards', + sa.Column('method_standard_id', sa.Integer(), nullable=False), + sa.Column('method_standard', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_standard_id'), + sa.UniqueConstraint('method_standard') + ) + op.create_table('methods', + sa.Column('method_id', sa.Integer(), nullable=False), + sa.Column('method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('method_category_id', sa.Integer(), nullable=True), + sa.Column('method_standard_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('detection_limits', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('procedure_reference_id', sa.Integer(), nullable=True), + sa.Column('method_url_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('method_id'), + sa.UniqueConstraint('method_name') + ) + op.create_index('idx_methods_method_name', 'methods', ['method_name'], unique=False) + op.create_table('organisms', + sa.Column('organism_id', sa.Integer(), nullable=False), + sa.Column('organism_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('organism_strain_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('organism_id') + ) + op.create_table('parameter_catagories', + sa.Column('parameter_catagory_id', sa.Integer(), nullable=False), + sa.Column('parameter_catagory', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('parameter_catagory_id') + ) + op.create_table('parameter_methods', + sa.Column('param_method_id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('param_method_id') + ) + op.create_table('parameter_units', + sa.Column('parameter_unit_id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('parameter_unit_id') + ) + op.create_index('idx_parameter_units_parameter_id', 'parameter_units', ['parameter_id'], unique=False) + op.create_index('idx_parameter_units_unit_id', 'parameter_units', ['unit_id'], unique=False) + op.create_table('parameters', + sa.Column('parameter_id', sa.Integer(), nullable=False), + sa.Column('parameter_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('parameter_category_id', sa.Integer(), nullable=True), + sa.Column('standard_unit_id', sa.Integer(), nullable=True), + sa.Column('calculated', sa.Boolean(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('typical_range_min', sa.Numeric(), nullable=True), + sa.Column('typical_range_max', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('parameter_id'), + sa.UniqueConstraint('parameter_name') + ) + op.create_table('particle_size', + sa.Column('particle_size_id', sa.Integer(), nullable=False), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('particle_length', sa.Integer(), nullable=True), + sa.Column('particle_width', sa.Integer(), nullable=True), + sa.Column('particle_height', sa.Integer(), nullable=True), + sa.Column('particle_units', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('particle_size_id') + ) + op.create_table('preprocessed_samples', + sa.Column('prepro_material_id', sa.Integer(), nullable=False), + sa.Column('prepro_material_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('biomass_sample_id', sa.Integer(), nullable=True), + sa.Column('prepro_method_id', sa.Integer(), nullable=True), + sa.Column('amount_before_drying_g', sa.Numeric(), nullable=True), + sa.Column('amount_after_drying', sa.Numeric(), nullable=True), + sa.Column('processing_date', sa.Date(), nullable=True), + sa.Column('storage_building', sa.Integer(), nullable=True), + sa.Column('amount_remaining_g', sa.Numeric(), nullable=True), + sa.Column('amount_as_of_date', sa.Date(), nullable=True), + sa.Column('prepro_analyst_id', sa.Integer(), nullable=True), + sa.Column('prepro_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prepro_material_id') + ) + op.create_index('idx_preprocessed_samples_biomass_sample_id', 'preprocessed_samples', ['biomass_sample_id'], unique=False) + op.create_index('idx_preprocessed_samples_prepro_method_id', 'preprocessed_samples', ['prepro_method_id'], unique=False) + op.create_table('preprocessing_methods', + sa.Column('prepro_method_id', sa.Integer(), nullable=False), + sa.Column('prepro_method', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('prepro_method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('prepro_temp_c', sa.Numeric(), nullable=True), + sa.Column('drying_step', sa.Boolean(), nullable=True), + sa.Column('method_ref_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('prepro_method_id') + ) + op.create_table('preprocessing_methods_abbreviations', + sa.Column('prepro_methods_abbrev_id', sa.Integer(), nullable=False), + sa.Column('prepro_method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prepro_methods_abbrev_id'), + sa.UniqueConstraint('prepro_method_abbrev') + ) + op.create_table('primary_product', + sa.Column('primary_product_id', sa.Integer(), nullable=False), + sa.Column('primary_product_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('primary_product_id'), + sa.UniqueConstraint('primary_product_name') + ) + op.create_table('product_type', + sa.Column('product_type_id', sa.Integer(), nullable=False), + sa.Column('product', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('product_type_id') + ) + op.create_table('provider_types', + sa.Column('provider_type_id', sa.Integer(), nullable=False), + sa.Column('provider_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('provider_type_id') + ) + op.create_table('providers', + sa.Column('provider_id', sa.Integer(), nullable=False), + sa.Column('provider_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('provider_affiliation', sa.Integer(), nullable=True), + sa.Column('provider_type_id', sa.Integer(), nullable=True), + sa.Column('anonymous', sa.Boolean(), nullable=True), + sa.PrimaryKeyConstraint('provider_id'), + sa.UniqueConstraint('provider_name') + ) + op.create_table('proximate_analysis', + sa.Column('prox_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prox_id') + ) + op.create_table('qc_results', + sa.Column('qc_result_id', sa.Integer(), nullable=False), + sa.Column('qc_result', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('qc_result_id'), + sa.UniqueConstraint('qc_result') + ) + op.create_table('raster_metadata', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('resolution', sa.Float(), nullable=True), + sa.Column('srid', sa.Integer(), nullable=True), + sa.Column('acquisition_date', sa.Date(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('references', + sa.Column('reference_id', sa.Integer(), nullable=False), + sa.Column('reference_title', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_author', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_publication', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_date', sa.Date(), nullable=True), + sa.Column('reference_doi_id', sa.Integer(), nullable=True), + sa.Column('url_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('reference_id') + ) + op.create_table('regions', + sa.Column('region_id', sa.Integer(), nullable=False), + sa.Column('region_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('region_id'), + sa.UniqueConstraint('region_name') + ) + op.create_table('rooms', + sa.Column('room_id', sa.Integer(), nullable=False), + sa.Column('room_number', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('building_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('room_id'), + sa.UniqueConstraint('room_number') + ) + op.create_table('soil_type', + sa.Column('soil_type_id', sa.Integer(), nullable=False), + sa.Column('soil_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('soil_location', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('soil_type_id'), + sa.UniqueConstraint('soil_type') + ) + op.create_table('source_names', + sa.Column('source_name_id', sa.Integer(), nullable=False), + sa.Column('source_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('source_name_id'), + sa.UniqueConstraint('source_name') + ) + op.create_table('source_types', + sa.Column('source_type_id', sa.Integer(), nullable=False), + sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('source_type_id'), + sa.UniqueConstraint('source_type') + ) + op.create_table('states', + sa.Column('state_id', sa.Integer(), nullable=False), + sa.Column('state_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('state_id'), + sa.UniqueConstraint('state_name') + ) + op.create_table('street_addresses', + sa.Column('street_address_id', sa.Integer(), nullable=False), + sa.Column('street_address', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('street_address_id') + ) + op.create_table('taxonomy', + sa.Column('taxonomy_id', sa.Integer(), nullable=False), + sa.Column('kingdom', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('phylum', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('order', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('family', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('genus', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('species', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('variety_subspecies_cultivar', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('taxonomy_id') + ) + op.create_table('testusers2', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('fullname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('nickname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('units', + sa.Column('unit_id', sa.Integer(), nullable=False), + sa.Column('unit', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('unit_id'), + sa.UniqueConstraint('unit') + ) + op.create_table('url', + sa.Column('url_id', sa.Integer(), nullable=False), + sa.Column('url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('url_id'), + sa.UniqueConstraint('url') + ) + op.create_table('vectorized_raster_polygons', + sa.Column('vectorized_ID', sa.Integer(), nullable=False), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('raster_id', sa.Integer(), nullable=True), + sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('mean_value', sa.Float(), nullable=True), + sa.Column('std_dev', sa.Float(), nullable=True), + sa.Column('area_m2', sa.Float(), nullable=True), + sa.Column('date_acquired', sa.Date(), nullable=True), + sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('vectorized_ID') + ) + op.create_table('xrf_analysis', + sa.Column('xrf_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('xrf_id') + ) + op.create_table('zips', + sa.Column('zip_id', sa.Integer(), nullable=False), + sa.Column('zip_code', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('zip_id'), + sa.UniqueConstraint('zip_code') + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('zips') + op.drop_table('xrf_analysis') + op.drop_table('vectorized_raster_polygons') + op.drop_table('url') + op.drop_table('units') + op.drop_table('testusers2') + op.drop_table('taxonomy') + op.drop_table('street_addresses') + op.drop_table('states') + op.drop_table('source_types') + op.drop_table('source_names') + op.drop_table('soil_type') + op.drop_table('rooms') + op.drop_table('regions') + op.drop_table('references') + op.drop_table('raster_metadata') + op.drop_table('qc_results') + op.drop_table('proximate_analysis') + op.drop_table('providers') + op.drop_table('provider_types') + op.drop_table('product_type') + op.drop_table('primary_product') + op.drop_table('preprocessing_methods_abbreviations') + op.drop_table('preprocessing_methods') + op.drop_index('idx_preprocessed_samples_prepro_method_id', table_name='preprocessed_samples') + op.drop_index('idx_preprocessed_samples_biomass_sample_id', table_name='preprocessed_samples') + op.drop_table('preprocessed_samples') + op.drop_table('particle_size') + op.drop_table('parameters') + op.drop_index('idx_parameter_units_unit_id', table_name='parameter_units') + op.drop_index('idx_parameter_units_parameter_id', table_name='parameter_units') + op.drop_table('parameter_units') + op.drop_table('parameter_methods') + op.drop_table('parameter_catagories') + op.drop_table('organisms') + op.drop_index('idx_methods_method_name', table_name='methods') + op.drop_table('methods') + op.drop_table('method_standards') + op.drop_index('idx_method_equipment_method_id', table_name='method_equipment') + op.drop_index('idx_method_equipment_equipment_id', table_name='method_equipment') + op.drop_table('method_equipment') + op.drop_table('method_categories') + op.drop_table('method_abbrevs') + op.drop_table('metadata') + op.drop_table('location_resolutions') + op.drop_table('import_log') + op.drop_table('icp_analysis') + op.drop_table('harvest_methods') + op.drop_table('geographic_locations') + op.drop_table('gasification_profile') + op.drop_table('fips') + op.drop_table('field_storage') + op.drop_index(op.f('ix_field_samples_source_codename_id'), table_name='field_samples') + op.drop_index(op.f('ix_field_samples_biomass_id'), table_name='field_samples') + op.drop_table('field_samples') + op.drop_table('fermentation_profile') + op.drop_table('external_usda') + op.drop_index('idx_external_phyllis2_biomass_id', table_name='external_phyllis2') + op.drop_index('idx_external_phyllis2_analysis_type_id', table_name='external_phyllis2') + op.drop_table('external_phyllis2') + op.drop_table('external_land_id') + op.drop_index('idx_external_inl_biofeedstock_library_biomass_id', table_name='external_inl_biofeedstock_library') + op.drop_table('external_inl_biofeedstock_library') + op.drop_table('external_ebmud') + op.drop_index('idx_external_dairy_one_parameter_id', table_name='external_dairy_one') + op.drop_index('idx_external_dairy_one_biomass_id', table_name='external_dairy_one') + op.drop_table('external_dairy_one') + op.drop_table('external_atip') + op.drop_index('idx_experiments_analysis_type_id', table_name='experiments') + op.drop_table('experiments') + op.drop_index('idx_experiment_methods_method_id', table_name='experiment_methods') + op.drop_index('idx_experiment_methods_experiment_id', table_name='experiment_methods') + op.drop_table('experiment_methods') + op.drop_table('equipment') + op.drop_table('doi') + op.drop_index('idx_data_sources_source_name_id', table_name='data_sources') + op.drop_table('data_sources') + op.drop_table('counties') + op.drop_table('compositional_analysis') + op.drop_table('collectors') + op.drop_table('collection_methods') + op.drop_table('cities') + op.drop_table('buildings') + op.drop_table('biomass_type') + op.drop_index(op.f('ix_biomass_test_biomass_test_name'), table_name='biomass_test') + op.drop_table('biomass_test') + op.drop_index(op.f('ix_biomass_quality_biomass_id'), table_name='biomass_quality') + op.drop_table('biomass_quality') + op.drop_index(op.f('ix_biomass_price_biomass_id'), table_name='biomass_price') + op.drop_table('biomass_price') + op.drop_index(op.f('ix_biomass_availability_biomass_id'), table_name='biomass_availability') + op.drop_table('biomass_availability') + op.drop_index(op.f('ix_biomass_biomass_type_id'), table_name='biomass') + op.drop_index(op.f('ix_biomass_biomass_name'), table_name='biomass') + op.drop_table('biomass') + op.drop_table('autoclave_profile') + op.drop_table('analyst_contact') + op.drop_table('analysis_types') + op.drop_index('uq_analysis_results_experiment_parameter_replicate', table_name='analysis_results') + op.drop_index('idx_analysis_results_parameter_id', table_name='analysis_results') + op.drop_table('analysis_results') + op.drop_table('analysis_replicate_id') + op.drop_table('analysis_abbreviations') + op.drop_table('ag_treatments') + op.drop_table('affiliations') + # ### end Alembic commands ### diff --git a/census.survey.mmd b/census.survey.mmd new file mode 100644 index 00000000..8ff952c9 --- /dev/null +++ b/census.survey.mmd @@ -0,0 +1,53 @@ +erDiagram +CensusRecord { + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} +Geography { + string state_name + string state_fips + string county_name + string county_fips + string geoid + string region_name + string agg_level_desc +} +SurveyRecord { + string period_desc + string freq_desc + string program_desc + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} +UsdaRecord { + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} + +CensusRecord ||--|o Geography : "geography" +SurveyRecord ||--|o Geography : "geography" +UsdaRecord ||--|o Geography : "geography" diff --git a/review_summary.txt b/review_summary.txt new file mode 100644 index 00000000..fcdf7f74 --- /dev/null +++ b/review_summary.txt @@ -0,0 +1,76 @@ +# Pull Request Review Summary + +This document summarizes key findings and documentation gaps discovered while setting up the project environment for testing. + +--- + +## 1. Environment Setup: `.env` File Creation + +**Finding:** The project requires a `.env` file to be created in the `resources/docker/` directory for the Docker services to function correctly. This step was not documented in the main `README.md`. + +**Recommendation:** Add the following instructions to the "ETL Pipeline (Prefect + Docker)" section of the main `README.md` to guide new users. + +**Added Documentation:** +```markdown +**Note**: Before starting the services for the first time, create the required environment file from the template: + +```bash +cp resources/docker/.env.example resources/docker/.env +``` +``` + +--- + +## 2. Database Migrations: Generating an Initial Migration + +**Finding:** The process for generating a new initial Alembic migration is not documented and was difficult to discover. The correct method involves using the dedicated `setup-db` service defined in `resources/docker/docker-compose.yml`, which was not mentioned in any high-level documentation. + +Initial attempts to run the `alembic` command inside the `prefect-worker` container failed because it does not have the necessary files or `PATH` configuration. + +**Correct Procedure for Initial Migration:** + +1. **Tear Down Services and Volumes:** Completely reset the database environment. + ```bash + pixi run teardown-services-volumes + ``` + +2. **Remove Old Migration Files:** Clear the existing migration history. + ```bash + rm alembic/versions/*.py + ``` + +3. **Generate New Migration:** Use the `setup-db` service to run the `alembic` command. This is the critical, undocumented step. + ```bash + docker-compose -f resources/docker/docker-compose.yml run --rm setup-db alembic revision --autogenerate -m "Initial migration" + ``` + +4. **Apply the Migration:** Start the services. The `setup-db` service will automatically apply the newly created migration upon startup. + ```bash + pixi run start-services + ``` + +**Recommendation:** This entire process should be clearly documented in a relevant location, such as the `ALEMBIC_WORKFLOW.md` or a new troubleshooting guide, to prevent confusion for future developers. The existence and purpose of the `setup-db` service is a key piece of information that is currently missing from the documentation. + +--- + +## 3. Accessing the Database + +**Finding:** The workflow for directly accessing the database to inspect data is not documented. It requires using the `psql` command inside the `db` container with the correct user and database name, which are defined in `resources/docker/.env.example`. + +**Correct Procedure for Listing Tables:** + +```bash +pixi run exec-db psql -U biocirv_user -d biocirv_db -c "\dt" +``` + +**Recommendation:** Add a section to the documentation explaining how to connect to the database for debugging and inspection purposes. + +--- + +## 4. Prefect API Connection + +**Finding:** When running a Prefect flow from the host machine (e.g., via `pixi run run-etl`), the client fails to connect to the Prefect server API. This is because the `PREFECT_API_URL` in the `.env` file is set to `http://0.0.0.0:4200/api`. This address is only valid for processes inside the same container, not for clients on the host. + +**Resolution:** The `PREFECT_API_URL` and `PREFECT_UI_API_URL` in `resources/docker/.env` were changed to `http://localhost:4200/api`. + +**Recommendation:** The `.env.example` file should be updated with the correct `localhost` address to prevent this issue for other developers. An explanation of the different network contexts (host vs. container) would also be beneficial in the documentation. From dca4ca695f75d44799c744875e05e086c2f324b2 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Tue, 18 Nov 2025 09:48:13 -0700 Subject: [PATCH 13/81] fixing alembic migration issues. Commenting out all SQLalchemy stuff for now --- README.md | 177 +++++++++++++++++- alembic/env.py | 16 +- ...n.py => 2eaabfd71d17_initial_migration.py} | 6 +- pixi.toml | 17 +- resources/docker/docker-compose.yml | 2 + 5 files changed, 203 insertions(+), 15 deletions(-) rename alembic/versions/{523eedbcaf6e_initial_migration.py => 2eaabfd71d17_initial_migration.py} (99%) diff --git a/README.md b/README.md index a58ea18b..5dc89ccc 100644 --- a/README.md +++ b/README.md @@ -35,11 +35,180 @@ run QGIS using pixi with the following command: pixi run qgis ``` -This will launch QGIS in the `gis` environment with all necessary dependencies -installed. +**Note**: On macOS, you may see a Python faulthandler error - this is expected +and can be ignored. See +[QGIS Issue #52987](https://github.com/qgis/QGIS/issues/52987). -For MacOS, there will be a Python error about faulthandler, which is expected -and can be ignored, see https://github.com/qgis/QGIS/issues/52987. +## Development + +### Running Tests + +```bash +# Run all tests +pixi run test + +# Run tests with coverage +pixi run test-cov +``` + +### Code Quality + +```bash +# Run pre-commit checks on staged files +pixi run pre-commit + +# Run pre-commit on all files (before PR) +pixi run pre-commit-all +``` + +### Available Pixi Tasks + +View all available tasks: + +```bash +pixi task list +``` + +Key tasks: + +- **Service Management**: `start-services`, `teardown-services`, + `service-status` +- **ETL Operations**: `deploy`, `run-etl` +- **Development**: `test`, `test-cov`, `pre-commit`, `pre-commit-all` +- **Applications**: `start-webservice`, `qgis` +- **Database**: `access-db`, `check-db-health` + +## Architecture + +### Namespace Packages + +This project uses **PEP 420 namespace packages** to organize code into +independently installable components that share a common namespace: + +- Each component has its own `pyproject.toml` and can be installed separately +- Shared models in `datamodels` are used by both `pipeline` and `webservice` +- Clear separation of concerns while maintaining type consistency + +### ETL Pipeline + +The ETL pipeline uses: + +- **Prefect**: Workflow orchestration and monitoring +- **Docker**: Containerized execution environment +- **PostgreSQL**: Data persistence +- **Google Sheets API**: Primary data source + +Pipeline architecture: + +1. **Extract**: Pull data from Google Sheets +2. **Transform**: Clean and normalize data with pandas +3. **Load**: Insert/update records in PostgreSQL via SQLModel + +### Database Models + +SQLModel-based models provide: + +- Type-safe database operations +- Automatic schema generation (via Alembic) +- Shared models across ETL and API components +- Pydantic validation + +## Project Components + +### 1. Data Models (`ca_biositing.datamodels`) + +Database models for: + +- Biomass data (field samples, measurements) +- Geographic locations +- Experiments and analysis +- Metadata and samples +- Organizations and contacts + +**Documentation**: +[`src/ca_biositing/datamodels/README.md`](src/ca_biositing/datamodels/README.md) + +### 2. ETL Pipeline (`ca_biositing.pipeline`) + +Prefect-orchestrated workflows for: + +- Data extraction from Google Sheets +- Data transformation and validation +- Database loading and updates +- Lookup table management + +**Documentation**: +[`src/ca_biositing/pipeline/README.md`](src/ca_biositing/pipeline/README.md) + +**Guides**: + +- [Docker Workflow](src/ca_biositing/pipeline/docs/DOCKER_WORKFLOW.md) +- [Prefect Workflow](src/ca_biositing/pipeline/docs/PREFECT_WORKFLOW.md) +- [ETL Development](src/ca_biositing/pipeline/docs/ETL_WORKFLOW.md) +- [Database Migrations](src/ca_biositing/pipeline/docs/ALEMBIC_WORKFLOW.md) + +### 3. Web Service (`ca_biositing.webservice`) + +FastAPI REST API providing: + +- Read access to database records +- Interactive API documentation (Swagger/OpenAPI) +- Type-safe endpoints using Pydantic + +**Documentation**: +[`src/ca_biositing/webservice/README.md`](src/ca_biositing/webservice/README.md) + +### 4. Deployment Resources (`resources/`) + +Docker and Prefect configuration for: + +- Service orchestration (Docker Compose) +- Prefect deployments +- Database initialization + +**Documentation**: [`resources/README.md`](resources/README.md) + +## Adding Dependencies + +### For Local Development (Pixi) + +```bash +# Add conda package to default environment +pixi add + +# Add PyPI package to default environment +pixi add --pypi + +# Add to specific feature (e.g., pipeline) +pixi add --feature pipeline --pypi +``` + +### For ETL Pipeline (Docker) + +The pipeline dependencies are managed by Pixi's `etl` environment feature in +`pixi.toml`. When you add dependencies and rebuild Docker images, they are +automatically included: + +```bash +# Add dependency to pipeline feature +pixi add --feature pipeline --pypi + +# Rebuild Docker images +pixi run rebuild-services + +# Restart services +pixi run start-services +``` + +## Environment Management + +This project uses **Pixi environments** for different workflows: + +- **`default`**: General development, testing, pre-commit hooks +- **`gis`**: QGIS and geospatial analysis tools +- **`etl`**: ETL pipeline (used in Docker containers) +- **`webservice`**: FastAPI web service +- **`frontend`**: Node.js/npm for frontend development ## Frontend Integration diff --git a/alembic/env.py b/alembic/env.py index 4b372e23..cd3a09ea 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -28,9 +28,9 @@ import importlib.util from pathlib import Path -# --- Import generated models --- -from ca_biositing.datamodels.schemas.generated.census_survey import * -from ca_biositing.datamodels.schemas.generated.geography import * +# --- Import generated models and their metadata --- +# from ca_biositing.datamodels.schemas.generated.census_survey import metadata as census_metadata +# from ca_biositing.datamodels.schemas.generated.geography import metadata as geography_metadata # --- Alembic Config object, provides access to alembic.ini values --- config = context.config @@ -49,11 +49,17 @@ # --- Metadata from your models for autogenerate --- # Combine metadata from all models # See: https://alembic.sqlalchemy.org/en/latest/autogenerate.html#affecting-the-autogenerate-process -for table in SQLModel.metadata.tables.values(): - table.tometadata(SQLModel.metadata) +# Start with the default SQLModel metadata target_metadata = SQLModel.metadata +# Manually merge metadata from generated modules +# for table in census_metadata.tables.values(): +# table.tometadata(target_metadata) +# +# for table in geography_metadata.tables.values(): +# table.tometadata(target_metadata) + def render_item(type_, obj, autogen_context): """Add custom imports to the migration template.""" diff --git a/alembic/versions/523eedbcaf6e_initial_migration.py b/alembic/versions/2eaabfd71d17_initial_migration.py similarity index 99% rename from alembic/versions/523eedbcaf6e_initial_migration.py rename to alembic/versions/2eaabfd71d17_initial_migration.py index 402bc49d..3273b864 100644 --- a/alembic/versions/523eedbcaf6e_initial_migration.py +++ b/alembic/versions/2eaabfd71d17_initial_migration.py @@ -1,8 +1,8 @@ """Initial migration -Revision ID: 523eedbcaf6e +Revision ID: 2eaabfd71d17 Revises: -Create Date: 2025-11-14 20:44:50.143083 +Create Date: 2025-11-18 16:35:19.779152 """ from typing import Sequence, Union @@ -12,7 +12,7 @@ import sqlmodel # revision identifiers, used by Alembic. -revision: str = '523eedbcaf6e' +revision: str = '2eaabfd71d17' down_revision: Union[str, Sequence[str], None] = None branch_labels: Union[str, Sequence[str], None] = None depends_on: Union[str, Sequence[str], None] = None diff --git a/pixi.toml b/pixi.toml index 1d81689f..02e590a2 100644 --- a/pixi.toml +++ b/pixi.toml @@ -64,9 +64,7 @@ start-services = { cmd = [ "resources/docker/docker-compose.yml", "up", "-d", -], description = "Start required services using Docker Compose.", depends-on = [ - "initial-migration", -] } +], description = "Start required services using Docker Compose." } teardown-services = { cmd = [ "docker-compose", "-f", @@ -176,6 +174,19 @@ restart-prefect-worker = { cmd = [ "prefect-worker", ], description = "Restart the Prefect worker service." } +migrate = { cmd = [ + "docker-compose", + "-f", + "resources/docker/docker-compose.yml", + "exec", + "prefect-worker", + "/bin/bash", + "-c", + "source /shell-hook.sh && alembic upgrade head", +], description = "Apply database migrations.", depends-on = [ + "start-services", +] } + [tasks.qgis] depends-on = [{ task = "run-qgis", environment = "gis" }] diff --git a/resources/docker/docker-compose.yml b/resources/docker/docker-compose.yml index 7328859f..8ad138b5 100644 --- a/resources/docker/docker-compose.yml +++ b/resources/docker/docker-compose.yml @@ -70,6 +70,8 @@ services: # Adding the flow code to the worker - ../prefect/run_prefect_flow.py:/app/run_prefect_flow.py - ../../credentials.json:/app/credentials.json + - ../../alembic:/app/alembic + - ../../alembic.ini:/app/alembic.ini depends_on: prefect-server: condition: service_healthy From b9c05600b47466ceb1442629b427b7f968ccbd23 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Tue, 18 Nov 2025 10:02:48 -0700 Subject: [PATCH 14/81] needed to clear alembic migrations first --- .../2eaabfd71d17_initial_migration.py | 877 ------------------ .../e15bda744fef_initial_migration.py | 877 ------------------ 2 files changed, 1754 deletions(-) delete mode 100644 alembic/versions/2eaabfd71d17_initial_migration.py delete mode 100644 alembic/versions/e15bda744fef_initial_migration.py diff --git a/alembic/versions/2eaabfd71d17_initial_migration.py b/alembic/versions/2eaabfd71d17_initial_migration.py deleted file mode 100644 index 3273b864..00000000 --- a/alembic/versions/2eaabfd71d17_initial_migration.py +++ /dev/null @@ -1,877 +0,0 @@ -"""Initial migration - -Revision ID: 2eaabfd71d17 -Revises: -Create Date: 2025-11-18 16:35:19.779152 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa -import sqlmodel - -# revision identifiers, used by Alembic. -revision: str = '2eaabfd71d17' -down_revision: Union[str, Sequence[str], None] = None -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.create_table('affiliations', - sa.Column('affiliation_id', sa.Integer(), nullable=False), - sa.Column('affiliation_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('affiliation_id'), - sa.UniqueConstraint('affiliation_name') - ) - op.create_table('ag_treatments', - sa.Column('ag_treatment_id', sa.Integer(), nullable=False), - sa.Column('ag_treatment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('ag_treatment_id') - ) - op.create_table('analysis_abbreviations', - sa.Column('analysis_abbreviations_id', sa.Integer(), nullable=False), - sa.Column('analysis_abbreviation', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_abbreviations_id'), - sa.UniqueConstraint('analysis_abbreviation') - ) - op.create_table('analysis_replicate_id', - sa.Column('analysis_replicate_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('analysis_types_id', sa.Integer(), nullable=True), - sa.Column('analysis_replicate_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_replicate_id') - ) - op.create_table('analysis_results', - sa.Column('result_id', sa.Integer(), nullable=False), - sa.Column('anlaysis_sample', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('replicate_no', sa.Integer(), nullable=True), - sa.Column('analysis_timestamp', sa.DateTime(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('qc_result_id', sa.Integer(), nullable=True), - sa.Column('measurement_equipment_id', sa.Integer(), nullable=True), - sa.Column('raw_data_url_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('analysis_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('result_id') - ) - op.create_index('idx_analysis_results_parameter_id', 'analysis_results', ['parameter_id'], unique=False) - op.create_index('uq_analysis_results_experiment_parameter_replicate', 'analysis_results', ['experiment_id', 'parameter_id', 'replicate_no'], unique=True) - op.create_table('analysis_types', - sa.Column('analysis_type_id', sa.Integer(), nullable=False), - sa.Column('analysis_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_type_id'), - sa.UniqueConstraint('analysis_name') - ) - op.create_table('analyst_contact', - sa.Column('analyst_id', sa.Integer(), nullable=False), - sa.Column('analyst_first_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_last_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_email', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_affiliation', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('analyst_id') - ) - op.create_table('autoclave_profile', - sa.Column('autoclave_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('autoclave_id') - ) - op.create_table('biomass', - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('biomass_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('primary_product_id', sa.Integer(), nullable=True), - sa.Column('taxonomy_id', sa.Integer(), nullable=True), - sa.Column('biomass_type_id', sa.Integer(), nullable=True), - sa.Column('biomass_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('biomass_id') - ) - op.create_index(op.f('ix_biomass_biomass_name'), 'biomass', ['biomass_name'], unique=False) - op.create_index(op.f('ix_biomass_biomass_type_id'), 'biomass', ['biomass_type_id'], unique=False) - op.create_table('biomass_availability', - sa.Column('availability_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('primary_product_id', sa.Integer(), nullable=True), - sa.Column('from_month', sa.Numeric(), nullable=True), - sa.Column('to_month', sa.Numeric(), nullable=True), - sa.Column('kg_low', sa.Numeric(), nullable=True), - sa.Column('kg_avg', sa.Numeric(), nullable=True), - sa.Column('kg_high', sa.Numeric(), nullable=True), - sa.Column('bdt_low', sa.Numeric(), nullable=True), - sa.Column('bdt_avg', sa.Numeric(), nullable=True), - sa.Column('bdt_high', sa.Numeric(), nullable=True), - sa.Column('data_source', sa.Integer(), nullable=True), - sa.Column('availability_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('availability_id') - ) - op.create_index(op.f('ix_biomass_availability_biomass_id'), 'biomass_availability', ['biomass_id'], unique=False) - op.create_table('biomass_price', - sa.Column('price_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('price_per_kg_low', sa.Numeric(), nullable=True), - sa.Column('price_per_kg_avg', sa.Numeric(), nullable=True), - sa.Column('price_per_kg_high', sa.Numeric(), nullable=True), - sa.Column('price_data_sources', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('price_id') - ) - op.create_index(op.f('ix_biomass_price_biomass_id'), 'biomass_price', ['biomass_id'], unique=False) - op.create_table('biomass_quality', - sa.Column('quality_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('expected_quality', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('output_feedstocks', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('convertibility', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('disposal_challenges', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('existing_markets', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('substitute_materials', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('regulatory_issues', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('quality_data_sources', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('quality_id') - ) - op.create_index(op.f('ix_biomass_quality_biomass_id'), 'biomass_quality', ['biomass_id'], unique=False) - op.create_table('biomass_test', - sa.Column('biomass_test_id', sa.Integer(), nullable=False), - sa.Column('biomass_test_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('biomass_test_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('biomass_test_id') - ) - op.create_index(op.f('ix_biomass_test_biomass_test_name'), 'biomass_test', ['biomass_test_name'], unique=False) - op.create_table('biomass_type', - sa.Column('biomass_type_id', sa.Integer(), nullable=False), - sa.Column('biomass_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('biomass_type_id'), - sa.UniqueConstraint('biomass_type') - ) - op.create_table('buildings', - sa.Column('building_id', sa.Integer(), nullable=False), - sa.Column('building_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('affiliation_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('building_id'), - sa.UniqueConstraint('building_name') - ) - op.create_table('cities', - sa.Column('city_id', sa.Integer(), nullable=False), - sa.Column('city_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('city_id'), - sa.UniqueConstraint('city_name') - ) - op.create_table('collection_methods', - sa.Column('collection_method_id', sa.Integer(), nullable=False), - sa.Column('collection_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('collection_method_id'), - sa.UniqueConstraint('collection_method_name') - ) - op.create_table('collectors', - sa.Column('collector_id', sa.Integer(), nullable=False), - sa.Column('collector_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('collector_affiliation', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('collector_id'), - sa.UniqueConstraint('collector_name') - ) - op.create_table('compositional_analysis', - sa.Column('cmp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('calculated_parameter_id', sa.Integer(), nullable=True), - sa.Column('calculated_parameter_value', sa.Numeric(), nullable=True), - sa.Column('calculated_parameter_unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('cmp_id') - ) - op.create_table('counties', - sa.Column('county_id', sa.Integer(), nullable=False), - sa.Column('county_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('county_id'), - sa.UniqueConstraint('county_name') - ) - op.create_table('data_sources', - sa.Column('source_id', sa.Integer(), nullable=False), - sa.Column('source_name_id', sa.Integer(), nullable=True), - sa.Column('source_type_id', sa.Integer(), nullable=True), - sa.Column('data_resolution_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('url_id', sa.Integer(), nullable=True), - sa.Column('import_timestamp', sa.DateTime(), nullable=True), - sa.PrimaryKeyConstraint('source_id') - ) - op.create_index('idx_data_sources_source_name_id', 'data_sources', ['source_name_id'], unique=False) - op.create_table('doi', - sa.Column('doi_id', sa.Integer(), nullable=False), - sa.Column('doi', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('doi_id') - ) - op.create_table('equipment', - sa.Column('equipment_id', sa.Integer(), nullable=False), - sa.Column('equipment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('equipment_room_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('equipment_id'), - sa.UniqueConstraint('equipment_name') - ) - op.create_table('experiment_methods', - sa.Column('experiment_method_id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('experiment_method_id') - ) - op.create_index('idx_experiment_methods_experiment_id', 'experiment_methods', ['experiment_id'], unique=False) - op.create_index('idx_experiment_methods_method_id', 'experiment_methods', ['method_id'], unique=False) - op.create_table('experiments', - sa.Column('experiment_id', sa.Integer(), nullable=False), - sa.Column('exper_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('gsheet_exper_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('analysis_abbrev_id', sa.Integer(), nullable=True), - sa.Column('exper_start_date', sa.Date(), nullable=True), - sa.Column('exper_duration', sa.Numeric(), nullable=True), - sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('exper_location_id', sa.Integer(), nullable=True), - sa.Column('exper_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('experiment_id'), - sa.UniqueConstraint('exper_uuid'), - sa.UniqueConstraint('gsheet_exper_id') - ) - op.create_index('idx_experiments_analysis_type_id', 'experiments', ['analysis_type_id'], unique=False) - op.create_table('external_atip', - sa.Column('atip_ID', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('atip_ID') - ) - op.create_table('external_dairy_one', - sa.Column('dairy_one_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('samples_count', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('accumulated_years_from', sa.Date(), nullable=True), - sa.Column('accumulated_years_to', sa.Date(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('dairy_one_id') - ) - op.create_index('idx_external_dairy_one_biomass_id', 'external_dairy_one', ['biomass_id'], unique=False) - op.create_index('idx_external_dairy_one_parameter_id', 'external_dairy_one', ['parameter_id'], unique=False) - op.create_table('external_ebmud', - sa.Column('ebmud_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('ebmud_id') - ) - op.create_table('external_inl_biofeedstock_library', - sa.Column('bfl_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('state_id', sa.Integer(), nullable=True), - sa.Column('affiliations_id', sa.Integer(), nullable=True), - sa.Column('harvest_method_id', sa.Integer(), nullable=True), - sa.Column('collection_method_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('accumulated_years_from', sa.Date(), nullable=True), - sa.Column('accumulated_years_to', sa.Date(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('bfl_id') - ) - op.create_index('idx_external_inl_biofeedstock_library_biomass_id', 'external_inl_biofeedstock_library', ['biomass_id'], unique=False) - op.create_table('external_land_id', - sa.Column('land_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('land_id') - ) - op.create_table('external_phyllis2', - sa.Column('phyllis_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('phyllis_id') - ) - op.create_index('idx_external_phyllis2_analysis_type_id', 'external_phyllis2', ['analysis_type_id'], unique=False) - op.create_index('idx_external_phyllis2_biomass_id', 'external_phyllis2', ['biomass_id'], unique=False) - op.create_table('external_usda', - sa.Column('usda_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('usda_id') - ) - op.create_table('fermentation_profile', - sa.Column('fp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('organism_id', sa.Integer(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('fp_id') - ) - op.create_table('field_samples', - sa.Column('sample_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('sample_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('source_codename_id', sa.Integer(), nullable=True), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('field_storage_id', sa.Integer(), nullable=True), - sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), - sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('collection_timestamp', sa.DateTime(), nullable=True), - sa.Column('collection_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_date', sa.Date(), nullable=True), - sa.Column('amount_collected_kg', sa.Numeric(), nullable=True), - sa.Column('provider_id', sa.Integer(), nullable=True), - sa.Column('collector_id', sa.Integer(), nullable=True), - sa.Column('basic_sample_info_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('created_at', sa.DateTime(), nullable=False), - sa.PrimaryKeyConstraint('sample_id') - ) - op.create_index(op.f('ix_field_samples_biomass_id'), 'field_samples', ['biomass_id'], unique=False) - op.create_index(op.f('ix_field_samples_source_codename_id'), 'field_samples', ['source_codename_id'], unique=False) - op.create_table('field_storage', - sa.Column('field_storage_id', sa.Integer(), nullable=False), - sa.Column('storage_method', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('field_storage_id'), - sa.UniqueConstraint('storage_method') - ) - op.create_table('fips', - sa.Column('fips_id', sa.Integer(), nullable=False), - sa.Column('fips_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('fips_id') - ) - op.create_table('gasification_profile', - sa.Column('gasification_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('gasification_id') - ) - op.create_table('geographic_locations', - sa.Column('location_id', sa.Integer(), nullable=False), - sa.Column('street_address_id', sa.Integer(), nullable=True), - sa.Column('city_id', sa.Integer(), nullable=True), - sa.Column('zip_id', sa.Integer(), nullable=True), - sa.Column('county_id', sa.Integer(), nullable=True), - sa.Column('state_id', sa.Integer(), nullable=True), - sa.Column('region_id', sa.Integer(), nullable=True), - sa.Column('fips_id', sa.Integer(), nullable=True), - sa.Column('latitude', sa.Numeric(), nullable=True), - sa.Column('longitude', sa.Numeric(), nullable=True), - sa.Column('location_resolution_id', sa.Integer(), nullable=True), - sa.Column('is_anonymous', sa.Boolean(), nullable=True), - sa.PrimaryKeyConstraint('location_id') - ) - op.create_table('harvest_methods', - sa.Column('harvest_method_id', sa.Integer(), nullable=False), - sa.Column('harvest_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('harvest_method_id'), - sa.UniqueConstraint('harvest_method_name') - ) - op.create_table('icp_analysis', - sa.Column('icp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('concentration_calculation_url_id', sa.Integer(), nullable=True), - sa.Column('result_wavelength', sa.Numeric(), nullable=True), - sa.Column('raw_url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('icp_id') - ) - op.create_table('import_log', - sa.Column('import_id', sa.Integer(), nullable=False), - sa.Column('import_timestamp', sa.DateTime(), nullable=True), - sa.Column('destination', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('source_file', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('records_imported', sa.Integer(), nullable=True), - sa.Column('import_status', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('error_log', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_user', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('import_id') - ) - op.create_table('location_resolutions', - sa.Column('location_resolution_id', sa.Integer(), nullable=False), - sa.Column('resolution_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('location_resolution_id'), - sa.UniqueConstraint('resolution_type') - ) - op.create_table('metadata', - sa.Column('metadata_id', sa.Integer(), nullable=False), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('ag_treatment_id', sa.Integer(), nullable=True), - sa.Column('last_application_date', sa.Date(), nullable=True), - sa.Column('treatment_amount_per_acre', sa.Numeric(), nullable=True), - sa.Column('soil_type', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('metadata_id') - ) - op.create_table('method_abbrevs', - sa.Column('method_abbrev_id', sa.Integer(), nullable=False), - sa.Column('method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_abbrev_id'), - sa.UniqueConstraint('method_abbrev') - ) - op.create_table('method_categories', - sa.Column('method_category_id', sa.Integer(), nullable=False), - sa.Column('method_category', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_category_id'), - sa.UniqueConstraint('method_category') - ) - op.create_table('method_equipment', - sa.Column('method_equipment_id', sa.Integer(), nullable=False), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('equipment_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('method_equipment_id') - ) - op.create_index('idx_method_equipment_equipment_id', 'method_equipment', ['equipment_id'], unique=False) - op.create_index('idx_method_equipment_method_id', 'method_equipment', ['method_id'], unique=False) - op.create_table('method_standards', - sa.Column('method_standard_id', sa.Integer(), nullable=False), - sa.Column('method_standard', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_standard_id'), - sa.UniqueConstraint('method_standard') - ) - op.create_table('methods', - sa.Column('method_id', sa.Integer(), nullable=False), - sa.Column('method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('method_category_id', sa.Integer(), nullable=True), - sa.Column('method_standard_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('detection_limits', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('procedure_reference_id', sa.Integer(), nullable=True), - sa.Column('method_url_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('method_id'), - sa.UniqueConstraint('method_name') - ) - op.create_index('idx_methods_method_name', 'methods', ['method_name'], unique=False) - op.create_table('organisms', - sa.Column('organism_id', sa.Integer(), nullable=False), - sa.Column('organism_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('organism_strain_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('organism_id') - ) - op.create_table('parameter_catagories', - sa.Column('parameter_catagory_id', sa.Integer(), nullable=False), - sa.Column('parameter_catagory', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('parameter_catagory_id') - ) - op.create_table('parameter_methods', - sa.Column('param_method_id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('param_method_id') - ) - op.create_table('parameter_units', - sa.Column('parameter_unit_id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('parameter_unit_id') - ) - op.create_index('idx_parameter_units_parameter_id', 'parameter_units', ['parameter_id'], unique=False) - op.create_index('idx_parameter_units_unit_id', 'parameter_units', ['unit_id'], unique=False) - op.create_table('parameters', - sa.Column('parameter_id', sa.Integer(), nullable=False), - sa.Column('parameter_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('parameter_category_id', sa.Integer(), nullable=True), - sa.Column('standard_unit_id', sa.Integer(), nullable=True), - sa.Column('calculated', sa.Boolean(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('typical_range_min', sa.Numeric(), nullable=True), - sa.Column('typical_range_max', sa.Numeric(), nullable=True), - sa.PrimaryKeyConstraint('parameter_id'), - sa.UniqueConstraint('parameter_name') - ) - op.create_table('particle_size', - sa.Column('particle_size_id', sa.Integer(), nullable=False), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('particle_length', sa.Integer(), nullable=True), - sa.Column('particle_width', sa.Integer(), nullable=True), - sa.Column('particle_height', sa.Integer(), nullable=True), - sa.Column('particle_units', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('particle_size_id') - ) - op.create_table('preprocessed_samples', - sa.Column('prepro_material_id', sa.Integer(), nullable=False), - sa.Column('prepro_material_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('biomass_sample_id', sa.Integer(), nullable=True), - sa.Column('prepro_method_id', sa.Integer(), nullable=True), - sa.Column('amount_before_drying_g', sa.Numeric(), nullable=True), - sa.Column('amount_after_drying', sa.Numeric(), nullable=True), - sa.Column('processing_date', sa.Date(), nullable=True), - sa.Column('storage_building', sa.Integer(), nullable=True), - sa.Column('amount_remaining_g', sa.Numeric(), nullable=True), - sa.Column('amount_as_of_date', sa.Date(), nullable=True), - sa.Column('prepro_analyst_id', sa.Integer(), nullable=True), - sa.Column('prepro_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prepro_material_id') - ) - op.create_index('idx_preprocessed_samples_biomass_sample_id', 'preprocessed_samples', ['biomass_sample_id'], unique=False) - op.create_index('idx_preprocessed_samples_prepro_method_id', 'preprocessed_samples', ['prepro_method_id'], unique=False) - op.create_table('preprocessing_methods', - sa.Column('prepro_method_id', sa.Integer(), nullable=False), - sa.Column('prepro_method', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('prepro_method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('prepro_temp_c', sa.Numeric(), nullable=True), - sa.Column('drying_step', sa.Boolean(), nullable=True), - sa.Column('method_ref_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('prepro_method_id') - ) - op.create_table('preprocessing_methods_abbreviations', - sa.Column('prepro_methods_abbrev_id', sa.Integer(), nullable=False), - sa.Column('prepro_method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prepro_methods_abbrev_id'), - sa.UniqueConstraint('prepro_method_abbrev') - ) - op.create_table('primary_product', - sa.Column('primary_product_id', sa.Integer(), nullable=False), - sa.Column('primary_product_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('primary_product_id'), - sa.UniqueConstraint('primary_product_name') - ) - op.create_table('product_type', - sa.Column('product_type_id', sa.Integer(), nullable=False), - sa.Column('product', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('product_type_id') - ) - op.create_table('provider_types', - sa.Column('provider_type_id', sa.Integer(), nullable=False), - sa.Column('provider_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('provider_type_id') - ) - op.create_table('providers', - sa.Column('provider_id', sa.Integer(), nullable=False), - sa.Column('provider_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('provider_affiliation', sa.Integer(), nullable=True), - sa.Column('provider_type_id', sa.Integer(), nullable=True), - sa.Column('anonymous', sa.Boolean(), nullable=True), - sa.PrimaryKeyConstraint('provider_id'), - sa.UniqueConstraint('provider_name') - ) - op.create_table('proximate_analysis', - sa.Column('prox_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prox_id') - ) - op.create_table('qc_results', - sa.Column('qc_result_id', sa.Integer(), nullable=False), - sa.Column('qc_result', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('qc_result_id'), - sa.UniqueConstraint('qc_result') - ) - op.create_table('raster_metadata', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('resolution', sa.Float(), nullable=True), - sa.Column('srid', sa.Integer(), nullable=True), - sa.Column('acquisition_date', sa.Date(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('references', - sa.Column('reference_id', sa.Integer(), nullable=False), - sa.Column('reference_title', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_author', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_publication', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_date', sa.Date(), nullable=True), - sa.Column('reference_doi_id', sa.Integer(), nullable=True), - sa.Column('url_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('reference_id') - ) - op.create_table('regions', - sa.Column('region_id', sa.Integer(), nullable=False), - sa.Column('region_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('region_id'), - sa.UniqueConstraint('region_name') - ) - op.create_table('rooms', - sa.Column('room_id', sa.Integer(), nullable=False), - sa.Column('room_number', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('building_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('room_id'), - sa.UniqueConstraint('room_number') - ) - op.create_table('soil_type', - sa.Column('soil_type_id', sa.Integer(), nullable=False), - sa.Column('soil_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('soil_location', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('soil_type_id'), - sa.UniqueConstraint('soil_type') - ) - op.create_table('source_names', - sa.Column('source_name_id', sa.Integer(), nullable=False), - sa.Column('source_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('source_name_id'), - sa.UniqueConstraint('source_name') - ) - op.create_table('source_types', - sa.Column('source_type_id', sa.Integer(), nullable=False), - sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('source_type_id'), - sa.UniqueConstraint('source_type') - ) - op.create_table('states', - sa.Column('state_id', sa.Integer(), nullable=False), - sa.Column('state_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('state_id'), - sa.UniqueConstraint('state_name') - ) - op.create_table('street_addresses', - sa.Column('street_address_id', sa.Integer(), nullable=False), - sa.Column('street_address', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('street_address_id') - ) - op.create_table('taxonomy', - sa.Column('taxonomy_id', sa.Integer(), nullable=False), - sa.Column('kingdom', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('phylum', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('order', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('family', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('genus', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('species', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('variety_subspecies_cultivar', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('taxonomy_id') - ) - op.create_table('testusers2', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('fullname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('nickname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('units', - sa.Column('unit_id', sa.Integer(), nullable=False), - sa.Column('unit', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('unit_id'), - sa.UniqueConstraint('unit') - ) - op.create_table('url', - sa.Column('url_id', sa.Integer(), nullable=False), - sa.Column('url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('url_id'), - sa.UniqueConstraint('url') - ) - op.create_table('vectorized_raster_polygons', - sa.Column('vectorized_ID', sa.Integer(), nullable=False), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('raster_id', sa.Integer(), nullable=True), - sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('mean_value', sa.Float(), nullable=True), - sa.Column('std_dev', sa.Float(), nullable=True), - sa.Column('area_m2', sa.Float(), nullable=True), - sa.Column('date_acquired', sa.Date(), nullable=True), - sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('vectorized_ID') - ) - op.create_table('xrf_analysis', - sa.Column('xrf_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('xrf_id') - ) - op.create_table('zips', - sa.Column('zip_id', sa.Integer(), nullable=False), - sa.Column('zip_code', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('zip_id'), - sa.UniqueConstraint('zip_code') - ) - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.drop_table('zips') - op.drop_table('xrf_analysis') - op.drop_table('vectorized_raster_polygons') - op.drop_table('url') - op.drop_table('units') - op.drop_table('testusers2') - op.drop_table('taxonomy') - op.drop_table('street_addresses') - op.drop_table('states') - op.drop_table('source_types') - op.drop_table('source_names') - op.drop_table('soil_type') - op.drop_table('rooms') - op.drop_table('regions') - op.drop_table('references') - op.drop_table('raster_metadata') - op.drop_table('qc_results') - op.drop_table('proximate_analysis') - op.drop_table('providers') - op.drop_table('provider_types') - op.drop_table('product_type') - op.drop_table('primary_product') - op.drop_table('preprocessing_methods_abbreviations') - op.drop_table('preprocessing_methods') - op.drop_index('idx_preprocessed_samples_prepro_method_id', table_name='preprocessed_samples') - op.drop_index('idx_preprocessed_samples_biomass_sample_id', table_name='preprocessed_samples') - op.drop_table('preprocessed_samples') - op.drop_table('particle_size') - op.drop_table('parameters') - op.drop_index('idx_parameter_units_unit_id', table_name='parameter_units') - op.drop_index('idx_parameter_units_parameter_id', table_name='parameter_units') - op.drop_table('parameter_units') - op.drop_table('parameter_methods') - op.drop_table('parameter_catagories') - op.drop_table('organisms') - op.drop_index('idx_methods_method_name', table_name='methods') - op.drop_table('methods') - op.drop_table('method_standards') - op.drop_index('idx_method_equipment_method_id', table_name='method_equipment') - op.drop_index('idx_method_equipment_equipment_id', table_name='method_equipment') - op.drop_table('method_equipment') - op.drop_table('method_categories') - op.drop_table('method_abbrevs') - op.drop_table('metadata') - op.drop_table('location_resolutions') - op.drop_table('import_log') - op.drop_table('icp_analysis') - op.drop_table('harvest_methods') - op.drop_table('geographic_locations') - op.drop_table('gasification_profile') - op.drop_table('fips') - op.drop_table('field_storage') - op.drop_index(op.f('ix_field_samples_source_codename_id'), table_name='field_samples') - op.drop_index(op.f('ix_field_samples_biomass_id'), table_name='field_samples') - op.drop_table('field_samples') - op.drop_table('fermentation_profile') - op.drop_table('external_usda') - op.drop_index('idx_external_phyllis2_biomass_id', table_name='external_phyllis2') - op.drop_index('idx_external_phyllis2_analysis_type_id', table_name='external_phyllis2') - op.drop_table('external_phyllis2') - op.drop_table('external_land_id') - op.drop_index('idx_external_inl_biofeedstock_library_biomass_id', table_name='external_inl_biofeedstock_library') - op.drop_table('external_inl_biofeedstock_library') - op.drop_table('external_ebmud') - op.drop_index('idx_external_dairy_one_parameter_id', table_name='external_dairy_one') - op.drop_index('idx_external_dairy_one_biomass_id', table_name='external_dairy_one') - op.drop_table('external_dairy_one') - op.drop_table('external_atip') - op.drop_index('idx_experiments_analysis_type_id', table_name='experiments') - op.drop_table('experiments') - op.drop_index('idx_experiment_methods_method_id', table_name='experiment_methods') - op.drop_index('idx_experiment_methods_experiment_id', table_name='experiment_methods') - op.drop_table('experiment_methods') - op.drop_table('equipment') - op.drop_table('doi') - op.drop_index('idx_data_sources_source_name_id', table_name='data_sources') - op.drop_table('data_sources') - op.drop_table('counties') - op.drop_table('compositional_analysis') - op.drop_table('collectors') - op.drop_table('collection_methods') - op.drop_table('cities') - op.drop_table('buildings') - op.drop_table('biomass_type') - op.drop_index(op.f('ix_biomass_test_biomass_test_name'), table_name='biomass_test') - op.drop_table('biomass_test') - op.drop_index(op.f('ix_biomass_quality_biomass_id'), table_name='biomass_quality') - op.drop_table('biomass_quality') - op.drop_index(op.f('ix_biomass_price_biomass_id'), table_name='biomass_price') - op.drop_table('biomass_price') - op.drop_index(op.f('ix_biomass_availability_biomass_id'), table_name='biomass_availability') - op.drop_table('biomass_availability') - op.drop_index(op.f('ix_biomass_biomass_type_id'), table_name='biomass') - op.drop_index(op.f('ix_biomass_biomass_name'), table_name='biomass') - op.drop_table('biomass') - op.drop_table('autoclave_profile') - op.drop_table('analyst_contact') - op.drop_table('analysis_types') - op.drop_index('uq_analysis_results_experiment_parameter_replicate', table_name='analysis_results') - op.drop_index('idx_analysis_results_parameter_id', table_name='analysis_results') - op.drop_table('analysis_results') - op.drop_table('analysis_replicate_id') - op.drop_table('analysis_abbreviations') - op.drop_table('ag_treatments') - op.drop_table('affiliations') - # ### end Alembic commands ### diff --git a/alembic/versions/e15bda744fef_initial_migration.py b/alembic/versions/e15bda744fef_initial_migration.py deleted file mode 100644 index 18517bc2..00000000 --- a/alembic/versions/e15bda744fef_initial_migration.py +++ /dev/null @@ -1,877 +0,0 @@ -"""Initial migration - -Revision ID: e15bda744fef -Revises: -Create Date: 2025-11-04 20:03:41.870493 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa -import sqlmodel - -# revision identifiers, used by Alembic. -revision: str = 'e15bda744fef' -down_revision: Union[str, Sequence[str], None] = None -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.create_table('affiliations', - sa.Column('affiliation_id', sa.Integer(), nullable=False), - sa.Column('affiliation_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('affiliation_id'), - sa.UniqueConstraint('affiliation_name') - ) - op.create_table('ag_treatments', - sa.Column('ag_treatment_id', sa.Integer(), nullable=False), - sa.Column('ag_treatment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('ag_treatment_id') - ) - op.create_table('analysis_abbreviations', - sa.Column('analysis_abbreviations_id', sa.Integer(), nullable=False), - sa.Column('analysis_abbreviation', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_abbreviations_id'), - sa.UniqueConstraint('analysis_abbreviation') - ) - op.create_table('analysis_replicate_id', - sa.Column('analysis_replicate_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('analysis_types_id', sa.Integer(), nullable=True), - sa.Column('analysis_replicate_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_replicate_id') - ) - op.create_table('analysis_results', - sa.Column('result_id', sa.Integer(), nullable=False), - sa.Column('anlaysis_sample', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('replicate_no', sa.Integer(), nullable=True), - sa.Column('analysis_timestamp', sa.DateTime(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('qc_result_id', sa.Integer(), nullable=True), - sa.Column('measurement_equipment_id', sa.Integer(), nullable=True), - sa.Column('raw_data_url_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('analysis_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('result_id') - ) - op.create_index('idx_analysis_results_parameter_id', 'analysis_results', ['parameter_id'], unique=False) - op.create_index('uq_analysis_results_experiment_parameter_replicate', 'analysis_results', ['experiment_id', 'parameter_id', 'replicate_no'], unique=True) - op.create_table('analysis_types', - sa.Column('analysis_type_id', sa.Integer(), nullable=False), - sa.Column('analysis_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_type_id'), - sa.UniqueConstraint('analysis_name') - ) - op.create_table('analyst_contact', - sa.Column('analyst_id', sa.Integer(), nullable=False), - sa.Column('analyst_first_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_last_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_email', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_affiliation', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('analyst_id') - ) - op.create_table('autoclave_profile', - sa.Column('autoclave_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('autoclave_id') - ) - op.create_table('biomass', - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('biomass_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('primary_product_id', sa.Integer(), nullable=True), - sa.Column('taxonomy_id', sa.Integer(), nullable=True), - sa.Column('biomass_type_id', sa.Integer(), nullable=True), - sa.Column('biomass_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('biomass_id') - ) - op.create_index(op.f('ix_biomass_biomass_name'), 'biomass', ['biomass_name'], unique=False) - op.create_index(op.f('ix_biomass_biomass_type_id'), 'biomass', ['biomass_type_id'], unique=False) - op.create_table('biomass_availability', - sa.Column('availability_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('primary_product_id', sa.Integer(), nullable=True), - sa.Column('from_month', sa.Numeric(), nullable=True), - sa.Column('to_month', sa.Numeric(), nullable=True), - sa.Column('kg_low', sa.Numeric(), nullable=True), - sa.Column('kg_avg', sa.Numeric(), nullable=True), - sa.Column('kg_high', sa.Numeric(), nullable=True), - sa.Column('bdt_low', sa.Numeric(), nullable=True), - sa.Column('bdt_avg', sa.Numeric(), nullable=True), - sa.Column('bdt_high', sa.Numeric(), nullable=True), - sa.Column('data_source', sa.Integer(), nullable=True), - sa.Column('availability_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('availability_id') - ) - op.create_index(op.f('ix_biomass_availability_biomass_id'), 'biomass_availability', ['biomass_id'], unique=False) - op.create_table('biomass_price', - sa.Column('price_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('price_per_kg_low', sa.Numeric(), nullable=True), - sa.Column('price_per_kg_avg', sa.Numeric(), nullable=True), - sa.Column('price_per_kg_high', sa.Numeric(), nullable=True), - sa.Column('price_data_sources', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('price_id') - ) - op.create_index(op.f('ix_biomass_price_biomass_id'), 'biomass_price', ['biomass_id'], unique=False) - op.create_table('biomass_quality', - sa.Column('quality_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('expected_quality', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('output_feedstocks', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('convertibility', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('disposal_challenges', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('existing_markets', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('substitute_materials', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('regulatory_issues', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('quality_data_sources', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('quality_id') - ) - op.create_index(op.f('ix_biomass_quality_biomass_id'), 'biomass_quality', ['biomass_id'], unique=False) - op.create_table('biomass_test', - sa.Column('biomass_test_id', sa.Integer(), nullable=False), - sa.Column('biomass_test_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('biomass_test_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('biomass_test_id') - ) - op.create_index(op.f('ix_biomass_test_biomass_test_name'), 'biomass_test', ['biomass_test_name'], unique=False) - op.create_table('biomass_type', - sa.Column('biomass_type_id', sa.Integer(), nullable=False), - sa.Column('biomass_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('biomass_type_id'), - sa.UniqueConstraint('biomass_type') - ) - op.create_table('buildings', - sa.Column('building_id', sa.Integer(), nullable=False), - sa.Column('building_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('affiliation_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('building_id'), - sa.UniqueConstraint('building_name') - ) - op.create_table('cities', - sa.Column('city_id', sa.Integer(), nullable=False), - sa.Column('city_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('city_id'), - sa.UniqueConstraint('city_name') - ) - op.create_table('collection_methods', - sa.Column('collection_method_id', sa.Integer(), nullable=False), - sa.Column('collection_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('collection_method_id'), - sa.UniqueConstraint('collection_method_name') - ) - op.create_table('collectors', - sa.Column('collector_id', sa.Integer(), nullable=False), - sa.Column('collector_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('collector_affiliation', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('collector_id'), - sa.UniqueConstraint('collector_name') - ) - op.create_table('compositional_analysis', - sa.Column('cmp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('calculated_parameter_id', sa.Integer(), nullable=True), - sa.Column('calculated_parameter_value', sa.Numeric(), nullable=True), - sa.Column('calculated_parameter_unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('cmp_id') - ) - op.create_table('counties', - sa.Column('county_id', sa.Integer(), nullable=False), - sa.Column('county_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('county_id'), - sa.UniqueConstraint('county_name') - ) - op.create_table('data_sources', - sa.Column('source_id', sa.Integer(), nullable=False), - sa.Column('source_name_id', sa.Integer(), nullable=True), - sa.Column('source_type_id', sa.Integer(), nullable=True), - sa.Column('data_resolution_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('url_id', sa.Integer(), nullable=True), - sa.Column('import_timestamp', sa.DateTime(), nullable=True), - sa.PrimaryKeyConstraint('source_id') - ) - op.create_index('idx_data_sources_source_name_id', 'data_sources', ['source_name_id'], unique=False) - op.create_table('doi', - sa.Column('doi_id', sa.Integer(), nullable=False), - sa.Column('doi', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('doi_id') - ) - op.create_table('equipment', - sa.Column('equipment_id', sa.Integer(), nullable=False), - sa.Column('equipment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('equipment_room_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('equipment_id'), - sa.UniqueConstraint('equipment_name') - ) - op.create_table('experiment_methods', - sa.Column('experiment_method_id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('experiment_method_id') - ) - op.create_index('idx_experiment_methods_experiment_id', 'experiment_methods', ['experiment_id'], unique=False) - op.create_index('idx_experiment_methods_method_id', 'experiment_methods', ['method_id'], unique=False) - op.create_table('experiments', - sa.Column('experiment_id', sa.Integer(), nullable=False), - sa.Column('exper_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('gsheet_exper_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('analysis_abbrev_id', sa.Integer(), nullable=True), - sa.Column('exper_start_date', sa.Date(), nullable=True), - sa.Column('exper_duration', sa.Numeric(), nullable=True), - sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('exper_location_id', sa.Integer(), nullable=True), - sa.Column('exper_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('experiment_id'), - sa.UniqueConstraint('exper_uuid'), - sa.UniqueConstraint('gsheet_exper_id') - ) - op.create_index('idx_experiments_analysis_type_id', 'experiments', ['analysis_type_id'], unique=False) - op.create_table('external_atip', - sa.Column('atip_ID', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('atip_ID') - ) - op.create_table('external_dairy_one', - sa.Column('dairy_one_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('samples_count', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('accumulated_years_from', sa.Date(), nullable=True), - sa.Column('accumulated_years_to', sa.Date(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('dairy_one_id') - ) - op.create_index('idx_external_dairy_one_biomass_id', 'external_dairy_one', ['biomass_id'], unique=False) - op.create_index('idx_external_dairy_one_parameter_id', 'external_dairy_one', ['parameter_id'], unique=False) - op.create_table('external_ebmud', - sa.Column('ebmud_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('ebmud_id') - ) - op.create_table('external_inl_biofeedstock_library', - sa.Column('bfl_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('state_id', sa.Integer(), nullable=True), - sa.Column('affiliations_id', sa.Integer(), nullable=True), - sa.Column('harvest_method_id', sa.Integer(), nullable=True), - sa.Column('collection_method_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('accumulated_years_from', sa.Date(), nullable=True), - sa.Column('accumulated_years_to', sa.Date(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('bfl_id') - ) - op.create_index('idx_external_inl_biofeedstock_library_biomass_id', 'external_inl_biofeedstock_library', ['biomass_id'], unique=False) - op.create_table('external_land_id', - sa.Column('land_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('land_id') - ) - op.create_table('external_phyllis2', - sa.Column('phyllis_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('phyllis_id') - ) - op.create_index('idx_external_phyllis2_analysis_type_id', 'external_phyllis2', ['analysis_type_id'], unique=False) - op.create_index('idx_external_phyllis2_biomass_id', 'external_phyllis2', ['biomass_id'], unique=False) - op.create_table('external_usda', - sa.Column('usda_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('usda_id') - ) - op.create_table('fermentation_profile', - sa.Column('fp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('organism_id', sa.Integer(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('fp_id') - ) - op.create_table('field_samples', - sa.Column('sample_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('sample_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('source_codename_id', sa.Integer(), nullable=True), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('field_storage_id', sa.Integer(), nullable=True), - sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), - sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('collection_timestamp', sa.DateTime(), nullable=True), - sa.Column('collection_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_date', sa.Date(), nullable=True), - sa.Column('amount_collected_kg', sa.Numeric(), nullable=True), - sa.Column('provider_id', sa.Integer(), nullable=True), - sa.Column('collector_id', sa.Integer(), nullable=True), - sa.Column('basic_sample_info_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('created_at', sa.DateTime(), nullable=False), - sa.PrimaryKeyConstraint('sample_id') - ) - op.create_index(op.f('ix_field_samples_biomass_id'), 'field_samples', ['biomass_id'], unique=False) - op.create_index(op.f('ix_field_samples_source_codename_id'), 'field_samples', ['source_codename_id'], unique=False) - op.create_table('field_storage', - sa.Column('field_storage_id', sa.Integer(), nullable=False), - sa.Column('storage_method', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('field_storage_id'), - sa.UniqueConstraint('storage_method') - ) - op.create_table('fips', - sa.Column('fips_id', sa.Integer(), nullable=False), - sa.Column('fips_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('fips_id') - ) - op.create_table('gasification_profile', - sa.Column('gasification_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('gasification_id') - ) - op.create_table('geographic_locations', - sa.Column('location_id', sa.Integer(), nullable=False), - sa.Column('street_address_id', sa.Integer(), nullable=True), - sa.Column('city_id', sa.Integer(), nullable=True), - sa.Column('zip_id', sa.Integer(), nullable=True), - sa.Column('county_id', sa.Integer(), nullable=True), - sa.Column('state_id', sa.Integer(), nullable=True), - sa.Column('region_id', sa.Integer(), nullable=True), - sa.Column('fips_id', sa.Integer(), nullable=True), - sa.Column('latitude', sa.Numeric(), nullable=True), - sa.Column('longitude', sa.Numeric(), nullable=True), - sa.Column('location_resolution_id', sa.Integer(), nullable=True), - sa.Column('is_anonymous', sa.Boolean(), nullable=True), - sa.PrimaryKeyConstraint('location_id') - ) - op.create_table('harvest_methods', - sa.Column('harvest_method_id', sa.Integer(), nullable=False), - sa.Column('harvest_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('harvest_method_id'), - sa.UniqueConstraint('harvest_method_name') - ) - op.create_table('icp_analysis', - sa.Column('icp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('concentration_calculation_url_id', sa.Integer(), nullable=True), - sa.Column('result_wavelength', sa.Numeric(), nullable=True), - sa.Column('raw_url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('icp_id') - ) - op.create_table('import_log', - sa.Column('import_id', sa.Integer(), nullable=False), - sa.Column('import_timestamp', sa.DateTime(), nullable=True), - sa.Column('destination', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('source_file', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('records_imported', sa.Integer(), nullable=True), - sa.Column('import_status', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('error_log', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_user', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('import_id') - ) - op.create_table('location_resolutions', - sa.Column('location_resolution_id', sa.Integer(), nullable=False), - sa.Column('resolution_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('location_resolution_id'), - sa.UniqueConstraint('resolution_type') - ) - op.create_table('metadata', - sa.Column('metadata_id', sa.Integer(), nullable=False), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('ag_treatment_id', sa.Integer(), nullable=True), - sa.Column('last_application_date', sa.Date(), nullable=True), - sa.Column('treatment_amount_per_acre', sa.Numeric(), nullable=True), - sa.Column('soil_type', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('metadata_id') - ) - op.create_table('method_abbrevs', - sa.Column('method_abbrev_id', sa.Integer(), nullable=False), - sa.Column('method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_abbrev_id'), - sa.UniqueConstraint('method_abbrev') - ) - op.create_table('method_categories', - sa.Column('method_category_id', sa.Integer(), nullable=False), - sa.Column('method_category', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_category_id'), - sa.UniqueConstraint('method_category') - ) - op.create_table('method_equipment', - sa.Column('method_equipment_id', sa.Integer(), nullable=False), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('equipment_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('method_equipment_id') - ) - op.create_index('idx_method_equipment_equipment_id', 'method_equipment', ['equipment_id'], unique=False) - op.create_index('idx_method_equipment_method_id', 'method_equipment', ['method_id'], unique=False) - op.create_table('method_standards', - sa.Column('method_standard_id', sa.Integer(), nullable=False), - sa.Column('method_standard', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_standard_id'), - sa.UniqueConstraint('method_standard') - ) - op.create_table('methods', - sa.Column('method_id', sa.Integer(), nullable=False), - sa.Column('method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('method_category_id', sa.Integer(), nullable=True), - sa.Column('method_standard_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('detection_limits', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('procedure_reference_id', sa.Integer(), nullable=True), - sa.Column('method_url_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('method_id'), - sa.UniqueConstraint('method_name') - ) - op.create_index('idx_methods_method_name', 'methods', ['method_name'], unique=False) - op.create_table('organisms', - sa.Column('organism_id', sa.Integer(), nullable=False), - sa.Column('organism_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('organism_strain_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('organism_id') - ) - op.create_table('parameter_catagories', - sa.Column('parameter_catagory_id', sa.Integer(), nullable=False), - sa.Column('parameter_catagory', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('parameter_catagory_id') - ) - op.create_table('parameter_methods', - sa.Column('param_method_id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('param_method_id') - ) - op.create_table('parameter_units', - sa.Column('parameter_unit_id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('parameter_unit_id') - ) - op.create_index('idx_parameter_units_parameter_id', 'parameter_units', ['parameter_id'], unique=False) - op.create_index('idx_parameter_units_unit_id', 'parameter_units', ['unit_id'], unique=False) - op.create_table('parameters', - sa.Column('parameter_id', sa.Integer(), nullable=False), - sa.Column('parameter_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('parameter_category_id', sa.Integer(), nullable=True), - sa.Column('standard_unit_id', sa.Integer(), nullable=True), - sa.Column('calculated', sa.Boolean(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('typical_range_min', sa.Numeric(), nullable=True), - sa.Column('typical_range_max', sa.Numeric(), nullable=True), - sa.PrimaryKeyConstraint('parameter_id'), - sa.UniqueConstraint('parameter_name') - ) - op.create_table('particle_size', - sa.Column('particle_size_id', sa.Integer(), nullable=False), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('particle_length', sa.Integer(), nullable=True), - sa.Column('particle_width', sa.Integer(), nullable=True), - sa.Column('particle_height', sa.Integer(), nullable=True), - sa.Column('particle_units', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('particle_size_id') - ) - op.create_table('preprocessed_samples', - sa.Column('prepro_material_id', sa.Integer(), nullable=False), - sa.Column('prepro_material_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('biomass_sample_id', sa.Integer(), nullable=True), - sa.Column('prepro_method_id', sa.Integer(), nullable=True), - sa.Column('amount_before_drying_g', sa.Numeric(), nullable=True), - sa.Column('amount_after_drying', sa.Numeric(), nullable=True), - sa.Column('processing_date', sa.Date(), nullable=True), - sa.Column('storage_building', sa.Integer(), nullable=True), - sa.Column('amount_remaining_g', sa.Numeric(), nullable=True), - sa.Column('amount_as_of_date', sa.Date(), nullable=True), - sa.Column('prepro_analyst_id', sa.Integer(), nullable=True), - sa.Column('prepro_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prepro_material_id') - ) - op.create_index('idx_preprocessed_samples_biomass_sample_id', 'preprocessed_samples', ['biomass_sample_id'], unique=False) - op.create_index('idx_preprocessed_samples_prepro_method_id', 'preprocessed_samples', ['prepro_method_id'], unique=False) - op.create_table('preprocessing_methods', - sa.Column('prepro_method_id', sa.Integer(), nullable=False), - sa.Column('prepro_method', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('prepro_method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('prepro_temp_c', sa.Numeric(), nullable=True), - sa.Column('drying_step', sa.Boolean(), nullable=True), - sa.Column('method_ref_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('prepro_method_id') - ) - op.create_table('preprocessing_methods_abbreviations', - sa.Column('prepro_methods_abbrev_id', sa.Integer(), nullable=False), - sa.Column('prepro_method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prepro_methods_abbrev_id'), - sa.UniqueConstraint('prepro_method_abbrev') - ) - op.create_table('primary_product', - sa.Column('primary_product_id', sa.Integer(), nullable=False), - sa.Column('primary_product_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('primary_product_id'), - sa.UniqueConstraint('primary_product_name') - ) - op.create_table('product_type', - sa.Column('product_type_id', sa.Integer(), nullable=False), - sa.Column('product', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('product_type_id') - ) - op.create_table('provider_types', - sa.Column('provider_type_id', sa.Integer(), nullable=False), - sa.Column('provider_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('provider_type_id') - ) - op.create_table('providers', - sa.Column('provider_id', sa.Integer(), nullable=False), - sa.Column('provider_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('provider_affiliation', sa.Integer(), nullable=True), - sa.Column('provider_type_id', sa.Integer(), nullable=True), - sa.Column('anonymous', sa.Boolean(), nullable=True), - sa.PrimaryKeyConstraint('provider_id'), - sa.UniqueConstraint('provider_name') - ) - op.create_table('proximate_analysis', - sa.Column('prox_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prox_id') - ) - op.create_table('qc_results', - sa.Column('qc_result_id', sa.Integer(), nullable=False), - sa.Column('qc_result', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('qc_result_id'), - sa.UniqueConstraint('qc_result') - ) - op.create_table('raster_metadata', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('resolution', sa.Float(), nullable=True), - sa.Column('srid', sa.Integer(), nullable=True), - sa.Column('acquisition_date', sa.Date(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('references', - sa.Column('reference_id', sa.Integer(), nullable=False), - sa.Column('reference_title', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_author', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_publication', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_date', sa.Date(), nullable=True), - sa.Column('reference_doi_id', sa.Integer(), nullable=True), - sa.Column('url_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('reference_id') - ) - op.create_table('regions', - sa.Column('region_id', sa.Integer(), nullable=False), - sa.Column('region_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('region_id'), - sa.UniqueConstraint('region_name') - ) - op.create_table('rooms', - sa.Column('room_id', sa.Integer(), nullable=False), - sa.Column('room_number', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('building_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('room_id'), - sa.UniqueConstraint('room_number') - ) - op.create_table('soil_type', - sa.Column('soil_type_id', sa.Integer(), nullable=False), - sa.Column('soil_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('soil_location', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('soil_type_id'), - sa.UniqueConstraint('soil_type') - ) - op.create_table('source_names', - sa.Column('source_name_id', sa.Integer(), nullable=False), - sa.Column('source_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('source_name_id'), - sa.UniqueConstraint('source_name') - ) - op.create_table('source_types', - sa.Column('source_type_id', sa.Integer(), nullable=False), - sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('source_type_id'), - sa.UniqueConstraint('source_type') - ) - op.create_table('states', - sa.Column('state_id', sa.Integer(), nullable=False), - sa.Column('state_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('state_id'), - sa.UniqueConstraint('state_name') - ) - op.create_table('street_addresses', - sa.Column('street_address_id', sa.Integer(), nullable=False), - sa.Column('street_address', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('street_address_id') - ) - op.create_table('taxonomy', - sa.Column('taxonomy_id', sa.Integer(), nullable=False), - sa.Column('kingdom', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('phylum', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('order', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('family', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('genus', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('species', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('variety_subspecies_cultivar', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('taxonomy_id') - ) - op.create_table('testusers2', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('fullname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('nickname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('units', - sa.Column('unit_id', sa.Integer(), nullable=False), - sa.Column('unit', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('unit_id'), - sa.UniqueConstraint('unit') - ) - op.create_table('url', - sa.Column('url_id', sa.Integer(), nullable=False), - sa.Column('url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('url_id'), - sa.UniqueConstraint('url') - ) - op.create_table('vectorized_raster_polygons', - sa.Column('vectorized_ID', sa.Integer(), nullable=False), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('raster_id', sa.Integer(), nullable=True), - sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('mean_value', sa.Float(), nullable=True), - sa.Column('std_dev', sa.Float(), nullable=True), - sa.Column('area_m2', sa.Float(), nullable=True), - sa.Column('date_acquired', sa.Date(), nullable=True), - sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('vectorized_ID') - ) - op.create_table('xrf_analysis', - sa.Column('xrf_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('xrf_id') - ) - op.create_table('zips', - sa.Column('zip_id', sa.Integer(), nullable=False), - sa.Column('zip_code', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('zip_id'), - sa.UniqueConstraint('zip_code') - ) - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.drop_table('zips') - op.drop_table('xrf_analysis') - op.drop_table('vectorized_raster_polygons') - op.drop_table('url') - op.drop_table('units') - op.drop_table('testusers2') - op.drop_table('taxonomy') - op.drop_table('street_addresses') - op.drop_table('states') - op.drop_table('source_types') - op.drop_table('source_names') - op.drop_table('soil_type') - op.drop_table('rooms') - op.drop_table('regions') - op.drop_table('references') - op.drop_table('raster_metadata') - op.drop_table('qc_results') - op.drop_table('proximate_analysis') - op.drop_table('providers') - op.drop_table('provider_types') - op.drop_table('product_type') - op.drop_table('primary_product') - op.drop_table('preprocessing_methods_abbreviations') - op.drop_table('preprocessing_methods') - op.drop_index('idx_preprocessed_samples_prepro_method_id', table_name='preprocessed_samples') - op.drop_index('idx_preprocessed_samples_biomass_sample_id', table_name='preprocessed_samples') - op.drop_table('preprocessed_samples') - op.drop_table('particle_size') - op.drop_table('parameters') - op.drop_index('idx_parameter_units_unit_id', table_name='parameter_units') - op.drop_index('idx_parameter_units_parameter_id', table_name='parameter_units') - op.drop_table('parameter_units') - op.drop_table('parameter_methods') - op.drop_table('parameter_catagories') - op.drop_table('organisms') - op.drop_index('idx_methods_method_name', table_name='methods') - op.drop_table('methods') - op.drop_table('method_standards') - op.drop_index('idx_method_equipment_method_id', table_name='method_equipment') - op.drop_index('idx_method_equipment_equipment_id', table_name='method_equipment') - op.drop_table('method_equipment') - op.drop_table('method_categories') - op.drop_table('method_abbrevs') - op.drop_table('metadata') - op.drop_table('location_resolutions') - op.drop_table('import_log') - op.drop_table('icp_analysis') - op.drop_table('harvest_methods') - op.drop_table('geographic_locations') - op.drop_table('gasification_profile') - op.drop_table('fips') - op.drop_table('field_storage') - op.drop_index(op.f('ix_field_samples_source_codename_id'), table_name='field_samples') - op.drop_index(op.f('ix_field_samples_biomass_id'), table_name='field_samples') - op.drop_table('field_samples') - op.drop_table('fermentation_profile') - op.drop_table('external_usda') - op.drop_index('idx_external_phyllis2_biomass_id', table_name='external_phyllis2') - op.drop_index('idx_external_phyllis2_analysis_type_id', table_name='external_phyllis2') - op.drop_table('external_phyllis2') - op.drop_table('external_land_id') - op.drop_index('idx_external_inl_biofeedstock_library_biomass_id', table_name='external_inl_biofeedstock_library') - op.drop_table('external_inl_biofeedstock_library') - op.drop_table('external_ebmud') - op.drop_index('idx_external_dairy_one_parameter_id', table_name='external_dairy_one') - op.drop_index('idx_external_dairy_one_biomass_id', table_name='external_dairy_one') - op.drop_table('external_dairy_one') - op.drop_table('external_atip') - op.drop_index('idx_experiments_analysis_type_id', table_name='experiments') - op.drop_table('experiments') - op.drop_index('idx_experiment_methods_method_id', table_name='experiment_methods') - op.drop_index('idx_experiment_methods_experiment_id', table_name='experiment_methods') - op.drop_table('experiment_methods') - op.drop_table('equipment') - op.drop_table('doi') - op.drop_index('idx_data_sources_source_name_id', table_name='data_sources') - op.drop_table('data_sources') - op.drop_table('counties') - op.drop_table('compositional_analysis') - op.drop_table('collectors') - op.drop_table('collection_methods') - op.drop_table('cities') - op.drop_table('buildings') - op.drop_table('biomass_type') - op.drop_index(op.f('ix_biomass_test_biomass_test_name'), table_name='biomass_test') - op.drop_table('biomass_test') - op.drop_index(op.f('ix_biomass_quality_biomass_id'), table_name='biomass_quality') - op.drop_table('biomass_quality') - op.drop_index(op.f('ix_biomass_price_biomass_id'), table_name='biomass_price') - op.drop_table('biomass_price') - op.drop_index(op.f('ix_biomass_availability_biomass_id'), table_name='biomass_availability') - op.drop_table('biomass_availability') - op.drop_index(op.f('ix_biomass_biomass_type_id'), table_name='biomass') - op.drop_index(op.f('ix_biomass_biomass_name'), table_name='biomass') - op.drop_table('biomass') - op.drop_table('autoclave_profile') - op.drop_table('analyst_contact') - op.drop_table('analysis_types') - op.drop_index('uq_analysis_results_experiment_parameter_replicate', table_name='analysis_results') - op.drop_index('idx_analysis_results_parameter_id', table_name='analysis_results') - op.drop_table('analysis_results') - op.drop_table('analysis_replicate_id') - op.drop_table('analysis_abbreviations') - op.drop_table('ag_treatments') - op.drop_table('affiliations') - # ### end Alembic commands ### From 120d608e5264271696a049acfaf41efd7da29932 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Tue, 18 Nov 2025 11:07:32 -0700 Subject: [PATCH 15/81] alembic issue fixed. sqlalchemy commented out for now --- README.md | 117 ++++++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 96 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index 5dc89ccc..114d504c 100644 --- a/README.md +++ b/README.md @@ -1,35 +1,110 @@ # ca-biositing -Discussion of general issues related to the project and protyping or research +A geospatial bioeconomy project for biositing analysis in California. This +repository provides tools for ETL pipelines to process data from Google Sheets +into PostgreSQL databases, geospatial analysis using QGIS, and a REST API for +data access. + +## Project Structure + +This project uses a **PEP 420 namespace package** structure with three main +components: + +- **`ca_biositing.datamodels`**: Shared SQLModel database models and database + configuration +- **`ca_biositing.pipeline`**: ETL pipelines orchestrated with Prefect, deployed + via Docker +- **`ca_biositing.webservice`**: FastAPI REST API for data access + +### Directory Layout + +```text +ca-biositing/ +├── src/ca_biositing/ # Namespace package root +│ ├── datamodels/ # Database models (SQLModel) +│ ├── pipeline/ # ETL pipelines (Prefect) +│ └── webservice/ # REST API (FastAPI) +├── resources/ # Deployment resources +│ ├── docker/ # Docker Compose configuration +│ └── prefect/ # Prefect deployment files +├── tests/ # Integration tests +├── pixi.toml # Pixi dependencies and tasks +└── pixi.lock # Dependency lock file +``` + +## Quick Start + +### Prerequisites + +- **Pixi** (v0.55.0+): + [Installation Guide](https://pixi.sh/latest/#installation) +- **Docker**: For running the ETL pipeline +- **Google Cloud credentials**: For Google Sheets access (optional) + +### Installation + +```bash +# Clone the repository +git clone https://github.com/uw-ssec/ca-biositing.git +cd ca-biositing + +# Install dependencies with Pixi +pixi install + +# Install pre-commit hooks +pixi run pre-commit-install +``` + +### Running Components + +#### ETL Pipeline (Prefect + Docker) + +**Note**: Before starting the services for the first time, create the required +environment file from the template: -## Relevant Links for project documentations and context +```bash +cp resources/docker/.env.example resources/docker/.env +``` -- eScience Slack channel: 🔒 - [#ssec-ca-biositing](https://escience-institute.slack.com/archives/C098GJCTTFE) -- SSEC Sharepoint (**INTERNAL SSEC ONLY**): 🔒 - [Projects/GeospatialBioeconomy](https://uwnetid.sharepoint.com/:f:/r/sites/og_ssec_escience/Shared%20Documents/Projects/GeospatialBioeconomy?csf=1&web=1&e=VBUGQG) -- Shared Sharepoint Directory: 🔒 - [SSEC CA Biositing Shared Folder](https://uwnetid.sharepoint.com/:f:/r/sites/og_ssec_escience/Shared%20Documents/Projects/GeospatialBioeconomy/SSEC%20CA%20Biositing%20Shared%20Folder?csf=1&web=1&e=p5wBel) +Then start and use the services: -## General Discussions +```bash +# 1. Create the initial database migration script +# (This is only needed once for a new database) +pixi run initial-migration -For general discussion, ideas, and resources please use the -[GitHub Discussions](https://github.com/uw-ssec/ca-biositing/discussions). -However, if there's an internal discussion that need to happen, please use the -slack channel provided. +# 2. Start all services (PostgreSQL, Prefect server, worker) +# This will also automatically apply any pending database migrations. +pixi run start-services -- Meeting Notes in GitHub: - [discussions/meetings](https://github.com/uw-ssec/ca-biositing/discussions/categories/meetings) +# 3. Deploy flows to Prefect +pixi run deploy -## Questions +# Run the ETL pipeline +pixi run run-etl -If you have any questions about our process, or locations of SSEC resources, -please ask [Anshul Tambay](https://github.com/atambay37). +# Monitor via Prefect UI: http://localhost:4200 + +# To apply new migrations after the initial setup +pixi run migrate + +# Stop services +pixi run teardown-services +``` -## QGIS +See [`resources/README.md`](resources/README.md) for detailed pipeline +documentation. + +#### Web Service (FastAPI) + +```bash +# Start the web service +pixi run start-webservice + +# Access API docs: http://localhost:8000/docs +``` -This project includes QGIS for geospatial analysis and visualization. You can -run QGIS using pixi with the following command: +#### QGIS (Geospatial Analysis) ```bash pixi run qgis From 6e4efcee70a86ef827cd3221d73e7c65db600f7a Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Wed, 19 Nov 2025 16:24:37 -0700 Subject: [PATCH 16/81] adding asyncpg to root pixi.toml --- pixi.toml | 20 ++++++-------------- 1 file changed, 6 insertions(+), 14 deletions(-) diff --git a/pixi.toml b/pixi.toml index 02e590a2..e5b60231 100644 --- a/pixi.toml +++ b/pixi.toml @@ -25,20 +25,12 @@ python = "~=3.12" pre-commit = ">=4.2.0,<5" pytest = ">=8.4.2,<9" pytest-cov = ">=7.0.0,<8" -sqlmodel = ">=0.0.19,<0.1" -alembic = ">=1.13.2,<2" -psycopg2 = ">=2.9.9,<3" -python-dotenv = ">=1.0.1,<2" -pandas = ">=2.2.0,<3" -pyjanitor = "*" -gspread = "*" -gspread-dataframe = "*" -pydantic-settings = "*" -google-auth-oauthlib = "*" -prefect = "*" -uvicorn = ">=0.30.0,<1" -fastapi = ">=0.115.0,<1" -linkml = "*" +pip = ">=25.2,<26" +docker-compose = ">=2.39.2,<3" +docker-cli = ">=28.3.1,<29" +testcontainers = ">=4.13.2,<5" +python-dotenv = ">=1.2.1,<2" +asyncpg = ">=0.29.0,<0.30" [tasks] pre-commit-all = "pre-commit run --all-files" From eee7e8622ceb6c32a4ce8234dd67a2b2703e5307 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Sun, 7 Dec 2025 20:24:49 -0700 Subject: [PATCH 17/81] rebasing to upstream main. 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a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml new file mode 100644 index 00000000..94d9f8d2 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml @@ -0,0 +1,32 @@ +id: https://w3id.org/ca_biositing +name: ca_biositing +title: CA Biositing Schema +description: >- + LinkML schema for the CA Biositing project, defining data models for + bioeconomy site selection, including resources, sampling, analysis, and + infrastructure. +license: https://creativecommons.org/publicdomain/zero/1.0/ +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + schema: http://schema.org/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - modules/core + - modules/resource_information + - modules/field_sampling + - modules/places + - modules/people + - modules/lineage + - modules/data_sources_metadata + - modules/sample_preparation + - modules/methods_parameters_units + - modules/experiment_equipment + - modules/general_analysis + - modules/aim1_records + - modules/aim2_records + - modules/external_data diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml new file mode 100644 index 00000000..179c4898 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml @@ -0,0 +1,123 @@ +id: https://w3id.org/ca_biositing/aim1_records +name: aim1_records +title: Aim 1 Records +description: Records for Aim 1 analysis. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - general_analysis + - experiment_equipment + - resource_information + - sample_preparation + - methods_parameters_units + - data_sources_metadata + +classes: + Aim1RecordBase: + is_a: BaseEntity + abstract: true + slots: + - dataset_id + - experiment_id + - resource_id + - sample_id + - technical_replicate_no + - technical_replicate_total + - method_id + - raw_data_id + - qc_pass + - note + + ProximateRecord: + is_a: Aim1RecordBase + description: Proximate analysis record. + + UltimateRecord: + is_a: Aim1RecordBase + description: Ultimate analysis record. + + CompositionalRecord: + is_a: Aim1RecordBase + description: Compositional analysis record. + + IcpRecord: + is_a: Aim1RecordBase + description: ICP analysis record. + + XrfRecord: + is_a: Aim1RecordBase + description: XRF analysis record. + slots: + - maybe_wavelength_nm + - maybe_intensity + - maybe_energy_slope + - maybe_energy_offset + + XrdRecord: + is_a: Aim1RecordBase + description: XRD analysis record. + slots: + - maybe_scan_low_nm + - maybe_scan_high_nm + + CalorimetryRecord: + is_a: Aim1RecordBase + description: Calorimetry analysis record. + + FtnirRecord: + is_a: Aim1RecordBase + description: FT-NIR analysis record. + + RgbRecord: + is_a: Aim1RecordBase + description: RGB analysis record. + +slots: + technical_replicate_no: + range: integer + description: Replicate number. + + technical_replicate_total: + range: integer + description: Total number of replicates. + + raw_data_id: + range: integer + description: Reference to FileObjectMetadata. + + qc_pass: + range: boolean + description: Whether the record passed QC. + + maybe_wavelength_nm: + range: decimal + description: Wavelength in nm. + + maybe_intensity: + range: decimal + description: Intensity. + + maybe_energy_slope: + range: decimal + description: Energy slope. + + maybe_energy_offset: + range: decimal + description: Energy offset. + + maybe_scan_low_nm: + range: integer + description: Low scan range in nm. + + maybe_scan_high_nm: + range: integer + description: High scan range in nm. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml new file mode 100644 index 00000000..416589b7 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml @@ -0,0 +1,143 @@ +id: https://w3id.org/ca_biositing/aim2_records +name: aim2_records +title: Aim 2 Records +description: Records for Aim 2 analysis. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - general_analysis + - experiment_equipment + - resource_information + - sample_preparation + - methods_parameters_units + - data_sources_metadata + - people + +classes: + Aim2RecordBase: + is_a: BaseEntity + abstract: true + slots: + - dataset_id + - experiment_id + - resource_id + - sample_id + - analyst_id + - raw_data_id + - qc_pass + - note + + PretreatmentRecord: + is_a: Aim2RecordBase + description: Pretreatment record. + slots: + - pretreatment_method_id + - eh_method_id + - reaction_block_id + - block_position + - temperature + - replicate_no + + FermentationRecord: + is_a: Aim2RecordBase + description: Fermentation record. + slots: + - strain_id + - pretreatment_method_id + - eh_method_id + - replicate_no + - well_position + - temperature + - agitation_rpm + - vessel_id + - analyte_detection_equipment_id + + GasificationRecord: + is_a: Aim2RecordBase + description: Gasification record. + slots: + - feedstock_mass + - bed_temperature + - gas_flow_rate + - technical_replicate_no + + AutoclaveRecord: + is_a: Aim2RecordBase + description: Autoclave record. + slots: + - technical_replicate_no + + Strain: + is_a: LookupBase + description: Strain used in fermentation. + slots: + - parent_strain_id + +slots: + pretreatment_method_id: + range: integer + description: Reference to Method (pretreatment). + + eh_method_id: + range: integer + description: Reference to Method (enzymatic hydrolysis). + + reaction_block_id: + range: integer + description: ID of the reaction block. + + block_position: + range: string + description: Position in the block. + + temperature: + range: decimal + description: Temperature. + + replicate_no: + range: integer + description: Replicate number. + + strain_id: + range: integer + description: Reference to Strain. + + well_position: + range: string + description: Position in the well. + + agitation_rpm: + range: decimal + description: Agitation in RPM. + + vessel_id: + range: integer + description: Reference to Equipment (vessel). + + analyte_detection_equipment_id: + range: integer + description: Reference to Equipment (detection). + + feedstock_mass: + range: decimal + description: Mass of feedstock. + + bed_temperature: + range: decimal + description: Bed temperature. + + gas_flow_rate: + range: decimal + description: Gas flow rate. + + parent_strain_id: + range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml new file mode 100644 index 00000000..987f0d1d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml @@ -0,0 +1,93 @@ +id: https://w3id.org/ca_biositing/analysis +name: analysis +title: Analysis Definitions +description: Datasets and observations. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - methods + +classes: + Dataset: + description: Dataset definition. + slots: + - id + - name + - record_type + - source_id + - start_date + - end_date + - description + slot_usage: + id: + identifier: true + range: integer + + Observation: + description: Observation data. + slots: + - id + - dataset_id + - record_type + - record_id + - parameter_id + - value + - unit_id + - dimension_type_id + - dimension_value + - dimension_unit_id + - note + slot_usage: + id: + identifier: true + range: integer + + DimensionType: + is_a: LookupBase + description: Type of dimension (e.g. timepoint, wavelength). + + AnalysisType: + is_a: LookupBase + description: Type of analysis. + +slots: + dataset_id: + range: integer + description: Reference to Dataset. + + record_type: + range: string + description: Type of record. + + record_id: + range: integer + description: ID of the record. + + value: + range: decimal + description: Value of the observation. + + unit_id: + range: integer + description: Reference to Unit. + + dimension_type_id: + range: integer + description: Reference to DimensionType. + + dimension_value: + range: decimal + description: Value of the dimension. + + dimension_unit_id: + range: integer + description: Reference to Unit (dimension). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml new file mode 100644 index 00000000..35cc271d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml @@ -0,0 +1,229 @@ +id: https://w3id.org/ca_biositing/analysis_records +name: analysis_records +title: Analysis Records +description: Specific analysis record types. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - analysis + - experiments + - methods + - sampling + - resources + +classes: + # Base Record Class (Mixin) + RecordBase: + mixin: true + slots: + - id + - dataset_id + - experiment_id + - resource_id + - sample_id + - technical_replicate_no + - technical_replicate_total + - method_id + - raw_data_id + - qc_pass + - note + slot_usage: + id: + identifier: true + range: integer + + ProximateRecord: + is_a: RecordBase + description: Proximate analysis record. + + UltimateRecord: + is_a: RecordBase + description: Ultimate analysis record. + + CompositionalRecord: + is_a: RecordBase + description: Compositional analysis record. + + IcpRecord: + is_a: RecordBase + description: ICP analysis record. + + XrfRecord: + is_a: RecordBase + description: XRF analysis record. + slots: + - maybe_wavelength_nm + - maybe_intensity + - maybe_energy_slope + - maybe_energy_offset + + XrdRecord: + is_a: RecordBase + description: XRD analysis record. + slots: + - maybe_scan_low_nm + - maybe_scan_high_nm + + CalorimetryRecord: + is_a: RecordBase + description: Calorimetry analysis record. + + FtnirRecord: + is_a: RecordBase + description: FT-NIR analysis record. + + RgbRecord: + is_a: RecordBase + description: RGB analysis record. + + PretreatmentRecord: + is_a: RecordBase + description: Pretreatment record. + slots: + - pretreatment_method + - eh_method_id + - reaction_block_id + - block_position + - temperature + - replicate_no + - analyst_id + + FermentationRecord: + is_a: RecordBase + description: Fermentation record. + slots: + - strain_id + - pretreatement_method_id + - eh_method_id + - replicate_no + - well_position + - temperature + - agitation_rpm + - vessel_id + - analyte_detection_equipment_id + - analyst_id + + GasificationRecord: + is_a: RecordBase + description: Gasification record. + slots: + - feedstock_mass + - bed_temperature + - gas_flow_rate + - analyst_id + + AutoclaveRecord: + is_a: RecordBase + description: Autoclave record. + slots: + - analyst_id + +slots: + technical_replicate_no: + range: integer + description: Technical replicate number. + + technical_replicate_total: + range: integer + description: Total technical replicates. + + raw_data_id: + range: integer + description: Reference to FileObjectMetadata. + + qc_pass: + range: boolean + description: Whether QC passed. + + maybe_wavelength_nm: + range: decimal + description: Wavelength in nm. + + maybe_intensity: + range: decimal + description: Intensity. + + maybe_energy_slope: + range: decimal + description: Energy slope. + + maybe_energy_offset: + range: decimal + description: Energy offset. + + maybe_scan_low_nm: + range: integer + description: Scan low nm. + + maybe_scan_high_nm: + range: integer + description: Scan high nm. + + pretreatment_method: + range: integer + description: Reference to Method (pretreatment). + + eh_method_id: + range: integer + description: Reference to Method (enzymatic hydrolysis). + + reaction_block_id: + range: integer + description: Reaction block ID. + + block_position: + range: string + description: Position in block. + + temperature: + range: decimal + description: Temperature. + + replicate_no: + range: integer + description: Replicate number. + + strain_id: + range: integer + description: Reference to Strain. + + pretreatement_method_id: + range: integer + description: Reference to Method (pretreatment). + + well_position: + range: string + description: Well position. + + agitation_rpm: + range: decimal + description: Agitation RPM. + + vessel_id: + range: integer + description: Reference to Equipment (vessel). + + analyte_detection_equipment_id: + range: integer + description: Reference to Equipment (detection). + + feedstock_mass: + range: decimal + description: Feedstock mass. + + bed_temperature: + range: decimal + description: Bed temperature. + + gas_flow_rate: + range: decimal + description: Gas flow rate. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml new file mode 100644 index 00000000..84eaa04c --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml @@ -0,0 +1,267 @@ +id: https://w3id.org/ca_biositing/core +name: core +title: Core Definitions +description: Base classes, lineage, and data source definitions. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + +classes: + BaseEntity: + mixin: true + description: Base entity included in all main entity tables. + slots: + - id + - created_at + - updated_at + - etl_run_id + - lineage_group_id + + LookupBase: + mixin: true + description: Base class for enum/ontology-like tables. + slots: + - id + - name + - description + - uri + + LineageGroup: + is_a: BaseEntity + description: Grouping for lineage information. + slots: + - note + + EntityLineage: + description: Lineage information for a specific entity. + slots: + - id + - lineage_group_id + - source_table + - source_row_id + - note + + EtlRun: + description: Information about an ETL run. + slots: + - id + - started_at + - completed_at + - pipeline_name + - status + - records_ingested + - note + slot_usage: + id: + identifier: true + range: string + + DataSource: + is_a: BaseEntity + description: Information about a data source. + slots: + - name + - description + - data_source_type_id + - full_title + - creator + - subject + - publisher + - contributor + - date + - type + - biocirv + - format + - language + - relation + - temporal_coverage + - location_coverage_id + - rights + - uri + + DataSourceType: + is_a: BaseEntity + description: Type of data source. + slots: + - source_type_id + + SourceType: + is_a: LookupBase + description: Lookup for source types (database, literature, etc.). + + LocationResolution: + is_a: LookupBase + description: Resolution of location coverage (nation, state, county, etc.). + + FileObjectMetadata: + is_a: BaseEntity + description: Metadata for file objects. + slots: + - data_source_id + - bucket_path + - file_format + - file_size + - checksum_md5 + - checksum_sha256 + +slots: + id: + identifier: true + range: integer + description: Unique identifier. + + created_at: + range: datetime + description: Timestamp when the record was created. + + updated_at: + range: datetime + description: Timestamp when the record was last updated. + + etl_run_id: + range: string + description: Identifier of the ETL run. + + lineage_group_id: + range: integer + description: Reference to the lineage group. + + name: + range: string + description: Name of the entity. + + description: + range: string + description: Description of the entity. + + uri: + range: uri + description: URI for the entity. + + note: + range: string + description: Additional notes. + + source_table: + range: string + description: Source table name. + + source_row_id: + range: string + description: Source row identifier. + + started_at: + range: datetime + description: Start time of the ETL run. + + completed_at: + range: datetime + description: Completion time of the ETL run. + + pipeline_name: + range: string + description: Name of the pipeline. + + status: + range: string + description: Status of the ETL run. + + records_ingested: + range: integer + description: Number of records ingested. + + data_source_type_id: + range: integer + description: Reference to data source type. + + full_title: + range: string + description: Full title of the data source. + + creator: + range: string + description: Creator of the data source. + + subject: + range: string + description: Subject of the data source. + + publisher: + range: string + description: Publisher of the data source. + + contributor: + range: string + description: Contributor to the data source. + + date: + range: datetime + description: Date associated with the data source. + + type: + range: string + description: Type of the data source. + + biocirv: + range: boolean + description: Whether the data source is internal to BioCirV. + + format: + range: string + description: Format of the data source. + + language: + range: string + description: Language of the data source. + + relation: + range: string + description: Relation of the data source. + + temporal_coverage: + range: string + description: Temporal coverage of the data source. + + location_coverage_id: + range: integer + description: Reference to location resolution. + + rights: + range: string + description: Rights associated with the data source. + + source_type_id: + range: integer + description: Reference to source type. + + data_source_id: + range: integer + description: Reference to data source. + + bucket_path: + range: string + description: Path to the file in the bucket. + + file_format: + range: string + description: Format of the file. + + file_size: + range: integer + description: Size of the file. + + checksum_md5: + range: string + description: MD5 checksum of the file. + + checksum_sha256: + range: string + description: SHA256 checksum of the file. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml new file mode 100644 index 00000000..7bb40074 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -0,0 +1,157 @@ +id: https://w3id.org/ca_biositing/data_sources_metadata +name: data_sources_metadata +title: Data Sources and Metadata +description: Data sources, types, and file metadata. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + DataSource: + is_a: BaseEntity + description: Source of data. + slots: + - name + - description + - data_source_type_id + - full_title + - creator + - subject + - publisher + - contributor + - date + - type + - biocirv + - format + - language + - relation + - temporal_coverage + - location_coverage_id + - rights + - uri + + DataSourceType: + is_a: LookupBase + description: Type of data source. + slots: + - source_type_id + + SourceType: + is_a: LookupBase + description: General source type. + + FileObjectMetadata: + is_a: BaseEntity + description: Metadata for file objects. + slots: + - data_source_id + - bucket_path + - file_format + - file_size + - checksum_md5 + - checksum_sha256 + + LocationResolution: + is_a: LookupBase + description: Resolution of location data. + +slots: + data_source_type_id: + range: integer + description: Reference to DataSourceType. + + source_type_id: + range: integer + description: Reference to SourceType. + + full_title: + range: string + description: Full title of the data source. + + creator: + range: string + description: Creator of the data source. + + subject: + range: string + description: Subject of the data source. + + publisher: + range: string + description: Publisher of the data source. + + contributor: + range: string + description: Contributor to the data source. + + date: + range: datetime + description: Date of the data source. + + type: + range: string + description: Type of the data source. + + biocirv: + range: boolean + description: Whether the data source is internal (BioCirV). + + format: + range: string + description: Format of the data source. + + language: + range: string + description: Language of the data source. + + relation: + range: string + description: Relation of the data source. + + temporal_coverage: + range: string + description: Temporal coverage of the data source. + + location_coverage_id: + range: integer + description: Reference to LocationResolution. + + rights: + range: string + description: Rights of the data source. + + uri: + range: string + description: URI of the resource. + + data_source_id: + range: integer + description: Reference to DataSource. + + bucket_path: + range: string + description: Path to the file in the bucket. + + file_format: + range: string + description: Format of the file. + + file_size: + range: integer + description: Size of the file in bytes. + + checksum_md5: + range: string + description: MD5 checksum of the file. + + checksum_sha256: + range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml new file mode 100644 index 00000000..4896706d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml @@ -0,0 +1,123 @@ +id: https://w3id.org/ca_biositing/experiment_equipment +name: experiment_equipment +title: Experiments and Equipment +description: Experimental data and equipment. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - places + - methods_parameters_units + - sample_preparation + - general_analysis + +classes: + Experiment: + is_a: BaseEntity + description: Experiment definition. + slots: + - analyst_id + - exper_start_date + - exper_duration + - exper_duration_unit_id + - exper_location_id + - description + + Equipment: + is_a: LookupBase + description: Equipment used in experiments. + slots: + - equipment_location_id + + ExperimentMethod: + description: Link between Experiment and Method. + slots: + - id + - experiment_id + - method_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentEquipment: + description: Link between Experiment and Equipment. + slots: + - id + - experiment_id + - equipment_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentAnalysis: + description: Link between Experiment and AnalysisType. + slots: + - id + - experiment_id + - analysis_type_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentPreparedSample: + description: Link between Experiment and PreparedSample. + slots: + - id + - experiment_id + - prepared_sample_id + slot_usage: + id: + identifier: true + range: integer + +slots: + analyst_id: + range: integer + description: Reference to Contact (analyst). + + exper_start_date: + range: date + description: Start date of the experiment. + + exper_duration: + range: decimal + description: Duration of the experiment. + + exper_duration_unit_id: + range: integer + description: Reference to Unit. + + exper_location_id: + range: integer + description: Reference to LocationAddress. + + equipment_location_id: + range: integer + description: Reference to LocationAddress. + + experiment_id: + range: integer + description: Reference to Experiment. + + equipment_id: + range: integer + description: Reference to Equipment. + + analysis_type_id: + range: integer + description: Reference to AnalysisType. + + prepared_sample_id: + range: integer + description: Reference to PreparedSample. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml new file mode 100644 index 00000000..56bf5322 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml @@ -0,0 +1,138 @@ +id: https://w3id.org/ca_biositing/experiments +name: experiments +title: Experiment Definitions +description: Experiments, equipment, and analysis. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - geography + - people + - methods + - sampling + - analysis + +classes: + Experiment: + is_a: BaseEntity + description: Experiment definition. + slots: + - analyst_id + - exper_start_date + - exper_duration + - exper_duration_unit_id + - exper_location_id + - description + + Equipment: + is_a: LookupBase + description: Equipment used in experiments. + slots: + - equipment_location_id + + ExperimentEquipment: + description: Link between experiment and equipment. + slots: + - id + - experiment_id + - equipment_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentAnalysis: + description: Link between experiment and analysis type. + slots: + - id + - experiment_id + - analysis_type_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentPreparedSample: + description: Link between experiment and prepared sample. + slots: + - id + - experiment_id + - prepared_sample_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentMethod: + description: Link between experiment and method. + slots: + - id + - experiment_id + - method_id + slot_usage: + id: + identifier: true + range: integer + + Strain: + is_a: LookupBase + description: Strain of organism. + slots: + - parent_strain_id + +slots: + analyst_id: + range: integer + description: Reference to Contact (analyst). + + exper_start_date: + range: date + description: Start date of experiment. + + exper_duration: + range: decimal + description: Duration of experiment. + + exper_duration_unit_id: + range: integer + description: Reference to Unit. + + exper_location_id: + range: integer + description: Reference to LocationAddress. + + equipment_location_id: + range: integer + description: Reference to LocationAddress. + + experiment_id: + range: integer + description: Reference to Experiment. + + equipment_id: + range: integer + description: Reference to Equipment. + + analysis_type_id: + range: integer + description: Reference to AnalysisType. + + prepared_sample_id: + range: integer + description: Reference to PreparedSample. + + method_id: + range: integer + description: Reference to Method. + + parent_strain_id: + range: integer + description: Reference to Strain (parent). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml new file mode 100644 index 00000000..519632c0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml @@ -0,0 +1,425 @@ +id: https://w3id.org/ca_biositing/external_data +name: external_data +title: External Data +description: External datasets (USDA, LandIQ, etc.). +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - general_analysis + - places + - resource_information + - methods_parameters_units + - data_sources_metadata + +classes: + UsdaDomain: + is_a: LookupBase + description: USDA domain. + + UsdaStatisticCategory: + is_a: LookupBase + description: USDA statistic category. + + UsdaSurveyProgram: + is_a: LookupBase + description: USDA survey program. + + UsdaCommodity: + is_a: LookupBase + description: USDA commodity. + slots: + - usda_source + - usda_code + - parent_commodity_id + + UsdaTermMap: + is_a: BaseEntity + description: Mapping of raw terms to USDA commodities. + slots: + - source_system + - source_context + - raw_term + - usda_commodity_id + - is_verified + - note + + ResourceUsdaCommodityMap: + is_a: BaseEntity + description: Mapping between resources/crops and USDA commodities. + slots: + - resource_id + - primary_crop_id + - usda_commodity_id + - match_tier + - note + + UsdaCensusRecord: + is_a: BaseEntity + description: USDA census record. + slots: + - dataset_id + - geoid + - commodity_code + - year + - source_reference + - note + + UsdaSurveyRecord: + is_a: BaseEntity + description: USDA survey record. + slots: + - dataset_id + - geoid + - commodity_code + - year + - survey_program_id + - survey_period + - reference_month + - seasonal_flag + - note + + UsdaMarketReport: + is_a: BaseEntity + description: USDA market report. + slots: + - slug_id + - slug_name + - report_series_title + - frequency + - office_name + - office_city_id + - office_state_fips + - source_id + + UsdaMarketRecord: + is_a: BaseEntity + description: USDA market record. + slots: + - report_id + - dataset_id + - report_begin_date + - report_end_date + - report_date + - commodity_id + - market_type_id + - market_type_catagory + - grp + - market_catagory_id + - class_ + - grade + - variety + - protein_pct + - application + - pkg + - sale_type + - price_unit_id + - freight + - trans_mode + + LandiqRecord: + is_a: BaseEntity + description: LandIQ record. + slots: + - dataset_id + - polygon_id + - main_crop + - secondary_crop + - tertiary_crop + - quaternary_crop + - confidence + - irrigated + - acres + - version + - note + + BillionTon2023Record: + is_a: BaseEntity + description: Billion Ton 2023 record. + slots: + - subclass_id + - resource_id + - geoid + - county_square_miles + - model_name + - scenario_name + - price_offered_usd + - production + - production_unit_id + - btu_ton + - production_energy_content + - energy_content_unit_id + - product_density_dtpersqmi + - land_source + + Polygon: + description: Geospatial polygon. + slots: + - id + - geoid + - geom + slot_usage: + id: + identifier: true + range: integer + +slots: + usda_source: + range: string + description: Source of the USDA definition (NASS, AMS). + + usda_code: + range: string + description: Official USDA code. + + parent_commodity_id: + range: integer + description: Reference to parent UsdaCommodity. + + source_system: + range: string + description: Source system (NASS, AMS). + + source_context: + range: string + description: Context of the source (Group, Slug ID). + + raw_term: + range: string + description: Raw term from the source. + + usda_commodity_id: + range: integer + description: Reference to UsdaCommodity. + + is_verified: + range: boolean + description: Whether the mapping is verified. + + match_tier: + range: string + description: Tier of the match. + + commodity_code: + range: integer + description: Reference to UsdaCommodity. + + year: + range: integer + description: Year of the record. + + source_reference: + range: string + description: Reference to the source. + + survey_program_id: + range: integer + description: Reference to UsdaSurveyProgram. + + survey_period: + range: string + description: Period of the survey. + + reference_month: + range: string + description: Reference month. + + seasonal_flag: + range: boolean + description: Whether the record is seasonal. + + slug_id: + range: integer + description: Slug ID. + + slug_name: + range: string + description: Slug name. + + report_series_title: + range: string + description: Title of the report series. + + frequency: + range: string + description: Frequency of the report. + + office_name: + range: string + description: Name of the office. + + office_city_id: + range: integer + description: Reference to LocationAddress. + + office_state_fips: + range: string + description: FIPS code of the office state. + + report_id: + range: integer + description: Reference to UsdaMarketReport. + + report_begin_date: + range: datetime + description: Begin date of the report. + + report_end_date: + range: datetime + description: End date of the report. + + report_date: + range: datetime + description: Date of the report. + + commodity_id: + range: integer + description: Reference to UsdaCommodity. + + market_type_id: + range: integer + description: ID of the market type. + + market_type_catagory: + range: string + description: Category of the market type. + + grp: + range: string + description: Group. + + market_catagory_id: + range: integer + description: ID of the market category. + + class_: + range: string + description: Class. + + grade: + range: string + description: Grade. + + variety: + range: string + description: Variety. + + protein_pct: + range: decimal + description: Protein percentage. + + application: + range: string + description: Application. + + pkg: + range: string + description: Package. + + sale_type: + range: string + description: Sale type. + + price_unit_id: + range: integer + description: Reference to Unit. + + freight: + range: string + description: Freight. + + trans_mode: + range: string + description: Transportation mode. + + polygon_id: + range: integer + description: Reference to Polygon. + + main_crop: + range: integer + description: Reference to PrimaryCrop. + + secondary_crop: + range: integer + description: Reference to PrimaryCrop. + + tertiary_crop: + range: integer + description: Reference to PrimaryCrop. + + quaternary_crop: + range: integer + description: Reference to PrimaryCrop. + + confidence: + range: integer + description: Confidence level. + + irrigated: + range: boolean + description: Whether the land is irrigated. + + acres: + range: float + description: Number of acres. + + subclass_id: + range: integer + description: Reference to ResourceSubclass. + + county_square_miles: + range: float + description: Square miles of the county. + + model_name: + range: string + description: Name of the model. + + scenario_name: + range: string + description: Name of the scenario. + + price_offered_usd: + range: decimal + description: Price offered in USD. + + production: + range: integer + description: Production amount. + + production_unit_id: + range: integer + description: Reference to Unit. + + btu_ton: + range: integer + description: BTU per ton. + + production_energy_content: + range: integer + description: Energy content of production. + + energy_content_unit_id: + range: integer + description: Reference to Unit. + + product_density_dtpersqmi: + range: decimal + description: Product density in dry tons per square mile. + + land_source: + range: string + description: Source of land data. + + geom: + range: string + description: Geometry (WKT or similar). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml new file mode 100644 index 00000000..9eaedfd7 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml @@ -0,0 +1,200 @@ +id: https://w3id.org/ca_biositing/field_sampling +name: field_sampling +title: Field Sampling +description: Field sampling and preparation. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - places + - people + - resource_information + - methods_parameters_units + +classes: + FieldSample: + is_a: BaseEntity + description: Sample collected from the field. + slots: + - name + - resource_id + - provider_id + - collector_id + - sample_collection_source + - amount_collected + - amount_collected_unit_id + - sampling_location_id + - field_storage_method_id + - field_storage_duration_value + - field_storage_duration_unit_id + - field_storage_location_id + - collection_timestamp + - collection_method_id + - harvest_method_id + - harvest_date + - field_sample_storage_location_id + - note + + FieldStorageMethod: + is_a: LookupBase + description: Method of field storage. + + CollectionMethod: + is_a: LookupBase + description: Method of collection. + + HarvestMethod: + is_a: LookupBase + description: Method of harvest. + + ProcessingMethod: + is_a: LookupBase + description: Method of processing. + + PhysicalCharacteristic: + is_a: BaseEntity + description: Physical characteristics of a sample. + slots: + - field_sample_id + - particle_length + - particle_width + - particle_height + - particle_unit_id + + SoilType: + is_a: LookupBase + description: Type of soil. + + AgTreatment: + is_a: LookupBase + description: Agricultural treatment. + + FieldSampleCondition: + is_a: BaseEntity + description: Condition of the field sample. + slots: + - field_sample_id + - ag_treatment_id + - last_application_date + - treatment_amount_per_acre + - processing_method_id + + LocationSoilType: + is_a: BaseEntity + description: Soil type at a location. + slots: + - location_id + - soil_type_id + +slots: + provider_id: + range: integer + description: Reference to Provider. + + collector_id: + range: integer + description: Reference to Contact (collector). + + sample_collection_source: + range: string + description: Source of sample collection. + + amount_collected: + range: decimal + description: Amount collected. + + amount_collected_unit_id: + range: integer + description: Reference to Unit. + + sampling_location_id: + range: integer + description: Reference to LocationAddress. + + field_storage_method_id: + range: integer + description: Reference to FieldStorageMethod. + + field_storage_duration_value: + range: decimal + description: Duration of field storage. + + field_storage_duration_unit_id: + range: integer + description: Reference to Unit. + + field_storage_location_id: + range: integer + description: Reference to LocationAddress. + + collection_timestamp: + range: datetime + description: Timestamp of collection. + + collection_method_id: + range: integer + description: Reference to CollectionMethod. + + harvest_method_id: + range: integer + description: Reference to HarvestMethod. + + harvest_date: + range: date + description: Date of harvest. + + field_sample_storage_location_id: + range: integer + description: Reference to LocationAddress. + + field_sample_id: + range: integer + description: Reference to FieldSample. + + particle_length: + range: decimal + description: Length of particle. + + particle_width: + range: decimal + description: Width of particle. + + particle_height: + range: decimal + description: Height of particle. + + particle_unit_id: + range: integer + description: Reference to Unit. + + ag_treatment_id: + range: integer + description: Reference to AgTreatment. + + last_application_date: + range: date + description: Date of last application. + + treatment_amount_per_acre: + range: float + description: Amount of treatment per acre. + + processing_method_id: + range: integer + description: Reference to ProcessingMethod. + + location_id: + range: integer + description: Reference to LocationAddress. + + soil_type_id: + range: integer + description: Reference to SoilType. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml new file mode 100644 index 00000000..cc8a195a --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml @@ -0,0 +1,93 @@ +id: https://w3id.org/ca_biositing/general_analysis +name: general_analysis +title: General Analysis +description: General analysis definitions. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - data_sources_metadata + - methods_parameters_units + +classes: + AnalysisType: + is_a: LookupBase + description: Type of analysis. + + Dataset: + is_a: BaseEntity + description: Dataset definition. + slots: + - name + - record_type + - source_id + - start_date + - end_date + - description + + DimensionType: + is_a: LookupBase + description: Type of dimension. + + Observation: + is_a: BaseEntity + description: Observation data. + slots: + - dataset_id + - record_type + - record_id + - parameter_id + - value + - unit_id + - dimension_type_id + - dimension_value + - dimension_unit_id + - note + +slots: + record_type: + range: string + description: Type of record. + + start_date: + range: date + description: Start date of the dataset. + + end_date: + range: date + description: End date of the dataset. + + dataset_id: + range: integer + description: Reference to Dataset. + + record_id: + range: integer + description: ID of the record. + + value: + range: decimal + description: Value of the observation. + + unit_id: + range: integer + description: Reference to Unit. + + dimension_type_id: + range: integer + description: Reference to DimensionType. + + dimension_value: + range: decimal + description: Value of the dimension. + + dimension_unit_id: + range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml new file mode 100644 index 00000000..32a8a880 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml @@ -0,0 +1,120 @@ +id: https://w3id.org/ca_biositing/geography +name: geography +title: Geography Definitions +description: Geospatial entities and locations. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + Geography: + description: Geographic region definition (e.g. county, state). + slots: + - geoid + - state_name + - state_fips + - county_name + - county_fips + - region_name + - agg_level_desc + slot_usage: + geoid: + identifier: true + + LocationAddress: + is_a: BaseEntity + description: Specific physical location. + slots: + - geography_id + - address_line1 + - address_line2 + - city + - zip + - lat + - lon + - is_anonymous + + Polygon: + description: Geospatial polygon definition. + slots: + - id + - geoid + - geom + slot_usage: + id: + identifier: true + range: integer + +slots: + geoid: + range: string + description: Geographic identifier. + + state_name: + range: string + description: Name of the state. + + state_fips: + range: string + description: FIPS code of the state. + + county_name: + range: string + description: Name of the county. + + county_fips: + range: string + description: FIPS code of the county. + + region_name: + range: string + description: Name of the region. + + agg_level_desc: + range: string + description: Description of the aggregation level. + + geography_id: + range: string + description: Reference to Geography geoid. + + address_line1: + range: string + description: Address line 1. + + address_line2: + range: string + description: Address line 2. + + city: + range: string + description: City name. + + zip: + range: string + description: ZIP code. + + lat: + range: float + description: Latitude. + + lon: + range: float + description: Longitude. + + is_anonymous: + range: boolean + description: Whether the location is anonymous. + + geom: + range: string # TODO: Define geometry type properly, maybe using a custom type or string for WKT + description: Geometry of the polygon. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure.yaml new file mode 100644 index 00000000..6ce9edf9 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure.yaml @@ -0,0 +1,1069 @@ +id: https://w3id.org/ca_biositing/infrastructure +name: infrastructure +title: Infrastructure +description: Infrastructure and facility data. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - general_analysis + - places + - resource_information + +classes: + FacilityRecord: + is_a: BaseEntity + description: Facility record. + slots: + - dataset_id + - facility_name + - location_id + - capacity_mw + - resource_id + - operator + - start_year + - note + + InfrastructureBiodieselPlants: + description: Biodiesel plants infrastructure. + slots: + - biodiesel_plant_id + - company + - bbi_index + - city + - state + - capacity_mmg_per_y + - feedstock + - status + - address + - coordinates + - latitude + - longitude + - source + slot_usage: + biodiesel_plant_id: + identifier: true + range: integer + + InfrastructureBiosolidsFacilities: + description: Biosolids facilities infrastructure. + slots: + - biosolid_facility_id + - report_submitted_date + - latitude + - longitude + - facility + - authority + - plant_type + - aqmd + - facility_address + - facility_city + - state + - facility_zip + - facility_county + - mailing_street_1 + - mailing_city + - mailing_state + - mailing_zip + - biosolids_number + - biosolids_contact + - biosolids_contact_phone + - biosolids_contact_email + - adwf + - potw_biosolids_generated + - twtds_biosolids_treated + - class_b_land_app + - class_b_applier + - class_a_compost + - class_a_heat_dried + - class_a_other + - class_a_other_applier + - twtds_transfer_to_second_preparer + - twtds_second_preparer_name + - adc_or_final_c + - landfill + - landfill_name + - surface_disposal + - deepwell_injection + - stored + - longterm_treatment + - other + - name_of_other + - incineration + slot_usage: + biosolid_facility_id: + identifier: true + range: integer + + InfrastructureCafoManureLocations: + description: CAFO manure locations infrastructure. + slots: + - cafo_manure_id + - latitude + - longitude + - owner_name + - facility_name + - address + - town + - state + - zip + - animal + - animal_feed_operation_type + - animal_units + - animal_count + - manure_total_solids + - source + - date_accessed + slot_usage: + cafo_manure_id: + identifier: true + range: integer + + InfrastructureEthanolBiorefineries: + description: Ethanol biorefineries infrastructure. + slots: + - ethanol_biorefinery_id + - name + - city + - state + - address + - type + - capacity_mgy + - production_mgy + - constr_exp + slot_usage: + ethanol_biorefinery_id: + identifier: true + range: integer + + InfrastructureLandfills: + description: Landfills infrastructure. + slots: + - project_id + - project_int_id + - ghgrp_id + - landfill_id + - landfill_name + - state + - physical_address + - city + - county + - zip_code + - latitude + - longitude + - ownership_type + - landfill_owner_orgs + - landfill_opened_year + - landfill_closure_year + - landfill_status + - waste_in_place + - waste_in_place_year + - lfg_system_in_place + - lfg_collected + - lfg_flared + - project_status + - project_name + - project_start_date + - project_shutdown_date + - project_type_category + - lfg_energy_project_type + - rng_delivery_method + - actual_mw_generation + - rated_mw_capacity + - lfg_flow_to_project + - direct_emission_reductions + - avoided_emission_reductions + slot_usage: + project_id: + identifier: true + range: string + + InfrastructureLivestockAnaerobicDigesters: + description: Livestock anaerobic digesters infrastructure. + slots: + - digester_id + - project_name + - project_type + - city + - state + - digester_type + - profile + - year_operational + - animal_type_class + - animal_types + - pop_feeding_digester + - total_pop_feeding_digester + - cattle + - dairy + - poultry + - swine + - codigestion + - biogas_generation_estimate + - electricity_generated + - biogas_end_uses + - methane_emission_reductions + - latitude + - longitude + slot_usage: + digester_id: + identifier: true + range: integer + + InfrastructureSafAndRenewableDieselPlants: + description: SAF and renewable diesel plants infrastructure. + slots: + - ibcc_index + - company + - city + - state + - country + - capacity + - feedstock + - products + - status + - address + - coordinates + - latitude + - longitude + slot_usage: + ibcc_index: + identifier: true + range: integer + + InfrastructureWastewaterTreatmentPlants: + description: Wastewater treatment plants infrastructure. + slots: + - plant_id + - name + - state + - codigestion + - flow_design_adjusted + - flow_average + - biosolids + - excess_flow + - biogas_utilized + - flaring + - excess_mass_loading_rate + - excess_mass_loading_rate_wet + - methane_production + - energy_content + - electric_kw + - thermal_mmbtu_d + - electric_kwh + - thermal_annual_mmbtu_y + - anaerobic_digestion_facility + - county + - dayload_bdt + - dayload + - equivalent_generation + - facility_type + - feedstock + - type + - city + - latitude + - longitude + - zipcode + slot_usage: + plant_id: + identifier: true + range: integer + + InfrastructureCombustionPlants: + description: Combustion plants infrastructure. + slots: + - combustion_fid + - objectid + - status + - city + - name + - county + - equivalent_generation + - np_mw + - cf + - yearload + - fuel + - notes + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + combustion_fid: + identifier: true + range: integer + + InfrastructureDistrictEnergySystems: + description: District energy systems infrastructure. + slots: + - des_fid + - cbg_id + - name + - system + - object_id + - city + - state + - primary_fuel + - secondary_fuel + - usetype + - cap_st + - cap_hw + - cap_cw + - chpcg_cap + - excess_c + - excess_h + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + des_fid: + identifier: true + range: integer + + InfrastructureFoodProcessingFacilities: + description: Food processing facilities infrastructure. + slots: + - processing_facility_id + - address + - county + - city + - company + - join_count + - master_type + - state + - subtype + - target_fid + - processing_type + - zip + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + processing_facility_id: + identifier: true + range: integer + + InfrastructureMswToEnergyAnaerobicDigesters: + description: MSW to energy anaerobic digesters infrastructure. + slots: + - wte_id + - city + - county + - equivalent_generation + - feedstock + - dayload + - dayload_bdt + - facility_type + - status + - notes + - source + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + wte_id: + identifier: true + range: integer + +slots: + facility_name: + range: string + description: Name of the facility. + + capacity_mw: + range: decimal + description: Capacity in MW. + + operator: + range: string + description: Operator of the facility. + + start_year: + range: integer + description: Start year of the facility. + + biodiesel_plant_id: + range: integer + description: ID of the biodiesel plant. + + company: + range: string + description: Company name. + + bbi_index: + range: integer + description: BBI index. + + city: + range: string + description: City. + + state: + range: string + description: State. + + capacity_mmg_per_y: + range: integer + description: Capacity in MMG per year. + + feedstock: + range: string + description: Feedstock. + + status: + range: string + description: Status. + + address: + range: string + description: Address. + + coordinates: + range: string + description: Coordinates. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. + + source: + range: string + description: Source. + + biosolid_facility_id: + range: integer + description: ID of the biosolids facility. + + report_submitted_date: + range: date + description: Date report submitted. + + facility: + range: string + description: Facility name. + + authority: + range: string + description: Authority. + + plant_type: + range: string + description: Plant type. + + aqmd: + range: string + description: AQMD. + + facility_address: + range: string + description: Facility address. + + facility_city: + range: string + description: Facility city. + + facility_zip: + range: string + description: Facility zip. + + facility_county: + range: string + description: Facility county. + + mailing_street_1: + range: string + description: Mailing street 1. + + mailing_city: + range: string + description: Mailing city. + + mailing_state: + range: string + description: Mailing state. + + mailing_zip: + range: string + description: Mailing zip. + + biosolids_number: + range: string + description: Biosolids number. + + biosolids_contact: + range: string + description: Biosolids contact. + + biosolids_contact_phone: + range: string + description: Biosolids contact phone. + + biosolids_contact_email: + range: string + description: Biosolids contact email. + + adwf: + range: decimal + description: ADWF. + + potw_biosolids_generated: + range: integer + description: POTW biosolids generated. + + twtds_biosolids_treated: + range: integer + description: TWTDS biosolids treated. + + class_b_land_app: + range: integer + description: Class B land application. + + class_b_applier: + range: string + description: Class B applier. + + class_a_compost: + range: integer + description: Class A compost. + + class_a_heat_dried: + range: integer + description: Class A heat dried. + + class_a_other: + range: integer + description: Class A other. + + class_a_other_applier: + range: string + description: Class A other applier. + + twtds_transfer_to_second_preparer: + range: integer + description: TWTDS transfer to second preparer. + + twtds_second_preparer_name: + range: string + description: TWTDS second preparer name. + + adc_or_final_c: + range: integer + description: ADC or final cover. + + landfill: + range: integer + description: Landfill. + + landfill_name: + range: string + description: Landfill name. + + surface_disposal: + range: integer + description: Surface disposal. + + deepwell_injection: + range: string + description: Deepwell injection. + + stored: + range: integer + description: Stored. + + longterm_treatment: + range: integer + description: Longterm treatment. + + other: + range: integer + description: Other. + + name_of_other: + range: string + description: Name of other. + + incineration: + range: integer + description: Incineration. + + cafo_manure_id: + range: integer + description: ID of the CAFO manure location. + + owner_name: + range: string + description: Owner name. + + town: + range: string + description: Town. + + zip: + range: string + description: Zip code. + + animal: + range: string + description: Animal. + + animal_feed_operation_type: + range: string + description: Animal feed operation type. + + animal_units: + range: integer + description: Animal units. + + animal_count: + range: integer + description: Animal count. + + manure_total_solids: + range: decimal + description: Manure total solids. + + date_accessed: + range: date + description: Date accessed. + + ethanol_biorefinery_id: + range: integer + description: ID of the ethanol biorefinery. + + type: + range: string + description: Type. + + capacity_mgy: + range: integer + description: Capacity in MGY. + + production_mgy: + range: integer + description: Production in MGY. + + constr_exp: + range: integer + description: Construction/expansion. + + project_id: + range: string + description: Project ID. + + project_int_id: + range: integer + description: Project integer ID. + + ghgrp_id: + range: string + description: GHGRP ID. + + landfill_id: + range: integer + description: Landfill ID. + + physical_address: + range: string + description: Physical address. + + county: + range: string + description: County. + + zip_code: + range: string + description: Zip code. + + ownership_type: + range: string + description: Ownership type. + + landfill_owner_orgs: + range: string + description: Landfill owner organizations. + + landfill_opened_year: + range: date + description: Landfill opened year. + + landfill_closure_year: + range: date + description: Landfill closure year. + + landfill_status: + range: string + description: Landfill status. + + waste_in_place: + range: integer + description: Waste in place. + + waste_in_place_year: + range: date + description: Waste in place year. + + lfg_system_in_place: + range: boolean + description: LFG system in place. + + lfg_collected: + range: decimal + description: LFG collected. + + lfg_flared: + range: decimal + description: LFG flared. + + project_status: + range: string + description: Project status. + + project_name: + range: string + description: Project name. + + project_start_date: + range: date + description: Project start date. + + project_shutdown_date: + range: date + description: Project shutdown date. + + project_type_category: + range: string + description: Project type category. + + lfg_energy_project_type: + range: string + description: LFG energy project type. + + rng_delivery_method: + range: string + description: RNG delivery method. + + actual_mw_generation: + range: decimal + description: Actual MW generation. + + rated_mw_capacity: + range: decimal + description: Rated MW capacity. + + lfg_flow_to_project: + range: decimal + description: LFG flow to project. + + direct_emission_reductions: + range: decimal + description: Direct emission reductions. + + avoided_emission_reductions: + range: decimal + description: Avoided emission reductions. + + digester_id: + range: integer + description: ID of the digester. + + project_type: + range: string + description: Project type. + + digester_type: + range: string + description: Digester type. + + profile: + range: string + description: Profile. + + year_operational: + range: date + description: Year operational. + + animal_type_class: + range: string + description: Animal type class. + + animal_types: + range: string + description: Animal types. + + pop_feeding_digester: + range: string + description: Population feeding digester. + + total_pop_feeding_digester: + range: integer + description: Total population feeding digester. + + cattle: + range: integer + description: Cattle. + + dairy: + range: integer + description: Dairy. + + poultry: + range: integer + description: Poultry. + + swine: + range: integer + description: Swine. + + codigestion: + range: string + description: Codigestion. + + biogas_generation_estimate: + range: integer + description: Biogas generation estimate. + + electricity_generated: + range: integer + description: Electricity generated. + + biogas_end_uses: + range: string + description: Biogas end uses. + + methane_emission_reductions: + range: integer + description: Methane emission reductions. + + ibcc_index: + range: integer + description: IBCC index. + + country: + range: string + description: Country. + + capacity: + range: string + description: Capacity. + + products: + range: string + description: Products. + + plant_id: + range: integer + description: ID of the plant. + + flow_design_adjusted: + range: decimal + description: Flow design adjusted. + + flow_average: + range: decimal + description: Flow average. + + biosolids: + range: decimal + description: Biosolids. + + excess_flow: + range: decimal + description: Excess flow. + + biogas_utilized: + range: boolean + description: Biogas utilized. + + flaring: + range: boolean + description: Flaring. + + excess_mass_loading_rate: + range: decimal + description: Excess mass loading rate. + + excess_mass_loading_rate_wet: + range: decimal + description: Excess mass loading rate wet. + + methane_production: + range: decimal + description: Methane production. + + energy_content: + range: decimal + description: Energy content. + + electric_kw: + range: decimal + description: Electric KW. + + thermal_mmbtu_d: + range: decimal + description: Thermal MMBTU/d. + + electric_kwh: + range: decimal + description: Electric KWh. + + thermal_annual_mmbtu_y: + range: decimal + description: Thermal annual MMBTU/y. + + anaerobic_digestion_facility: + range: string + description: Anaerobic digestion facility. + + dayload_bdt: + range: decimal + description: Dayload BDT. + + dayload: + range: decimal + description: Dayload. + + equivalent_generation: + range: decimal + description: Equivalent generation. + + facility_type: + range: string + description: Facility type. + + zipcode: + range: string + description: Zipcode. + + combustion_fid: + range: integer + description: Combustion FID. + + objectid: + range: integer + description: Object ID. + + np_mw: + range: decimal + description: NP MW. + + cf: + range: decimal + description: CF. + + yearload: + range: integer + description: Yearload. + + fuel: + range: string + description: Fuel. + + notes: + range: string + description: Notes. + + wkt_geom: + range: string + description: WKT geometry. + + geom: + range: string + description: Geometry. + + des_fid: + range: integer + description: DES FID. + + cbg_id: + range: integer + description: CBG ID. + + system: + range: string + description: System. + + object_id: + range: integer + description: Object ID. + + primary_fuel: + range: string + description: Primary fuel. + + secondary_fuel: + range: string + description: Secondary fuel. + + usetype: + range: string + description: Use type. + + cap_st: + range: decimal + description: Cap ST. + + cap_hw: + range: decimal + description: Cap HW. + + cap_cw: + range: decimal + description: Cap CW. + + chpcg_cap: + range: decimal + description: CHPCG Cap. + + excess_c: + range: decimal + description: Excess C. + + excess_h: + range: decimal + description: Excess H. + + processing_facility_id: + range: integer + description: Processing facility ID. + + join_count: + range: integer + description: Join count. + + master_type: + range: string + description: Master type. + + subtype: + range: string + description: Subtype. + + target_fid: + range: integer + description: Target FID. + + processing_type: + range: string + description: Processing type. + + wte_id: + range: integer + description: WTE ID. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml new file mode 100644 index 00000000..b0014c90 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml @@ -0,0 +1,84 @@ +id: https://w3id.org/ca_biositing/lineage +name: lineage +title: Lineage Definitions +description: Data lineage and ETL tracking. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + LineageGroup: + is_a: BaseEntity + description: Grouping of lineage entities. + slots: + - name + - description + + EntityLineage: + description: Lineage relationship between entities. + slots: + - id + - parent_entity_id + - child_entity_id + - lineage_group_id + - relationship_type + slot_usage: + id: + identifier: true + range: integer + + EtlRun: + is_a: BaseEntity + description: ETL run information. + slots: + - run_id + - start_time + - end_time + - status + - log_uri + +slots: + parent_entity_id: + range: integer + description: ID of the parent entity. + + child_entity_id: + range: integer + description: ID of the child entity. + + lineage_group_id: + range: integer + description: Reference to LineageGroup. + + relationship_type: + range: string + description: Type of relationship. + + run_id: + range: string + description: Unique identifier for the ETL run. + + start_time: + range: datetime + description: Start time of the run. + + end_time: + range: datetime + description: End time of the run. + + status: + range: string + description: Status of the run. + + log_uri: + range: string + description: URI to the run logs. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml new file mode 100644 index 00000000..d370f253 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml @@ -0,0 +1,120 @@ +id: https://w3id.org/ca_biositing/methods +name: methods +title: Methods and Parameters +description: Methods, parameters, and units. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + Unit: + is_a: LookupBase + description: Unit of measurement. + + Method: + is_a: BaseEntity + description: Analytical method. + slots: + - name + - method_abbrev_id + - method_category_id + - method_standard_id + - description + - detection_limits + - source_id + + MethodAbbrev: + is_a: LookupBase + description: Abbreviation for a method. + + MethodCategory: + is_a: LookupBase + description: Category of a method. + + MethodStandard: + is_a: LookupBase + description: Standard associated with a method. + + Parameter: + is_a: BaseEntity + description: Parameter measured. + slots: + - name + - standard_unit_id + - calculated + - description + + ParameterCategory: + is_a: LookupBase + description: Category of a parameter. + + ParameterCategoryParameter: + description: Link between parameter and category. + slots: + - id + - parameter_id + - parameter_category_id + slot_usage: + id: + identifier: true + range: integer + + ParameterUnit: + description: Link between parameter and alternate units. + slots: + - id + - parameter_id + - alternate_unit_id + slot_usage: + id: + identifier: true + range: integer + +slots: + method_abbrev_id: + range: integer + description: Reference to MethodAbbrev. + + method_category_id: + range: integer + description: Reference to MethodCategory. + + method_standard_id: + range: integer + description: Reference to MethodStandard. + + detection_limits: + range: string + description: Detection limits of the method. + + source_id: + range: integer + description: Reference to DataSource. + + standard_unit_id: + range: integer + description: Reference to Unit (standard). + + calculated: + range: boolean + description: Whether the parameter is calculated. + + parameter_id: + range: integer + description: Reference to Parameter. + + parameter_category_id: + range: integer + description: Reference to ParameterCategory. + + alternate_unit_id: + range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml new file mode 100644 index 00000000..1f4b0c5d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml @@ -0,0 +1,122 @@ +id: https://w3id.org/ca_biositing/methods_parameters_units +name: methods_parameters_units +title: Methods, Parameters, and Units +description: Analytical methods, parameters, and units of measurement. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - data_sources_metadata + +classes: + Unit: + is_a: LookupBase + description: Unit of measurement. + + Method: + is_a: BaseEntity + description: Analytical method. + slots: + - name + - method_abbrev_id + - method_category_id + - method_standard_id + - description + - detection_limits + - source_id + + MethodAbbrev: + is_a: LookupBase + description: Abbreviation for method. + + MethodCategory: + is_a: LookupBase + description: Category of method. + + MethodStandard: + is_a: LookupBase + description: Standard associated with the method. + + Parameter: + is_a: BaseEntity + description: Parameter being measured. + slots: + - name + - standard_unit_id + - calculated + - description + + ParameterCategory: + is_a: LookupBase + description: Category of parameter. + + ParameterCategoryParameter: + description: Link between Parameter and ParameterCategory. + slots: + - id + - parameter_id + - parameter_category_id + slot_usage: + id: + identifier: true + range: integer + + ParameterUnit: + description: Link between Parameter and Unit (alternate units). + slots: + - id + - parameter_id + - alternate_unit_id + slot_usage: + id: + identifier: true + range: integer + +slots: + method_abbrev_id: + range: integer + description: Reference to MethodAbbrev. + + method_category_id: + range: integer + description: Reference to MethodCategory. + + method_standard_id: + range: integer + description: Reference to MethodStandard. + + detection_limits: + range: string + description: Detection limits of the method. + + source_id: + range: integer + description: Reference to DataSource. + + standard_unit_id: + range: integer + description: Reference to Unit. + + calculated: + range: boolean + description: Whether the parameter is calculated. + + parameter_id: + range: integer + description: Reference to Parameter. + + parameter_category_id: + range: integer + description: Reference to ParameterCategory. + + alternate_unit_id: + range: integer + description: Reference to Unit. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml new file mode 100644 index 00000000..818bce18 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml @@ -0,0 +1,65 @@ +id: https://w3id.org/ca_biositing/people +name: people +title: People Definitions +description: Contact and provider information. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + +classes: + Contact: + description: Contact information for a person. + slots: + - id + - first_name + - last_name + - email + - affiliation + slot_usage: + id: + identifier: true + range: integer + + Provider: + description: Provider information. + slots: + - id + - codename + slot_usage: + id: + identifier: true + range: integer + +slots: + id: + identifier: true + range: integer + description: Unique identifier. + + first_name: + range: string + description: First name. + + last_name: + range: string + description: Last name. + + email: + range: string + description: Email address. + + affiliation: + range: string + description: Affiliation. + + codename: + range: string + description: Codename for the provider. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml new file mode 100644 index 00000000..7cd2c18b --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml @@ -0,0 +1,73 @@ +id: https://w3id.org/ca_biositing/places +name: places +title: Places Definitions +description: Geographic locations and addresses. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + Geography: + is_a: BaseEntity + description: Geographic location. + slots: + - geoid + - name + - type + - geometry + slot_usage: + geoid: + identifier: true + + LocationAddress: + is_a: BaseEntity + description: Physical address. + slots: + - street_address + - city + - state + - zip_code + - country + - geoid + +slots: + geoid: + range: string + description: Unique identifier for geography. + + type: + range: string + description: Type of geography (e.g. county, state). + + geometry: + range: string + description: WKT geometry. + + street_address: + range: string + description: Street address. + + city: + range: string + description: City. + + state: + range: string + description: State. + + zip_code: + range: string + description: ZIP code. + + country: + range: string + description: Country. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml new file mode 100644 index 00000000..28d31e47 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml @@ -0,0 +1,178 @@ +id: https://w3id.org/ca_biositing/resource_information +name: resource_information +title: Resource Information +description: Biomass resources and their classifications. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - places + +classes: + Resource: + is_a: BaseEntity + description: Biomass resource definition. + slots: + - name + - primary_crop_id + - resource_class_id + - resource_subclass_id + - note + + ResourceClass: + is_a: LookupBase + description: Classification of resources. + + ResourceSubclass: + is_a: LookupBase + description: Sub-classification of resources. + + PrimaryCrop: + is_a: LookupBase + description: Primary crop definition. + slots: + - note + + ResourceAvailability: + is_a: BaseEntity + description: Availability of a resource in a location. + slots: + - resource_id + - geoid + - from_month + - to_month + - year_round + - note + + ResourceCounterfactual: + is_a: BaseEntity + description: Counterfactual uses of a resource. + slots: + - geoid + - resource_id + - counterfactual_description + - animal_bedding_percent + - animal_bedding_source_id + - animal_feed_percent + - animal_feed_source_id + - bioelectricty_percent + - bioelectricty_source_id + - burn_percent + - burn_source_id + - compost_percent + - compost_source_id + - landfill_percent + - landfill_source_id + - counterfactual_date + - note + + ResourceMorphology: + description: Morphology of a resource. + slots: + - id + - resource_id + - morphology_uri + slot_usage: + id: + identifier: true + range: integer + +slots: + primary_crop_id: + range: integer + description: Reference to PrimaryCrop. + + resource_class_id: + range: integer + description: Reference to ResourceClass. + + resource_subclass_id: + range: integer + description: Reference to ResourceSubclass. + + resource_id: + range: integer + description: Reference to Resource. + + geoid: + range: string + description: Reference to Geography. + + from_month: + range: integer + description: Start month of availability. + + to_month: + range: integer + description: End month of availability. + + year_round: + range: boolean + description: Whether available year-round. + + counterfactual_description: + range: string + description: Description of counterfactual scenario. + + animal_bedding_percent: + range: decimal + description: Percentage used for animal bedding. + + animal_bedding_source_id: + range: integer + description: Source for animal bedding data. + + animal_feed_percent: + range: decimal + description: Percentage used for animal feed. + + animal_feed_source_id: + range: integer + description: Source for animal feed data. + + bioelectricty_percent: + range: decimal + description: Percentage used for bioelectricity. + + bioelectricty_source_id: + range: integer + description: Source for bioelectricity data. + + burn_percent: + range: decimal + description: Percentage burned. + + burn_source_id: + range: integer + description: Source for burn data. + + compost_percent: + range: decimal + description: Percentage composted. + + compost_source_id: + range: integer + description: Source for compost data. + + landfill_percent: + range: decimal + description: Percentage landfilled. + + landfill_source_id: + range: integer + description: Source for landfill data. + + counterfactual_date: + range: date + description: Date of counterfactual data. + + morphology_uri: + range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml new file mode 100644 index 00000000..f3d26ede --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml @@ -0,0 +1,178 @@ +id: https://w3id.org/ca_biositing/resources +name: resources +title: Resource Definitions +description: Biomass resources and their classifications. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - geography + +classes: + Resource: + is_a: BaseEntity + description: Biomass resource definition. + slots: + - name + - primary_crop_id + - resource_class_id + - resource_subclass_id + - note + + ResourceClass: + is_a: LookupBase + description: Classification of resources. + + ResourceSubclass: + is_a: LookupBase + description: Sub-classification of resources. + + PrimaryCrop: + is_a: LookupBase + description: Primary crop definition. + slots: + - note + + ResourceAvailability: + is_a: BaseEntity + description: Availability of a resource in a location. + slots: + - resource_id + - geoid + - from_month + - to_month + - year_round + - note + + ResourceCounterfactual: + is_a: BaseEntity + description: Counterfactual uses of a resource. + slots: + - geoid + - resource_id + - counterfactual_description + - animal_bedding_percent + - animal_bedding_source_id + - animal_feed_percent + - animal_feed_source_id + - bioelectricty_percent + - bioelectricty_source_id + - burn_percent + - burn_source_id + - compost_percent + - compost_source_id + - landfill_percent + - landfill_source_id + - counterfactual_date + - note + + ResourceMorphology: + description: Morphology of a resource. + slots: + - id + - resource_id + - morphology_uri + slot_usage: + id: + identifier: true + range: integer + +slots: + primary_crop_id: + range: integer + description: Reference to PrimaryCrop. + + resource_class_id: + range: integer + description: Reference to ResourceClass. + + resource_subclass_id: + range: integer + description: Reference to ResourceSubclass. + + resource_id: + range: integer + description: Reference to Resource. + + geoid: + range: string + description: Reference to Geography. + + from_month: + range: integer + description: Start month of availability. + + to_month: + range: integer + description: End month of availability. + + year_round: + range: boolean + description: Whether available year-round. + + counterfactual_description: + range: string + description: Description of counterfactual scenario. + + animal_bedding_percent: + range: decimal + description: Percentage used for animal bedding. + + animal_bedding_source_id: + range: integer + description: Source for animal bedding data. + + animal_feed_percent: + range: decimal + description: Percentage used for animal feed. + + animal_feed_source_id: + range: integer + description: Source for animal feed data. + + bioelectricty_percent: + range: decimal + description: Percentage used for bioelectricity. + + bioelectricty_source_id: + range: integer + description: Source for bioelectricity data. + + burn_percent: + range: decimal + description: Percentage burned. + + burn_source_id: + range: integer + description: Source for burn data. + + compost_percent: + range: decimal + description: Percentage composted. + + compost_source_id: + range: integer + description: Source for compost data. + + landfill_percent: + range: decimal + description: Percentage landfilled. + + landfill_source_id: + range: integer + description: Source for landfill data. + + counterfactual_date: + range: date + description: Date of counterfactual data. + + morphology_uri: + range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation.yaml new file mode 100644 index 00000000..758bb6c8 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation.yaml @@ -0,0 +1,70 @@ +id: https://w3id.org/ca_biositing/sample_preparation +name: sample_preparation +title: Sample Preparation +description: Sample preparation methods and records. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - field_sampling + - people + +classes: + PreparationMethod: + is_a: BaseEntity + description: Method of sample preparation. + slots: + - name + - description + - prep_method_abbrev_id + - prep_temp_c + - uri + - drying_step + + PreparationMethodAbbreviation: + is_a: LookupBase + description: Abbreviation for preparation method. + + PreparedSample: + is_a: BaseEntity + description: Sample that has been prepared. + slots: + - name + - field_sample_id + - prep_method_id + - prep_date + - preparer_id + - note + +slots: + prep_method_abbrev_id: + range: integer + description: Reference to PreparationMethodAbbreviation. + + prep_temp_c: + range: decimal + description: Preparation temperature in Celsius. + + drying_step: + range: boolean + description: Whether drying step was involved. + + prep_method_id: + range: integer + description: Reference to PreparationMethod. + + prep_date: + range: date + description: Date of preparation. + + preparer_id: + range: integer + description: Reference to Contact (preparer). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml new file mode 100644 index 00000000..9b449f57 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml @@ -0,0 +1,250 @@ +id: https://w3id.org/ca_biositing/sampling +name: sampling +title: Sampling Definitions +description: Field sampling and preparation. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - geography + - people + - resources + - methods + +classes: + FieldSample: + is_a: BaseEntity + description: Sample collected from the field. + slots: + - name + - resource_id + - provider_id + - collector_id + - sample_collection_source + - amount_collected + - amount_collected_unit_id + - sampling_location_id + - field_storage_method_id + - field_storage_duration_value + - field_storage_duration_unit_id + - field_storage_location_id + - collection_timestamp + - collection_method_id + - harvest_method_id + - harvest_date + - field_sample_storage_location_id + - note + + FieldStorageMethod: + is_a: LookupBase + description: Method of field storage. + + CollectionMethod: + is_a: LookupBase + description: Method of collection. + + HarvestMethod: + is_a: LookupBase + description: Method of harvest. + + ProcessingMethod: + is_a: LookupBase + description: Method of processing. + + PhysicalCharacteristic: + is_a: BaseEntity + description: Physical characteristics of a sample. + slots: + - field_sample_id + - particle_length + - particle_width + - particle_height + - particle_unit_id + + SoilType: + is_a: LookupBase + description: Type of soil. + + AgTreatment: + is_a: LookupBase + description: Agricultural treatment. + + FieldSampleCondition: + is_a: BaseEntity + description: Condition of the field sample. + slots: + - field_sample_id + - ag_treatment_id + - last_application_date + - treatment_amount_per_acre + - processing_method_id + + LocationSoilType: + is_a: BaseEntity + description: Soil type at a location. + slots: + - location_id + - soil_type_id + + PreparationMethod: + is_a: BaseEntity + description: Method of sample preparation. + slots: + - name + - description + - prep_method_abbrev_id + - prep_temp_c + - uri + - drying_step + + PreparationMethodAbbreviation: + is_a: LookupBase + description: Abbreviation for preparation method. + + PreparedSample: + is_a: BaseEntity + description: Sample prepared for analysis. + slots: + - name + - field_sample_id + - prep_method_id + - prep_date + - preparer_id + - note + +slots: + provider_id: + range: integer + description: Reference to Provider. + + collector_id: + range: integer + description: Reference to Contact (collector). + + sample_collection_source: + range: string + description: Source of sample collection. + + amount_collected: + range: decimal + description: Amount collected. + + amount_collected_unit_id: + range: integer + description: Reference to Unit. + + sampling_location_id: + range: integer + description: Reference to LocationAddress. + + field_storage_method_id: + range: integer + description: Reference to FieldStorageMethod. + + field_storage_duration_value: + range: decimal + description: Duration of field storage. + + field_storage_duration_unit_id: + range: integer + description: Reference to Unit. + + field_storage_location_id: + range: integer + description: Reference to LocationAddress. + + collection_timestamp: + range: datetime + description: Timestamp of collection. + + collection_method_id: + range: integer + description: Reference to CollectionMethod. + + harvest_method_id: + range: integer + description: Reference to HarvestMethod. + + harvest_date: + range: date + description: Date of harvest. + + field_sample_storage_location_id: + range: integer + description: Reference to LocationAddress. + + field_sample_id: + range: integer + description: Reference to FieldSample. + + particle_length: + range: decimal + description: Length of particle. + + particle_width: + range: decimal + description: Width of particle. + + particle_height: + range: decimal + description: Height of particle. + + particle_unit_id: + range: integer + description: Reference to Unit. + + ag_treatment_id: + range: integer + description: Reference to AgTreatment. + + last_application_date: + range: date + description: Date of last application. + + treatment_amount_per_acre: + range: float + description: Amount of treatment per acre. + + processing_method_id: + range: integer + description: Reference to ProcessingMethod. + + location_id: + range: integer + description: Reference to LocationAddress. + + soil_type_id: + range: integer + description: Reference to SoilType. + + prep_method_abbrev_id: + range: integer + description: Reference to PreparationMethodAbbreviation. + + prep_temp_c: + range: decimal + description: Preparation temperature in Celsius. + + drying_step: + range: boolean + description: Whether drying step was included. + + prep_method_id: + range: integer + description: Reference to PreparationMethod. + + prep_date: + range: date + description: Date of preparation. + + preparer_id: + range: integer + description: Reference to Contact (preparer). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/initial_linkML_conversion/dbdiagram_dump.md b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/initial_linkML_conversion/dbdiagram_dump.md new file mode 100644 index 00000000..4583cf2c --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/initial_linkML_conversion/dbdiagram_dump.md @@ -0,0 +1,981 @@ +/////////////////////////////////////////////////////////// // BASE ENTITY +(included in all main entity tables) // id int [pk, increment] // created_at +datetime [default: `current_timestamp`] // updated_at datetime [default: +`current_timestamp`] // etl_run_id string // lineage_group_id int [ref: > +lineage_group.id] /////////////////////////////////////////////////////////// + +// LookupBase for enum/ontology-like tables // id int [pk, increment] // name +string [not null, unique] // description string // uri string +/////////////////////////////////////////////////////////// + +//===================TABLE GROUPS================== TableGroup "Resource +Information" [color: #1E69FD] { resource resource_class resource_subclass +primary_crop resource_availability resource_counterfactual resource_morphology } + +TableGroup "Field Sampling" [color: #d35400] { field_sample field_storage_method +collection_method harvest_method physical_characteristic soil_type ag_treatment +field_sample_condition processing_method location_soil_type } + +TableGroup "Places" { geography location_address } + +TableGroup "People" { provider contact } + +TableGroup "Lineage" { lineage_group entity_lineage etl_run } + +TableGroup "Data Sources & Metadata" [color: #990D0D]{ data_source +data_source_type source_type file_object_metadata location_resolution } + +TableGroup "Sample Preparation" [color:#F7AC5E] { preparation_method +preparation_method_abbreviation prepared_sample } + +TableGroup "Methods, Parameters, Units" [color: #F0B7B7]{ unit method_abbrev +method_category method_standard parameter_category method parameter +parameter_unit + +} + +TableGroup "Experiment, Equipment" [color: #CDFC9F]{ experiment +experiment_method equipment experiment_analysis experiment_equipment +experiment_prepared_sample } + +TableGroup "General Analysis" [color: #A15CF5]{ analysis_type observation +dataset dimension_type } + +TableGroup "Aim2 Records" [color: #cc0000]{ fermentation_record +gasification_record pretreatment_record autoclave_record strain } + +TableGroup "Aim1 Records" [color: #ffc84f] { proximate_record +compositional_record ultimate_record icp_record calorimetry_record xrf_record +xrd_record rgb_record ftnir_record } + +TableGroup "External Data" [color:#20b2aa] { usda_census_record //usda_commodity +//usda_commodity_to_primary_crop usda_domain usda_statistic_category +usda_survey_program usda_survey_record usda_market_record +billion_ton_2023_record landiq_record polygon //I think this is used to +essentially get all polygons in a county? + +} + +TableGroup "Infrastructure" [color:#6495ed]{ facility_record +infrastructure_biodiesel_plants infrastructure_biosolids_facilities +infrastructure_cafo_manure_locations infrastructure_ethanol_biorefineries +infrastructure_landfills infrastructure_livestock_anaerobic_digesters +infrastructure_saf_and_renewable_diesel_plants +infrastructure_wastewater_treatment_plants infrastructure_combustion_plants +infrastructure_district_energy_systems infrastructure_food_processing_facilities +infrastructure_msw_to_energy_anaerobic_digesters } + +/////////////////////////////////////////////////////////// // LINEAGE TABLES +/////////////////////////////////////////////////////////// + +Table lineage_group { id int [pk, increment] etl_run_id string [ref:> +etl_run.id] note text } + +Table entity_lineage { id int [pk, increment] lineage_group_id int [not null, +ref: > lineage_group.id] source_table string [not null] // sheet or raw table +source_row_id string [not null] // row index or key note text } + +Table etl_run { id string [pk] // UUID started_at datetime completed_at datetime +pipeline_name string status string // success/failure/partial records_ingested +int note text } + +/////////////////////////////////////////////////////////// // RESOURCE +/////////////////////////////////////////////////////////// + +Table resource { // BaseEntity id int [pk, increment] created_at datetime +[default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] + +// Domain fields name string [not null, unique] primary_crop_id int [not null, +ref: > primary_crop.id] resource_class_id int [not null, ref: > +resource_class.id] resource_subclass_id int [ref: > resource_subclass.id] note +text } + +Table resource_class { // LookupBase id int [pk, increment] name string [not +null, unique] description string uri string } + +Table resource_subclass { // LookupBase id int [pk, increment] name string [not +null, unique] description string uri string } + +/////////////////////////////////////////////////////////// // PRIMARY CROP +/////////////////////////////////////////////////////////// + +Table primary_crop { // LookupBase (+ ontology) id int [pk, increment] name +string [not null, unique] description string uri string note text } + +/////////////////////////////////////////////////////////// // RESOURCE +AVAILABILITY /////////////////////////////////////////////////////////// + +Table resource_availability { // BaseEntity id int [pk, increment] created_at +datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] + +// Domain fields resource_id int [not null, ref: > resource.id] geoid string +[not null, ref: > geography.geoid] + +from_month int to_month int year_round boolean note text } + +/////////////////////////////////////////////////////////// // RESOURCE +COUNTERFACTUAL /////////////////////////////////////////////////////////// + +Table resource_counterfactual { // BaseEntity id int [pk, increment] created_at +datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] // Domain fields geoid string [not null, ref: > +geography.geoid] //location resource_id int [not null, ref: > resource.id] +counterfactual_description text //animal is too broad. Want just livestock and +poultry animal_bedding_percent decimal animal_bedding_source_id int [ref:> +data_source.id] animal_feed_percent decimal animal_feed_source_id int [ref:> +data_source.id] bioelectricty_percent decimal bioelectricty_source_id int [ref:> +data_source.id] burn_percent decimal burn_source_id int [ref:> data_source.id] +compost_percent decimal compost_source_id int [ref:> data_source.id] +landfill_percent decimal landfill_source_id int [ref:> data_source.id] +counterfactual_date date //contained in source. Set a base year as a disclaimer +//scenario identifier note text } + +/////////////////////////////////////////////////////////// // RESOURCE +MORPHOLOGY (many-to-many) +/////////////////////////////////////////////////////////// + +//'Check morphology ontology with Andrea' Table resource_morphology { id int +[pk, increment] resource_id int [not null, ref: > resource.id] morphology_uri +string [not null] // ontology URI for plant part (stem, shell, leaf…) } + +/////////////////////////////////////////////////////////// // GEOGRAPHY / +PLACES /////////////////////////////////////////////////////////// + +Table geography { geoid string [pk] state_name string state_fips string +county_name string county_fips string region_name string agg_level_desc string } + +Table location_address { id int [pk, increment] geography_id string [ref: > +geography.geoid] address_line1 string address_line2 string city string zip +string lat float lon float is_anonymous boolean } + +/////////////////////////////////////////////////////////// // NOTES +/////////////////////////////////////////////////////////// + +///////////////////////////////////////////////////////// // FIELD SAMPLES TABLE +GROUP //////////////////////////////////////////////////////// + +Table field_sample [headercolor: #d35400] { //Base entity id int [pk, increment] +created_at datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] //Domain Specific name string [not null, note: "e.g., +Ene-WaHu018"] //Should link perfectly to Gsheet sample name resource_id integer +[not null, ref: > resource.id] provider_id integer [ref: > provider.id] // needs +to be anon //add this! collector_id integer [ref: > contact.id] +sample_collection_source text //this is kind of free for all in the sample +metadata gsheet amount_collected decimal //consider making not null +amount_collected_unit_id integer [ref:> unit.id] //consider making not null +//source_codename_id integer [note: "Anonymized source identifier"] //not sure +what to do with this? Should we keep? sampling_location_id integer [not null, +ref: > location_address.id] // needs to be anon. May be null if from external +sources //I think we can do this via permissions in the database itself... +field_storage_method_id integer [ref: > field_storage_method.id] +field_storage_duration_value decimal field_storage_duration_unit_id integer +[ref:> unit.id] field_storage_location_id integer [ref:> location_address.id] // +nullable; may be same as sampling_location_id collection_timestamp timestamp +collection_method_id integer [ref: > collection_method.id] harvest_method_id +integer [ref: > harvest_method.id] harvest_date date //soil_type_id integer +[ref:> soil_type.id] //I am not sure I like this here. Maybe morve to +field_sample_condition? field_sample_storage_location_id integer [ref:> +location_address.id] //Used to describe where the sample is now note text + +indexes { resource_id //will we use this often enough to index? +//source_codename_id } } + +Table field_storage_method [headercolor: #d35400]{ // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +description string uri string } + +Table collection_method [headercolor: #d35400]{ // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +description string uri string } + +Table harvest_method [headercolor: #d35400]{ // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +description string uri string } + +Table processing_method [headercolor: #d35400]{ // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +description string uri string } + +//consider moving this to the analysis table group Table physical_characteristic +[headercolor: #d35400]{ //Base entity id int [pk, increment] created_at datetime +[default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] // field_sample_id integer [not null, ref: > field_sample.id] +particle_length decimal particle_width decimal particle_height decimal +particle_unit_id integer [ref:> unit.id] //Could add index in here } + +Table soil_type [headercolor: #d35400] { // LookupBase for enum/ontology-like +tables id int [pk, increment] name string [not null, unique] description string +uri string //soil_location integer [ref: > geography.id] //not sure if this +should be in a different "Base" table } + +Table ag_treatment [headercolor: #d35400] { // LookupBase for enum/ontology-like +tables id int [pk, increment] name string [not null, unique] description string +uri string } + +Table field_sample_condition [headercolor: #d35400] { //Would like to find a +better name for this table, or maybe break it apart //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] // field_sample_id int [not null, ref:> +field_sample.id] ag_treatment_id int [not null, ref:> ag_treatment.id] +last_application_date date [note: "if applicable"] treatment_amount_per_acre +float processing_method_id int [ref:> processing_method.id] } + +Table location_soil_type [headercolor: #d35400] { //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] //Domain specific location_id int [not null, ref:> +location_address.id] soil_type_id int [not null, ref:> soil_type.id] } + +///////////////////////////////////////////////////////// ///////// UNITS +//////////////// //////////////////////////////////////////////////////// + +Table unit { id int [pk, increment] name string [not null, unique] // e.g., +"cm", "kg", "m3" description string //can be longform like centimeter, +kilograms, cubic meters uri url } + +//////////////////////////////////////////////////////// ///////SAMPLE +PREPARATION///////////// +//////////////////////////////////////////////////////// + +Table preparation_method [headercolor: #F7AC5E] { //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] // name string [note: "As Is, Knife Mill (2mm), Oven +Dry"] description text prep_method_abbrev_id integer [ref:- +preparation_method_abbreviation.id] prep_temp_c decimal //I feel like this +should just be in the method right? uri string //ideally a protocols.io linked +DOI drying_step boolean //I think this should also just be in the method +//method_ref_id integer //[ref: > references.reference_id] } + +Table preparation_method_abbreviation [headercolor: #F7AC5E] { // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +description string uri string } + +Table prepared_sample [headercolor: #f7ac5e] { //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] // name string // this should correspond with +prepro_material_name in Gsheets. field_sample_id integer [not null, ref:- +field_sample.id] prep_method_id integer [not null, ref:- preparation_method.id] +//amount_before_drying decimal //amount_after_drying decimal prep_date date +//storage_location_id integer [ref: > location_address.id] //We may want this to +be location with a room. Need to ask James how specific the storage location is +for the samples cus in th Gsheets it is only the building //amount_remaining +decimal //amount_remaining_unit_id integer [ref:> unit.id] //amount_as_of_date +date preparer_id integer //[ref: > analysts_contact.analyst_id] note text + +indexes { field_sample_id prep_method_id } + +} + +//////////////////////////////////////////////////////// ///////DATA SOURCES AND +METADATA///////////// //////////////////////////////////////////////////////// + +Table data_source [headercolor: #990D0D] { //Base entity id int [pk, increment] +created_at datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] // name string [not null] //a short english identifier for the +source, such as the in-text citation (e.g. "Smith 2019" "BT23" "ForageOne") +description text //purpose of the data maybe. Unabbreviated names +data_source_type_id int [not null, ref:- data_source_type.id] // Foreign key +referenceing source_types full_title string [not null] creator string subject +string publisher string contributor string date datetime type string [not null] +biocirv boolean // e.g. "External data" = FALSE, "Internal data" = TRUE format +string language string relation string temporal_coverage daterange //The spatial +or temporal topic of the resource. location_coverage int [ref:> +location_resolution.id] rights string uri string [not null] } + +Table data_source_type [headercolor: #990D0D] { //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] // source_type_id int [ref: > source_type.id] } + +Table location_resolution [headercolor: #990D0D] { //nation, state, county, +region, etc // LookupBase for enum/ontology-like tables id int [pk, increment] +name string [not null, unique] //database, literature, internal, etc description +string uri string } + +Table source_type [headercolor: #990D0D]{ // LookupBase for enum/ontology-like +tables id int [pk, increment] name string [not null, unique] //database, +literature, industry report, government report, etc description string uri +string } + +Table file_object_metadata [headercolor: #990D0D] { //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] // data_source_id int [ref: > data_source.id] +bucket_path string file_format string file_size int checksum_md5 string +checksum_sha256 string } + +//THIS IS FOR LATER WHEN WE DO ANALYSIS RESULTS //analysis_result_file_object { +// analysis_result_id int [ref: > analysis_result.id] // file_object_id int +[ref: > file_object.id] // primary key (analysis_result_id, file_object_id) //} + +///////////////////////// ////// METHODS, PARAMETERS, UNITS +///////////////////////// + +Table method [headercolor: #F0B7B7] { //Base entity id int [pk, increment] +created_at datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] //Domain fields name string [unique] method_abbrev_id int +[ref: > method_abbrev.id] // Foreign key referencing method_abbrevs +method_category_id int [ref: > method_category.id] // Foreign key referencing +method_categories method_standard_id int [ref: > method_standard.id] // Foreign +key referencing method_standards description text detection_limits text //maybe +make this substantial in the future source_id int [ref: > data_source.id] +//protocols.io + +indexes { name } } + +Table method_abbrev [headercolor: #F0B7B7] { // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +// e.g. ICP, Ult description string uri string } + +Table method_category [headercolor: #F0B7B7] { //still need to better define +what this would be... // LookupBase for enum/ontology-like tables id int [pk, +increment] name string [not null, unique] //"ICP method, CompAna method, dry, +wet" description string uri string } + +Table method_standard [headercolor: #F0B7B7] { // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +// Standard associated with the method (e.g., AOAC 997.02, TAPPI T203) +description string uri string } + +Table parameter [headercolor:#F0B7B7] { //Base entity id int [pk, increment] +created_at datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] // name string [not null, unique] //parameter_category_id +integer [ref: > parameter_catagory.id] //"Fermentation, Minerals, Elements, +Compositional Analysis, etc" standard_unit_id integer [ref : > unit.id] +//Expected unit of a result. Is this the right way to do this? Should we use a +different //table to facilitate the identification and coercing of mismathed +units across internal and external datasets? //alternate_units text [note: "JSON +array of alternative units"] //I think I have eled this in the parameter_units +bridge table calculated boolean [note:"if not calculated then it is measured +directly. E.g glucose vs glucan"] description text //typical_range_min decimal +//typical_range_max decimal } + +Table parameter_catagory_parameter [headercolor: #F0B7B7] { id int [pk, +increment] parameter_id int [not null, ref: > parameter.id] +parameter_catagory_id int [not null, ref: > parameter_category.id] } + +Table parameter_category [headercolor: #F0B7B7] { //need to better define // +LookupBase for enum/ontology-like tables id int [pk, increment] name string [not +null, unique] //[note: "Fermentation, Minerals, Elements, Compositional +Analysis, etc"] description string uri string } + +Table parameter_unit [headercolor: #F0B7B7] { id integer [pk] parameter_id +integer [ref: > parameter.id] //contains the standard unit alternate_unit_id +integer [not null, ref:> unit.id] } + +Ref: "experiment_prepared_sample"."id" < +"experiment_prepared_sample"."prepared_sample_id" + +///////////////////////// ////// Experiments, Equipment +///////////////////////// + +Table experiment { id int [pk, increment] // Primary key created_at datetime +[default: `current_timestamp`] // When this row was created updated_at datetime +[default: `current_timestamp`] // Last updated timestamp + +// ETL tracking / provenance etl_run_id string [note: "ETL process that +generated this experiment row"] lineage_group_id int [ref: > lineage_group.id, +note: "Links to original source data (sheet, row, file, etc.)"] + +// Domain-specific fields analyst_id int [note: "Person responsible for +experiment"] exper_start_date date [note: "Date the experiment started"] +exper_duration decimal [note: "Duration of experiment"] exper_duration_unit_id +int [ref: > unit.id, note: "Unit for exper_duration, e.g., days, hours"] +exper_location_id int [ref: > location_address.id, note: "Where the experiment +was performed"] description text [note: "Optional notes or description of the +experiment"] } + +Table equipment [headercolor: #CDFC9F]{ // LookupBase for enum/ontology-like +tables id int [pk, increment] name string [not null, unique] // description +string uri string // equipment_location_id integer [ref: > location_address.id] +//from room can access building, affiliation, address, etc } + +Table experiment_equipment [headercolor: #CDFC9F]{ id int [pk] experiment_id int +[not null, ref: > experiment.id] equipment_id int [not null, ref: > +equipment.id] } + +Table experiment_analysis [headercolor: #CDFC9F] { id int [pk, increment] +experiment_id int [ref:> experiment.id] analysis_type_id int [ref:> +analysis_type.id] } + +Table experiment_prepared_sample [headercolor: #CDFC9F] { id int [pk, increment] +experiment_id int [ref:> experiment.id] prepared_sample_id int [ref:> +prepared_sample.id] } + +Table experiment_method [headercolor: #CDFC9F] { id int [pk] experiment_id int +[ref: > experiment.id] method_id int [ref: > method.id] + +indexes { method_id experiment_id } } //====================================== +// DATASET TABLE //====================================== + +//A dataset is defined by a publisher and the time //period over which it took +observations which are grouped //but non-redundant. //so that methodology and +observation space is the same.? + +//Ex: LandIQ is a record_type but there are multiple years of //LandIQ data so +record_type is insufficient to differentiate //a polygon from 2020 and 2022. + +//Ex. Phyllis2 is a publisher, but it releases data in sections //based on +analysis type so we will import "Phyllis 2 Proximate //analysis" "Phyllis 2 +Ultimate Analysis" as datasets. //What is the problem though just have Phyllis2 +as a dataset that //is an aggregation of those datasets? + +//Ex: BioCirV is a publisher that takes data across a timeframe. //Should we +differentiate Aim1 and Aim2? I vote no. + +Table dataset { id int [pk, increment] name string // Human-readable dataset +name record_type string [note: "Determines which child record table rows belong +to this dataset"] // e.g. "ultimate_record", "compositional_record" +//experiment_id int [ref: > experiment.id, note: "Nullable; only applies for +lab-produced datasets"] source_id int [ref:> data_source.id] start_date date +end_date date description text } + +//=========================================================== // OBSERVATION +TABLE (parameter/value pairs) +//=========================================================== + +Table observation { id int [pk, increment] dataset_id int [ref: > dataset.id] + +// Polymorphic link to child record table record_type string [note: "ENUM of +child record tables"] record_id int [note: "Points to ID in table defined by +record_type"] + +parameter_id int [ref: > parameter.id] value decimal unit_id int [ref: > +unit.id] + +// Optional dimensions (e.g., timepoint for timeseries data, wavelength, +replicate time) dimension_type_id int [ref: > dimension_type.id] dimension_value +decimal dimension_unit_id int [ref: > unit.id] + +//observation_source_id int [ref: > data_source.id] note text + +indexes { (dataset_id, record_id, parameter_id) } } + +//=========================================================== // CHILD RECORD +TABLES – ANALYTICAL DATA +//=========================================================== + +//A record is the surrounding information needed to understand an observation. +//Record tables give context for the parameter + value + unit //from the +observation table. They explain which data groupings (samples, experiments, +//and datasets) that these observations belong to. + +//A technical replicate is defined by a sample and a given experiment +//(analyst, on a day, at a time, on a machine) + +//A sample replicate is defined by a sample and an analytical method + +////////////////////////////////////////////////// ////// INTERNAL RECORD BASE +CLASS///////////////// ////////////////////////////////////////////////// + +//id int [pk, increment] //dataset_id int [ref: > dataset.id] //experiment_id +int [ref: > experiment.id] //resource_id int [ref:> resource.id] //sample_id int +[ref: > prepared_sample.id] //technical_replicate_no int //which replicate this +record represents //technical_replicate_total int //total number of replicates +for a sample //method_id int [ref: > method.id] //we suspect this will be +captured in the experiment_id //raw_data_id int [ref:> file_object_metadata.id] +//qc_pass boolean //note text + +////////////////////////////////////////////////// + +Table proximate_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref: > prepared_sample.id] technical_replicate_no +int //which replicate this record represents technical_replicate_total int +//total number of replicates for a sample method_id int [ref: > method.id] //we +suspect this will be captured in the experiment_id //equipment_id int [ref: > +equipment.id] //we suspect this will be captured in the experiment_id +//analyst_id int [ref: > contact.id] //we suspect this will be captured in the +experiment_id raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean +note text } + +Table ultimate_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref: > prepared_sample.id] technical_replicate_no +int //which replicate this record represents technical_replicate_total int +//total number of replicates for a sample method_id int [ref: > method.id] +//equipment_id int [ref: > equipment.id] //analyst_id int [ref: > contact.id] +raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note text } + +Table compositional_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref: > prepared_sample.id] technical_replicate_no +int //which replicate this record represents technical_replicate_total int +//total number of replicates for a sample method_id int [ref: > method.id] +//equipment_id int [ref: > equipment.id] //analyst_id int [ref: > contact.id] +raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note text } + +Table icp_record { id int [pk, increment] dataset_id int [ref: > dataset.id] +experiment_id int [ref: > experiment.id] resource_id int [ref:> resource.id] +sample_id int [ref: > prepared_sample.id] technical_replicate_no int //which +replicate this record represents technical_replicate_total int //total number of +replicates for a sample method_id int [ref: > method.id] //equipment_id int +[ref: > equipment.id] //analyst_id int [ref: > contact.id] raw_data_id int +[ref:> file_object_metadata.id] qc_pass boolean note text } + +Table xrf_record { id int [pk, increment] dataset_id int [ref: > dataset.id] +experiment_id int [ref: > experiment.id] resource_id int [ref:> resource.id] +sample_id int [ref: > prepared_sample.id] technical_replicate_no int //which +replicate this record represents technical_replicate_total int //total number of +replicates for a sample method_id int [ref: > method.id] maybe_wavelength_nm +decimal ////might be in the method maybe_intensity decimal //might be in the +method maybe_energy_slope decimal //might be in the method maybe_energy_offset +decimal //might be in the method //equipment_id int [ref: > equipment.id] +//analyst_id int [ref: > contact.id] raw_data_id int [ref:> +file_object_metadata.id] qc_pass boolean note text } + +Table xrd_record { id int [pk, increment] dataset_id int [ref: > dataset.id] +experiment_id int [ref: > experiment.id] resource_id int [ref:> resource.id] +sample_id int [ref: > prepared_sample.id] technical_replicate_no int //which +replicate this record represents technical_replicate_total int //total number of +replicates for a sample maybe_scan_low_nm int ////might be in the method +maybe_scan_high_nm int ////might be in the method method_id int [ref: > +method.id] //equipment_id int [ref: > equipment.id] //analyst_id int [ref: > +contact.id] raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note +text } + +Table calorimetry_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref: > prepared_sample.id] technical_replicate_no +int //which replicate this record represents technical_replicate_total int +//total number of replicates for a sample method_id int [ref: > method.id] +//equipment_id int [ref: > equipment.id] //analyst_id int [ref: > contact.id] +raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note text } + +Table ftnir_record { id int [pk, increment] dataset_id int [ref: > dataset.id] +experiment_id int [ref: > experiment.id] resource_id int [ref:> resource.id] +sample_id int [ref: > prepared_sample.id] technical_replicate_no int //which +replicate this record represents technical_replicate_total int //total number of +replicates for a sample method_id int [ref: > method.id] //equipment_id int +[ref: > equipment.id] //analyst_id int [ref: > contact.id] raw_data_id int +[ref:> file_object_metadata.id] qc_pass boolean note text } + +Table rgb_record { id int [pk, increment] dataset_id int [ref: > dataset.id] +experiment_id int [ref: > experiment.id] resource_id int [ref:> resource.id] +sample_id int [ref: > prepared_sample.id] technical_replicate_no int //which +replicate this record represents technical_replicate_total int //total number of +replicates for a sample method_id int [ref: > method.id] //equipment_id int +[ref: > equipment.id] //analyst_id int [ref: > contact.id] raw_data_id int +[ref:> file_object_metadata.id] qc_pass boolean note text } + +///////////////////////////////////// ////// AIM2 EXPERIMENTAL DATA +///////////////////////////////////// + +Table pretreatment_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref: > prepared_sample.id] pretreatment_method int +[ref:> method.id] eh_method_id int [ref:> method.id] reaction_block_id int +block_position varchar temperature decimal replicate_no int analyst_id int +[ref:> contact.id] qc_pass boolean note text } + +Table fermentation_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref: > +resource.id] //this is denormalized, but maybe necessary for external data +sample_id int [ref: > prepared_sample.id] strain_id int [ref:> strain.id] +pretreatement_method_id int [ref:> method.id] //decon method in gsheet +eh_method_id int [ref:> method.id] //enzymatic hydrolysis method replicate_no +int well_position varchar temperature decimal //ph decimal //Is this at the +beginning? End? agitation_rpm decimal vessel_id int [ref:> equipment.id] +analyte_detection_equipment_id int [ref:> equipment.id] analyst_id int [ref: > +contact.id] raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note +text } + +Table gasification_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref: > +resource.id] //this is denormalized, but maybe necessary for external data +sample_id int [ref:> prepared_sample.id] feedstock_mass decimal bed_temperature +decimal gas_flow_rate decimal technical_replicate_no int analyst_id int [ref: > +contact.id] raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note +text } + +Table autoclave_record { id int [pk, increment] dataset_id int [ref:> +dataset.id] experiment_id int [ref:> experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref:> prepared_sample.id] technical_replicate_no int +analyst_id int [ref: > contact.id] raw_data_id int [ref:> +file_object_metadata.id] qc_pass boolean note text } + +//=========================================================== // CHILD RECORD +TABLES – USDA DATA //=========================================================== + +//I want to create a base "usda_record" class that will be used for both +usda_census and usda_survey //records. I would also like to explore the class +also being applicable to usda_market type records, //although these are much +more different. + +Table usda_census_record [headercolor: #ffc72f] { id int [pk, increment] +dataset_id int [ref: > dataset.id] geoid int [ref:> geography.geoid] +commodity_code int [ref: > usda_commodity.id] year int source_reference string +// this may be the same as any other source attribute note text } + +Table usda_survey_record [headercolor: #ffc72f] { id int [pk, increment] +dataset_id int [ref: > dataset.id] geoid int [ref:> geography.geoid] +commodity_code int [ref: > usda_commodity.id] year int survey_program_id int +[ref: > usda_survey_program.id] survey_period string reference_month string +seasonal_flag boolean note text } + +//=========================================================== // CHILD RECORD +TABLE – USDA MARKET NEWS +//=========================================================== + +Table usda_market_report [headercolor: #ffc72f]{ id int [pk, increment] + +// IDENTIFIERS slug_id int [not null, note: "The constant MARS ID, e.g., 3667. +Defines the 'Series'."] slug_name string report_series_title string //e.g. +"Feedstuffs Report" + +// FREQUENCY & ORIGIN frequency string // e.g., "Monthly", "Weekly" office_name +varchar office_city_id int [ref:> location_address.id] office_state_fips varchar +[ref:> geography.geoid] source int [ref : - data_source.id] //might be +unnecessary since data can be looked up by slug_id and data in this table + +// Note: Splitting this table is NORMALIZATION. // It prevents repeating +'Monthly Feedstuffs Report' 10,000 times. } + +Table usda_market_record [headercolor: #ffc72f] { id int [pk, increment] +report_id int [not null, ref: > usda_market_report.id] dataset_id int [ref:> +dataset.id] //office_name varchar //office_city_id int [ref:> +location_address.id] //office_state_fips varchar [ref:> geography.geoid] +report_begin_date datetime //This report refers to the report_end_date datetime +report_date datetime //not sure how this differs from the other dates, but it is +earlier... //published_date datetime commodity_id int [not null, ref: > +usda_commodity.id] //primary_crop_id int [not null, ref:> primary_crop.id] +//assumes we can control what USDA market data we input and import only data for +primary crops in our database. otherwise the "not null" designation may present +issue market_type_id int //[ref:> market_type.id] market_type_catagory varchar +//this could be normalized, but it is all just "summary" in the example data +//slug_id int //slug_name string //report_title string grp string +market_catagory_id int // [ref;> market_catagory.id] class string grade string +variety string protein_pct decimal application string pkg string // sale_type +string //"FOB" (Free on Board - buyer pays shipping) or "Delivered" (seller pays +shipping) price_unit_id int [ref:> unit.id] //price_min decimal //these all go +into the parameter unit observation table //price_max decimal //price_min_change +decimal //price_min_direction varchar //price_max_change decimal +//price_max_direction decimal //avg_price decimal //avg_price_year_ago decimal +freight string trans_mode string } + +//=========================================================== // CHILD RECORD +TABLE – LAND IQ //=========================================================== + +//I think I may want to create a base "polygon" or "geometry" record type //for +geospatial records. Please log this and flag for discussion later. + +Table landiq_record [headercolor: #808080] { id int [pk, increment] dataset_id +int [ref: > dataset.id] polygon_id int [ref: > polygon.id] main_crop int [ref: > +primary_crop.id] secondary_crop int [ref: > primary_crop.id] tertiary_crop int +[ref: > primary_crop.id] quaternary_crop int [ref: > primary_crop.id] confidence +int irrigated boolean acres float version string note text } + +//=========================================================== // CHILD RECORD +TABLE – FACILITY/INFRASTRUCTURE DATA +//=========================================================== + +Table facility_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] facility_name string location_id int [ref: > location_address.id] +capacity_mw decimal resource_id int [ref:> resource.id] //could have multiple +resources per facility. For example almond shells and hulls. operator string +start_year int note text } + +//INFRASTRUCTURE RECORD SET PLACEHOLDER. + +//These records are for now to be simply modeled as + +//==================== TABLE GROUP ========================= +//==================== INFRASTRUCTURE INDUSTRIAL DATASETS +========================= + +Table infrastructure_biodiesel_plants [headercolor: #008B8B] { // two joined +datasets biodiesel_plant_id integer [pk] company varchar bbi_index integer // +blank for some companies city varchar state char(2) [note: "convert to state +abbreviation"] // some rows have whole names written out; reduce to +abbreviations capacity_mmg_per_y integer // should it be integer? feedstock +varchar [note: "multiselect"] // blank for some companies status varchar [note: +"select ; options listed are either 'operational' or 'idle'"] // blank for some +companies address varchar // blank for some companies coordinates varchar [note: +"currently string, convert to geometric point"] // blank for some companies +latitude decimal longitude decimal source text [note: "change to url later"] } + +Table infrastructure_biosolids_facilities [headercolor: #008B8B] { // lots of +mixed all-caps and proper formatting biosolid_facility_id integer [pk] +report_submitted_date date // one row says "06-Kan-24" - correct typo and +convert to date latitude decimal longitude decimal facility varchar authority +varchar plant_type varchar [note: "multiselect"] aqmd varchar // some blank +entries. could also make multiselect if we had a unified format? e.g. "feather +river" and "feather river aqmd" is the same facility_address varchar // some +blank facility_city varchar // some blank state varchar(2) facility_zip varchar +// some blank facility_county varchar // some blank (make multiselect?) +mailing_street_1 varchar // some blank mailing_city varchar // some blank (make +multiselect?) mailing_state varchar(2) // some blank? mailing_zip varchar +biosolids_number varchar // add custom check alter - should be CALX###### +biosolids_contact varchar biosolids_contact_phone varchar // convert to single +custom format biosolids_contact_email varchar // convert to single custom format +adwf decimal potw_biosolids_generated integer twtds_biosolids_treated integer // +very blank class_b_land_app integer // very blank class_b_applier varchar // +very blank class_a_compost integer // very blank class_a_heat_dried integer // +very blank class_a_other integer // very blank class_a_other_applier varchar // +very blank twtds_transfer_to_second_preparer int // very blank +twtds_second_preparer_name varchar [note: "sometimes multiple preparers are +reported along with respective amt of biosolids transferred"] adc_or_final_c +integer // very blank landfill integer landfill_name varchar // very blank +surface_disposal integer // VERY blank deepwell_injection varchar //I don't even +know what is this stored integer // has some random varchar content in there +longterm_treatment integer // very blank other integer // very blank +name_of_other varchar incineration integer Note: "probably could change to a +long format? a lot of blank fields and random columns near the bottom" } + +Table infrastructure_cafo_manure_locations [headercolor: #008B8B] { +cafo_manure_id integer [pk] latitude decimal longitude decimal owner_name +varchar // very blank facility_name varchar address varchar town varchar state +varchar(2) zip varchar(5) animal varchar [note: "select"] +animal_feed_operation_type varchar [note:"select"] animal_units integer // +partially blank animal_count integer // partially blank; also some of them end +with 333, 667, or 000? are these calculations? manure_total_solids decimal +[note: "million gallons a year"] source text [note: "change to url later"] +date_accessed date } + +Table infrastructure_ethanol_biorefineries [headercolor: #008B8B] { +ethanol_biorefinery_id integer [pk] name varchar city varchar state varchar(2) +address varchar type varchar [note: "multiselect"] capacity_mgy integer +production_mgy integer constr_exp integer // don't know what this is } + +Table infrastructure_landfills [headercolor: #008B8B] { project_int_id integer +project_id varchar [pk] ghgrp_id varchar landfill_id integer landfill_name +varchar state varchar(2) physical_address text city varchar county varchar +zip_code varchar latitude decimal longitude decimal ownership_type varchar +[note: "select, either Public or Private"] landfill_owner_orgs varchar +landfill_opened_year date [note: "year only; should it be int or date?"] +landfill_closure_year date [note: "year only; should it be int or date?"] +landfill_status varchar [note: "select"] waste_in_place integer [note: "in +tons"] waste_in_place_year date [note: "assuming year collected?"] +lfg_system_in_place boolean [note: "currently yes/no"] lfg_collected decimal +[note: "in mmscfd"] lfg_flared decimal [note: "in mmscfd"] project_status +varchar [note: "select"] project_name varchar [note: "select?"] +project_start_date date project_shutdown_date date // very empty +project_type_category varchar [note: "select"] lfg_energy_project_type varchar +[note: "select"] rng_delivery_method varchar actual_mw_generation decimal +rated_mw_capacity decimal lfg_flow_to_project decimal [note: "mmscfd"] +direct_emission_reductions decimal [note: "MMTCO2e/yr for current year"] +avoided_emission_reductions decimal [note: "MMTCO2e/yr for current year"] } + +Table infrastructure_livestock_anaerobic_digesters [headercolor: #008B8B] { +digester_id integer [pk] project_name varchar project_type varchar [note: +"select or multiselect"] city varchar state varchar(2) digester_type varchar +[note: "select or multiselect"] profile text [note: "url"] year_operational date +[note: "year only"] animal_type_class varchar [note: "select"] animal_types +varchar [note: "multiselect"] pop_feeding_digester varchar [note: "either single +integer or multiple integers separated by a semicolon"] // is this even +necessary? total_pop_feeding_digester integer cattle integer dairy integer +poultry integer swine integer codigestion varchar [note: "multiselect"] +biogas_generation_estimate integer [note: "cu/ft per day"] electricity_generated +integer [note: "kWh/yr"] biogas_end_uses varchar [note: "multiselect"] +methane_emission_reductions integer [note: "metric tons CO2e/yr"] latitude +decimal longitude decimal } + +Table infrastructure_saf_and_renewable_diesel_plants [headercolor: #008B8B] { +ibcc_index integer [pk] company varchar city varchar state varchar(2) country +varchar capacity varchar [note: "mmg per yr; mostly integers with some strings +in the format '#/#' where # is a number"] feedstock varchar [note: +"multiselect"] products varchar [note: "multiselect"] status varchar [note: +"multiselect"] address text coordinates text latitude decimal longitude decimal +} + +Table infrastructure_wastewater_treatment_plants [headercolor: #008B8B] { +plant_id integer [pk] name varchar state varchar(2) codigestion boolean [note: +"currently 0/1"] flow_design_adjusted decimal [note: "MGD"] flow_average decimal +[note: "MGD"] biosolids decimal [note: "BDT/yr"] excess_flow decimal [note: +"MGD"] biogas_utilized boolean [note: "currently 0/1"] flaring boolean [note: +"currently 0/1"] excess_mass_loading_rate decimal [note: "BDT/d"] +excess_mass_loading_rate_wet decimal [note: "tons per day?"] methane_production +decimal [note: "cubic ft/d"] energy_content decimal [note: "BTU/d"] electric_kw +decimal thermal_mmbtu_d decimal electric_kwh decimal thermal_annual_mmbtu_y +decimal anaerobic_digestion_facility varchar // partially blank county varchar +// partially blank dayload_bdt decimal // for ca only dayload decimal // what's +the difference between this and the prev one? for ca only equivalent_generation +decimal // for ca only facility_type varchar [note: "select"] // for ca only +feedstock varchar [note: "select"] // for ca only type varchar [note: "select"] +// for ca only city varchar latitude decimal longitude decimal zipcode varchar } + +Table infrastructure_combustion_plants [headercolor: #008B8B] { combustion_fid +integer [pk] objectid integer // several object ids are 0 status varchar [note: +"select: active, retired, unknown"] // has a random 0 in there. does that mean +unknown city varchar name varchar county varchar equivalent_generation decimal +np_mw decimal // what does this mean? look up cf decimal // what does this mean? +yearload integer [note: "in bdt"] fuel varchar [note: "select WDS, MSW, AB"] +notes varchar [note: "optional field, blanks replaced by zeroes"] type varchar +[note: "all COMB_pts; is it necessary"] wkt_geom text geom point latitude +decimal longitude decimal } + +Table infrastructure_district_energy_systems [headercolor: #008B8B] { des_fid +integer [pk] cbg_id integer name varchar system varchar // partially blank +object_id integer city varchar state varchar(2) primary_fuel varchar [note: +"selection of NG, E/Electric"] secondary_fuel varchar [note: "selection"] // +partially blank usetype varchar [note: "selection btwn College, +Downtown/Utility, Healthcare, Airport, Gov, Military"] cap_st decimal // what +does this mean? cap_hw decimal // what does this mean? cap_cw decimal // what +does this mean? chpcg_cap decimal // what does this mean? excess_c decimal +[note: 'all zeroes'] excess_h decimal [note: 'all zeroes'] type varchar [note: +'all DES_CBG'] wkt_geom text geom point latitude decimal longitude decimal } + +Table infrastructure_food_processing_facilities [headercolor: #008B8B] { +processing_facility_id integer [pk] address varchar county varchar city varchar +company varchar join_count integer // unsure if this is necessary. could omit? +master_type varchar [note: 'select; this is the main crop'] state varchar(2) +subtype varchar [note: 'select; this is also crop/product type'] target_fid +integer // lots of zeroes processing_type varchar [note: 'select'] zip varchar +type varchar [note: 'all PROC'] // unsure if this is needed wkt_geom text geom +point latitude decimal longitude decimal } + +Table infrastructure_msw_to_energy_anaerobic_digesters [headercolor: #008B8B] { +wte_id integer [pk] city varchar county varchar equivalent_generation decimal // +note: number stored as text feedstock varchar [note: 'multiselect'] dayload +decimal // note: number stored as text dayload_bdt decimal // note: number +stored as text facility_type varchar [note: 'select'] status varchar [note: +'select'] notes text source text type varchar [note: 'all W2E_pts'] // unsure if +needed wkt_geom text geom point latitude decimal longitude decimal } + +//=========================================================== // CHILD RECORD +TABLE – BT23 //=========================================================== + +Table billion_ton_2023_record [headercolor: #EB801B] { id int [pk, increment] +subclass_id int [ref:> resource_subclass.id] resource_id int [ref:> resource.id] +geoid varchar [ref:> geography.geoid] county_square_miles float model_name +varchar //enumerated list with POLYSIS, NASS, etc. scenario_name varchar +//Enumerated list of near-term, mature-market, etc price_offered_usd decimal +production int production_unit_id int [ref:> unit.id] btu_ton int +production_energy_content int energy_content_unit_id int [ref:> unit.id] +product_density_dtpersqmi decimal land_source varchar } + +/////////////////////////////////////////////////////////////// +/////////////////////////////////////////////////////////////// Table +usda_domain [headercolor: #ffc72f] { //domain still needs linkage! id int [pk, +increment] name string [not null, unique] description string uri string } + +// Table usda_commodity [headercolor: #ffc72f] { // id int [pk, increment] // +name string [not null, unique] // description string // uri string // } + +// Table usda_commodity_to_primary_crop [headercolor: #ffc72f] { // +usda_commodity_id int [ref: > usda_commodity.id] // primary_crop_id int [ref: > +primary_crop.id] // } + +Table usda_statistic_category [headercolor: #ffc72f] { id int [pk, increment] +name string [not null, unique] description string uri string } + +Table usda_survey_program [headercolor: #ffc72f] { id int [pk, increment] name +string [not null, unique] description string uri string } + +Table dimension_type [headercolor: #A15CF5] { id int [pk, increment] name string +[not null, unique, note: "E.g., TIMEPOINT, WAVELENGTH, DEPTH"] description text +uri string } + +Table analysis_type [headercolor: #A15CF5] { //we may want to be careful +difference between analysis and methods // LookupBase for enum/ontology-like +tables id int [pk, increment] name string [not null, unique, note: "X-Ray +Fluorescence analysis, Proximate analysis, Chemical Composition, Fermentation +Profile, etc"] // description string uri string // } + +Table polygon [headercolor: #808080] { id int [pk] geoid string [ref: > +geography.geoid] geom geometry } + +Table strain { // LookupBase for enum/ontology-like tables id int [pk, +increment] name string [not null, unique, note: "X-Ray Fluorescence analysis, +Proximate analysis, Chemical Composition, Fermentation Profile, etc"] // +parent_strain_id int [ref:> strain.id, note: "recursive"] description string uri +string // + +} + +# // ========================================== // USDA HIERARCHY & MAPPING // + +TableGroup "Resource Ontology Mapping" [color: #5D6D7E] { usda_commodity +resource_usda_commodity_map // usda_term_map // <--- The Dictionary (Raw Text -> +Clean USDA Node) + +} + +Table usda_commodity { // LookupBase id int [pk, increment] name string [not +null] // e.g., "Almonds", "Tree Nuts", "Rice, Long Grain" usda_source string // +"usda_source" = Who OWNS this official definition? // - "NASS": It is a census +crop (e.g., Almonds). // - "AMS": It is a market term not tracked by NASS (e.g., +Almond Hulls). usda_code string [note: "The official code used by USDA API"] + +// The Cleanup Mechanism (Self-Referencing Hierarchy) parent_commodity_id int +[ref: > usda_commodity.id, note: "If this is 'Almonds Hulls', parent might be +'Almonds'. There might be another row where commodity code is 'Almonds', and its +parent would be 'Tree Nuts'. 'Tree Nuts' would have NULL listed for parent."] +//Gemini has promised that the USDA NASS API already has structured commodity +relations so it should be a programmable task. + +description string uri string + +Note: ''' + +# ETL INGESTION RULE + +1. **Ingest NASS First:** The NASS API is the primary source of truth. + Programmatically populate this table using NASS "Group" -> "Commodity" -> + "Class" hierarchy. +2. **Ingest AMS Second:** The AMS API (Market Data) is messy. - When Python + encounters a term in AMS (e.g., "Almond Hulls"), it must check this table. - + If the term exists (from NASS), link to it. - If the term is NEW, create a + new node here with usda_source = "AMS". - **Manual Step:** A human must + periodically review new "AMS" nodes and link them to their NASS parent (e.g., + Link "Almond Hulls" -> "Almonds"). ''' } + +Table usda_term_map { id int [pk, increment] + +// THE INPUT (The Messy Reality) source_system string [note: " 'NASS' or 'AMS' +"] // "source_system" = Where did we FIND this specific messy text string. // We +need this so if we re-run the ingestion script, we know which rules apply (NASS +data is prioritized, AMS data is referenced and then added if not already +captured) source_context string [note: "For AMS: The Slug ID (e.g. 3667). For +NASS: The Group."] // "source_context" = The container where we found it. // - +For NASS: The Group Name (e.g., "Tree Nuts"). // - For AMS: The Slug ID (e.g., +"3668" = "Monthly National Grain and Oilseed Processor Feedstuff Report"). +raw_term string [not null, note: "The exact string from the API, e.g., 'Hulls', +'Hull/Shell Mix'"] + +// THE OUTPUT (The Decision) usda_commodity_id int [ref: > usda_commodity.id] +//We review this manually. + +// METADATA is_verified boolean [default: false] //Note whether we've confirmed +mapping note text } + +Table resource_usda_commodity_map { id int [pk, increment] + +// 1. THE INTERNAL TARGET (Who is asking?) // We allow linking to EITHER a +specific resource OR a general crop resource_id int [ref: > resource.id, null] +// Specific: "Almond Hulls" primary_crop_id int [ref: > primary_crop.id, null] +// General: "Almonds" + +// 2. THE EXTERNAL SOURCE (Who has the data?) usda_commodity_id int [ref: > +usda_commodity.id, not null] + +// 3. THE LOGIC (How good is the match?) match_tier string [not null, note: +"ENUM: 'DIRECT_MATCH', 'CROP_FALLBACK', 'AGGREGATE_PARENT'"] + +// Metadata created_at datetime [default: `current_timestamp`] note text [note: +"Explanation of why this link was made"] + +// LOGIC: A row must have EITHER a resource_id OR a primary_crop_id, but not +both null. } + +///////////////////////////////////////////////////////////// //////////// +PEOPLE ////////////// +//////////////////////////////////////////////////////////// + +Table contact { id int [pk] first_name varchar last_name varchar email varchar +[unique] affiliation varchar //maybe link to an enumerated list } + +Table provider { id int [pk] codename string } diff --git a/src/ca_biositing/datamodels/pyproject.toml b/src/ca_biositing/datamodels/pyproject.toml index 9d9a5d1c..6b4f49ee 100644 --- a/src/ca_biositing/datamodels/pyproject.toml +++ b/src/ca_biositing/datamodels/pyproject.toml @@ -27,6 +27,8 @@ dependencies = [ "psycopg2-binary>=2.9.6,<3", "pydantic>=2.0.0", "pydantic-settings>=2.0.0", + "linkml>=1.8.0", + "sqlalchemy>=2.0.0", ] [project.urls] diff --git a/src/pipeline/README.md b/src/pipeline/README.md deleted file mode 100644 index f2db60b9..00000000 --- a/src/pipeline/README.md +++ /dev/null @@ -1,168 +0,0 @@ -# ETL Pipeline Project - -This project implements a modular ETL (Extract, Transform, Load) pipeline that -extracts data from Google Sheets (or other sources), transforms it using Python, -and loads it into a PostgreSQL database. The entire environment is containerized -with Docker. - ---- - -## Core Workflows - -This project has three key development workflows. For detailed, step-by-step -instructions, please refer to the dedicated workflow guides. A high-level -overview is provided here to give conceptual understanding before you begin. - -### 1. Docker Environment Management - -- **Purpose:** Managing the lifecycle of your development containers (app and - database). -- **Details:** For starting, stopping, and rebuilding your environment. -- **[See the full guide: DOCKER_WORKFLOW.md](../../docs/pipeline/DOCKER_WORKFLOW.md)** - -### 2. Database Schema Migrations (Alembic) - -- **Purpose:** Making and applying changes to the database schema (e.g., adding - tables or columns). -- **Details:** How to automatically generate and apply migration scripts based - on your SQLModel changes. -- **[See the full guide: ALEMBIC_WORKFLOW.md](../../docs/pipeline/ALEMBIC_WORKFLOW.md)** - -### 3. ETL Pipeline Development (Prefect) - -- **Purpose:** Running the ETL pipeline and adding new data pipelines using - Prefect's "flow of flows" pattern. -- **Details:** The `run_prefect_flow.py` script acts as a master orchestrator - that runs all individual pipeline flows defined in the `src/flows/` directory. - To add a new pipeline, you must create a new flow file and add it to the - master flow. -- **[See the full guide: ETL_WORKFLOW.md](../../docs/pipeline/ETL_WORKFLOW.md)** - -### 4. Creating New Database Models - -- **Purpose:** Adding a new table to the database schema. -- **Details:** Use the `model_template.py` to define your new table, then follow - the Alembic workflow to generate and apply the migration. -- **[See the model template: src/models/templates/model_template.py](./src/models/templates/model_template.py)** -- **[See the migration guide: ALEMBIC_WORKFLOW.md](../../docs/pipeline/ALEMBIC_WORKFLOW.md)** - ---- - -## Local Development Environment (Pixi) - -This project uses **Pixi** to manage dependencies and run tasks for local -development. This environment is used for both running the application locally -and for code quality tools like `pre-commit`. The Docker container also uses -Pixi to install dependencies. - -**1. Install Pixi:** - -- Follow the official instructions to - [install Pixi](https://pixi.sh/latest/installation/) on your system. - -**2. Install Local Dependencies:** - -- Once Pixi is installed, navigate to the `ca-biositing` root directory and run: - - ```bash - pixi install - ``` - - This will install the required local tools (like `pre-commit`) into a managed - environment. - - If you have issues with the install on Windows, you may need to command: - - ``` - pixi workspace platform add win-64 - ``` - - Once pixi is installed, run the following command to set up pre-commit checks - on every commit: - - ```bash - pixi run pre-commit-install - ``` - -**3. Activate the Local Environment:** - -- To activate this environment in your shell, run: - - ```bash - pixi shell - ``` - - This command is the equivalent of a traditional `source venv/bin/activate`. - You will see a prefix in your shell prompt indicating that the environment is - active. You can now run commands like `pre-commit` directly. - ---- - -## Getting Started - -Follow these steps to set up and run the project for the first time. - -**1. Google Cloud Setup:** - -- To allow the application to access Google Sheets, you must first create a - service account and generate a `credentials.json` file. -- **[Follow the full guide here: GCP_SETUP.md](../../docs/pipeline/GCP_SETUP.md)** - -**2. Environment Setup:** - -- Create a `.env` file in the project root directory by copying the - `.env.example` file. -- The database connection settings (e.g., `POSTGRES_USER`) are used to connect - to the PostgreSQL container. The default values in `.env.example` are - sufficient for local development. You do not need to change them unless you - have a custom setup. - -**3. Build the Docker Image:** - -- From the project root directory, build the Docker image. - - ```bash - docker-compose build - ``` - -**4. Start the Services:** - -- Start the application and database containers in detached mode. - - ```bash - docker-compose up -d - ``` - -**5. Apply Database Migrations:** - -- The first time you start the project, you need to apply the database - migrations to create the tables. This command applies existing migrations; you - only need to consult the Alembic workflow guide when creating _new_ - migrations. - - ```bash - docker-compose exec app pixi run alembic upgrade head - ``` - -The environment is now fully set up and running. - ---- - -## Project Structure - -This `pipeline` directory is a self-contained ETL project located within the -larger `ca-biositing` repository. Here is a brief overview of its key -directories: - -``` -pipeline/ -├── alembic/ # Database migration scripts -├── etl/ -│ ├── extract/ # ETL Task: Modules for extracting data -│ ├── transform/ # ETL Task: Modules for transforming data -│ ├── load/ # ETL Task: Modules for loading data -│ └── templates/ # Templates for new ETL modules -├── flows/ # Prefect Flows: Individual pipeline definitions -├── models/ # SQLModel class definitions (database tables) -└── utils/ # Shared utility functions -``` From cbf8242a404f6471d75d179e6c993c47ec7de1ff Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Mon, 8 Dec 2025 09:22:39 -0700 Subject: [PATCH 19/81] AI hallucinations are messing up yaml files. Attempting to fix. --- .../datamodels/linkml/modules/analysis.yaml | 12 + .../linkml/modules/analysis_records.yaml | 4 + .../datamodels/linkml/modules/core.yaml | 166 -- .../linkml/modules/data_sources_metadata.yaml | 144 +- .../datamodels/linkml/modules/lineage.yaml | 73 +- .../datamodels/linkml/modules/places.yaml | 78 +- .../schemas/generated/aim2_records.py | 0 .../schemas/generated/analysis_records.py | 1919 +++++++++++++++++ .../schemas/generated/census_survey.py | 132 -- .../schemas/generated/field_sampling.py | 0 .../datamodels/schemas/generated/geography.py | 29 - src/ca_biositing/datamodels/generate_sqla.py | 49 + .../pipeline/utils/database_interaction.ipynb | 177 +- 13 files changed, 2254 insertions(+), 529 deletions(-) create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py create mode 100644 src/ca_biositing/datamodels/generate_sqla.py diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml index 987f0d1d..456b876d 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml @@ -91,3 +91,15 @@ slots: dimension_unit_id: range: integer description: Reference to Unit (dimension). + + source_id: + range: integer + description: Reference to Source. + + start_date: + range: datetime + description: Start date of the dataset. + + end_date: + range: datetime + description: End date of the dataset. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml index 35cc271d..4ec92ee7 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml @@ -227,3 +227,7 @@ slots: gas_flow_rate: range: decimal description: Gas flow rate. + + sample_id: + range: integer + description: Reference to Sample. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml index 84eaa04c..234b9b4f 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml @@ -34,84 +34,6 @@ classes: - description - uri - LineageGroup: - is_a: BaseEntity - description: Grouping for lineage information. - slots: - - note - - EntityLineage: - description: Lineage information for a specific entity. - slots: - - id - - lineage_group_id - - source_table - - source_row_id - - note - - EtlRun: - description: Information about an ETL run. - slots: - - id - - started_at - - completed_at - - pipeline_name - - status - - records_ingested - - note - slot_usage: - id: - identifier: true - range: string - - DataSource: - is_a: BaseEntity - description: Information about a data source. - slots: - - name - - description - - data_source_type_id - - full_title - - creator - - subject - - publisher - - contributor - - date - - type - - biocirv - - format - - language - - relation - - temporal_coverage - - location_coverage_id - - rights - - uri - - DataSourceType: - is_a: BaseEntity - description: Type of data source. - slots: - - source_type_id - - SourceType: - is_a: LookupBase - description: Lookup for source types (database, literature, etc.). - - LocationResolution: - is_a: LookupBase - description: Resolution of location coverage (nation, state, county, etc.). - - FileObjectMetadata: - is_a: BaseEntity - description: Metadata for file objects. - slots: - - data_source_id - - bucket_path - - file_format - - file_size - - checksum_md5 - - checksum_sha256 - slots: id: identifier: true @@ -177,91 +99,3 @@ slots: records_ingested: range: integer description: Number of records ingested. - - data_source_type_id: - range: integer - description: Reference to data source type. - - full_title: - range: string - description: Full title of the data source. - - creator: - range: string - description: Creator of the data source. - - subject: - range: string - description: Subject of the data source. - - publisher: - range: string - description: Publisher of the data source. - - contributor: - range: string - description: Contributor to the data source. - - date: - range: datetime - description: Date associated with the data source. - - type: - range: string - description: Type of the data source. - - biocirv: - range: boolean - description: Whether the data source is internal to BioCirV. - - format: - range: string - description: Format of the data source. - - language: - range: string - description: Language of the data source. - - relation: - range: string - description: Relation of the data source. - - temporal_coverage: - range: string - description: Temporal coverage of the data source. - - location_coverage_id: - range: integer - description: Reference to location resolution. - - rights: - range: string - description: Rights associated with the data source. - - source_type_id: - range: integer - description: Reference to source type. - - data_source_id: - range: integer - description: Reference to data source. - - bucket_path: - range: string - description: Path to the file in the bucket. - - file_format: - range: string - description: Format of the file. - - file_size: - range: integer - description: Size of the file. - - checksum_md5: - range: string - description: MD5 checksum of the file. - - checksum_sha256: - range: string - description: SHA256 checksum of the file. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index 7bb40074..fab12584 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -14,6 +14,7 @@ default_range: string imports: - linkml:types - core + - field_sampling classes: DataSource: @@ -22,136 +23,49 @@ classes: slots: - name - description - - data_source_type_id - - full_title - - creator - - subject - - publisher - - contributor - - date - - type - - biocirv - - format - - language - - relation - - temporal_coverage - - location_coverage_id - - rights - uri + - publication_date + - version + - publisher + - author + - license + - note - DataSourceType: - is_a: LookupBase - description: Type of data source. - slots: - - source_type_id - - SourceType: - is_a: LookupBase - description: General source type. - - FileObjectMetadata: + MetadataSample: is_a: BaseEntity - description: Metadata for file objects. + description: Metadata for a field sample. slots: - - data_source_id - - bucket_path - - file_format - - file_size - - checksum_md5 - - checksum_sha256 - - LocationResolution: - is_a: LookupBase - description: Resolution of location data. + - field_sample_id + - metadata_key + - metadata_value + - metadata_type + - note slots: - data_source_type_id: - range: integer - description: Reference to DataSourceType. - - source_type_id: - range: integer - description: Reference to SourceType. - - full_title: - range: string - description: Full title of the data source. - - creator: - range: string - description: Creator of the data source. - - subject: - range: string - description: Subject of the data source. - - publisher: - range: string - description: Publisher of the data source. - - contributor: - range: string - description: Contributor to the data source. - - date: - range: datetime - description: Date of the data source. - - type: - range: string - description: Type of the data source. - - biocirv: - range: boolean - description: Whether the data source is internal (BioCirV). - - format: - range: string - description: Format of the data source. - - language: - range: string - description: Language of the data source. - - relation: - range: string - description: Relation of the data source. - - temporal_coverage: - range: string - description: Temporal coverage of the data source. - - location_coverage_id: - range: integer - description: Reference to LocationResolution. + publication_date: + range: date + description: Date of publication. - rights: + version: range: string - description: Rights of the data source. + description: Version of the data source. - uri: + author: range: string - description: URI of the resource. + description: Author of the data source. - data_source_id: - range: integer - description: Reference to DataSource. - - bucket_path: + license: range: string - description: Path to the file in the bucket. + description: License of the data source. - file_format: + metadata_key: range: string - description: Format of the file. - - file_size: - range: integer - description: Size of the file in bytes. + description: Key for the metadata. - checksum_md5: + metadata_value: range: string - description: MD5 checksum of the file. + description: Value for the metadata. - checksum_sha256: + metadata_type: range: string + description: Type of the metadata value (e.g. string, int, float). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml index b0014c90..6d0fd301 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml @@ -17,68 +17,39 @@ imports: classes: LineageGroup: - is_a: BaseEntity - description: Grouping of lineage entities. + description: Grouping for lineage information. slots: - - name - - description + - id + - etl_run_id + - note + slot_usage: + id: + identifier: true + range: integer EntityLineage: - description: Lineage relationship between entities. + description: Lineage information for a specific entity. slots: - id - - parent_entity_id - - child_entity_id - lineage_group_id - - relationship_type + - source_table + - source_row_id + - note slot_usage: id: identifier: true range: integer EtlRun: - is_a: BaseEntity - description: ETL run information. + description: Information about an ETL run. slots: - - run_id - - start_time - - end_time + - id + - started_at + - completed_at + - pipeline_name - status - - log_uri - -slots: - parent_entity_id: - range: integer - description: ID of the parent entity. - - child_entity_id: - range: integer - description: ID of the child entity. - - lineage_group_id: - range: integer - description: Reference to LineageGroup. - - relationship_type: - range: string - description: Type of relationship. - - run_id: - range: string - description: Unique identifier for the ETL run. - - start_time: - range: datetime - description: Start time of the run. - - end_time: - range: datetime - description: End time of the run. - - status: - range: string - description: Status of the run. - - log_uri: - range: string - description: URI to the run logs. + - records_ingested + - note + slot_usage: + id: + identifier: true diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml index 7cd2c18b..5a6342d3 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml @@ -17,13 +17,15 @@ imports: classes: Geography: - is_a: BaseEntity description: Geographic location. slots: - geoid - - name - - type - - geometry + - state_name + - state_fips + - county_name + - county_fips + - region_name + - agg_level_desc slot_usage: geoid: identifier: true @@ -32,42 +34,72 @@ classes: is_a: BaseEntity description: Physical address. slots: - - street_address + - geography_id + - address_line1 + - address_line2 - city - - state - - zip_code - - country - - geoid + - zip + - lat + - lon + - is_anonymous slots: geoid: range: string description: Unique identifier for geography. - type: + state_name: range: string - description: Type of geography (e.g. county, state). + description: State name. - geometry: + state_fips: range: string - description: WKT geometry. + description: State FIPS code. - street_address: + county_name: range: string - description: Street address. + description: County name. - city: + county_fips: range: string - description: City. + description: County FIPS code. - state: + region_name: range: string - description: State. + description: Region name. - zip_code: + agg_level_desc: range: string - description: ZIP code. + description: Aggregation level description. - country: + geography_id: range: string - description: Country. + description: Reference to Geography. + + address_line1: + range: string + description: Address line 1. + + address_line2: + range: string + description: Address line 2. + + city: + range: string + description: City. + + zip: + range: string + description: ZIP code. + + lat: + range: float + description: Latitude. + + lon: + range: float + description: Longitude. + + is_anonymous: + range: boolean + description: Whether the location is anonymous. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py new file mode 100644 index 00000000..e69de29b diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py new file mode 100644 index 00000000..c7ac9023 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py @@ -0,0 +1,1919 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class RecordBase(Base): + """ + + """ + __tablename__ = 'RecordBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"RecordBase(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class EntityLineage(Base): + """ + Lineage information for a specific entity. + """ + __tablename__ = 'EntityLineage' + + id = Column(Integer(), primary_key=True, nullable=False ) + lineage_group_id = Column(Integer()) + source_table = Column(Text()) + source_row_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" + + + + + + +class EtlRun(Base): + """ + Information about an ETL run. + """ + __tablename__ = 'EtlRun' + + id = Column(Text(), primary_key=True, nullable=False ) + started_at = Column(DateTime()) + completed_at = Column(DateTime()) + pipeline_name = Column(Text()) + status = Column(Text()) + records_ingested = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" + + + + + + +class Dataset(Base): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(DateTime()) + end_date = Column(DateTime()) + description = Column(Text()) + + + def __repr__(self): + return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" + + + + + + +class Observation(Base): + """ + Observation data. + """ + __tablename__ = 'Observation' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon definition. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between experiment and equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between experiment and analysis type. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between experiment and prepared sample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between experiment and method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ProximateRecord(RecordBase): + """ + Proximate analysis record. + """ + __tablename__ = 'ProximateRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"ProximateRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UltimateRecord(RecordBase): + """ + Ultimate analysis record. + """ + __tablename__ = 'UltimateRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"UltimateRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CompositionalRecord(RecordBase): + """ + Compositional analysis record. + """ + __tablename__ = 'CompositionalRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"CompositionalRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class IcpRecord(RecordBase): + """ + ICP analysis record. + """ + __tablename__ = 'IcpRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"IcpRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrfRecord(RecordBase): + """ + XRF analysis record. + """ + __tablename__ = 'XrfRecord' + + maybe_wavelength_nm = Column(Numeric()) + maybe_intensity = Column(Numeric()) + maybe_energy_slope = Column(Numeric()) + maybe_energy_offset = Column(Numeric()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrdRecord(RecordBase): + """ + XRD analysis record. + """ + __tablename__ = 'XrdRecord' + + maybe_scan_low_nm = Column(Integer()) + maybe_scan_high_nm = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CalorimetryRecord(RecordBase): + """ + Calorimetry analysis record. + """ + __tablename__ = 'CalorimetryRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"CalorimetryRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FtnirRecord(RecordBase): + """ + FT-NIR analysis record. + """ + __tablename__ = 'FtnirRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"FtnirRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class RgbRecord(RecordBase): + """ + RGB analysis record. + """ + __tablename__ = 'RgbRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"RgbRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PretreatmentRecord(RecordBase): + """ + Pretreatment record. + """ + __tablename__ = 'PretreatmentRecord' + + pretreatment_method = Column(Integer()) + eh_method_id = Column(Integer()) + reaction_block_id = Column(Integer()) + block_position = Column(Text()) + temperature = Column(Numeric()) + replicate_no = Column(Integer()) + analyst_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"PretreatmentRecord(pretreatment_method={self.pretreatment_method},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FermentationRecord(RecordBase): + """ + Fermentation record. + """ + __tablename__ = 'FermentationRecord' + + strain_id = Column(Integer()) + pretreatement_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + replicate_no = Column(Integer()) + well_position = Column(Text()) + temperature = Column(Numeric()) + agitation_rpm = Column(Numeric()) + vessel_id = Column(Integer()) + analyte_detection_equipment_id = Column(Integer()) + analyst_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"FermentationRecord(strain_id={self.strain_id},pretreatement_method_id={self.pretreatement_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class GasificationRecord(RecordBase): + """ + Gasification record. + """ + __tablename__ = 'GasificationRecord' + + feedstock_mass = Column(Numeric()) + bed_temperature = Column(Numeric()) + gas_flow_rate = Column(Numeric()) + analyst_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AutoclaveRecord(RecordBase): + """ + Autoclave record. + """ + __tablename__ = 'AutoclaveRecord' + + analyst_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"AutoclaveRecord(analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LineageGroup(BaseEntity): + """ + Grouping for lineage information. + """ + __tablename__ = 'LineageGroup' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LineageGroup(note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Information about a data source. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) + publisher = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) + uri = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},uri={self.uri},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Lookup for source types (database, literature, etc.). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of location coverage (nation, state, county, etc.). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for file objects. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension (e.g. timepoint, wavelength). + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample prepared for analysis. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Strain(LookupBase): + """ + Strain of organism. + """ + __tablename__ = 'Strain' + + parent_strain_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py deleted file mode 100644 index 158c32a4..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py +++ /dev/null @@ -1,132 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class USDARecord(Base): - """ - Base class for USDA agricultural data records. - """ - __tablename__ = 'USDARecord' - - id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) - year = Column(Integer(), nullable=False ) - crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) - variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) - unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) - value = Column(Float()) - bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) - class_desc = Column(Text()) - domain_desc = Column(Text()) - source = Column(Text()) - notes = Column(Text()) - geography_id = Column(Integer(), ForeignKey('Geography.id')) - geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) - - - def __repr__(self): - return f"USDARecord(id={self.id},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" - - - - - - -class Geography(Base): - """ - Reference table for U.S. geographic identifiers. - """ - __tablename__ = 'Geography' - - id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - geoid = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(id={self.id},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},geoid={self.geoid},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class CensusRecord(USDARecord): - """ - A USDA Census of Agriculture record (every 5 years). - """ - __tablename__ = 'CensusRecord' - - id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) - year = Column(Integer(), nullable=False ) - crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) - variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) - unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) - value = Column(Float()) - bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) - class_desc = Column(Text()) - domain_desc = Column(Text()) - source = Column(Text()) - notes = Column(Text()) - geography_id = Column(Integer(), ForeignKey('Geography.id')) - geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) - - - def __repr__(self): - return f"CensusRecord(id={self.id},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SurveyRecord(USDARecord): - """ - A USDA Survey record (annual, seasonal, or periodic). - """ - __tablename__ = 'SurveyRecord' - - id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) - period_desc = Column(Text()) - freq_desc = Column(Text()) - program_desc = Column(Text()) - year = Column(Integer(), nullable=False ) - crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) - variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) - unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) - value = Column(Float()) - bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) - class_desc = Column(Text()) - domain_desc = Column(Text()) - source = Column(Text()) - notes = Column(Text()) - geography_id = Column(Integer(), ForeignKey('Geography.id')) - geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) - - - def __repr__(self): - return f"SurveyRecord(id={self.id},period_desc={self.period_desc},freq_desc={self.freq_desc},program_desc={self.program_desc},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py new file mode 100644 index 00000000..e69de29b diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py deleted file mode 100644 index dcc8a564..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py +++ /dev/null @@ -1,29 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class Geography(Base): - """ - Reference table for U.S. geographic identifiers. - """ - __tablename__ = 'Geography' - - id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - geoid = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(id={self.id},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},geoid={self.geoid},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" diff --git a/src/ca_biositing/datamodels/generate_sqla.py b/src/ca_biositing/datamodels/generate_sqla.py new file mode 100644 index 00000000..54fe4a59 --- /dev/null +++ b/src/ca_biositing/datamodels/generate_sqla.py @@ -0,0 +1,49 @@ +import os +import subprocess +from pathlib import Path + +def generate_sqla(): + """ + Generates SQLAlchemy models from LinkML schema modules. + """ + base_dir = Path(__file__).parent + linkml_dir = base_dir / "ca_biositing/datamodels/linkml" + modules_dir = linkml_dir / "modules" + output_dir = base_dir / "ca_biositing/datamodels/schemas/generated" + + # Ensure output directory exists + output_dir.mkdir(parents=True, exist_ok=True) + + # Generate for modules + for yaml_file in modules_dir.glob("*.yaml"): + module_name = yaml_file.stem + output_file = output_dir / f"{module_name}.py" + print(f"Generating {output_file} from {yaml_file}...") + + cmd = [ + "python", "-m", "linkml.generators.sqlalchemygen", + "--no-mergeimports", + str(yaml_file) + ] + + with open(output_file, "w") as f: + subprocess.run(cmd, stdout=f, check=True) + + # Generate for main schema + main_yaml = linkml_dir / "ca_biositing.yaml" + main_output = output_dir / "ca_biositing.py" + print(f"Generating {main_output} from {main_yaml}...") + + cmd = [ + "python", "-m", "linkml.generators.sqlalchemygen", + "--no-mergeimports", + str(main_yaml) + ] + + with open(main_output, "w") as f: + subprocess.run(cmd, stdout=f, check=True) + + print("Generation complete.") + +if __name__ == "__main__": + generate_sqla() diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb index 41d5e443..671f288a 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb @@ -23,9 +23,17 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Libraries and models imported successfully.\n" + ] + } + ], "source": [ "import pandas as pd\n", "from sqlmodel import create_engine, Session, select\n", @@ -53,9 +61,17 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Database engine created. Ready to connect to: postgresql+psycopg2://biocirv_user:@localhost:5432/biocirv_db\n" + ] + } + ], "source": [ "DATABASE_URL = \"postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db\"\n", "\n", @@ -77,9 +93,19 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "- Loaded 0 records from 'field_samples'.\n", + "- Loaded 0 records from 'geographic_locations'.\n", + "- Loaded 18 records from 'primary_product'.\n" + ] + } + ], "source": [ "field_samples_df = None\n", "locations_df = None\n", @@ -111,9 +137,118 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "analysis_type_id", + "rawType": "int64", + "type": "integer" + }, + { + "name": "analysis_name", + "rawType": "object", + "type": "string" + } + ], + "ref": "29cf402a-5519-4cf9-9c5d-27d39dd02736", + "rows": [ + [ + "1", + "Proximate analysis" + ], + [ + "2", + "ICP-OES" + ], + [ + "3", + "Chemical composition" + ], + [ + "4", + "XRF analysis" + ], + [ + "5", + "Ultimate analysis" + ] + ], + "shape": { + "columns": 1, + "rows": 5 + } + }, + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
analysis_name
analysis_type_id
1Proximate analysis
2ICP-OES
3Chemical composition
4XRF analysis
5Ultimate analysis
\n", + "
" + ], + "text/plain": [ + " analysis_name\n", + "analysis_type_id \n", + "1 Proximate analysis\n", + "2 ICP-OES\n", + "3 Chemical composition\n", + "4 XRF analysis\n", + "5 Ultimate analysis" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "df2 = pd.read_sql(\"SELECT * FROM analysis_types\", engine)\n", "df2 = df2.set_index(\"analysis_type_id\")\n", @@ -134,9 +269,17 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Skipping join because 'field_samples' table is empty.\n" + ] + } + ], "source": [ "merged_df = None\n", "\n", @@ -169,9 +312,17 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "No data to display.\n" + ] + } + ], "source": [ "if merged_df is not None:\n", " display(merged_df.head())\n", @@ -196,7 +347,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.14.0" + "version": "3.13.9" } }, "nbformat": 4, From a4758c8190d8b2f8859d52e265c04d85d1d54ace Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Mon, 8 Dec 2025 10:50:11 -0700 Subject: [PATCH 20/81] generated sqla from linkml.STILL NEEDS A CHECK. Next up alembic. --- .../linkml/modules/aim1_records.yaml | 4 + .../linkml/modules/aim2_records.yaml | 24 +- .../linkml/modules/data_sources_metadata.yaml | 61 +- .../linkml/modules/experiment_equipment.yaml | 4 + .../schemas/generated/aim1_records.py | 1707 ++++++++++++ .../schemas/generated/aim2_records.py | 1565 +++++++++++ .../datamodels/schemas/generated/analysis.py | 375 +++ .../schemas/generated/analysis_records.py | 224 -- .../schemas/generated/ca_biositing.py | 2403 +++++++++++++++++ .../datamodels/schemas/generated/core.py | 46 + .../generated/data_sources_metadata.py | 1000 +++++++ .../schemas/generated/experiment_equipment.py | 1341 +++++++++ .../schemas/generated/experiments.py | 1224 +++++++++ .../schemas/generated/external_data.py | 1527 +++++++++++ .../schemas/generated/field_sampling.py | 1000 +++++++ .../schemas/generated/general_analysis.py | 1118 ++++++++ .../datamodels/schemas/generated/geography.py | 125 + .../schemas/generated/infrastructure.py | 1595 +++++++++++ .../datamodels/schemas/generated/lineage.py | 109 + .../datamodels/schemas/generated/methods.py | 275 ++ .../generated/methods_parameters_units.py | 1000 +++++++ .../datamodels/schemas/generated/people.py | 44 + .../datamodels/schemas/generated/places.py | 106 + .../schemas/generated/resource_information.py | 307 +++ .../datamodels/schemas/generated/resources.py | 326 +++ .../schemas/generated/sample_preparation.py | 1089 ++++++++ .../datamodels/schemas/generated/sampling.py | 964 +++++++ 27 files changed, 19323 insertions(+), 240 deletions(-) create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml index 179c4898..fc2ae1ff 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml @@ -121,3 +121,7 @@ slots: maybe_scan_high_nm: range: integer description: High scan range in nm. + + sample_id: + range: integer + description: Reference to PreparedSample. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml index 416589b7..8eabaa1f 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml @@ -35,6 +35,8 @@ classes: - raw_data_id - qc_pass - note + - technical_replicate_total + - technical_replicate_no PretreatmentRecord: is_a: Aim2RecordBase @@ -68,13 +70,11 @@ classes: - feedstock_mass - bed_temperature - gas_flow_rate - - technical_replicate_no AutoclaveRecord: is_a: Aim2RecordBase description: Autoclave record. - slots: - - technical_replicate_no + slots: [] Strain: is_a: LookupBase @@ -141,3 +141,21 @@ slots: parent_strain_id: range: integer + + sample_id: + range: integer + + raw_data_id: + range: integer + description: Reference to FileObjectMetadata. + + qc_pass: + range: boolean + description: Whether the record passed QC. + + technical_replicate_no: + range: integer + description: Replicate number. + + technical_replicate_total: + range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index fab12584..cc20fe83 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -31,15 +31,30 @@ classes: - license - note - MetadataSample: + FileObjectMetadata: is_a: BaseEntity - description: Metadata for a field sample. + description: Metadata for a file object. slots: - - field_sample_id - - metadata_key - - metadata_value - - metadata_type - - note + - data_source_id + - bucket_path + - file_format + - file_size + - checksum_md5 + - checksum_sha256 + + DataSourceType: + is_a: BaseEntity + description: Type of data source. + slots: + - source_type_id + + LocationResolution: + is_a: LookupBase + description: Resolution of the location (e.g. nation, state, county). + + SourceType: + is_a: LookupBase + description: Type of source (e.g. database, literature). slots: publication_date: @@ -50,6 +65,10 @@ slots: range: string description: Version of the data source. + publisher: + range: string + description: Publisher of the data source. + author: range: string description: Author of the data source. @@ -58,14 +77,30 @@ slots: range: string description: License of the data source. - metadata_key: + data_source_id: + range: integer + description: Reference to DataSource. + + bucket_path: + range: string + description: Path to the file in the bucket. + + file_format: range: string - description: Key for the metadata. + description: Format of the file. + + file_size: + range: integer + description: Size of the file in bytes. - metadata_value: + checksum_md5: range: string - description: Value for the metadata. + description: MD5 checksum of the file. - metadata_type: + checksum_sha256: range: string - description: Type of the metadata value (e.g. string, int, float). + description: SHA256 checksum of the file. + + source_type_id: + range: integer + description: Reference to SourceType. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml index 4896706d..bc76394b 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml @@ -121,3 +121,7 @@ slots: prepared_sample_id: range: integer description: Reference to PreparedSample. + + method_id: + range: integer + description: Reference to Method. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py new file mode 100644 index 00000000..9893aae0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py @@ -0,0 +1,1707 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between Experiment and Method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between Experiment and Equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between Experiment and AnalysisType. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between Experiment and PreparedSample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class Aim1RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'Aim1RecordBase' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProximateRecord(Aim1RecordBase): + """ + Proximate analysis record. + """ + __tablename__ = 'ProximateRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UltimateRecord(Aim1RecordBase): + """ + Ultimate analysis record. + """ + __tablename__ = 'UltimateRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CompositionalRecord(Aim1RecordBase): + """ + Compositional analysis record. + """ + __tablename__ = 'CompositionalRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class IcpRecord(Aim1RecordBase): + """ + ICP analysis record. + """ + __tablename__ = 'IcpRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrfRecord(Aim1RecordBase): + """ + XRF analysis record. + """ + __tablename__ = 'XrfRecord' + + maybe_wavelength_nm = Column(Numeric()) + maybe_intensity = Column(Numeric()) + maybe_energy_slope = Column(Numeric()) + maybe_energy_offset = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrdRecord(Aim1RecordBase): + """ + XRD analysis record. + """ + __tablename__ = 'XrdRecord' + + maybe_scan_low_nm = Column(Integer()) + maybe_scan_high_nm = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CalorimetryRecord(Aim1RecordBase): + """ + Calorimetry analysis record. + """ + __tablename__ = 'CalorimetryRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FtnirRecord(Aim1RecordBase): + """ + FT-NIR analysis record. + """ + __tablename__ = 'FtnirRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class RgbRecord(Aim1RecordBase): + """ + RGB analysis record. + """ + __tablename__ = 'RgbRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py index e69de29b..e212029e 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py @@ -0,0 +1,1565 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between Experiment and Method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between Experiment and Equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between Experiment and AnalysisType. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between Experiment and PreparedSample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class Aim2RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'Aim2RecordBase' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Strain(LookupBase): + """ + Strain used in fermentation. + """ + __tablename__ = 'Strain' + + parent_strain_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PretreatmentRecord(Aim2RecordBase): + """ + Pretreatment record. + """ + __tablename__ = 'PretreatmentRecord' + + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + reaction_block_id = Column(Integer()) + block_position = Column(Text()) + temperature = Column(Numeric()) + replicate_no = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FermentationRecord(Aim2RecordBase): + """ + Fermentation record. + """ + __tablename__ = 'FermentationRecord' + + strain_id = Column(Integer()) + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + replicate_no = Column(Integer()) + well_position = Column(Text()) + temperature = Column(Numeric()) + agitation_rpm = Column(Numeric()) + vessel_id = Column(Integer()) + analyte_detection_equipment_id = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class GasificationRecord(Aim2RecordBase): + """ + Gasification record. + """ + __tablename__ = 'GasificationRecord' + + feedstock_mass = Column(Numeric()) + bed_temperature = Column(Numeric()) + gas_flow_rate = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AutoclaveRecord(Aim2RecordBase): + """ + Autoclave record. + """ + __tablename__ = 'AutoclaveRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py new file mode 100644 index 00000000..31e8b6fb --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py @@ -0,0 +1,375 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Dataset(Base): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(DateTime()) + end_date = Column(DateTime()) + description = Column(Text()) + + + def __repr__(self): + return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" + + + + + + +class Observation(Base): + """ + Observation data. + """ + __tablename__ = 'Observation' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class DimensionType(LookupBase): + """ + Type of dimension (e.g. timepoint, wavelength). + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py index c7ac9023..44a65db4 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py @@ -77,50 +77,6 @@ def __repr__(self): -class EntityLineage(Base): - """ - Lineage information for a specific entity. - """ - __tablename__ = 'EntityLineage' - - id = Column(Integer(), primary_key=True, nullable=False ) - lineage_group_id = Column(Integer()) - source_table = Column(Text()) - source_row_id = Column(Text()) - note = Column(Text()) - - - def __repr__(self): - return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" - - - - - - -class EtlRun(Base): - """ - Information about an ETL run. - """ - __tablename__ = 'EtlRun' - - id = Column(Text(), primary_key=True, nullable=False ) - started_at = Column(DateTime()) - completed_at = Column(DateTime()) - pipeline_name = Column(Text()) - status = Column(Text()) - records_ingested = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" - - - - - - class Dataset(Base): """ Dataset definition. @@ -829,186 +785,6 @@ def __repr__(self): -class LineageGroup(BaseEntity): - """ - Grouping for lineage information. - """ - __tablename__ = 'LineageGroup' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LineageGroup(note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Information about a data source. - """ - __tablename__ = 'DataSource' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - uri = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},uri={self.uri},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source. - """ - __tablename__ = 'DataSourceType' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Lookup for source types (database, literature, etc.). - """ - __tablename__ = 'SourceType' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of location coverage (nation, state, county, etc.). - """ - __tablename__ = 'LocationResolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for file objects. - """ - __tablename__ = 'FileObjectMetadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - class DimensionType(LookupBase): """ Type of dimension (e.g. timepoint, wavelength). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py new file mode 100644 index 00000000..bbbb9a74 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py @@ -0,0 +1,2403 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class LineageGroup(Base): + """ + Grouping for lineage information. + """ + __tablename__ = 'LineageGroup' + + id = Column(Integer(), primary_key=True, nullable=False ) + etl_run_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"LineageGroup(id={self.id},etl_run_id={self.etl_run_id},note={self.note},)" + + + + + + +class EntityLineage(Base): + """ + Lineage information for a specific entity. + """ + __tablename__ = 'EntityLineage' + + id = Column(Integer(), primary_key=True, nullable=False ) + lineage_group_id = Column(Integer()) + source_table = Column(Text()) + source_row_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" + + + + + + +class EtlRun(Base): + """ + Information about an ETL run. + """ + __tablename__ = 'EtlRun' + + id = Column(Integer(), primary_key=True, nullable=False ) + started_at = Column(DateTime()) + completed_at = Column(DateTime()) + pipeline_name = Column(Text()) + status = Column(Text()) + records_ingested = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between Experiment and Method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between Experiment and Equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between Experiment and AnalysisType. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between Experiment and PreparedSample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Aim1RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'Aim1RecordBase' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Aim2RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'Aim2RecordBase' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Strain(LookupBase): + """ + Strain used in fermentation. + """ + __tablename__ = 'Strain' + + parent_strain_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaDomain(LookupBase): + """ + USDA domain. + """ + __tablename__ = 'UsdaDomain' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaDomain(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaStatisticCategory(LookupBase): + """ + USDA statistic category. + """ + __tablename__ = 'UsdaStatisticCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaStatisticCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyProgram(LookupBase): + """ + USDA survey program. + """ + __tablename__ = 'UsdaSurveyProgram' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaSurveyProgram(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCommodity(LookupBase): + """ + USDA commodity. + """ + __tablename__ = 'UsdaCommodity' + + usda_source = Column(Text()) + usda_code = Column(Text()) + parent_commodity_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaTermMap(BaseEntity): + """ + Mapping of raw terms to USDA commodities. + """ + __tablename__ = 'UsdaTermMap' + + source_system = Column(Text()) + source_context = Column(Text()) + raw_term = Column(Text()) + usda_commodity_id = Column(Integer()) + is_verified = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceUsdaCommodityMap(BaseEntity): + """ + Mapping between resources/crops and USDA commodities. + """ + __tablename__ = 'ResourceUsdaCommodityMap' + + resource_id = Column(Integer()) + primary_crop_id = Column(Integer()) + usda_commodity_id = Column(Integer()) + match_tier = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCensusRecord(BaseEntity): + """ + USDA census record. + """ + __tablename__ = 'UsdaCensusRecord' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + source_reference = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyRecord(BaseEntity): + """ + USDA survey record. + """ + __tablename__ = 'UsdaSurveyRecord' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + survey_program_id = Column(Integer()) + survey_period = Column(Text()) + reference_month = Column(Text()) + seasonal_flag = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketReport(BaseEntity): + """ + USDA market report. + """ + __tablename__ = 'UsdaMarketReport' + + slug_id = Column(Integer()) + slug_name = Column(Text()) + report_series_title = Column(Text()) + frequency = Column(Text()) + office_name = Column(Text()) + office_city_id = Column(Integer()) + office_state_fips = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketReport(slug_id={self.slug_id},slug_name={self.slug_name},report_series_title={self.report_series_title},frequency={self.frequency},office_name={self.office_name},office_city_id={self.office_city_id},office_state_fips={self.office_state_fips},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketRecord(BaseEntity): + """ + USDA market record. + """ + __tablename__ = 'UsdaMarketRecord' + + report_id = Column(Integer()) + dataset_id = Column(Integer()) + report_begin_date = Column(DateTime()) + report_end_date = Column(DateTime()) + report_date = Column(DateTime()) + commodity_id = Column(Integer()) + market_type_id = Column(Integer()) + market_type_catagory = Column(Text()) + grp = Column(Text()) + market_catagory_id = Column(Integer()) + class_ = Column(Text()) + grade = Column(Text()) + variety = Column(Text()) + protein_pct = Column(Numeric()) + application = Column(Text()) + pkg = Column(Text()) + sale_type = Column(Text()) + price_unit_id = Column(Integer()) + freight = Column(Text()) + trans_mode = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_catagory={self.market_type_catagory},grp={self.grp},market_catagory_id={self.market_catagory_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LandiqRecord(BaseEntity): + """ + LandIQ record. + """ + __tablename__ = 'LandiqRecord' + + dataset_id = Column(Integer()) + polygon_id = Column(Integer()) + main_crop = Column(Integer()) + secondary_crop = Column(Integer()) + tertiary_crop = Column(Integer()) + quaternary_crop = Column(Integer()) + confidence = Column(Integer()) + irrigated = Column(Boolean()) + acres = Column(Float()) + version = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class BillionTon2023Record(BaseEntity): + """ + Billion Ton 2023 record. + """ + __tablename__ = 'BillionTon2023Record' + + subclass_id = Column(Integer()) + resource_id = Column(Integer()) + geoid = Column(Text()) + county_square_miles = Column(Float()) + model_name = Column(Text()) + scenario_name = Column(Text()) + price_offered_usd = Column(Numeric()) + production = Column(Integer()) + production_unit_id = Column(Integer()) + btu_ton = Column(Integer()) + production_energy_content = Column(Integer()) + energy_content_unit_id = Column(Integer()) + product_density_dtpersqmi = Column(Numeric()) + land_source = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BillionTon2023Record(subclass_id={self.subclass_id},resource_id={self.resource_id},geoid={self.geoid},county_square_miles={self.county_square_miles},model_name={self.model_name},scenario_name={self.scenario_name},price_offered_usd={self.price_offered_usd},production={self.production},production_unit_id={self.production_unit_id},btu_ton={self.btu_ton},production_energy_content={self.production_energy_content},energy_content_unit_id={self.energy_content_unit_id},product_density_dtpersqmi={self.product_density_dtpersqmi},land_source={self.land_source},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProximateRecord(Aim1RecordBase): + """ + Proximate analysis record. + """ + __tablename__ = 'ProximateRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UltimateRecord(Aim1RecordBase): + """ + Ultimate analysis record. + """ + __tablename__ = 'UltimateRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CompositionalRecord(Aim1RecordBase): + """ + Compositional analysis record. + """ + __tablename__ = 'CompositionalRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class IcpRecord(Aim1RecordBase): + """ + ICP analysis record. + """ + __tablename__ = 'IcpRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrfRecord(Aim1RecordBase): + """ + XRF analysis record. + """ + __tablename__ = 'XrfRecord' + + maybe_wavelength_nm = Column(Numeric()) + maybe_intensity = Column(Numeric()) + maybe_energy_slope = Column(Numeric()) + maybe_energy_offset = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrdRecord(Aim1RecordBase): + """ + XRD analysis record. + """ + __tablename__ = 'XrdRecord' + + maybe_scan_low_nm = Column(Integer()) + maybe_scan_high_nm = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CalorimetryRecord(Aim1RecordBase): + """ + Calorimetry analysis record. + """ + __tablename__ = 'CalorimetryRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FtnirRecord(Aim1RecordBase): + """ + FT-NIR analysis record. + """ + __tablename__ = 'FtnirRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class RgbRecord(Aim1RecordBase): + """ + RGB analysis record. + """ + __tablename__ = 'RgbRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PretreatmentRecord(Aim2RecordBase): + """ + Pretreatment record. + """ + __tablename__ = 'PretreatmentRecord' + + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + reaction_block_id = Column(Integer()) + block_position = Column(Text()) + temperature = Column(Numeric()) + replicate_no = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FermentationRecord(Aim2RecordBase): + """ + Fermentation record. + """ + __tablename__ = 'FermentationRecord' + + strain_id = Column(Integer()) + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + replicate_no = Column(Integer()) + well_position = Column(Text()) + temperature = Column(Numeric()) + agitation_rpm = Column(Numeric()) + vessel_id = Column(Integer()) + analyte_detection_equipment_id = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class GasificationRecord(Aim2RecordBase): + """ + Gasification record. + """ + __tablename__ = 'GasificationRecord' + + feedstock_mass = Column(Numeric()) + bed_temperature = Column(Numeric()) + gas_flow_rate = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AutoclaveRecord(Aim2RecordBase): + """ + Autoclave record. + """ + __tablename__ = 'AutoclaveRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py new file mode 100644 index 00000000..1f2a5b30 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py @@ -0,0 +1,46 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py new file mode 100644 index 00000000..e8ad5281 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py @@ -0,0 +1,1000 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py new file mode 100644 index 00000000..542f4cd0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py @@ -0,0 +1,1341 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ExperimentMethod(Base): + """ + Link between Experiment and Method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between Experiment and Equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between Experiment and AnalysisType. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between Experiment and PreparedSample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py new file mode 100644 index 00000000..c34d8d9a --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py @@ -0,0 +1,1224 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ExperimentEquipment(Base): + """ + Link between experiment and equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between experiment and analysis type. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between experiment and prepared sample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between experiment and method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon definition. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Dataset(Base): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(DateTime()) + end_date = Column(DateTime()) + description = Column(Text()) + + + def __repr__(self): + return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" + + + + + + +class Observation(Base): + """ + Observation data. + """ + __tablename__ = 'Observation' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" + + + + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Strain(LookupBase): + """ + Strain of organism. + """ + __tablename__ = 'Strain' + + parent_strain_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample prepared for analysis. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension (e.g. timepoint, wavelength). + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py new file mode 100644 index 00000000..16cf80f9 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py @@ -0,0 +1,1527 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Polygon(Base): + """ + Geospatial polygon. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class UsdaDomain(LookupBase): + """ + USDA domain. + """ + __tablename__ = 'UsdaDomain' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaDomain(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaStatisticCategory(LookupBase): + """ + USDA statistic category. + """ + __tablename__ = 'UsdaStatisticCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaStatisticCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyProgram(LookupBase): + """ + USDA survey program. + """ + __tablename__ = 'UsdaSurveyProgram' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaSurveyProgram(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCommodity(LookupBase): + """ + USDA commodity. + """ + __tablename__ = 'UsdaCommodity' + + usda_source = Column(Text()) + usda_code = Column(Text()) + parent_commodity_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaTermMap(BaseEntity): + """ + Mapping of raw terms to USDA commodities. + """ + __tablename__ = 'UsdaTermMap' + + source_system = Column(Text()) + source_context = Column(Text()) + raw_term = Column(Text()) + usda_commodity_id = Column(Integer()) + is_verified = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceUsdaCommodityMap(BaseEntity): + """ + Mapping between resources/crops and USDA commodities. + """ + __tablename__ = 'ResourceUsdaCommodityMap' + + resource_id = Column(Integer()) + primary_crop_id = Column(Integer()) + usda_commodity_id = Column(Integer()) + match_tier = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCensusRecord(BaseEntity): + """ + USDA census record. + """ + __tablename__ = 'UsdaCensusRecord' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + source_reference = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyRecord(BaseEntity): + """ + USDA survey record. + """ + __tablename__ = 'UsdaSurveyRecord' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + survey_program_id = Column(Integer()) + survey_period = Column(Text()) + reference_month = Column(Text()) + seasonal_flag = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketReport(BaseEntity): + """ + USDA market report. + """ + __tablename__ = 'UsdaMarketReport' + + slug_id = Column(Integer()) + slug_name = Column(Text()) + report_series_title = Column(Text()) + frequency = Column(Text()) + office_name = Column(Text()) + office_city_id = Column(Integer()) + office_state_fips = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketReport(slug_id={self.slug_id},slug_name={self.slug_name},report_series_title={self.report_series_title},frequency={self.frequency},office_name={self.office_name},office_city_id={self.office_city_id},office_state_fips={self.office_state_fips},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketRecord(BaseEntity): + """ + USDA market record. + """ + __tablename__ = 'UsdaMarketRecord' + + report_id = Column(Integer()) + dataset_id = Column(Integer()) + report_begin_date = Column(DateTime()) + report_end_date = Column(DateTime()) + report_date = Column(DateTime()) + commodity_id = Column(Integer()) + market_type_id = Column(Integer()) + market_type_catagory = Column(Text()) + grp = Column(Text()) + market_catagory_id = Column(Integer()) + class_ = Column(Text()) + grade = Column(Text()) + variety = Column(Text()) + protein_pct = Column(Numeric()) + application = Column(Text()) + pkg = Column(Text()) + sale_type = Column(Text()) + price_unit_id = Column(Integer()) + freight = Column(Text()) + trans_mode = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_catagory={self.market_type_catagory},grp={self.grp},market_catagory_id={self.market_catagory_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LandiqRecord(BaseEntity): + """ + LandIQ record. + """ + __tablename__ = 'LandiqRecord' + + dataset_id = Column(Integer()) + polygon_id = Column(Integer()) + main_crop = Column(Integer()) + secondary_crop = Column(Integer()) + tertiary_crop = Column(Integer()) + quaternary_crop = Column(Integer()) + confidence = Column(Integer()) + irrigated = Column(Boolean()) + acres = Column(Float()) + version = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class BillionTon2023Record(BaseEntity): + """ + Billion Ton 2023 record. + """ + __tablename__ = 'BillionTon2023Record' + + subclass_id = Column(Integer()) + resource_id = Column(Integer()) + geoid = Column(Text()) + county_square_miles = Column(Float()) + model_name = Column(Text()) + scenario_name = Column(Text()) + price_offered_usd = Column(Numeric()) + production = Column(Integer()) + production_unit_id = Column(Integer()) + btu_ton = Column(Integer()) + production_energy_content = Column(Integer()) + energy_content_unit_id = Column(Integer()) + product_density_dtpersqmi = Column(Numeric()) + land_source = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BillionTon2023Record(subclass_id={self.subclass_id},resource_id={self.resource_id},geoid={self.geoid},county_square_miles={self.county_square_miles},model_name={self.model_name},scenario_name={self.scenario_name},price_offered_usd={self.price_offered_usd},production={self.production},production_unit_id={self.production_unit_id},btu_ton={self.btu_ton},production_energy_content={self.production_energy_content},energy_content_unit_id={self.energy_content_unit_id},product_density_dtpersqmi={self.product_density_dtpersqmi},land_source={self.land_source},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py index e69de29b..f941eeae 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py @@ -0,0 +1,1000 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py new file mode 100644 index 00000000..bffb89f8 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py @@ -0,0 +1,1118 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py new file mode 100644 index 00000000..acb4d3c4 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py @@ -0,0 +1,125 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon definition. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py new file mode 100644 index 00000000..76adbad5 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py @@ -0,0 +1,1595 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class InfrastructureBiodieselPlants(Base): + """ + Biodiesel plants infrastructure. + """ + __tablename__ = 'InfrastructureBiodieselPlants' + + biodiesel_plant_id = Column(Integer(), primary_key=True, nullable=False ) + company = Column(Text()) + bbi_index = Column(Integer()) + city = Column(Text()) + state = Column(Text()) + capacity_mmg_per_y = Column(Integer()) + feedstock = Column(Text()) + status = Column(Text()) + address = Column(Text()) + coordinates = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + source = Column(Text()) + + + def __repr__(self): + return f"InfrastructureBiodieselPlants(biodiesel_plant_id={self.biodiesel_plant_id},company={self.company},bbi_index={self.bbi_index},city={self.city},state={self.state},capacity_mmg_per_y={self.capacity_mmg_per_y},feedstock={self.feedstock},status={self.status},address={self.address},coordinates={self.coordinates},latitude={self.latitude},longitude={self.longitude},source={self.source},)" + + + + + + +class InfrastructureBiosolidsFacilities(Base): + """ + Biosolids facilities infrastructure. + """ + __tablename__ = 'InfrastructureBiosolidsFacilities' + + biosolid_facility_id = Column(Integer(), primary_key=True, nullable=False ) + report_submitted_date = Column(Date()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + facility = Column(Text()) + authority = Column(Text()) + plant_type = Column(Text()) + aqmd = Column(Text()) + facility_address = Column(Text()) + facility_city = Column(Text()) + state = Column(Text()) + facility_zip = Column(Text()) + facility_county = Column(Text()) + mailing_street_1 = Column(Text()) + mailing_city = Column(Text()) + mailing_state = Column(Text()) + mailing_zip = Column(Text()) + biosolids_number = Column(Text()) + biosolids_contact = Column(Text()) + biosolids_contact_phone = Column(Text()) + biosolids_contact_email = Column(Text()) + adwf = Column(Numeric()) + potw_biosolids_generated = Column(Integer()) + twtds_biosolids_treated = Column(Integer()) + class_b_land_app = Column(Integer()) + class_b_applier = Column(Text()) + class_a_compost = Column(Integer()) + class_a_heat_dried = Column(Integer()) + class_a_other = Column(Integer()) + class_a_other_applier = Column(Text()) + twtds_transfer_to_second_preparer = Column(Integer()) + twtds_second_preparer_name = Column(Text()) + adc_or_final_c = Column(Integer()) + landfill = Column(Integer()) + landfill_name = Column(Text()) + surface_disposal = Column(Integer()) + deepwell_injection = Column(Text()) + stored = Column(Integer()) + longterm_treatment = Column(Integer()) + other = Column(Integer()) + name_of_other = Column(Text()) + incineration = Column(Integer()) + + + def __repr__(self): + return f"InfrastructureBiosolidsFacilities(biosolid_facility_id={self.biosolid_facility_id},report_submitted_date={self.report_submitted_date},latitude={self.latitude},longitude={self.longitude},facility={self.facility},authority={self.authority},plant_type={self.plant_type},aqmd={self.aqmd},facility_address={self.facility_address},facility_city={self.facility_city},state={self.state},facility_zip={self.facility_zip},facility_county={self.facility_county},mailing_street_1={self.mailing_street_1},mailing_city={self.mailing_city},mailing_state={self.mailing_state},mailing_zip={self.mailing_zip},biosolids_number={self.biosolids_number},biosolids_contact={self.biosolids_contact},biosolids_contact_phone={self.biosolids_contact_phone},biosolids_contact_email={self.biosolids_contact_email},adwf={self.adwf},potw_biosolids_generated={self.potw_biosolids_generated},twtds_biosolids_treated={self.twtds_biosolids_treated},class_b_land_app={self.class_b_land_app},class_b_applier={self.class_b_applier},class_a_compost={self.class_a_compost},class_a_heat_dried={self.class_a_heat_dried},class_a_other={self.class_a_other},class_a_other_applier={self.class_a_other_applier},twtds_transfer_to_second_preparer={self.twtds_transfer_to_second_preparer},twtds_second_preparer_name={self.twtds_second_preparer_name},adc_or_final_c={self.adc_or_final_c},landfill={self.landfill},landfill_name={self.landfill_name},surface_disposal={self.surface_disposal},deepwell_injection={self.deepwell_injection},stored={self.stored},longterm_treatment={self.longterm_treatment},other={self.other},name_of_other={self.name_of_other},incineration={self.incineration},)" + + + + + + +class InfrastructureCafoManureLocations(Base): + """ + CAFO manure locations infrastructure. + """ + __tablename__ = 'InfrastructureCafoManureLocations' + + cafo_manure_id = Column(Integer(), primary_key=True, nullable=False ) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + owner_name = Column(Text()) + facility_name = Column(Text()) + address = Column(Text()) + town = Column(Text()) + state = Column(Text()) + zip = Column(Text()) + animal = Column(Text()) + animal_feed_operation_type = Column(Text()) + animal_units = Column(Integer()) + animal_count = Column(Integer()) + manure_total_solids = Column(Numeric()) + source = Column(Text()) + date_accessed = Column(Date()) + + + def __repr__(self): + return f"InfrastructureCafoManureLocations(cafo_manure_id={self.cafo_manure_id},latitude={self.latitude},longitude={self.longitude},owner_name={self.owner_name},facility_name={self.facility_name},address={self.address},town={self.town},state={self.state},zip={self.zip},animal={self.animal},animal_feed_operation_type={self.animal_feed_operation_type},animal_units={self.animal_units},animal_count={self.animal_count},manure_total_solids={self.manure_total_solids},source={self.source},date_accessed={self.date_accessed},)" + + + + + + +class InfrastructureEthanolBiorefineries(Base): + """ + Ethanol biorefineries infrastructure. + """ + __tablename__ = 'InfrastructureEthanolBiorefineries' + + ethanol_biorefinery_id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + city = Column(Text()) + state = Column(Text()) + address = Column(Text()) + type = Column(Text()) + capacity_mgy = Column(Integer()) + production_mgy = Column(Integer()) + constr_exp = Column(Integer()) + + + def __repr__(self): + return f"InfrastructureEthanolBiorefineries(ethanol_biorefinery_id={self.ethanol_biorefinery_id},name={self.name},city={self.city},state={self.state},address={self.address},type={self.type},capacity_mgy={self.capacity_mgy},production_mgy={self.production_mgy},constr_exp={self.constr_exp},)" + + + + + + +class InfrastructureLandfills(Base): + """ + Landfills infrastructure. + """ + __tablename__ = 'InfrastructureLandfills' + + project_id = Column(Text(), primary_key=True, nullable=False ) + project_int_id = Column(Integer()) + ghgrp_id = Column(Text()) + landfill_id = Column(Integer()) + landfill_name = Column(Text()) + state = Column(Text()) + physical_address = Column(Text()) + city = Column(Text()) + county = Column(Text()) + zip_code = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + ownership_type = Column(Text()) + landfill_owner_orgs = Column(Text()) + landfill_opened_year = Column(Date()) + landfill_closure_year = Column(Date()) + landfill_status = Column(Text()) + waste_in_place = Column(Integer()) + waste_in_place_year = Column(Date()) + lfg_system_in_place = Column(Boolean()) + lfg_collected = Column(Numeric()) + lfg_flared = Column(Numeric()) + project_status = Column(Text()) + project_name = Column(Text()) + project_start_date = Column(Date()) + project_shutdown_date = Column(Date()) + project_type_category = Column(Text()) + lfg_energy_project_type = Column(Text()) + rng_delivery_method = Column(Text()) + actual_mw_generation = Column(Numeric()) + rated_mw_capacity = Column(Numeric()) + lfg_flow_to_project = Column(Numeric()) + direct_emission_reductions = Column(Numeric()) + avoided_emission_reductions = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureLandfills(project_id={self.project_id},project_int_id={self.project_int_id},ghgrp_id={self.ghgrp_id},landfill_id={self.landfill_id},landfill_name={self.landfill_name},state={self.state},physical_address={self.physical_address},city={self.city},county={self.county},zip_code={self.zip_code},latitude={self.latitude},longitude={self.longitude},ownership_type={self.ownership_type},landfill_owner_orgs={self.landfill_owner_orgs},landfill_opened_year={self.landfill_opened_year},landfill_closure_year={self.landfill_closure_year},landfill_status={self.landfill_status},waste_in_place={self.waste_in_place},waste_in_place_year={self.waste_in_place_year},lfg_system_in_place={self.lfg_system_in_place},lfg_collected={self.lfg_collected},lfg_flared={self.lfg_flared},project_status={self.project_status},project_name={self.project_name},project_start_date={self.project_start_date},project_shutdown_date={self.project_shutdown_date},project_type_category={self.project_type_category},lfg_energy_project_type={self.lfg_energy_project_type},rng_delivery_method={self.rng_delivery_method},actual_mw_generation={self.actual_mw_generation},rated_mw_capacity={self.rated_mw_capacity},lfg_flow_to_project={self.lfg_flow_to_project},direct_emission_reductions={self.direct_emission_reductions},avoided_emission_reductions={self.avoided_emission_reductions},)" + + + + + + +class InfrastructureLivestockAnaerobicDigesters(Base): + """ + Livestock anaerobic digesters infrastructure. + """ + __tablename__ = 'InfrastructureLivestockAnaerobicDigesters' + + digester_id = Column(Integer(), primary_key=True, nullable=False ) + project_name = Column(Text()) + project_type = Column(Text()) + city = Column(Text()) + state = Column(Text()) + digester_type = Column(Text()) + profile = Column(Text()) + year_operational = Column(Date()) + animal_type_class = Column(Text()) + animal_types = Column(Text()) + pop_feeding_digester = Column(Text()) + total_pop_feeding_digester = Column(Integer()) + cattle = Column(Integer()) + dairy = Column(Integer()) + poultry = Column(Integer()) + swine = Column(Integer()) + codigestion = Column(Text()) + biogas_generation_estimate = Column(Integer()) + electricity_generated = Column(Integer()) + biogas_end_uses = Column(Text()) + methane_emission_reductions = Column(Integer()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureLivestockAnaerobicDigesters(digester_id={self.digester_id},project_name={self.project_name},project_type={self.project_type},city={self.city},state={self.state},digester_type={self.digester_type},profile={self.profile},year_operational={self.year_operational},animal_type_class={self.animal_type_class},animal_types={self.animal_types},pop_feeding_digester={self.pop_feeding_digester},total_pop_feeding_digester={self.total_pop_feeding_digester},cattle={self.cattle},dairy={self.dairy},poultry={self.poultry},swine={self.swine},codigestion={self.codigestion},biogas_generation_estimate={self.biogas_generation_estimate},electricity_generated={self.electricity_generated},biogas_end_uses={self.biogas_end_uses},methane_emission_reductions={self.methane_emission_reductions},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureSafAndRenewableDieselPlants(Base): + """ + SAF and renewable diesel plants infrastructure. + """ + __tablename__ = 'InfrastructureSafAndRenewableDieselPlants' + + ibcc_index = Column(Integer(), primary_key=True, nullable=False ) + company = Column(Text()) + city = Column(Text()) + state = Column(Text()) + country = Column(Text()) + capacity = Column(Text()) + feedstock = Column(Text()) + products = Column(Text()) + status = Column(Text()) + address = Column(Text()) + coordinates = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureSafAndRenewableDieselPlants(ibcc_index={self.ibcc_index},company={self.company},city={self.city},state={self.state},country={self.country},capacity={self.capacity},feedstock={self.feedstock},products={self.products},status={self.status},address={self.address},coordinates={self.coordinates},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureWastewaterTreatmentPlants(Base): + """ + Wastewater treatment plants infrastructure. + """ + __tablename__ = 'InfrastructureWastewaterTreatmentPlants' + + plant_id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + state = Column(Text()) + codigestion = Column(Text()) + flow_design_adjusted = Column(Numeric()) + flow_average = Column(Numeric()) + biosolids = Column(Numeric()) + excess_flow = Column(Numeric()) + biogas_utilized = Column(Boolean()) + flaring = Column(Boolean()) + excess_mass_loading_rate = Column(Numeric()) + excess_mass_loading_rate_wet = Column(Numeric()) + methane_production = Column(Numeric()) + energy_content = Column(Numeric()) + electric_kw = Column(Numeric()) + thermal_mmbtu_d = Column(Numeric()) + electric_kwh = Column(Numeric()) + thermal_annual_mmbtu_y = Column(Numeric()) + anaerobic_digestion_facility = Column(Text()) + county = Column(Text()) + dayload_bdt = Column(Numeric()) + dayload = Column(Numeric()) + equivalent_generation = Column(Numeric()) + facility_type = Column(Text()) + feedstock = Column(Text()) + type = Column(Text()) + city = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + zipcode = Column(Text()) + + + def __repr__(self): + return f"InfrastructureWastewaterTreatmentPlants(plant_id={self.plant_id},name={self.name},state={self.state},codigestion={self.codigestion},flow_design_adjusted={self.flow_design_adjusted},flow_average={self.flow_average},biosolids={self.biosolids},excess_flow={self.excess_flow},biogas_utilized={self.biogas_utilized},flaring={self.flaring},excess_mass_loading_rate={self.excess_mass_loading_rate},excess_mass_loading_rate_wet={self.excess_mass_loading_rate_wet},methane_production={self.methane_production},energy_content={self.energy_content},electric_kw={self.electric_kw},thermal_mmbtu_d={self.thermal_mmbtu_d},electric_kwh={self.electric_kwh},thermal_annual_mmbtu_y={self.thermal_annual_mmbtu_y},anaerobic_digestion_facility={self.anaerobic_digestion_facility},county={self.county},dayload_bdt={self.dayload_bdt},dayload={self.dayload},equivalent_generation={self.equivalent_generation},facility_type={self.facility_type},feedstock={self.feedstock},type={self.type},city={self.city},latitude={self.latitude},longitude={self.longitude},zipcode={self.zipcode},)" + + + + + + +class InfrastructureCombustionPlants(Base): + """ + Combustion plants infrastructure. + """ + __tablename__ = 'InfrastructureCombustionPlants' + + combustion_fid = Column(Integer(), primary_key=True, nullable=False ) + objectid = Column(Integer()) + status = Column(Text()) + city = Column(Text()) + name = Column(Text()) + county = Column(Text()) + equivalent_generation = Column(Numeric()) + np_mw = Column(Numeric()) + cf = Column(Numeric()) + yearload = Column(Integer()) + fuel = Column(Text()) + notes = Column(Text()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureCombustionPlants(combustion_fid={self.combustion_fid},objectid={self.objectid},status={self.status},city={self.city},name={self.name},county={self.county},equivalent_generation={self.equivalent_generation},np_mw={self.np_mw},cf={self.cf},yearload={self.yearload},fuel={self.fuel},notes={self.notes},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureDistrictEnergySystems(Base): + """ + District energy systems infrastructure. + """ + __tablename__ = 'InfrastructureDistrictEnergySystems' + + des_fid = Column(Integer(), primary_key=True, nullable=False ) + cbg_id = Column(Integer()) + name = Column(Text()) + system = Column(Text()) + object_id = Column(Integer()) + city = Column(Text()) + state = Column(Text()) + primary_fuel = Column(Text()) + secondary_fuel = Column(Text()) + usetype = Column(Text()) + cap_st = Column(Numeric()) + cap_hw = Column(Numeric()) + cap_cw = Column(Numeric()) + chpcg_cap = Column(Numeric()) + excess_c = Column(Numeric()) + excess_h = Column(Numeric()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureDistrictEnergySystems(des_fid={self.des_fid},cbg_id={self.cbg_id},name={self.name},system={self.system},object_id={self.object_id},city={self.city},state={self.state},primary_fuel={self.primary_fuel},secondary_fuel={self.secondary_fuel},usetype={self.usetype},cap_st={self.cap_st},cap_hw={self.cap_hw},cap_cw={self.cap_cw},chpcg_cap={self.chpcg_cap},excess_c={self.excess_c},excess_h={self.excess_h},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureFoodProcessingFacilities(Base): + """ + Food processing facilities infrastructure. + """ + __tablename__ = 'InfrastructureFoodProcessingFacilities' + + processing_facility_id = Column(Integer(), primary_key=True, nullable=False ) + address = Column(Text()) + county = Column(Text()) + city = Column(Text()) + company = Column(Text()) + join_count = Column(Integer()) + master_type = Column(Text()) + state = Column(Text()) + subtype = Column(Text()) + target_fid = Column(Integer()) + processing_type = Column(Text()) + zip = Column(Text()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureFoodProcessingFacilities(processing_facility_id={self.processing_facility_id},address={self.address},county={self.county},city={self.city},company={self.company},join_count={self.join_count},master_type={self.master_type},state={self.state},subtype={self.subtype},target_fid={self.target_fid},processing_type={self.processing_type},zip={self.zip},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureMswToEnergyAnaerobicDigesters(Base): + """ + MSW to energy anaerobic digesters infrastructure. + """ + __tablename__ = 'InfrastructureMswToEnergyAnaerobicDigesters' + + wte_id = Column(Integer(), primary_key=True, nullable=False ) + city = Column(Text()) + county = Column(Text()) + equivalent_generation = Column(Numeric()) + feedstock = Column(Text()) + dayload = Column(Numeric()) + dayload_bdt = Column(Numeric()) + facility_type = Column(Text()) + status = Column(Text()) + notes = Column(Text()) + source = Column(Text()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureMswToEnergyAnaerobicDigesters(wte_id={self.wte_id},city={self.city},county={self.county},equivalent_generation={self.equivalent_generation},feedstock={self.feedstock},dayload={self.dayload},dayload_bdt={self.dayload_bdt},facility_type={self.facility_type},status={self.status},notes={self.notes},source={self.source},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class FacilityRecord(BaseEntity): + """ + Facility record. + """ + __tablename__ = 'FacilityRecord' + + dataset_id = Column(Integer()) + facility_name = Column(Text()) + location_id = Column(Integer()) + capacity_mw = Column(Numeric()) + resource_id = Column(Integer()) + operator = Column(Text()) + start_year = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FacilityRecord(dataset_id={self.dataset_id},facility_name={self.facility_name},location_id={self.location_id},capacity_mw={self.capacity_mw},resource_id={self.resource_id},operator={self.operator},start_year={self.start_year},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py new file mode 100644 index 00000000..56bbfa6d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py @@ -0,0 +1,109 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class LineageGroup(Base): + """ + Grouping for lineage information. + """ + __tablename__ = 'LineageGroup' + + id = Column(Integer(), primary_key=True, nullable=False ) + etl_run_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"LineageGroup(id={self.id},etl_run_id={self.etl_run_id},note={self.note},)" + + + + + + +class EntityLineage(Base): + """ + Lineage information for a specific entity. + """ + __tablename__ = 'EntityLineage' + + id = Column(Integer(), primary_key=True, nullable=False ) + lineage_group_id = Column(Integer()) + source_table = Column(Text()) + source_row_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" + + + + + + +class EtlRun(Base): + """ + Information about an ETL run. + """ + __tablename__ = 'EtlRun' + + id = Column(Integer(), primary_key=True, nullable=False ) + started_at = Column(DateTime()) + completed_at = Column(DateTime()) + pipeline_name = Column(Text()) + status = Column(Text()) + records_ingested = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py new file mode 100644 index 00000000..7aceee05 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py @@ -0,0 +1,275 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py new file mode 100644 index 00000000..3b0c7511 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py @@ -0,0 +1,1000 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py new file mode 100644 index 00000000..c5825f29 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py @@ -0,0 +1,44 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py new file mode 100644 index 00000000..f721c286 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py @@ -0,0 +1,106 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py new file mode 100644 index 00000000..9350f964 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py @@ -0,0 +1,307 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py new file mode 100644 index 00000000..cb16a4a0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py @@ -0,0 +1,326 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon definition. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py new file mode 100644 index 00000000..9f3eb1e5 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py @@ -0,0 +1,1089 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py new file mode 100644 index 00000000..d37b7688 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py @@ -0,0 +1,964 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon definition. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample prepared for analysis. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } From cecc4d930c4db68c7802f67934d9c6afa3e081af Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Mon, 8 Dec 2025 13:02:38 -0700 Subject: [PATCH 21/81] feat: generated sqlA now is being read by Alembic and schema was successfully migrated --- alembic/env.py | 26 +- .../301006b4795f_initial_migration.py | 32 - .../e22149be0d9c_initial_migration.py | 1111 +++++++++++++++++ 3 files changed, 1125 insertions(+), 44 deletions(-) delete mode 100644 alembic/versions/301006b4795f_initial_migration.py create mode 100644 alembic/versions/e22149be0d9c_initial_migration.py diff --git a/alembic/env.py b/alembic/env.py index cd3a09ea..068e73bb 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -13,17 +13,18 @@ load_dotenv(dotenv_path=PROJECT_ROOT / ".env") # Looks for .env in the project root by default # --- Import your models so Alembic knows about them --- -from ca_biositing.datamodels.biomass import * -from ca_biositing.datamodels.data_and_references import * -from ca_biositing.datamodels.experiments_analysis import * -from ca_biositing.datamodels.external_datasets import * -from ca_biositing.datamodels.geographic_locations import * -from ca_biositing.datamodels.metadata_samples import * -from ca_biositing.datamodels.organizations import * -from ca_biositing.datamodels.people_contacts import * -from ca_biositing.datamodels.sample_preprocessing import * -from ca_biositing.datamodels.specific_aalysis_results import * -from ca_biositing.datamodels.user import * +# from ca_biositing.datamodels.biomass import * +# from ca_biositing.datamodels.data_and_references import * +# from ca_biositing.datamodels.experiments_analysis import * +# from ca_biositing.datamodels.external_datasets import * +# from ca_biositing.datamodels.geographic_locations import * +# from ca_biositing.datamodels.metadata_samples import * +# from ca_biositing.datamodels.organizations import * +# from ca_biositing.datamodels.people_contacts import * +# from ca_biositing.datamodels.sample_preprocessing import * +# from ca_biositing.datamodels.specific_aalysis_results import * +# from ca_biositing.datamodels.user import * +from ca_biositing.datamodels.schemas.generated.ca_biositing import * from sqlmodel import SQLModel import importlib.util from pathlib import Path @@ -51,7 +52,8 @@ # See: https://alembic.sqlalchemy.org/en/latest/autogenerate.html#affecting-the-autogenerate-process # Start with the default SQLModel metadata -target_metadata = SQLModel.metadata +# target_metadata = SQLModel.metadata +target_metadata = Base.metadata # Manually merge metadata from generated modules # for table in census_metadata.tables.values(): diff --git a/alembic/versions/301006b4795f_initial_migration.py b/alembic/versions/301006b4795f_initial_migration.py deleted file mode 100644 index 8e4f7afd..00000000 --- a/alembic/versions/301006b4795f_initial_migration.py +++ /dev/null @@ -1,32 +0,0 @@ -"""Initial migration - -Revision ID: 301006b4795f -Revises: e15bda744fef -Create Date: 2025-11-12 20:54:01.573577 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '301006b4795f' -down_revision: Union[str, Sequence[str], None] = 'e15bda744fef' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### diff --git a/alembic/versions/e22149be0d9c_initial_migration.py b/alembic/versions/e22149be0d9c_initial_migration.py new file mode 100644 index 00000000..574739e6 --- /dev/null +++ b/alembic/versions/e22149be0d9c_initial_migration.py @@ -0,0 +1,1111 @@ +"""Initial migration + +Revision ID: e22149be0d9c +Revises: +Create Date: 2025-12-08 18:01:48.554213 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'e22149be0d9c' +down_revision: Union[str, Sequence[str], None] = None +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('AgTreatment', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Aim1RecordBase', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Aim2RecordBase', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('AnalysisType', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('AutoclaveRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('BaseEntity', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('BillionTon2023Record', + sa.Column('subclass_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('county_square_miles', sa.Float(), nullable=True), + sa.Column('model_name', sa.Text(), nullable=True), + sa.Column('scenario_name', sa.Text(), nullable=True), + sa.Column('price_offered_usd', sa.Numeric(), nullable=True), + sa.Column('production', sa.Integer(), nullable=True), + sa.Column('production_unit_id', sa.Integer(), nullable=True), + sa.Column('btu_ton', sa.Integer(), nullable=True), + sa.Column('production_energy_content', sa.Integer(), nullable=True), + sa.Column('energy_content_unit_id', sa.Integer(), nullable=True), + sa.Column('product_density_dtpersqmi', sa.Numeric(), nullable=True), + sa.Column('land_source', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('CalorimetryRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('CollectionMethod', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('CompositionalRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Contact', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('first_name', sa.Text(), nullable=True), + sa.Column('last_name', sa.Text(), nullable=True), + sa.Column('email', sa.Text(), nullable=True), + sa.Column('affiliation', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('DataSource', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.Column('publication_date', sa.Date(), nullable=True), + sa.Column('version', sa.Text(), nullable=True), + sa.Column('publisher', sa.Text(), nullable=True), + sa.Column('author', sa.Text(), nullable=True), + sa.Column('license', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('DataSourceType', + sa.Column('source_type_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Dataset', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('record_type', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('start_date', sa.Date(), nullable=True), + sa.Column('end_date', sa.Date(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('DimensionType', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('EntityLineage', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.Column('source_table', sa.Text(), nullable=True), + sa.Column('source_row_id', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Equipment', + sa.Column('equipment_location_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('EtlRun', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('started_at', sa.DateTime(), nullable=True), + sa.Column('completed_at', sa.DateTime(), nullable=True), + sa.Column('pipeline_name', sa.Text(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('records_ingested', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Experiment', + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('exper_start_date', sa.Date(), nullable=True), + sa.Column('exper_duration', sa.Numeric(), nullable=True), + sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('exper_location_id', sa.Integer(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ExperimentAnalysis', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ExperimentEquipment', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('equipment_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ExperimentMethod', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ExperimentPreparedSample', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('prepared_sample_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FermentationRecord', + sa.Column('strain_id', sa.Integer(), nullable=True), + sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), + sa.Column('eh_method_id', sa.Integer(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('well_position', sa.Text(), nullable=True), + sa.Column('temperature', sa.Numeric(), nullable=True), + sa.Column('agitation_rpm', sa.Numeric(), nullable=True), + sa.Column('vessel_id', sa.Integer(), nullable=True), + sa.Column('analyte_detection_equipment_id', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FieldSample', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('provider_id', sa.Integer(), nullable=True), + sa.Column('collector_id', sa.Integer(), nullable=True), + sa.Column('sample_collection_source', sa.Text(), nullable=True), + sa.Column('amount_collected', sa.Numeric(), nullable=True), + sa.Column('amount_collected_unit_id', sa.Integer(), nullable=True), + sa.Column('sampling_location_id', sa.Integer(), nullable=True), + sa.Column('field_storage_method_id', sa.Integer(), nullable=True), + sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), + sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('field_storage_location_id', sa.Integer(), nullable=True), + sa.Column('collection_timestamp', sa.DateTime(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_date', sa.Date(), nullable=True), + sa.Column('field_sample_storage_location_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FieldSampleCondition', + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('ag_treatment_id', sa.Integer(), nullable=True), + sa.Column('last_application_date', sa.Date(), nullable=True), + sa.Column('treatment_amount_per_acre', sa.Float(), nullable=True), + sa.Column('processing_method_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FieldStorageMethod', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FileObjectMetadata', + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('bucket_path', sa.Text(), nullable=True), + sa.Column('file_format', sa.Text(), nullable=True), + sa.Column('file_size', sa.Integer(), nullable=True), + sa.Column('checksum_md5', sa.Text(), nullable=True), + sa.Column('checksum_sha256', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FtnirRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('GasificationRecord', + sa.Column('feedstock_mass', sa.Numeric(), nullable=True), + sa.Column('bed_temperature', sa.Numeric(), nullable=True), + sa.Column('gas_flow_rate', sa.Numeric(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Geography', + sa.Column('geoid', sa.Text(), nullable=False), + sa.Column('state_name', sa.Text(), nullable=True), + sa.Column('state_fips', sa.Text(), nullable=True), + sa.Column('county_name', sa.Text(), nullable=True), + sa.Column('county_fips', sa.Text(), nullable=True), + sa.Column('region_name', sa.Text(), nullable=True), + sa.Column('agg_level_desc', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('geoid') + ) + op.create_table('HarvestMethod', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('IcpRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LandiqRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('polygon_id', sa.Integer(), nullable=True), + sa.Column('main_crop', sa.Integer(), nullable=True), + sa.Column('secondary_crop', sa.Integer(), nullable=True), + sa.Column('tertiary_crop', sa.Integer(), nullable=True), + sa.Column('quaternary_crop', sa.Integer(), nullable=True), + sa.Column('confidence', sa.Integer(), nullable=True), + sa.Column('irrigated', sa.Boolean(), nullable=True), + sa.Column('acres', sa.Float(), nullable=True), + sa.Column('version', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LineageGroup', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LocationAddress', + sa.Column('geography_id', sa.Text(), nullable=True), + sa.Column('address_line1', sa.Text(), nullable=True), + sa.Column('address_line2', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('zip', sa.Text(), nullable=True), + sa.Column('lat', sa.Float(), nullable=True), + sa.Column('lon', sa.Float(), nullable=True), + sa.Column('is_anonymous', sa.Boolean(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LocationResolution', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LocationSoilType', + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('soil_type_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LookupBase', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Method', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('method_category_id', sa.Integer(), nullable=True), + sa.Column('method_standard_id', sa.Integer(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('detection_limits', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('MethodAbbrev', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('MethodCategory', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('MethodStandard', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Observation', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('record_type', sa.Text(), nullable=True), + sa.Column('record_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('dimension_type_id', sa.Integer(), nullable=True), + sa.Column('dimension_value', sa.Numeric(), nullable=True), + sa.Column('dimension_unit_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Parameter', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('standard_unit_id', sa.Integer(), nullable=True), + sa.Column('calculated', sa.Boolean(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ParameterCategory', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ParameterCategoryParameter', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_category_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ParameterUnit', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('alternate_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PhysicalCharacteristic', + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('particle_length', sa.Numeric(), nullable=True), + sa.Column('particle_width', sa.Numeric(), nullable=True), + sa.Column('particle_height', sa.Numeric(), nullable=True), + sa.Column('particle_unit_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Polygon', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PreparationMethod', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('prep_method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('prep_temp_c', sa.Numeric(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.Column('drying_step', sa.Boolean(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PreparationMethodAbbreviation', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PreparedSample', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('prep_method_id', sa.Integer(), nullable=True), + sa.Column('prep_date', sa.Date(), nullable=True), + sa.Column('preparer_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PretreatmentRecord', + sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), + sa.Column('eh_method_id', sa.Integer(), nullable=True), + sa.Column('reaction_block_id', sa.Integer(), nullable=True), + sa.Column('block_position', sa.Text(), nullable=True), + sa.Column('temperature', sa.Numeric(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PrimaryCrop', + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ProcessingMethod', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Provider', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('codename', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ProximateRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Resource', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('primary_crop_id', sa.Integer(), nullable=True), + sa.Column('resource_class_id', sa.Integer(), nullable=True), + sa.Column('resource_subclass_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceAvailability', + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('from_month', sa.Integer(), nullable=True), + sa.Column('to_month', sa.Integer(), nullable=True), + sa.Column('year_round', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceClass', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceCounterfactual', + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('counterfactual_description', sa.Text(), nullable=True), + sa.Column('animal_bedding_percent', sa.Numeric(), nullable=True), + sa.Column('animal_bedding_source_id', sa.Integer(), nullable=True), + sa.Column('animal_feed_percent', sa.Numeric(), nullable=True), + sa.Column('animal_feed_source_id', sa.Integer(), nullable=True), + sa.Column('bioelectricty_percent', sa.Numeric(), nullable=True), + sa.Column('bioelectricty_source_id', sa.Integer(), nullable=True), + sa.Column('burn_percent', sa.Numeric(), nullable=True), + sa.Column('burn_source_id', sa.Integer(), nullable=True), + sa.Column('compost_percent', sa.Numeric(), nullable=True), + sa.Column('compost_source_id', sa.Integer(), nullable=True), + sa.Column('landfill_percent', sa.Numeric(), nullable=True), + sa.Column('landfill_source_id', sa.Integer(), nullable=True), + sa.Column('counterfactual_date', sa.Date(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceMorphology', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('morphology_uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceSubclass', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceUsdaCommodityMap', + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('primary_crop_id', sa.Integer(), nullable=True), + sa.Column('usda_commodity_id', sa.Integer(), nullable=True), + sa.Column('match_tier', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('RgbRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('SoilType', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('SourceType', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Strain', + sa.Column('parent_strain_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UltimateRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Unit', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaCensusRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('commodity_code', sa.Integer(), nullable=True), + sa.Column('year', sa.Integer(), nullable=True), + sa.Column('source_reference', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaCommodity', + sa.Column('usda_source', sa.Text(), nullable=True), + sa.Column('usda_code', sa.Text(), nullable=True), + sa.Column('parent_commodity_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaDomain', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaMarketRecord', + sa.Column('report_id', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('report_begin_date', sa.DateTime(), nullable=True), + sa.Column('report_end_date', sa.DateTime(), nullable=True), + sa.Column('report_date', sa.DateTime(), nullable=True), + sa.Column('commodity_id', sa.Integer(), nullable=True), + sa.Column('market_type_id', sa.Integer(), nullable=True), + sa.Column('market_type_catagory', sa.Text(), nullable=True), + sa.Column('grp', sa.Text(), nullable=True), + sa.Column('market_catagory_id', sa.Integer(), nullable=True), + sa.Column('class_', sa.Text(), nullable=True), + sa.Column('grade', sa.Text(), nullable=True), + sa.Column('variety', sa.Text(), nullable=True), + sa.Column('protein_pct', sa.Numeric(), nullable=True), + sa.Column('application', sa.Text(), nullable=True), + sa.Column('pkg', sa.Text(), nullable=True), + sa.Column('sale_type', sa.Text(), nullable=True), + sa.Column('price_unit_id', sa.Integer(), nullable=True), + sa.Column('freight', sa.Text(), nullable=True), + sa.Column('trans_mode', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaMarketReport', + sa.Column('slug_id', sa.Integer(), nullable=True), + sa.Column('slug_name', sa.Text(), nullable=True), + sa.Column('report_series_title', sa.Text(), nullable=True), + sa.Column('frequency', sa.Text(), nullable=True), + sa.Column('office_name', sa.Text(), nullable=True), + sa.Column('office_city_id', sa.Integer(), nullable=True), + sa.Column('office_state_fips', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaStatisticCategory', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaSurveyProgram', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaSurveyRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('commodity_code', sa.Integer(), nullable=True), + sa.Column('year', sa.Integer(), nullable=True), + sa.Column('survey_program_id', sa.Integer(), nullable=True), + sa.Column('survey_period', sa.Text(), nullable=True), + sa.Column('reference_month', sa.Text(), nullable=True), + sa.Column('seasonal_flag', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaTermMap', + sa.Column('source_system', sa.Text(), nullable=True), + sa.Column('source_context', sa.Text(), nullable=True), + sa.Column('raw_term', sa.Text(), nullable=True), + sa.Column('usda_commodity_id', sa.Integer(), nullable=True), + sa.Column('is_verified', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('XrdRecord', + sa.Column('maybe_scan_low_nm', sa.Integer(), nullable=True), + sa.Column('maybe_scan_high_nm', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('XrfRecord', + sa.Column('maybe_wavelength_nm', sa.Numeric(), nullable=True), + sa.Column('maybe_intensity', sa.Numeric(), nullable=True), + sa.Column('maybe_energy_slope', sa.Numeric(), nullable=True), + sa.Column('maybe_energy_offset', sa.Numeric(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('XrfRecord') + op.drop_table('XrdRecord') + op.drop_table('UsdaTermMap') + op.drop_table('UsdaSurveyRecord') + op.drop_table('UsdaSurveyProgram') + op.drop_table('UsdaStatisticCategory') + op.drop_table('UsdaMarketReport') + op.drop_table('UsdaMarketRecord') + op.drop_table('UsdaDomain') + op.drop_table('UsdaCommodity') + op.drop_table('UsdaCensusRecord') + op.drop_table('Unit') + op.drop_table('UltimateRecord') + op.drop_table('Strain') + op.drop_table('SourceType') + op.drop_table('SoilType') + op.drop_table('RgbRecord') + op.drop_table('ResourceUsdaCommodityMap') + op.drop_table('ResourceSubclass') + op.drop_table('ResourceMorphology') + op.drop_table('ResourceCounterfactual') + op.drop_table('ResourceClass') + op.drop_table('ResourceAvailability') + op.drop_table('Resource') + op.drop_table('ProximateRecord') + op.drop_table('Provider') + op.drop_table('ProcessingMethod') + op.drop_table('PrimaryCrop') + op.drop_table('PretreatmentRecord') + op.drop_table('PreparedSample') + op.drop_table('PreparationMethodAbbreviation') + op.drop_table('PreparationMethod') + op.drop_table('Polygon') + op.drop_table('PhysicalCharacteristic') + op.drop_table('ParameterUnit') + op.drop_table('ParameterCategoryParameter') + op.drop_table('ParameterCategory') + op.drop_table('Parameter') + op.drop_table('Observation') + op.drop_table('MethodStandard') + op.drop_table('MethodCategory') + op.drop_table('MethodAbbrev') + op.drop_table('Method') + op.drop_table('LookupBase') + op.drop_table('LocationSoilType') + op.drop_table('LocationResolution') + op.drop_table('LocationAddress') + op.drop_table('LineageGroup') + op.drop_table('LandiqRecord') + op.drop_table('IcpRecord') + op.drop_table('HarvestMethod') + op.drop_table('Geography') + op.drop_table('GasificationRecord') + op.drop_table('FtnirRecord') + op.drop_table('FileObjectMetadata') + op.drop_table('FieldStorageMethod') + op.drop_table('FieldSampleCondition') + op.drop_table('FieldSample') + op.drop_table('FermentationRecord') + op.drop_table('ExperimentPreparedSample') + op.drop_table('ExperimentMethod') + op.drop_table('ExperimentEquipment') + op.drop_table('ExperimentAnalysis') + op.drop_table('Experiment') + op.drop_table('EtlRun') + op.drop_table('Equipment') + op.drop_table('EntityLineage') + op.drop_table('DimensionType') + op.drop_table('Dataset') + op.drop_table('DataSourceType') + op.drop_table('DataSource') + op.drop_table('Contact') + op.drop_table('CompositionalRecord') + op.drop_table('CollectionMethod') + op.drop_table('CalorimetryRecord') + op.drop_table('BillionTon2023Record') + op.drop_table('BaseEntity') + op.drop_table('AutoclaveRecord') + op.drop_table('AnalysisType') + op.drop_table('Aim2RecordBase') + op.drop_table('Aim1RecordBase') + op.drop_table('AgTreatment') + # ### end Alembic commands ### From 7987cdabf4c7b0cce714f82c6b5bc9ff3bf2a53e Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Mon, 8 Dec 2025 15:45:01 -0700 Subject: [PATCH 22/81] feat: sqla to alembic complete. new pixi task. docs updated. --- README.md | 14 +- ...2618fe6b09b_rename_tables_to_snake_case.py | 2192 +++++++++++++++++ ...8c837616b_adding_a_test_to_landiqrecord.py | 32 + pixi.toml | 2 + src/ca_biositing/datamodels/README.md | 175 +- .../linkml/modules/external_data.yaml | 5 + .../schemas/generated/aim1_records.py | 120 +- .../schemas/generated/aim2_records.py | 112 +- .../datamodels/schemas/generated/analysis.py | 30 +- .../schemas/generated/analysis_records.py | 122 +- .../schemas/generated/ca_biositing.py | 167 +- .../datamodels/schemas/generated/core.py | 4 +- .../generated/data_sources_metadata.py | 74 +- .../schemas/generated/experiment_equipment.py | 100 +- .../schemas/generated/experiments.py | 94 +- .../schemas/generated/external_data.py | 111 +- .../schemas/generated/field_sampling.py | 74 +- .../schemas/generated/general_analysis.py | 82 +- .../datamodels/schemas/generated/geography.py | 10 +- .../schemas/generated/infrastructure.py | 108 +- .../datamodels/schemas/generated/lineage.py | 10 +- .../datamodels/schemas/generated/methods.py | 22 +- .../generated/methods_parameters_units.py | 74 +- .../datamodels/schemas/generated/people.py | 4 +- .../datamodels/schemas/generated/places.py | 8 +- .../schemas/generated/resource_information.py | 22 +- .../datamodels/schemas/generated/resources.py | 24 +- .../schemas/generated/sample_preparation.py | 80 +- .../datamodels/schemas/generated/sampling.py | 72 +- .../datamodels/{ => utils}/generate_sqla.py | 39 +- .../utils/orchestrate_schema_update.py | 58 + 31 files changed, 3205 insertions(+), 836 deletions(-) create mode 100644 alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py create mode 100644 alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py rename src/ca_biositing/datamodels/{ => utils}/generate_sqla.py (54%) create mode 100644 src/ca_biositing/datamodels/utils/orchestrate_schema_update.py diff --git a/README.md b/README.md index 114d504c..3eacc3b9 100644 --- a/README.md +++ b/README.md @@ -10,8 +10,8 @@ data access. This project uses a **PEP 420 namespace package** structure with three main components: -- **`ca_biositing.datamodels`**: Shared SQLModel database models and database - configuration +- **`ca_biositing.datamodels`**: Shared LinkML/SQLModel database models and + database configuration - **`ca_biositing.pipeline`**: ETL pipelines orchestrated with Prefect, deployed via Docker - **`ca_biositing.webservice`**: FastAPI REST API for data access @@ -152,6 +152,7 @@ Key tasks: - **Development**: `test`, `test-cov`, `pre-commit`, `pre-commit-all` - **Applications**: `start-webservice`, `qgis` - **Database**: `access-db`, `check-db-health` +- **Datamodels**: `update-schema`, `migrate` ## Architecture @@ -181,6 +182,15 @@ Pipeline architecture: ### Database Models +We use a **LinkML-first approach** for defining our data schema. The workflow +is: + +1. **LinkML Schema**: The schema is defined in YAML files (source of truth). +2. **SQLAlchemy Generation**: Python classes are automatically generated from + LinkML. +3. **Alembic Migrations**: Database migrations are generated from the Python + classes. + SQLModel-based models provide: - Type-safe database operations diff --git a/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py b/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py new file mode 100644 index 00000000..22464c6b --- /dev/null +++ b/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py @@ -0,0 +1,2192 @@ +"""rename_tables_to_snake_case + +Revision ID: 42618fe6b09b +Revises: e22149be0d9c +Create Date: 2025-12-08 21:37:30.253589 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa +from sqlalchemy.dialects import postgresql + +# revision identifiers, used by Alembic. +revision: str = '42618fe6b09b' +down_revision: Union[str, Sequence[str], None] = 'e22149be0d9c' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('ag_treatment', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('aim1_record_base', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('aim2_record_base', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('analysis_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('autoclave_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('base_entity', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('billion_ton2023_record', + sa.Column('subclass_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('county_square_miles', sa.Float(), nullable=True), + sa.Column('model_name', sa.Text(), nullable=True), + sa.Column('scenario_name', sa.Text(), nullable=True), + sa.Column('price_offered_usd', sa.Numeric(), nullable=True), + sa.Column('production', sa.Integer(), nullable=True), + sa.Column('production_unit_id', sa.Integer(), nullable=True), + sa.Column('btu_ton', sa.Integer(), nullable=True), + sa.Column('production_energy_content', sa.Integer(), nullable=True), + sa.Column('energy_content_unit_id', sa.Integer(), nullable=True), + sa.Column('product_density_dtpersqmi', sa.Numeric(), nullable=True), + sa.Column('land_source', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('calorimetry_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('collection_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('compositional_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('contact', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('first_name', sa.Text(), nullable=True), + sa.Column('last_name', sa.Text(), nullable=True), + sa.Column('email', sa.Text(), nullable=True), + sa.Column('affiliation', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('data_source', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.Column('publication_date', sa.Date(), nullable=True), + sa.Column('version', sa.Text(), nullable=True), + sa.Column('publisher', sa.Text(), nullable=True), + sa.Column('author', sa.Text(), nullable=True), + sa.Column('license', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('data_source_type', + sa.Column('source_type_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('dataset', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('record_type', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('start_date', sa.Date(), nullable=True), + sa.Column('end_date', sa.Date(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('dimension_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('entity_lineage', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.Column('source_table', sa.Text(), nullable=True), + sa.Column('source_row_id', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('equipment', + sa.Column('equipment_location_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('etl_run', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('started_at', sa.DateTime(), nullable=True), + sa.Column('completed_at', sa.DateTime(), nullable=True), + sa.Column('pipeline_name', sa.Text(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('records_ingested', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment', + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('exper_start_date', sa.Date(), nullable=True), + sa.Column('exper_duration', sa.Numeric(), nullable=True), + sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('exper_location_id', sa.Integer(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_analysis', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_equipment', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('equipment_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_prepared_sample', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('prepared_sample_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('fermentation_record', + sa.Column('strain_id', sa.Integer(), nullable=True), + sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), + sa.Column('eh_method_id', sa.Integer(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('well_position', sa.Text(), nullable=True), + sa.Column('temperature', sa.Numeric(), nullable=True), + sa.Column('agitation_rpm', sa.Numeric(), nullable=True), + sa.Column('vessel_id', sa.Integer(), nullable=True), + sa.Column('analyte_detection_equipment_id', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('field_sample', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('provider_id', sa.Integer(), nullable=True), + sa.Column('collector_id', sa.Integer(), nullable=True), + sa.Column('sample_collection_source', sa.Text(), nullable=True), + sa.Column('amount_collected', sa.Numeric(), nullable=True), + sa.Column('amount_collected_unit_id', sa.Integer(), nullable=True), + sa.Column('sampling_location_id', sa.Integer(), nullable=True), + sa.Column('field_storage_method_id', sa.Integer(), nullable=True), + sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), + sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('field_storage_location_id', sa.Integer(), nullable=True), + sa.Column('collection_timestamp', sa.DateTime(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_date', sa.Date(), nullable=True), + sa.Column('field_sample_storage_location_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('field_sample_condition', + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('ag_treatment_id', sa.Integer(), nullable=True), + sa.Column('last_application_date', sa.Date(), nullable=True), + sa.Column('treatment_amount_per_acre', sa.Float(), nullable=True), + sa.Column('processing_method_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('field_storage_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('file_object_metadata', + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('bucket_path', sa.Text(), nullable=True), + sa.Column('file_format', sa.Text(), nullable=True), + sa.Column('file_size', sa.Integer(), nullable=True), + sa.Column('checksum_md5', sa.Text(), nullable=True), + sa.Column('checksum_sha256', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ftnir_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('gasification_record', + sa.Column('feedstock_mass', sa.Numeric(), nullable=True), + sa.Column('bed_temperature', sa.Numeric(), nullable=True), + sa.Column('gas_flow_rate', sa.Numeric(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('geography', + sa.Column('geoid', sa.Text(), nullable=False), + sa.Column('state_name', sa.Text(), nullable=True), + sa.Column('state_fips', sa.Text(), nullable=True), + sa.Column('county_name', sa.Text(), nullable=True), + sa.Column('county_fips', sa.Text(), nullable=True), + sa.Column('region_name', sa.Text(), nullable=True), + sa.Column('agg_level_desc', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('geoid') + ) + op.create_table('harvest_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('icp_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('landiq_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('polygon_id', sa.Integer(), nullable=True), + sa.Column('main_crop', sa.Integer(), nullable=True), + sa.Column('secondary_crop', sa.Integer(), nullable=True), + sa.Column('tertiary_crop', sa.Integer(), nullable=True), + sa.Column('quaternary_crop', sa.Integer(), nullable=True), + sa.Column('confidence', sa.Integer(), nullable=True), + sa.Column('irrigated', sa.Boolean(), nullable=True), + sa.Column('acres', sa.Float(), nullable=True), + sa.Column('version', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('lineage_group', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('location_address', + sa.Column('geography_id', sa.Text(), nullable=True), + sa.Column('address_line1', sa.Text(), nullable=True), + sa.Column('address_line2', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('zip', sa.Text(), nullable=True), + sa.Column('lat', sa.Float(), nullable=True), + sa.Column('lon', sa.Float(), nullable=True), + sa.Column('is_anonymous', sa.Boolean(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('location_resolution', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('location_soil_type', + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('soil_type_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('lookup_base', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('method_category_id', sa.Integer(), nullable=True), + sa.Column('method_standard_id', sa.Integer(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('detection_limits', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method_abbrev', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method_category', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method_standard', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('observation', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('record_type', sa.Text(), nullable=True), + sa.Column('record_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('dimension_type_id', sa.Integer(), nullable=True), + sa.Column('dimension_value', sa.Numeric(), nullable=True), + sa.Column('dimension_unit_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('standard_unit_id', sa.Integer(), nullable=True), + sa.Column('calculated', sa.Boolean(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter_category', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter_category_parameter', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_category_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter_unit', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('alternate_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('physical_characteristic', + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('particle_length', sa.Numeric(), nullable=True), + sa.Column('particle_width', sa.Numeric(), nullable=True), + sa.Column('particle_height', sa.Numeric(), nullable=True), + sa.Column('particle_unit_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('polygon', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('preparation_method', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('prep_method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('prep_temp_c', sa.Numeric(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.Column('drying_step', sa.Boolean(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('preparation_method_abbreviation', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('prepared_sample', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('prep_method_id', sa.Integer(), nullable=True), + sa.Column('prep_date', sa.Date(), nullable=True), + sa.Column('preparer_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('pretreatment_record', + sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), + sa.Column('eh_method_id', sa.Integer(), nullable=True), + sa.Column('reaction_block_id', sa.Integer(), nullable=True), + sa.Column('block_position', sa.Text(), nullable=True), + sa.Column('temperature', sa.Numeric(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('primary_crop', + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('processing_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('provider', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('codename', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('proximate_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('primary_crop_id', sa.Integer(), nullable=True), + sa.Column('resource_class_id', sa.Integer(), nullable=True), + sa.Column('resource_subclass_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_availability', + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('from_month', sa.Integer(), nullable=True), + sa.Column('to_month', sa.Integer(), nullable=True), + sa.Column('year_round', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_class', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_counterfactual', + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('counterfactual_description', sa.Text(), nullable=True), + sa.Column('animal_bedding_percent', sa.Numeric(), nullable=True), + sa.Column('animal_bedding_source_id', sa.Integer(), nullable=True), + sa.Column('animal_feed_percent', sa.Numeric(), nullable=True), + sa.Column('animal_feed_source_id', sa.Integer(), nullable=True), + sa.Column('bioelectricty_percent', sa.Numeric(), nullable=True), + sa.Column('bioelectricty_source_id', sa.Integer(), nullable=True), + sa.Column('burn_percent', sa.Numeric(), nullable=True), + sa.Column('burn_source_id', sa.Integer(), nullable=True), + sa.Column('compost_percent', sa.Numeric(), nullable=True), + sa.Column('compost_source_id', sa.Integer(), nullable=True), + sa.Column('landfill_percent', sa.Numeric(), nullable=True), + sa.Column('landfill_source_id', sa.Integer(), nullable=True), + sa.Column('counterfactual_date', sa.Date(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_morphology', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('morphology_uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_subclass', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_usda_commodity_map', + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('primary_crop_id', sa.Integer(), nullable=True), + sa.Column('usda_commodity_id', sa.Integer(), nullable=True), + sa.Column('match_tier', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('rgb_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('soil_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('source_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('strain', + sa.Column('parent_strain_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ultimate_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('unit', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_census_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('commodity_code', sa.Integer(), nullable=True), + sa.Column('year', sa.Integer(), nullable=True), + sa.Column('source_reference', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_commodity', + sa.Column('usda_source', sa.Text(), nullable=True), + sa.Column('usda_code', sa.Text(), nullable=True), + sa.Column('parent_commodity_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_domain', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_market_record', + sa.Column('report_id', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('report_begin_date', sa.DateTime(), nullable=True), + sa.Column('report_end_date', sa.DateTime(), nullable=True), + sa.Column('report_date', sa.DateTime(), nullable=True), + sa.Column('commodity_id', sa.Integer(), nullable=True), + sa.Column('market_type_id', sa.Integer(), nullable=True), + sa.Column('market_type_catagory', sa.Text(), nullable=True), + sa.Column('grp', sa.Text(), nullable=True), + sa.Column('market_catagory_id', sa.Integer(), nullable=True), + sa.Column('class_', sa.Text(), nullable=True), + sa.Column('grade', sa.Text(), nullable=True), + sa.Column('variety', sa.Text(), nullable=True), + sa.Column('protein_pct', sa.Numeric(), nullable=True), + sa.Column('application', sa.Text(), nullable=True), + sa.Column('pkg', sa.Text(), nullable=True), + sa.Column('sale_type', sa.Text(), nullable=True), + sa.Column('price_unit_id', sa.Integer(), nullable=True), + sa.Column('freight', sa.Text(), nullable=True), + sa.Column('trans_mode', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_market_report', + sa.Column('slug_id', sa.Integer(), nullable=True), + sa.Column('slug_name', sa.Text(), nullable=True), + sa.Column('report_series_title', sa.Text(), nullable=True), + sa.Column('frequency', sa.Text(), nullable=True), + sa.Column('office_name', sa.Text(), nullable=True), + sa.Column('office_city_id', sa.Integer(), nullable=True), + sa.Column('office_state_fips', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_statistic_category', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_survey_program', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_survey_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('commodity_code', sa.Integer(), nullable=True), + sa.Column('year', sa.Integer(), nullable=True), + sa.Column('survey_program_id', sa.Integer(), nullable=True), + sa.Column('survey_period', sa.Text(), nullable=True), + sa.Column('reference_month', sa.Text(), nullable=True), + sa.Column('seasonal_flag', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_term_map', + sa.Column('source_system', sa.Text(), nullable=True), + sa.Column('source_context', sa.Text(), nullable=True), + sa.Column('raw_term', sa.Text(), nullable=True), + sa.Column('usda_commodity_id', sa.Integer(), nullable=True), + sa.Column('is_verified', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('xrd_record', + sa.Column('maybe_scan_low_nm', sa.Integer(), nullable=True), + sa.Column('maybe_scan_high_nm', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('xrf_record', + sa.Column('maybe_wavelength_nm', sa.Numeric(), nullable=True), + sa.Column('maybe_intensity', sa.Numeric(), nullable=True), + sa.Column('maybe_energy_slope', sa.Numeric(), nullable=True), + sa.Column('maybe_energy_offset', sa.Numeric(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.drop_table('UsdaMarketRecord') + op.drop_table('ResourceAvailability') + op.drop_table('PreparedSample') + op.drop_table('UsdaStatisticCategory') + op.drop_table('PrimaryCrop') + op.drop_table('BaseEntity') + op.drop_table('ResourceCounterfactual') + op.drop_table('UltimateRecord') + op.drop_table('SourceType') + op.drop_table('Contact') + op.drop_table('DataSourceType') + op.drop_table('ParameterUnit') + op.drop_table('Parameter') + op.drop_table('UsdaTermMap') + op.drop_table('Experiment') + op.drop_table('ParameterCategory') + op.drop_table('ExperimentEquipment') + op.drop_table('Aim1RecordBase') + op.drop_table('Geography') + op.drop_table('Method') + op.drop_table('LineageGroup') + op.drop_table('RgbRecord') + op.drop_table('MethodStandard') + op.drop_table('PretreatmentRecord') + op.drop_table('ResourceSubclass') + op.drop_table('UsdaMarketReport') + op.drop_table('Polygon') + op.drop_table('LocationResolution') + op.drop_table('ResourceMorphology') + op.drop_table('AutoclaveRecord') + op.drop_table('DimensionType') + op.drop_table('CompositionalRecord') + op.drop_table('PhysicalCharacteristic') + op.drop_table('Aim2RecordBase') + op.drop_table('UsdaCensusRecord') + op.drop_table('ResourceUsdaCommodityMap') + op.drop_table('AnalysisType') + op.drop_table('ParameterCategoryParameter') + op.drop_table('ExperimentAnalysis') + op.drop_table('UsdaDomain') + op.drop_table('HarvestMethod') + op.drop_table('LookupBase') + op.drop_table('FtnirRecord') + op.drop_table('Resource') + op.drop_table('Equipment') + op.drop_table('DataSource') + op.drop_table('ResourceClass') + op.drop_table('LocationAddress') + op.drop_table('UsdaSurveyRecord') + op.drop_table('FermentationRecord') + op.drop_table('XrdRecord') + op.drop_table('AgTreatment') + op.drop_table('ExperimentMethod') + op.drop_table('Dataset') + op.drop_table('LocationSoilType') + op.drop_table('FieldSampleCondition') + op.drop_table('XrfRecord') + op.drop_table('MethodAbbrev') + op.drop_table('Provider') + op.drop_table('LandiqRecord') + op.drop_table('EntityLineage') + op.drop_table('Unit') + op.drop_table('CalorimetryRecord') + op.drop_table('ExperimentPreparedSample') + op.drop_table('CollectionMethod') + op.drop_table('IcpRecord') + op.drop_table('PreparationMethodAbbreviation') + op.drop_table('BillionTon2023Record') + op.drop_table('ProcessingMethod') + op.drop_table('EtlRun') + op.drop_table('FileObjectMetadata') + op.drop_table('MethodCategory') + op.drop_table('GasificationRecord') + op.drop_table('UsdaCommodity') + op.drop_table('PreparationMethod') + op.drop_table('Observation') + op.drop_table('SoilType') + op.drop_table('FieldSample') + op.drop_table('FieldStorageMethod') + op.drop_table('Strain') + op.drop_table('ProximateRecord') + op.drop_table('UsdaSurveyProgram') + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('UsdaSurveyProgram', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaSurveyProgram_pkey')) + ) + op.create_table('ProximateRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ProximateRecord_pkey')) + ) + op.create_table('Strain', + sa.Column('parent_strain_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Strain_pkey')) + ) + op.create_table('FieldStorageMethod', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FieldStorageMethod_pkey')) + ) + op.create_table('FieldSample', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('provider_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('collector_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_collection_source', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('amount_collected', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('amount_collected_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sampling_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('field_storage_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('field_storage_duration_value', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('field_storage_duration_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('field_storage_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('collection_timestamp', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('collection_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('harvest_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('harvest_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('field_sample_storage_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FieldSample_pkey')) + ) + op.create_table('SoilType', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('SoilType_pkey')) + ) + op.create_table('Observation', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('record_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('record_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('value', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dimension_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dimension_value', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('dimension_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Observation_pkey')) + ) + op.create_table('PreparationMethod', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('prep_method_abbrev_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prep_temp_c', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('drying_step', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PreparationMethod_pkey')) + ) + op.create_table('UsdaCommodity', + sa.Column('usda_source', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('usda_code', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('parent_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaCommodity_pkey')) + ) + op.create_table('GasificationRecord', + sa.Column('feedstock_mass', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('bed_temperature', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('gas_flow_rate', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('GasificationRecord_pkey')) + ) + op.create_table('MethodCategory', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('MethodCategory_pkey')) + ) + op.create_table('FileObjectMetadata', + sa.Column('data_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('bucket_path', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('file_format', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('file_size', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('checksum_md5', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('checksum_sha256', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FileObjectMetadata_pkey')) + ) + op.create_table('EtlRun', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('started_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('completed_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('pipeline_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('records_ingested', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('EtlRun_pkey')) + ) + op.create_table('ProcessingMethod', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ProcessingMethod_pkey')) + ) + op.create_table('BillionTon2023Record', + sa.Column('subclass_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county_square_miles', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('model_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('scenario_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('price_offered_usd', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('production', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('production_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('btu_ton', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('production_energy_content', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('energy_content_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('product_density_dtpersqmi', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('land_source', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('BillionTon2023Record_pkey')) + ) + op.create_table('PreparationMethodAbbreviation', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PreparationMethodAbbreviation_pkey')) + ) + op.create_table('IcpRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('IcpRecord_pkey')) + ) + op.create_table('CollectionMethod', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('CollectionMethod_pkey')) + ) + op.create_table('ExperimentPreparedSample', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prepared_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ExperimentPreparedSample_pkey')) + ) + op.create_table('CalorimetryRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('CalorimetryRecord_pkey')) + ) + op.create_table('Unit', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Unit_pkey')) + ) + op.create_table('EntityLineage', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('source_table', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_row_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('EntityLineage_pkey')) + ) + op.create_table('LandiqRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('polygon_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('main_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('secondary_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('tertiary_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('quaternary_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('confidence', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('irrigated', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('acres', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('version', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LandiqRecord_pkey')) + ) + op.create_table('Provider', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('codename', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Provider_pkey')) + ) + op.create_table('MethodAbbrev', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('MethodAbbrev_pkey')) + ) + op.create_table('XrfRecord', + sa.Column('maybe_wavelength_nm', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('maybe_intensity', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('maybe_energy_slope', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('maybe_energy_offset', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('XrfRecord_pkey')) + ) + op.create_table('FieldSampleCondition', + sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('ag_treatment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('last_application_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('treatment_amount_per_acre', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('processing_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FieldSampleCondition_pkey')) + ) + op.create_table('LocationSoilType', + sa.Column('location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('soil_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LocationSoilType_pkey')) + ) + op.create_table('Dataset', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('record_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('start_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('end_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Dataset_pkey')) + ) + op.create_table('ExperimentMethod', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ExperimentMethod_pkey')) + ) + op.create_table('AgTreatment', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('AgTreatment_pkey')) + ) + op.create_table('XrdRecord', + sa.Column('maybe_scan_low_nm', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('maybe_scan_high_nm', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('XrdRecord_pkey')) + ) + op.create_table('FermentationRecord', + sa.Column('strain_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('pretreatment_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('eh_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('well_position', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('temperature', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('agitation_rpm', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('vessel_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyte_detection_equipment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FermentationRecord_pkey')) + ) + op.create_table('UsdaSurveyRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('commodity_code', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('year', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('survey_program_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('survey_period', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('reference_month', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('seasonal_flag', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaSurveyRecord_pkey')) + ) + op.create_table('LocationAddress', + sa.Column('geography_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('address_line1', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('address_line2', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('zip', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lat', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('lon', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('is_anonymous', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LocationAddress_pkey')) + ) + op.create_table('ResourceClass', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceClass_pkey')) + ) + op.create_table('DataSource', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('publication_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('version', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('publisher', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('author', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('license', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('DataSource_pkey')) + ) + op.create_table('Equipment', + sa.Column('equipment_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Equipment_pkey')) + ) + op.create_table('Resource', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('primary_crop_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_class_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_subclass_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Resource_pkey')) + ) + op.create_table('FtnirRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FtnirRecord_pkey')) + ) + op.create_table('LookupBase', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LookupBase_pkey')) + ) + op.create_table('HarvestMethod', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('HarvestMethod_pkey')) + ) + op.create_table('UsdaDomain', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaDomain_pkey')) + ) + op.create_table('ExperimentAnalysis', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analysis_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ExperimentAnalysis_pkey')) + ) + op.create_table('ParameterCategoryParameter', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('parameter_category_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ParameterCategoryParameter_pkey')) + ) + op.create_table('AnalysisType', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('AnalysisType_pkey')) + ) + op.create_table('ResourceUsdaCommodityMap', + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('primary_crop_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('usda_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('match_tier', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceUsdaCommodityMap_pkey')) + ) + op.create_table('UsdaCensusRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('commodity_code', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('year', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('source_reference', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaCensusRecord_pkey')) + ) + op.create_table('Aim2RecordBase', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Aim2RecordBase_pkey')) + ) + op.create_table('PhysicalCharacteristic', + sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('particle_length', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('particle_width', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('particle_height', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('particle_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PhysicalCharacteristic_pkey')) + ) + op.create_table('CompositionalRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('CompositionalRecord_pkey')) + ) + op.create_table('DimensionType', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('DimensionType_pkey')) + ) + op.create_table('AutoclaveRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('AutoclaveRecord_pkey')) + ) + op.create_table('ResourceMorphology', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('morphology_uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceMorphology_pkey')) + ) + op.create_table('LocationResolution', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LocationResolution_pkey')) + ) + op.create_table('Polygon', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('geom', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Polygon_pkey')) + ) + op.create_table('UsdaMarketReport', + sa.Column('slug_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('slug_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('report_series_title', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('frequency', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('office_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('office_city_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('office_state_fips', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaMarketReport_pkey')) + ) + op.create_table('ResourceSubclass', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceSubclass_pkey')) + ) + op.create_table('PretreatmentRecord', + sa.Column('pretreatment_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('eh_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('reaction_block_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('block_position', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('temperature', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PretreatmentRecord_pkey')) + ) + op.create_table('MethodStandard', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('MethodStandard_pkey')) + ) + op.create_table('RgbRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('RgbRecord_pkey')) + ) + op.create_table('LineageGroup', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LineageGroup_pkey')) + ) + op.create_table('Method', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('method_abbrev_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_category_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_standard_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('detection_limits', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Method_pkey')) + ) + op.create_table('Geography', + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=False), + sa.Column('state_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state_fips', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county_fips', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('region_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('agg_level_desc', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('geoid', name=op.f('Geography_pkey')) + ) + op.create_table('Aim1RecordBase', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Aim1RecordBase_pkey')) + ) + op.create_table('ExperimentEquipment', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('equipment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ExperimentEquipment_pkey')) + ) + op.create_table('ParameterCategory', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ParameterCategory_pkey')) + ) + op.create_table('Experiment', + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('exper_start_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('exper_duration', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('exper_duration_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('exper_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Experiment_pkey')) + ) + op.create_table('UsdaTermMap', + sa.Column('source_system', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_context', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('raw_term', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('usda_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('is_verified', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaTermMap_pkey')) + ) + op.create_table('Parameter', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('standard_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calculated', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Parameter_pkey')) + ) + op.create_table('ParameterUnit', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('alternate_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ParameterUnit_pkey')) + ) + op.create_table('DataSourceType', + sa.Column('source_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('DataSourceType_pkey')) + ) + op.create_table('Contact', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('first_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('last_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('email', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('affiliation', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Contact_pkey')) + ) + op.create_table('SourceType', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('SourceType_pkey')) + ) + op.create_table('UltimateRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UltimateRecord_pkey')) + ) + op.create_table('ResourceCounterfactual', + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('counterfactual_description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('animal_bedding_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('animal_bedding_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('animal_feed_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('animal_feed_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('bioelectricty_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('bioelectricty_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('burn_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('burn_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('compost_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('compost_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('landfill_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('landfill_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('counterfactual_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceCounterfactual_pkey')) + ) + op.create_table('BaseEntity', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('BaseEntity_pkey')) + ) + op.create_table('PrimaryCrop', + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PrimaryCrop_pkey')) + ) + op.create_table('UsdaStatisticCategory', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaStatisticCategory_pkey')) + ) + op.create_table('PreparedSample', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prep_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prep_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('preparer_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PreparedSample_pkey')) + ) + op.create_table('ResourceAvailability', + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('from_month', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('to_month', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('year_round', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceAvailability_pkey')) + ) + op.create_table('UsdaMarketRecord', + sa.Column('report_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('report_begin_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('report_end_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('report_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('market_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('market_type_catagory', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('grp', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('market_catagory_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('class_', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('grade', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('variety', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('protein_pct', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('application', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('pkg', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('sale_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('price_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('freight', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('trans_mode', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaMarketRecord_pkey')) + ) + op.drop_table('xrf_record') + op.drop_table('xrd_record') + op.drop_table('usda_term_map') + op.drop_table('usda_survey_record') + op.drop_table('usda_survey_program') + op.drop_table('usda_statistic_category') + op.drop_table('usda_market_report') + op.drop_table('usda_market_record') + op.drop_table('usda_domain') + op.drop_table('usda_commodity') + op.drop_table('usda_census_record') + op.drop_table('unit') + op.drop_table('ultimate_record') + op.drop_table('strain') + op.drop_table('source_type') + op.drop_table('soil_type') + op.drop_table('rgb_record') + op.drop_table('resource_usda_commodity_map') + op.drop_table('resource_subclass') + op.drop_table('resource_morphology') + op.drop_table('resource_counterfactual') + op.drop_table('resource_class') + op.drop_table('resource_availability') + op.drop_table('resource') + op.drop_table('proximate_record') + op.drop_table('provider') + op.drop_table('processing_method') + op.drop_table('primary_crop') + op.drop_table('pretreatment_record') + op.drop_table('prepared_sample') + op.drop_table('preparation_method_abbreviation') + op.drop_table('preparation_method') + op.drop_table('polygon') + op.drop_table('physical_characteristic') + op.drop_table('parameter_unit') + op.drop_table('parameter_category_parameter') + op.drop_table('parameter_category') + op.drop_table('parameter') + op.drop_table('observation') + op.drop_table('method_standard') + op.drop_table('method_category') + op.drop_table('method_abbrev') + op.drop_table('method') + op.drop_table('lookup_base') + op.drop_table('location_soil_type') + op.drop_table('location_resolution') + op.drop_table('location_address') + op.drop_table('lineage_group') + op.drop_table('landiq_record') + op.drop_table('icp_record') + op.drop_table('harvest_method') + op.drop_table('geography') + op.drop_table('gasification_record') + op.drop_table('ftnir_record') + op.drop_table('file_object_metadata') + op.drop_table('field_storage_method') + op.drop_table('field_sample_condition') + op.drop_table('field_sample') + op.drop_table('fermentation_record') + op.drop_table('experiment_prepared_sample') + op.drop_table('experiment_method') + op.drop_table('experiment_equipment') + op.drop_table('experiment_analysis') + op.drop_table('experiment') + op.drop_table('etl_run') + op.drop_table('equipment') + op.drop_table('entity_lineage') + op.drop_table('dimension_type') + op.drop_table('dataset') + op.drop_table('data_source_type') + op.drop_table('data_source') + op.drop_table('contact') + op.drop_table('compositional_record') + op.drop_table('collection_method') + op.drop_table('calorimetry_record') + op.drop_table('billion_ton2023_record') + op.drop_table('base_entity') + op.drop_table('autoclave_record') + op.drop_table('analysis_type') + op.drop_table('aim2_record_base') + op.drop_table('aim1_record_base') + op.drop_table('ag_treatment') + # ### end Alembic commands ### diff --git a/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py b/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py new file mode 100644 index 00000000..c1db3ff6 --- /dev/null +++ b/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py @@ -0,0 +1,32 @@ +"""adding a test to landiqrecord + +Revision ID: b838c837616b +Revises: 42618fe6b09b +Create Date: 2025-12-08 22:33:34.608783 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'b838c837616b' +down_revision: Union[str, Sequence[str], None] = '42618fe6b09b' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('landiq_record', sa.Column('test', sa.Text(), nullable=True)) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column('landiq_record', 'test') + # ### end Alembic commands ### diff --git a/pixi.toml b/pixi.toml index 7c291ac7..bfb9ea0e 100644 --- a/pixi.toml +++ b/pixi.toml @@ -179,6 +179,8 @@ migrate = { cmd = [ "start-services", ] } +update-schema = { cmd = "python src/ca_biositing/datamodels/utils/orchestrate_schema_update.py", description = "Orchestrate schema update: generate models, rebuild services, and create migration." } + [tasks.qgis] depends-on = [{ task = "run-qgis", environment = "gis" }] diff --git a/src/ca_biositing/datamodels/README.md b/src/ca_biositing/datamodels/README.md index a363db01..75239724 100644 --- a/src/ca_biositing/datamodels/README.md +++ b/src/ca_biositing/datamodels/README.md @@ -9,13 +9,42 @@ etc.). The `ca_biositing.datamodels` package provides: -- **Database Models**: SQLModel classes representing database tables for - biomass, geographic locations, experiments, samples, and more +- **LinkML Schema**: The single source of truth for the data model, defined in + YAML. +- **Generated Database Models**: SQLModel classes automatically generated from + the LinkML schema. - **Database Configuration**: Database connection and session management - utilities + utilities. - **Model Configuration**: Shared configuration for model behavior using - Pydantic Settings -- **Type Safety**: Full type annotations for all models and fields + Pydantic Settings. +- **Type Safety**: Full type annotations for all models and fields. + +## Schema Management Workflow + +We use **LinkML** as the source of truth for our data schema. The workflow for +making schema changes is: + +1. **Modify LinkML Schema**: Edit the YAML files in + `src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/`. +2. **Update Schema**: Run the orchestration command to generate Python models, + rebuild services, and create a migration. + ```bash + pixi run update-schema -m "Description of changes" + ``` + This command performs the following steps: + - Cleans the generated models directory. + - Generates new SQLAlchemy/SQLModel classes from the LinkML schema. + - Rebuilds the Docker services to include the new code. + - Starts the services. + - Generates an Alembic migration script. +3. **Apply Migration**: Apply the changes to the database. + ```bash + pixi run migrate + ``` + +The generated Python models are saved in +`src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/`. **Do +not edit these files directly.** Always modify the LinkML schema and regenerate. ## Structure @@ -24,20 +53,16 @@ src/ca_biositing/datamodels/ ├── ca_biositing/ │ └── datamodels/ │ ├── __init__.py # Package initialization and version -│ ├── biomass.py # Biomass-related models (FieldSample, Biomass, etc.) │ ├── config.py # Model configuration │ ├── database.py # Database connection setup -│ ├── data_and_references.py # Data and reference models -│ ├── experiments_analysis.py # Experiment analysis models -│ ├── external_datasets.py # External dataset models -│ ├── geographic_locations.py # Geographic location models -│ ├── metadata_samples.py # Sample metadata models -│ ├── organizations.py # Organization models -│ ├── people_contacts.py # People and contact models -│ ├── sample_preprocessing.py # Sample preprocessing models -│ ├── specific_aalysis_results.py # Analysis results models -│ ├── user.py # User models -│ └── templates/ # Model templates for new tables +│ ├── linkml/ # LinkML schema source files +│ │ ├── ca_biositing.yaml # Main schema entrypoint +│ │ └── modules/ # Modular schema definitions +│ ├── schemas/ +│ │ └── generated/ # Generated SQLModel classes (DO NOT EDIT) +│ └── utils/ # Schema management scripts +│ ├── generate_sqla.py # Script to generate models from LinkML +│ └── orchestrate_schema_update.py # Orchestration script ├── tests/ │ ├── __init__.py │ ├── conftest.py # Pytest fixtures and configuration @@ -76,32 +101,34 @@ pip install -e . ### Importing Models +Models are generated into separate modules based on the LinkML schema structure. +You should import them from `ca_biositing.datamodels.schemas.generated`. + ```python -from ca_biositing.datamodels.biomass import ( - Biomass, - FieldSample, - BiomassType, - PrimaryProduct +from ca_biositing.datamodels.schemas.generated.resource_information import ( + Resource, + ResourceClass, + PrimaryCrop ) -from ca_biositing.datamodels.geographic_locations import ( - GeographicLocation, - City, - State +from ca_biositing.datamodels.schemas.generated.field_sampling import FieldSample +from ca_biositing.datamodels.schemas.generated.places import ( + Geography, + LocationAddress ) # Create a model instance sample = FieldSample( - biomass_id=1, - sample_name="Sample-001", - amount_collected_kg=50.5 + name="Sample-001", + resource_id=1, + amount_collected=50.5 ) ``` ### Database Operations ```python -from sqlmodel import Session, create_engine -from ca_biositing.datamodels.biomass import Biomass +from sqlmodel import Session, create_engine, select +from ca_biositing.datamodels.schemas.generated.resource_information import Resource # Create engine and session engine = create_engine("postgresql://user:pass@localhost/dbname") @@ -109,11 +136,12 @@ engine = create_engine("postgresql://user:pass@localhost/dbname") # Use with SQLModel Session with Session(engine) as session: # Query models - biomass_items = session.query(Biomass).all() + statement = select(Resource) + resources = session.exec(statement).all() # Add new records - new_biomass = Biomass(biomass_name="Corn Stover") - session.add(new_biomass) + new_resource = Resource(name="Corn Stover") + session.add(new_resource) session.commit() ``` @@ -142,42 +170,49 @@ pixi run pytest src/ca_biositing/datamodels --cov=ca_biositing.datamodels --cov- See `tests/README.md` for detailed information about the test suite. -## Model Categories +## Model Categories (LinkML Modules) + +The schema is organized into modular YAML files in `linkml/modules/`. Each +module generates a corresponding Python file in `schemas/generated/`. -### Biomass Models (`biomass.py`) +### Core & Infrastructure -Core models for biomass entities, field samples, and related data: +- **`core.yaml`**: Base classes and shared types used across the schema. +- **`infrastructure.yaml`**: Infrastructure-related entities (e.g., + `InfrastructureType`, `Infrastructure`). +- **`places.yaml`**: Geographic location models (`GeographicLocation`, `City`, + `State`, `County`, `Region`, `FIPS`). +- **`people.yaml`**: People and contact information (`Person`, `ContactInfo`, + `Role`). +- **`data_sources_metadata.yaml`**: Metadata about data sources and references + (`DataSource`, `Reference`). -- `Biomass`: Core biomass entity -- `FieldSample`: Sample metadata collected in the field -- `BiomassType`: Lookup table for biomass types -- `PrimaryProduct`: Lookup table for primary products -- `BiomassAvailability`: Seasonal and quantitative availability -- `BiomassQuality`: Qualitative attributes -- `BiomassPrice`: Pricing information -- `HarvestMethod`, `CollectionMethod`, `FieldStorage`: Lookup tables +### Biomass & Sampling -### Geographic Models (`geographic_locations.py`) +- **`resource_information.yaml`**: Core biomass entities (`Biomass`, + `BiomassType`, `PrimaryProduct`, `BiomassAvailability`, `BiomassQuality`, + `BiomassPrice`). +- **`field_sampling.yaml`**: Field sampling data (`FieldSample`, + `HarvestMethod`, `CollectionMethod`, `FieldStorage`). +- **`sample_preparation.yaml`**: Sample preprocessing steps + (`SamplePreprocessing`, `PreprocessingMethod`). +- **`lineage.yaml`**: Tracking sample lineage (`SampleLineage`). -Models for location data (can be anonymized): +### Experiments & Analysis -- `GeographicLocation`: Main geographic location entity -- `StreetAddress`, `City`, `Zip`, `County`, `State`, `Region`: Location - components -- `FIPS`: FIPS codes -- `LocationResolution`: Resolution types (GPS, county, etc.) +- **`experiment_equipment.yaml`**: Experimental setup and equipment + (`Experiment`, `Equipment`). +- **`methods_parameters_units.yaml`**: Methods, parameters, and units (`Method`, + `Parameter`, `Unit`). +- **`general_analysis.yaml`**: General analysis results (`AnalysisResult`, + `AnalysisType`). +- **`aim1_records.yaml`**: Specific records for Aim 1 (`Aim1Record`). +- **`aim2_records.yaml`**: Specific records for Aim 2 (`Aim2Record`). -### Other Model Files +### External Data -- `data_and_references.py`: Data sources and references -- `experiments_analysis.py`: Experimental analysis data -- `external_datasets.py`: External dataset integration -- `metadata_samples.py`: Sample metadata -- `organizations.py`: Organization information -- `people_contacts.py`: People and contact information -- `sample_preprocessing.py`: Sample preprocessing steps -- `specific_aalysis_results.py`: Analysis results -- `user.py`: User management +- **`external_data.yaml`**: Integration with external datasets + (`ExternalDataset`). ## Dependencies @@ -201,16 +236,12 @@ pixi run pre-commit run --files src/ca_biositing/datamodels/**/* ### Adding New Models -1. Create or modify model files in `ca_biositing/datamodels/` -2. Follow the existing patterns (use SQLModel, Field definitions, type hints) -3. Add corresponding tests in `tests/` -4. Generate Alembic migrations if needed (see main project documentation) -5. Run tests and pre-commit checks - -### Model Templates - -Template files are available in `ca_biositing/datamodels/templates/` to help -create new models following the project conventions. +1. **Modify LinkML**: Add the new class to the appropriate YAML file in + `linkml/modules/`. +2. **Update Schema**: Run `pixi run update-schema -m "Add new model"`. +3. **Verify**: Check the generated file in `schemas/generated/` to ensure it + looks correct. +4. **Apply**: Run `pixi run migrate` to update the database. ## Package Information diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml index 519632c0..cfca5168 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml @@ -140,6 +140,7 @@ classes: - acres - version - note + - test BillionTon2023Record: is_a: BaseEntity @@ -423,3 +424,7 @@ slots: geom: range: string description: Geometry (WKT or similar). + + test: + range: string + description: A test slot. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py index 9893aae0..6a5fd758 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -96,7 +96,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -115,7 +115,7 @@ class ExperimentMethod(Base): """ Link between Experiment and Method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -134,7 +134,7 @@ class ExperimentEquipment(Base): """ Link between Experiment and Equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -153,7 +153,7 @@ class ExperimentAnalysis(Base): """ Link between Experiment and AnalysisType. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -172,7 +172,7 @@ class ExperimentPreparedSample(Base): """ Link between Experiment and PreparedSample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -191,7 +191,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -210,7 +210,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -231,7 +231,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -249,7 +249,7 @@ class Aim1RecordBase(BaseEntity): """ """ - __tablename__ = 'Aim1RecordBase' + __tablename__ = 'aim1_record_base' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -285,7 +285,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -310,7 +310,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -342,7 +342,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -367,7 +367,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) @@ -403,7 +403,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -437,7 +437,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -462,7 +462,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -495,7 +495,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -520,7 +520,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -545,7 +545,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -570,7 +570,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -600,7 +600,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -625,7 +625,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -657,7 +657,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -682,7 +682,7 @@ class PreparedSample(BaseEntity): """ Sample that has been prepared. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -714,7 +714,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -749,7 +749,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -781,7 +781,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -808,7 +808,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -833,7 +833,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -858,7 +858,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -890,7 +890,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -916,7 +916,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -947,7 +947,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -972,7 +972,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -997,7 +997,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1023,7 +1023,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -1055,7 +1055,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -1098,7 +1098,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -1142,7 +1142,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1167,7 +1167,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1192,7 +1192,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1217,7 +1217,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1242,7 +1242,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1273,7 +1273,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1298,7 +1298,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1323,7 +1323,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1354,7 +1354,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -1382,7 +1382,7 @@ class ProximateRecord(Aim1RecordBase): """ Proximate analysis record. """ - __tablename__ = 'ProximateRecord' + __tablename__ = 'proximate_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1418,7 +1418,7 @@ class UltimateRecord(Aim1RecordBase): """ Ultimate analysis record. """ - __tablename__ = 'UltimateRecord' + __tablename__ = 'ultimate_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1454,7 +1454,7 @@ class CompositionalRecord(Aim1RecordBase): """ Compositional analysis record. """ - __tablename__ = 'CompositionalRecord' + __tablename__ = 'compositional_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1490,7 +1490,7 @@ class IcpRecord(Aim1RecordBase): """ ICP analysis record. """ - __tablename__ = 'IcpRecord' + __tablename__ = 'icp_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1526,7 +1526,7 @@ class XrfRecord(Aim1RecordBase): """ XRF analysis record. """ - __tablename__ = 'XrfRecord' + __tablename__ = 'xrf_record' maybe_wavelength_nm = Column(Numeric()) maybe_intensity = Column(Numeric()) @@ -1566,7 +1566,7 @@ class XrdRecord(Aim1RecordBase): """ XRD analysis record. """ - __tablename__ = 'XrdRecord' + __tablename__ = 'xrd_record' maybe_scan_low_nm = Column(Integer()) maybe_scan_high_nm = Column(Integer()) @@ -1604,7 +1604,7 @@ class CalorimetryRecord(Aim1RecordBase): """ Calorimetry analysis record. """ - __tablename__ = 'CalorimetryRecord' + __tablename__ = 'calorimetry_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1640,7 +1640,7 @@ class FtnirRecord(Aim1RecordBase): """ FT-NIR analysis record. """ - __tablename__ = 'FtnirRecord' + __tablename__ = 'ftnir_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1676,7 +1676,7 @@ class RgbRecord(Aim1RecordBase): """ RGB analysis record. """ - __tablename__ = 'RgbRecord' + __tablename__ = 'rgb_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py index e212029e..b282c9da 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -96,7 +96,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -115,7 +115,7 @@ class ExperimentMethod(Base): """ Link between Experiment and Method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -134,7 +134,7 @@ class ExperimentEquipment(Base): """ Link between Experiment and Equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -153,7 +153,7 @@ class ExperimentAnalysis(Base): """ Link between Experiment and AnalysisType. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -172,7 +172,7 @@ class ExperimentPreparedSample(Base): """ Link between Experiment and PreparedSample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -191,7 +191,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -210,7 +210,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -231,7 +231,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -249,7 +249,7 @@ class Aim2RecordBase(BaseEntity): """ """ - __tablename__ = 'Aim2RecordBase' + __tablename__ = 'aim2_record_base' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -285,7 +285,7 @@ class Strain(LookupBase): """ Strain used in fermentation. """ - __tablename__ = 'Strain' + __tablename__ = 'strain' parent_strain_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -311,7 +311,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -336,7 +336,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -368,7 +368,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -393,7 +393,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) @@ -429,7 +429,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -463,7 +463,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -488,7 +488,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -521,7 +521,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -546,7 +546,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -571,7 +571,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -596,7 +596,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -626,7 +626,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -651,7 +651,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -683,7 +683,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -708,7 +708,7 @@ class PreparedSample(BaseEntity): """ Sample that has been prepared. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -740,7 +740,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -775,7 +775,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -807,7 +807,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -834,7 +834,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -859,7 +859,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -884,7 +884,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -916,7 +916,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -942,7 +942,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -973,7 +973,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -998,7 +998,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1023,7 +1023,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1049,7 +1049,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -1081,7 +1081,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -1124,7 +1124,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -1168,7 +1168,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1193,7 +1193,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1218,7 +1218,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1243,7 +1243,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1268,7 +1268,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1299,7 +1299,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1324,7 +1324,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1349,7 +1349,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1380,7 +1380,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -1408,7 +1408,7 @@ class PretreatmentRecord(Aim2RecordBase): """ Pretreatment record. """ - __tablename__ = 'PretreatmentRecord' + __tablename__ = 'pretreatment_record' pretreatment_method_id = Column(Integer()) eh_method_id = Column(Integer()) @@ -1450,7 +1450,7 @@ class FermentationRecord(Aim2RecordBase): """ Fermentation record. """ - __tablename__ = 'FermentationRecord' + __tablename__ = 'fermentation_record' strain_id = Column(Integer()) pretreatment_method_id = Column(Integer()) @@ -1495,7 +1495,7 @@ class GasificationRecord(Aim2RecordBase): """ Gasification record. """ - __tablename__ = 'GasificationRecord' + __tablename__ = 'gasification_record' feedstock_mass = Column(Numeric()) bed_temperature = Column(Numeric()) @@ -1534,7 +1534,7 @@ class AutoclaveRecord(Aim2RecordBase): """ Autoclave record. """ - __tablename__ = 'AutoclaveRecord' + __tablename__ = 'autoclave_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py index 31e8b6fb..f860432f 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py @@ -13,7 +13,7 @@ class Dataset(Base): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -36,7 +36,7 @@ class Observation(Base): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -63,7 +63,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -84,7 +84,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -104,7 +104,7 @@ class ParameterCategoryParameter(Base): """ Link between parameter and category. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -123,7 +123,7 @@ class ParameterUnit(Base): """ Link between parameter and alternate units. """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -142,7 +142,7 @@ class DimensionType(LookupBase): """ Type of dimension (e.g. timepoint, wavelength). """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -167,7 +167,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -192,7 +192,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -217,7 +217,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -250,7 +250,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for a method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -275,7 +275,7 @@ class MethodCategory(LookupBase): """ Category of a method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -300,7 +300,7 @@ class MethodStandard(LookupBase): """ Standard associated with a method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -325,7 +325,7 @@ class Parameter(BaseEntity): """ Parameter measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -355,7 +355,7 @@ class ParameterCategory(LookupBase): """ Category of a parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py index 44a65db4..b8968702 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py @@ -13,7 +13,7 @@ class RecordBase(Base): """ """ - __tablename__ = 'RecordBase' + __tablename__ = 'record_base' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -40,7 +40,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -61,7 +61,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -81,7 +81,7 @@ class Dataset(Base): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -104,7 +104,7 @@ class Observation(Base): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -131,7 +131,7 @@ class Geography(Base): """ Geographic region definition (e.g. county, state). """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -154,7 +154,7 @@ class Polygon(Base): """ Geospatial polygon definition. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -173,7 +173,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -194,7 +194,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -212,7 +212,7 @@ class ParameterCategoryParameter(Base): """ Link between parameter and category. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -231,7 +231,7 @@ class ParameterUnit(Base): """ Link between parameter and alternate units. """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -250,7 +250,7 @@ class ExperimentEquipment(Base): """ Link between experiment and equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -269,7 +269,7 @@ class ExperimentAnalysis(Base): """ Link between experiment and analysis type. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -288,7 +288,7 @@ class ExperimentPreparedSample(Base): """ Link between experiment and prepared sample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -307,7 +307,7 @@ class ExperimentMethod(Base): """ Link between experiment and method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -326,7 +326,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -345,7 +345,7 @@ class ProximateRecord(RecordBase): """ Proximate analysis record. """ - __tablename__ = 'ProximateRecord' + __tablename__ = 'proximate_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -377,7 +377,7 @@ class UltimateRecord(RecordBase): """ Ultimate analysis record. """ - __tablename__ = 'UltimateRecord' + __tablename__ = 'ultimate_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -409,7 +409,7 @@ class CompositionalRecord(RecordBase): """ Compositional analysis record. """ - __tablename__ = 'CompositionalRecord' + __tablename__ = 'compositional_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -441,7 +441,7 @@ class IcpRecord(RecordBase): """ ICP analysis record. """ - __tablename__ = 'IcpRecord' + __tablename__ = 'icp_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -473,7 +473,7 @@ class XrfRecord(RecordBase): """ XRF analysis record. """ - __tablename__ = 'XrfRecord' + __tablename__ = 'xrf_record' maybe_wavelength_nm = Column(Numeric()) maybe_intensity = Column(Numeric()) @@ -509,7 +509,7 @@ class XrdRecord(RecordBase): """ XRD analysis record. """ - __tablename__ = 'XrdRecord' + __tablename__ = 'xrd_record' maybe_scan_low_nm = Column(Integer()) maybe_scan_high_nm = Column(Integer()) @@ -543,7 +543,7 @@ class CalorimetryRecord(RecordBase): """ Calorimetry analysis record. """ - __tablename__ = 'CalorimetryRecord' + __tablename__ = 'calorimetry_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -575,7 +575,7 @@ class FtnirRecord(RecordBase): """ FT-NIR analysis record. """ - __tablename__ = 'FtnirRecord' + __tablename__ = 'ftnir_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -607,7 +607,7 @@ class RgbRecord(RecordBase): """ RGB analysis record. """ - __tablename__ = 'RgbRecord' + __tablename__ = 'rgb_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -639,7 +639,7 @@ class PretreatmentRecord(RecordBase): """ Pretreatment record. """ - __tablename__ = 'PretreatmentRecord' + __tablename__ = 'pretreatment_record' pretreatment_method = Column(Integer()) eh_method_id = Column(Integer()) @@ -678,7 +678,7 @@ class FermentationRecord(RecordBase): """ Fermentation record. """ - __tablename__ = 'FermentationRecord' + __tablename__ = 'fermentation_record' strain_id = Column(Integer()) pretreatement_method_id = Column(Integer()) @@ -720,7 +720,7 @@ class GasificationRecord(RecordBase): """ Gasification record. """ - __tablename__ = 'GasificationRecord' + __tablename__ = 'gasification_record' feedstock_mass = Column(Numeric()) bed_temperature = Column(Numeric()) @@ -756,7 +756,7 @@ class AutoclaveRecord(RecordBase): """ Autoclave record. """ - __tablename__ = 'AutoclaveRecord' + __tablename__ = 'autoclave_record' analyst_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -789,7 +789,7 @@ class DimensionType(LookupBase): """ Type of dimension (e.g. timepoint, wavelength). """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -814,7 +814,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -839,7 +839,7 @@ class LocationAddress(BaseEntity): """ Specific physical location. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -873,7 +873,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -898,7 +898,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -931,7 +931,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for a method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -956,7 +956,7 @@ class MethodCategory(LookupBase): """ Category of a method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -981,7 +981,7 @@ class MethodStandard(LookupBase): """ Standard associated with a method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1006,7 +1006,7 @@ class Parameter(BaseEntity): """ Parameter measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -1036,7 +1036,7 @@ class ParameterCategory(LookupBase): """ Category of a parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1061,7 +1061,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -1105,7 +1105,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1130,7 +1130,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1155,7 +1155,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1180,7 +1180,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1205,7 +1205,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1236,7 +1236,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1261,7 +1261,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1286,7 +1286,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1317,7 +1317,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -1345,7 +1345,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -1377,7 +1377,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1402,7 +1402,7 @@ class PreparedSample(BaseEntity): """ Sample prepared for analysis. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -1434,7 +1434,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -1466,7 +1466,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1492,7 +1492,7 @@ class Strain(LookupBase): """ Strain of organism. """ - __tablename__ = 'Strain' + __tablename__ = 'strain' parent_strain_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1518,7 +1518,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -1549,7 +1549,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1574,7 +1574,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1599,7 +1599,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1625,7 +1625,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -1657,7 +1657,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py index bbbb9a74..87fb054a 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -73,7 +73,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -96,7 +96,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -117,7 +117,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -135,7 +135,7 @@ class LineageGroup(Base): """ Grouping for lineage information. """ - __tablename__ = 'LineageGroup' + __tablename__ = 'lineage_group' id = Column(Integer(), primary_key=True, nullable=False ) etl_run_id = Column(Text()) @@ -154,7 +154,7 @@ class EntityLineage(Base): """ Lineage information for a specific entity. """ - __tablename__ = 'EntityLineage' + __tablename__ = 'entity_lineage' id = Column(Integer(), primary_key=True, nullable=False ) lineage_group_id = Column(Integer()) @@ -175,7 +175,7 @@ class EtlRun(Base): """ Information about an ETL run. """ - __tablename__ = 'EtlRun' + __tablename__ = 'etl_run' id = Column(Integer(), primary_key=True, nullable=False ) started_at = Column(DateTime()) @@ -198,7 +198,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -217,7 +217,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -236,7 +236,7 @@ class ExperimentMethod(Base): """ Link between Experiment and Method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -255,7 +255,7 @@ class ExperimentEquipment(Base): """ Link between Experiment and Equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -274,7 +274,7 @@ class ExperimentAnalysis(Base): """ Link between Experiment and AnalysisType. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -293,7 +293,7 @@ class ExperimentPreparedSample(Base): """ Link between Experiment and PreparedSample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -312,7 +312,7 @@ class Polygon(Base): """ Geospatial polygon. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -331,7 +331,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -362,7 +362,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -387,7 +387,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -412,7 +412,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -438,7 +438,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -470,7 +470,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -513,7 +513,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -557,7 +557,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -582,7 +582,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -607,7 +607,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -632,7 +632,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -657,7 +657,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -688,7 +688,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -713,7 +713,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -738,7 +738,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -769,7 +769,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -797,7 +797,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -831,7 +831,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -866,7 +866,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -898,7 +898,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -925,7 +925,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -950,7 +950,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -975,7 +975,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -1007,7 +1007,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1032,7 +1032,7 @@ class PreparedSample(BaseEntity): """ Sample that has been prepared. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -1064,7 +1064,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1089,7 +1089,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -1122,7 +1122,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1147,7 +1147,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1172,7 +1172,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1197,7 +1197,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -1227,7 +1227,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1252,7 +1252,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -1284,7 +1284,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1310,7 +1310,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1335,7 +1335,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -1367,7 +1367,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1392,7 +1392,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) @@ -1428,7 +1428,7 @@ class Aim1RecordBase(BaseEntity): """ """ - __tablename__ = 'Aim1RecordBase' + __tablename__ = 'aim1_record_base' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1464,7 +1464,7 @@ class Aim2RecordBase(BaseEntity): """ """ - __tablename__ = 'Aim2RecordBase' + __tablename__ = 'aim2_record_base' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1500,7 +1500,7 @@ class Strain(LookupBase): """ Strain used in fermentation. """ - __tablename__ = 'Strain' + __tablename__ = 'strain' parent_strain_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1526,7 +1526,7 @@ class UsdaDomain(LookupBase): """ USDA domain. """ - __tablename__ = 'UsdaDomain' + __tablename__ = 'usda_domain' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1551,7 +1551,7 @@ class UsdaStatisticCategory(LookupBase): """ USDA statistic category. """ - __tablename__ = 'UsdaStatisticCategory' + __tablename__ = 'usda_statistic_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1576,7 +1576,7 @@ class UsdaSurveyProgram(LookupBase): """ USDA survey program. """ - __tablename__ = 'UsdaSurveyProgram' + __tablename__ = 'usda_survey_program' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1601,7 +1601,7 @@ class UsdaCommodity(LookupBase): """ USDA commodity. """ - __tablename__ = 'UsdaCommodity' + __tablename__ = 'usda_commodity' usda_source = Column(Text()) usda_code = Column(Text()) @@ -1629,7 +1629,7 @@ class UsdaTermMap(BaseEntity): """ Mapping of raw terms to USDA commodities. """ - __tablename__ = 'UsdaTermMap' + __tablename__ = 'usda_term_map' source_system = Column(Text()) source_context = Column(Text()) @@ -1661,7 +1661,7 @@ class ResourceUsdaCommodityMap(BaseEntity): """ Mapping between resources/crops and USDA commodities. """ - __tablename__ = 'ResourceUsdaCommodityMap' + __tablename__ = 'resource_usda_commodity_map' resource_id = Column(Integer()) primary_crop_id = Column(Integer()) @@ -1692,7 +1692,7 @@ class UsdaCensusRecord(BaseEntity): """ USDA census record. """ - __tablename__ = 'UsdaCensusRecord' + __tablename__ = 'usda_census_record' dataset_id = Column(Integer()) geoid = Column(Text()) @@ -1724,7 +1724,7 @@ class UsdaSurveyRecord(BaseEntity): """ USDA survey record. """ - __tablename__ = 'UsdaSurveyRecord' + __tablename__ = 'usda_survey_record' dataset_id = Column(Integer()) geoid = Column(Text()) @@ -1759,7 +1759,7 @@ class UsdaMarketReport(BaseEntity): """ USDA market report. """ - __tablename__ = 'UsdaMarketReport' + __tablename__ = 'usda_market_report' slug_id = Column(Integer()) slug_name = Column(Text()) @@ -1793,7 +1793,7 @@ class UsdaMarketRecord(BaseEntity): """ USDA market record. """ - __tablename__ = 'UsdaMarketRecord' + __tablename__ = 'usda_market_record' report_id = Column(Integer()) dataset_id = Column(Integer()) @@ -1839,7 +1839,7 @@ class LandiqRecord(BaseEntity): """ LandIQ record. """ - __tablename__ = 'LandiqRecord' + __tablename__ = 'landiq_record' dataset_id = Column(Integer()) polygon_id = Column(Integer()) @@ -1852,6 +1852,7 @@ class LandiqRecord(BaseEntity): acres = Column(Float()) version = Column(Text()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1860,7 +1861,7 @@ class LandiqRecord(BaseEntity): def __repr__(self): - return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1876,7 +1877,7 @@ class BillionTon2023Record(BaseEntity): """ Billion Ton 2023 record. """ - __tablename__ = 'BillionTon2023Record' + __tablename__ = 'billion_ton2023_record' subclass_id = Column(Integer()) resource_id = Column(Integer()) @@ -1916,7 +1917,7 @@ class ProximateRecord(Aim1RecordBase): """ Proximate analysis record. """ - __tablename__ = 'ProximateRecord' + __tablename__ = 'proximate_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1952,7 +1953,7 @@ class UltimateRecord(Aim1RecordBase): """ Ultimate analysis record. """ - __tablename__ = 'UltimateRecord' + __tablename__ = 'ultimate_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1988,7 +1989,7 @@ class CompositionalRecord(Aim1RecordBase): """ Compositional analysis record. """ - __tablename__ = 'CompositionalRecord' + __tablename__ = 'compositional_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -2024,7 +2025,7 @@ class IcpRecord(Aim1RecordBase): """ ICP analysis record. """ - __tablename__ = 'IcpRecord' + __tablename__ = 'icp_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -2060,7 +2061,7 @@ class XrfRecord(Aim1RecordBase): """ XRF analysis record. """ - __tablename__ = 'XrfRecord' + __tablename__ = 'xrf_record' maybe_wavelength_nm = Column(Numeric()) maybe_intensity = Column(Numeric()) @@ -2100,7 +2101,7 @@ class XrdRecord(Aim1RecordBase): """ XRD analysis record. """ - __tablename__ = 'XrdRecord' + __tablename__ = 'xrd_record' maybe_scan_low_nm = Column(Integer()) maybe_scan_high_nm = Column(Integer()) @@ -2138,7 +2139,7 @@ class CalorimetryRecord(Aim1RecordBase): """ Calorimetry analysis record. """ - __tablename__ = 'CalorimetryRecord' + __tablename__ = 'calorimetry_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -2174,7 +2175,7 @@ class FtnirRecord(Aim1RecordBase): """ FT-NIR analysis record. """ - __tablename__ = 'FtnirRecord' + __tablename__ = 'ftnir_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -2210,7 +2211,7 @@ class RgbRecord(Aim1RecordBase): """ RGB analysis record. """ - __tablename__ = 'RgbRecord' + __tablename__ = 'rgb_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -2246,7 +2247,7 @@ class PretreatmentRecord(Aim2RecordBase): """ Pretreatment record. """ - __tablename__ = 'PretreatmentRecord' + __tablename__ = 'pretreatment_record' pretreatment_method_id = Column(Integer()) eh_method_id = Column(Integer()) @@ -2288,7 +2289,7 @@ class FermentationRecord(Aim2RecordBase): """ Fermentation record. """ - __tablename__ = 'FermentationRecord' + __tablename__ = 'fermentation_record' strain_id = Column(Integer()) pretreatment_method_id = Column(Integer()) @@ -2333,7 +2334,7 @@ class GasificationRecord(Aim2RecordBase): """ Gasification record. """ - __tablename__ = 'GasificationRecord' + __tablename__ = 'gasification_record' feedstock_mass = Column(Numeric()) bed_temperature = Column(Numeric()) @@ -2372,7 +2373,7 @@ class AutoclaveRecord(Aim2RecordBase): """ Autoclave record. """ - __tablename__ = 'AutoclaveRecord' + __tablename__ = 'autoclave_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py index 1f2a5b30..20ba55a2 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py index e8ad5281..48fe18d7 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -98,7 +98,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -116,7 +116,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -135,7 +135,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -154,7 +154,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -173,7 +173,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -208,7 +208,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -240,7 +240,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -267,7 +267,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -292,7 +292,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -317,7 +317,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -351,7 +351,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -382,7 +382,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -407,7 +407,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -432,7 +432,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -458,7 +458,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -490,7 +490,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -533,7 +533,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -558,7 +558,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -591,7 +591,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -616,7 +616,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -641,7 +641,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -666,7 +666,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -696,7 +696,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -721,7 +721,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -765,7 +765,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -790,7 +790,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -815,7 +815,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -840,7 +840,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -865,7 +865,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -896,7 +896,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -921,7 +921,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -946,7 +946,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -977,7 +977,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py index 542f4cd0..3f2ab322 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py @@ -13,7 +13,7 @@ class ExperimentMethod(Base): """ Link between Experiment and Method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -32,7 +32,7 @@ class ExperimentEquipment(Base): """ Link between Experiment and Equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -51,7 +51,7 @@ class ExperimentAnalysis(Base): """ Link between Experiment and AnalysisType. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -70,7 +70,7 @@ class ExperimentPreparedSample(Base): """ Link between Experiment and PreparedSample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -89,7 +89,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -110,7 +110,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -130,7 +130,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -153,7 +153,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -172,7 +172,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -191,7 +191,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -212,7 +212,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -230,7 +230,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -249,7 +249,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -281,7 +281,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -307,7 +307,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -341,7 +341,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -366,7 +366,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -399,7 +399,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -424,7 +424,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -449,7 +449,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -474,7 +474,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -504,7 +504,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -529,7 +529,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -573,7 +573,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -598,7 +598,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -623,7 +623,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -648,7 +648,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -673,7 +673,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -704,7 +704,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -729,7 +729,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -754,7 +754,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -785,7 +785,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -813,7 +813,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -845,7 +845,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -870,7 +870,7 @@ class PreparedSample(BaseEntity): """ Sample that has been prepared. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -902,7 +902,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -937,7 +937,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -969,7 +969,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -996,7 +996,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1021,7 +1021,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1046,7 +1046,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -1077,7 +1077,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1102,7 +1102,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1127,7 +1127,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1153,7 +1153,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -1185,7 +1185,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -1228,7 +1228,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1253,7 +1253,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -1285,7 +1285,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1310,7 +1310,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py index c34d8d9a..4d5b8097 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py @@ -13,7 +13,7 @@ class ExperimentEquipment(Base): """ Link between experiment and equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -32,7 +32,7 @@ class ExperimentAnalysis(Base): """ Link between experiment and analysis type. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -51,7 +51,7 @@ class ExperimentPreparedSample(Base): """ Link between experiment and prepared sample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -70,7 +70,7 @@ class ExperimentMethod(Base): """ Link between experiment and method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -89,7 +89,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -110,7 +110,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -130,7 +130,7 @@ class Geography(Base): """ Geographic region definition (e.g. county, state). """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -153,7 +153,7 @@ class Polygon(Base): """ Geospatial polygon definition. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -172,7 +172,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -193,7 +193,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -211,7 +211,7 @@ class ParameterCategoryParameter(Base): """ Link between parameter and category. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -230,7 +230,7 @@ class ParameterUnit(Base): """ Link between parameter and alternate units. """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -249,7 +249,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -268,7 +268,7 @@ class Dataset(Base): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -291,7 +291,7 @@ class Observation(Base): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -318,7 +318,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -350,7 +350,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -376,7 +376,7 @@ class Strain(LookupBase): """ Strain of organism. """ - __tablename__ = 'Strain' + __tablename__ = 'strain' parent_strain_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -402,7 +402,7 @@ class LocationAddress(BaseEntity): """ Specific physical location. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -436,7 +436,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -461,7 +461,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -494,7 +494,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for a method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -519,7 +519,7 @@ class MethodCategory(LookupBase): """ Category of a method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -544,7 +544,7 @@ class MethodStandard(LookupBase): """ Standard associated with a method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -569,7 +569,7 @@ class Parameter(BaseEntity): """ Parameter measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -599,7 +599,7 @@ class ParameterCategory(LookupBase): """ Category of a parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -624,7 +624,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -655,7 +655,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -680,7 +680,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -705,7 +705,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -731,7 +731,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -763,7 +763,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -806,7 +806,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -850,7 +850,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -875,7 +875,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -900,7 +900,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -925,7 +925,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -950,7 +950,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -981,7 +981,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1006,7 +1006,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1031,7 +1031,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1062,7 +1062,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -1090,7 +1090,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -1122,7 +1122,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1147,7 +1147,7 @@ class PreparedSample(BaseEntity): """ Sample prepared for analysis. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -1179,7 +1179,7 @@ class DimensionType(LookupBase): """ Type of dimension (e.g. timepoint, wavelength). """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1204,7 +1204,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py index 16cf80f9..c1e3bad5 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py @@ -13,7 +13,7 @@ class Polygon(Base): """ Geospatial polygon. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -32,7 +32,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -53,7 +53,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -73,7 +73,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -92,7 +92,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -111,7 +111,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -134,7 +134,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -153,7 +153,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -174,7 +174,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -192,7 +192,7 @@ class UsdaDomain(LookupBase): """ USDA domain. """ - __tablename__ = 'UsdaDomain' + __tablename__ = 'usda_domain' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -217,7 +217,7 @@ class UsdaStatisticCategory(LookupBase): """ USDA statistic category. """ - __tablename__ = 'UsdaStatisticCategory' + __tablename__ = 'usda_statistic_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -242,7 +242,7 @@ class UsdaSurveyProgram(LookupBase): """ USDA survey program. """ - __tablename__ = 'UsdaSurveyProgram' + __tablename__ = 'usda_survey_program' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -267,7 +267,7 @@ class UsdaCommodity(LookupBase): """ USDA commodity. """ - __tablename__ = 'UsdaCommodity' + __tablename__ = 'usda_commodity' usda_source = Column(Text()) usda_code = Column(Text()) @@ -295,7 +295,7 @@ class UsdaTermMap(BaseEntity): """ Mapping of raw terms to USDA commodities. """ - __tablename__ = 'UsdaTermMap' + __tablename__ = 'usda_term_map' source_system = Column(Text()) source_context = Column(Text()) @@ -327,7 +327,7 @@ class ResourceUsdaCommodityMap(BaseEntity): """ Mapping between resources/crops and USDA commodities. """ - __tablename__ = 'ResourceUsdaCommodityMap' + __tablename__ = 'resource_usda_commodity_map' resource_id = Column(Integer()) primary_crop_id = Column(Integer()) @@ -358,7 +358,7 @@ class UsdaCensusRecord(BaseEntity): """ USDA census record. """ - __tablename__ = 'UsdaCensusRecord' + __tablename__ = 'usda_census_record' dataset_id = Column(Integer()) geoid = Column(Text()) @@ -390,7 +390,7 @@ class UsdaSurveyRecord(BaseEntity): """ USDA survey record. """ - __tablename__ = 'UsdaSurveyRecord' + __tablename__ = 'usda_survey_record' dataset_id = Column(Integer()) geoid = Column(Text()) @@ -425,7 +425,7 @@ class UsdaMarketReport(BaseEntity): """ USDA market report. """ - __tablename__ = 'UsdaMarketReport' + __tablename__ = 'usda_market_report' slug_id = Column(Integer()) slug_name = Column(Text()) @@ -459,7 +459,7 @@ class UsdaMarketRecord(BaseEntity): """ USDA market record. """ - __tablename__ = 'UsdaMarketRecord' + __tablename__ = 'usda_market_record' report_id = Column(Integer()) dataset_id = Column(Integer()) @@ -505,7 +505,7 @@ class LandiqRecord(BaseEntity): """ LandIQ record. """ - __tablename__ = 'LandiqRecord' + __tablename__ = 'landiq_record' dataset_id = Column(Integer()) polygon_id = Column(Integer()) @@ -518,6 +518,7 @@ class LandiqRecord(BaseEntity): acres = Column(Float()) version = Column(Text()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -526,7 +527,7 @@ class LandiqRecord(BaseEntity): def __repr__(self): - return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -542,7 +543,7 @@ class BillionTon2023Record(BaseEntity): """ Billion Ton 2023 record. """ - __tablename__ = 'BillionTon2023Record' + __tablename__ = 'billion_ton2023_record' subclass_id = Column(Integer()) resource_id = Column(Integer()) @@ -582,7 +583,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -617,7 +618,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -649,7 +650,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -676,7 +677,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -701,7 +702,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -726,7 +727,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -751,7 +752,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -784,7 +785,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -809,7 +810,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -834,7 +835,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -859,7 +860,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -889,7 +890,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -914,7 +915,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -939,7 +940,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -971,7 +972,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -996,7 +997,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) @@ -1032,7 +1033,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -1066,7 +1067,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -1097,7 +1098,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1122,7 +1123,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1147,7 +1148,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1173,7 +1174,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -1205,7 +1206,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -1248,7 +1249,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -1292,7 +1293,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1317,7 +1318,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1342,7 +1343,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1367,7 +1368,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1392,7 +1393,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1423,7 +1424,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1448,7 +1449,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1473,7 +1474,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1504,7 +1505,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py index f941eeae..6fed28ad 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -98,7 +98,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -116,7 +116,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -135,7 +135,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -154,7 +154,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -173,7 +173,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -217,7 +217,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -242,7 +242,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -267,7 +267,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -292,7 +292,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -317,7 +317,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -348,7 +348,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -373,7 +373,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -398,7 +398,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -429,7 +429,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -457,7 +457,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -491,7 +491,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -522,7 +522,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -547,7 +547,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -572,7 +572,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -598,7 +598,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -630,7 +630,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -673,7 +673,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -708,7 +708,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -740,7 +740,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -767,7 +767,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -792,7 +792,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -817,7 +817,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -842,7 +842,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -875,7 +875,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -900,7 +900,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -925,7 +925,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -950,7 +950,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -980,7 +980,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py index bffb89f8..5b4bbd8c 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -98,7 +98,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -116,7 +116,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -135,7 +135,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -154,7 +154,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -173,7 +173,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -198,7 +198,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -230,7 +230,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -255,7 +255,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) @@ -291,7 +291,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -326,7 +326,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -358,7 +358,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -385,7 +385,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -410,7 +410,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -435,7 +435,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -469,7 +469,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -500,7 +500,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -525,7 +525,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -550,7 +550,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -576,7 +576,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -608,7 +608,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -651,7 +651,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -676,7 +676,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -709,7 +709,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -734,7 +734,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -759,7 +759,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -784,7 +784,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -814,7 +814,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -839,7 +839,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -883,7 +883,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -908,7 +908,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -933,7 +933,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -958,7 +958,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -983,7 +983,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1014,7 +1014,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1039,7 +1039,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1064,7 +1064,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1095,7 +1095,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py index acb4d3c4..2de38d94 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py @@ -13,7 +13,7 @@ class Geography(Base): """ Geographic region definition (e.g. county, state). """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -36,7 +36,7 @@ class Polygon(Base): """ Geospatial polygon definition. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -55,7 +55,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -76,7 +76,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -96,7 +96,7 @@ class LocationAddress(BaseEntity): """ Specific physical location. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py index 76adbad5..20dfafc8 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py @@ -13,7 +13,7 @@ class InfrastructureBiodieselPlants(Base): """ Biodiesel plants infrastructure. """ - __tablename__ = 'InfrastructureBiodieselPlants' + __tablename__ = 'infrastructure_biodiesel_plants' biodiesel_plant_id = Column(Integer(), primary_key=True, nullable=False ) company = Column(Text()) @@ -42,7 +42,7 @@ class InfrastructureBiosolidsFacilities(Base): """ Biosolids facilities infrastructure. """ - __tablename__ = 'InfrastructureBiosolidsFacilities' + __tablename__ = 'infrastructure_biosolids_facilities' biosolid_facility_id = Column(Integer(), primary_key=True, nullable=False ) report_submitted_date = Column(Date()) @@ -100,7 +100,7 @@ class InfrastructureCafoManureLocations(Base): """ CAFO manure locations infrastructure. """ - __tablename__ = 'InfrastructureCafoManureLocations' + __tablename__ = 'infrastructure_cafo_manure_locations' cafo_manure_id = Column(Integer(), primary_key=True, nullable=False ) latitude = Column(Numeric()) @@ -132,7 +132,7 @@ class InfrastructureEthanolBiorefineries(Base): """ Ethanol biorefineries infrastructure. """ - __tablename__ = 'InfrastructureEthanolBiorefineries' + __tablename__ = 'infrastructure_ethanol_biorefineries' ethanol_biorefinery_id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -157,7 +157,7 @@ class InfrastructureLandfills(Base): """ Landfills infrastructure. """ - __tablename__ = 'InfrastructureLandfills' + __tablename__ = 'infrastructure_landfills' project_id = Column(Text(), primary_key=True, nullable=False ) project_int_id = Column(Integer()) @@ -207,7 +207,7 @@ class InfrastructureLivestockAnaerobicDigesters(Base): """ Livestock anaerobic digesters infrastructure. """ - __tablename__ = 'InfrastructureLivestockAnaerobicDigesters' + __tablename__ = 'infrastructure_livestock_anaerobic_digesters' digester_id = Column(Integer(), primary_key=True, nullable=False ) project_name = Column(Text()) @@ -246,7 +246,7 @@ class InfrastructureSafAndRenewableDieselPlants(Base): """ SAF and renewable diesel plants infrastructure. """ - __tablename__ = 'InfrastructureSafAndRenewableDieselPlants' + __tablename__ = 'infrastructure_saf_and_renewable_diesel_plants' ibcc_index = Column(Integer(), primary_key=True, nullable=False ) company = Column(Text()) @@ -275,7 +275,7 @@ class InfrastructureWastewaterTreatmentPlants(Base): """ Wastewater treatment plants infrastructure. """ - __tablename__ = 'InfrastructureWastewaterTreatmentPlants' + __tablename__ = 'infrastructure_wastewater_treatment_plants' plant_id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -321,7 +321,7 @@ class InfrastructureCombustionPlants(Base): """ Combustion plants infrastructure. """ - __tablename__ = 'InfrastructureCombustionPlants' + __tablename__ = 'infrastructure_combustion_plants' combustion_fid = Column(Integer(), primary_key=True, nullable=False ) objectid = Column(Integer()) @@ -354,7 +354,7 @@ class InfrastructureDistrictEnergySystems(Base): """ District energy systems infrastructure. """ - __tablename__ = 'InfrastructureDistrictEnergySystems' + __tablename__ = 'infrastructure_district_energy_systems' des_fid = Column(Integer(), primary_key=True, nullable=False ) cbg_id = Column(Integer()) @@ -391,7 +391,7 @@ class InfrastructureFoodProcessingFacilities(Base): """ Food processing facilities infrastructure. """ - __tablename__ = 'InfrastructureFoodProcessingFacilities' + __tablename__ = 'infrastructure_food_processing_facilities' processing_facility_id = Column(Integer(), primary_key=True, nullable=False ) address = Column(Text()) @@ -424,7 +424,7 @@ class InfrastructureMswToEnergyAnaerobicDigesters(Base): """ MSW to energy anaerobic digesters infrastructure. """ - __tablename__ = 'InfrastructureMswToEnergyAnaerobicDigesters' + __tablename__ = 'infrastructure_msw_to_energy_anaerobic_digesters' wte_id = Column(Integer(), primary_key=True, nullable=False ) city = Column(Text()) @@ -456,7 +456,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -477,7 +477,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -497,7 +497,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -520,7 +520,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -541,7 +541,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -559,7 +559,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -578,7 +578,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -597,7 +597,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -616,7 +616,7 @@ class FacilityRecord(BaseEntity): """ Facility record. """ - __tablename__ = 'FacilityRecord' + __tablename__ = 'facility_record' dataset_id = Column(Integer()) facility_name = Column(Text()) @@ -650,7 +650,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -685,7 +685,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -717,7 +717,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -744,7 +744,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -769,7 +769,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -794,7 +794,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -828,7 +828,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -859,7 +859,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -884,7 +884,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -909,7 +909,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -935,7 +935,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -967,7 +967,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -1010,7 +1010,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1035,7 +1035,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -1068,7 +1068,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1093,7 +1093,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1118,7 +1118,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1143,7 +1143,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -1173,7 +1173,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1198,7 +1198,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -1242,7 +1242,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1267,7 +1267,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1292,7 +1292,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1317,7 +1317,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1342,7 +1342,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1373,7 +1373,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1398,7 +1398,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1423,7 +1423,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1454,7 +1454,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -1482,7 +1482,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1507,7 +1507,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -1539,7 +1539,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1564,7 +1564,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py index 56bbfa6d..c1fb6e9a 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py @@ -13,7 +13,7 @@ class LineageGroup(Base): """ Grouping for lineage information. """ - __tablename__ = 'LineageGroup' + __tablename__ = 'lineage_group' id = Column(Integer(), primary_key=True, nullable=False ) etl_run_id = Column(Text()) @@ -32,7 +32,7 @@ class EntityLineage(Base): """ Lineage information for a specific entity. """ - __tablename__ = 'EntityLineage' + __tablename__ = 'entity_lineage' id = Column(Integer(), primary_key=True, nullable=False ) lineage_group_id = Column(Integer()) @@ -53,7 +53,7 @@ class EtlRun(Base): """ Information about an ETL run. """ - __tablename__ = 'EtlRun' + __tablename__ = 'etl_run' id = Column(Integer(), primary_key=True, nullable=False ) started_at = Column(DateTime()) @@ -76,7 +76,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -97,7 +97,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py index 7aceee05..5a5c33e9 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py @@ -13,7 +13,7 @@ class ParameterCategoryParameter(Base): """ Link between parameter and category. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -32,7 +32,7 @@ class ParameterUnit(Base): """ Link between parameter and alternate units. """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -51,7 +51,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -72,7 +72,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -92,7 +92,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -117,7 +117,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -150,7 +150,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for a method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -175,7 +175,7 @@ class MethodCategory(LookupBase): """ Category of a method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -200,7 +200,7 @@ class MethodStandard(LookupBase): """ Standard associated with a method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -225,7 +225,7 @@ class Parameter(BaseEntity): """ Parameter measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -255,7 +255,7 @@ class ParameterCategory(LookupBase): """ Category of a parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py index 3b0c7511..4e50f484 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py @@ -13,7 +13,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -32,7 +32,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -51,7 +51,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -72,7 +72,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -92,7 +92,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -115,7 +115,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -136,7 +136,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -154,7 +154,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -173,7 +173,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -198,7 +198,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -231,7 +231,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -256,7 +256,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -281,7 +281,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -306,7 +306,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -336,7 +336,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -361,7 +361,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -395,7 +395,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -426,7 +426,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -451,7 +451,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -476,7 +476,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -502,7 +502,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -534,7 +534,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -577,7 +577,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -621,7 +621,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -646,7 +646,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -671,7 +671,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -696,7 +696,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -721,7 +721,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -752,7 +752,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -777,7 +777,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -802,7 +802,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -833,7 +833,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -861,7 +861,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -896,7 +896,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -928,7 +928,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -955,7 +955,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -980,7 +980,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py index c5825f29..7eacc534 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py @@ -13,7 +13,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -34,7 +34,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py index f721c286..4eccd8ac 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py @@ -13,7 +13,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -36,7 +36,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -57,7 +57,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -77,7 +77,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py index 9350f964..b1d3d70e 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py @@ -13,7 +13,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -32,7 +32,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -53,7 +53,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -73,7 +73,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -96,7 +96,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -127,7 +127,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -152,7 +152,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -177,7 +177,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -203,7 +203,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -235,7 +235,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -278,7 +278,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py index cb16a4a0..bec06909 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py @@ -13,7 +13,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -32,7 +32,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -53,7 +53,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -73,7 +73,7 @@ class Geography(Base): """ Geographic region definition (e.g. county, state). """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -96,7 +96,7 @@ class Polygon(Base): """ Geospatial polygon definition. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -115,7 +115,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -146,7 +146,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -171,7 +171,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -196,7 +196,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -222,7 +222,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -254,7 +254,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -297,7 +297,7 @@ class LocationAddress(BaseEntity): """ Specific physical location. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py index 9f3eb1e5..a3da8a03 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -98,7 +98,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -116,7 +116,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -135,7 +135,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -154,7 +154,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -173,7 +173,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -205,7 +205,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -230,7 +230,7 @@ class PreparedSample(BaseEntity): """ Sample that has been prepared. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -262,7 +262,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -296,7 +296,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -327,7 +327,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -352,7 +352,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -377,7 +377,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -403,7 +403,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -435,7 +435,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -478,7 +478,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -522,7 +522,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -547,7 +547,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -572,7 +572,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -597,7 +597,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -622,7 +622,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -653,7 +653,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -678,7 +678,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -703,7 +703,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -734,7 +734,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -762,7 +762,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -797,7 +797,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -829,7 +829,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -856,7 +856,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -881,7 +881,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -906,7 +906,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -931,7 +931,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -964,7 +964,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -989,7 +989,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1014,7 +1014,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1039,7 +1039,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -1069,7 +1069,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py index d37b7688..63f68798 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic region definition (e.g. county, state). """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class Polygon(Base): """ Geospatial polygon definition. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -96,7 +96,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -117,7 +117,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -135,7 +135,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -154,7 +154,7 @@ class ParameterCategoryParameter(Base): """ Link between parameter and category. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -173,7 +173,7 @@ class ParameterUnit(Base): """ Link between parameter and alternate units. """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -192,7 +192,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -236,7 +236,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -261,7 +261,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -286,7 +286,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -311,7 +311,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -336,7 +336,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -367,7 +367,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -392,7 +392,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -417,7 +417,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -448,7 +448,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -476,7 +476,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -508,7 +508,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -533,7 +533,7 @@ class PreparedSample(BaseEntity): """ Sample prepared for analysis. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -565,7 +565,7 @@ class LocationAddress(BaseEntity): """ Specific physical location. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -599,7 +599,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -630,7 +630,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -655,7 +655,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -680,7 +680,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -706,7 +706,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -738,7 +738,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -781,7 +781,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -806,7 +806,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -839,7 +839,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for a method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -864,7 +864,7 @@ class MethodCategory(LookupBase): """ Category of a method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -889,7 +889,7 @@ class MethodStandard(LookupBase): """ Standard associated with a method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -914,7 +914,7 @@ class Parameter(BaseEntity): """ Parameter measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -944,7 +944,7 @@ class ParameterCategory(LookupBase): """ Category of a parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/generate_sqla.py b/src/ca_biositing/datamodels/utils/generate_sqla.py similarity index 54% rename from src/ca_biositing/datamodels/generate_sqla.py rename to src/ca_biositing/datamodels/utils/generate_sqla.py index 54fe4a59..50c0825f 100644 --- a/src/ca_biositing/datamodels/generate_sqla.py +++ b/src/ca_biositing/datamodels/utils/generate_sqla.py @@ -1,12 +1,39 @@ import os +import re import subprocess from pathlib import Path +def to_snake_case(name): + """Converts PascalCase to snake_case.""" + s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name) + return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower() + +def post_process_file(file_path): + """ + Post-processes the generated file to convert table names to snake_case. + """ + with open(file_path, 'r') as f: + content = f.read() + + # Regex to find __tablename__ assignments + # Matches: __tablename__ = 'SomeName' + pattern = r"__tablename__ = '([A-Za-z0-9]+)'" + + def replace_tablename(match): + original_name = match.group(1) + snake_name = to_snake_case(original_name) + return f"__tablename__ = '{snake_name}'" + + new_content = re.sub(pattern, replace_tablename, content) + + with open(file_path, 'w') as f: + f.write(new_content) + def generate_sqla(): """ Generates SQLAlchemy models from LinkML schema modules. """ - base_dir = Path(__file__).parent + base_dir = Path(__file__).parent.parent linkml_dir = base_dir / "ca_biositing/datamodels/linkml" modules_dir = linkml_dir / "modules" output_dir = base_dir / "ca_biositing/datamodels/schemas/generated" @@ -14,6 +41,12 @@ def generate_sqla(): # Ensure output directory exists output_dir.mkdir(parents=True, exist_ok=True) + # Clean output directory + print(f"Cleaning output directory: {output_dir}") + for file in output_dir.glob("*.py"): + if file.name != "__init__.py": + file.unlink() + # Generate for modules for yaml_file in modules_dir.glob("*.yaml"): module_name = yaml_file.stem @@ -29,6 +62,8 @@ def generate_sqla(): with open(output_file, "w") as f: subprocess.run(cmd, stdout=f, check=True) + post_process_file(output_file) + # Generate for main schema main_yaml = linkml_dir / "ca_biositing.yaml" main_output = output_dir / "ca_biositing.py" @@ -43,6 +78,8 @@ def generate_sqla(): with open(main_output, "w") as f: subprocess.run(cmd, stdout=f, check=True) + post_process_file(main_output) + print("Generation complete.") if __name__ == "__main__": diff --git a/src/ca_biositing/datamodels/utils/orchestrate_schema_update.py b/src/ca_biositing/datamodels/utils/orchestrate_schema_update.py new file mode 100644 index 00000000..07281d32 --- /dev/null +++ b/src/ca_biositing/datamodels/utils/orchestrate_schema_update.py @@ -0,0 +1,58 @@ +import subprocess +import sys +import argparse +import shlex +from pathlib import Path + +def run_command(command, cwd=None): + print(f"Running: {command}") + try: + # If command is a string, use shell=True. If list, use shell=False. + shell = isinstance(command, str) + subprocess.run(command, shell=shell, check=True, cwd=cwd) + except subprocess.CalledProcessError as e: + print(f"Error running command: {command}") + sys.exit(e.returncode) + +def main(): + parser = argparse.ArgumentParser(description="Orchestrate schema update workflow.") + parser.add_argument("-m", "--message", required=True, help="Migration message") + args = parser.parse_args() + + # 1. Generate SQLAlchemy models + print("--- Generating SQLAlchemy models ---") + script_path = Path(__file__).parent / "generate_sqla.py" + run_command(f"python {script_path}") + + # 2. Rebuild services + print("--- Rebuilding services ---") + # We assume we are in the project root or pixi handles the path + run_command("pixi run rebuild-services") + + # 3. Start services + print("--- Starting services ---") + run_command("pixi run start-services") + + # 4. Generate migration + print(f"--- Generating migration: {args.message} ---") + + # Construct the bash command to run inside the container + # usage of shlex.quote ensures the message is safely quoted for the inner bash shell + safe_message = shlex.quote(args.message) + inner_cmd = f"source /shell-hook.sh && alembic revision --autogenerate -m {safe_message}" + + # We invoke docker-compose directly via pixi to avoid potential argument parsing issues + # with pixi task aliases when handling complex nested quotes. + cmd = [ + "pixi", "run", "docker-compose", + "-f", "resources/docker/docker-compose.yml", + "exec", "prefect-worker", + "/bin/bash", "-c", inner_cmd + ] + run_command(cmd) + + print("--- Schema update orchestration complete! ---") + print("Don't forget to run 'pixi run migrate' to apply the changes.") + +if __name__ == "__main__": + main() From 1a4e470074b5676f485957b7ece64f3a24b98ce7 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Tue, 9 Dec 2025 15:58:44 -0700 Subject: [PATCH 23/81] quick clean up before push to upstream --- ...n.py => 1e9784d75e62_initial_migration.py} | 335 +-- ...2618fe6b09b_rename_tables_to_snake_case.py | 2192 ----------------- ...8c837616b_adding_a_test_to_landiqrecord.py | 32 - .../ca_biositing/datamodels/biomass.py | 306 --- .../ca_biositing/datamodels/config.py | 37 - .../datamodels/data_and_references.py | 85 - .../ca_biositing/datamodels/database.py | 27 - .../datamodels/experiments_analysis.py | 296 --- .../datamodels/external_datasets.py | 295 --- .../datamodels/geographic_locations.py | 113 - .../datamodels/linkml/modules/resources.yaml | 2 - .../datamodels/metadata_samples.py | 79 - .../ca_biositing/datamodels/organizations.py | 46 - .../datamodels/people_contacts.py | 59 - .../datamodels/sample_preprocessing.py | 68 - .../datamodels/specific_aalysis_results.py | 199 -- .../ca_biositing/datamodels/user.py | 13 - 17 files changed, 168 insertions(+), 4016 deletions(-) rename alembic/versions/{e22149be0d9c_initial_migration.py => 1e9784d75e62_initial_migration.py} (88%) delete mode 100644 alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py delete mode 100644 alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/biomass.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/config.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/data_and_references.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/database.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/experiments_analysis.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/external_datasets.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/geographic_locations.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/metadata_samples.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/organizations.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/people_contacts.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/sample_preprocessing.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/specific_aalysis_results.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/user.py diff --git a/alembic/versions/e22149be0d9c_initial_migration.py b/alembic/versions/1e9784d75e62_initial_migration.py similarity index 88% rename from alembic/versions/e22149be0d9c_initial_migration.py rename to alembic/versions/1e9784d75e62_initial_migration.py index 574739e6..83745dc2 100644 --- a/alembic/versions/e22149be0d9c_initial_migration.py +++ b/alembic/versions/1e9784d75e62_initial_migration.py @@ -1,8 +1,8 @@ """Initial migration -Revision ID: e22149be0d9c +Revision ID: 1e9784d75e62 Revises: -Create Date: 2025-12-08 18:01:48.554213 +Create Date: 2025-12-08 22:50:05.973054 """ from typing import Sequence, Union @@ -12,7 +12,7 @@ # revision identifiers, used by Alembic. -revision: str = 'e22149be0d9c' +revision: str = '1e9784d75e62' down_revision: Union[str, Sequence[str], None] = None branch_labels: Union[str, Sequence[str], None] = None depends_on: Union[str, Sequence[str], None] = None @@ -21,14 +21,14 @@ def upgrade() -> None: """Upgrade schema.""" # ### commands auto generated by Alembic - please adjust! ### - op.create_table('AgTreatment', + op.create_table('ag_treatment', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Aim1RecordBase', + op.create_table('aim1_record_base', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -46,7 +46,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Aim2RecordBase', + op.create_table('aim2_record_base', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -64,14 +64,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('AnalysisType', + op.create_table('analysis_type', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('AutoclaveRecord', + op.create_table('autoclave_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -89,7 +89,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('BaseEntity', + op.create_table('base_entity', sa.Column('id', sa.Integer(), nullable=False), sa.Column('created_at', sa.DateTime(), nullable=True), sa.Column('updated_at', sa.DateTime(), nullable=True), @@ -97,7 +97,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('BillionTon2023Record', + op.create_table('billion_ton2023_record', sa.Column('subclass_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('geoid', sa.Text(), nullable=True), @@ -119,7 +119,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('CalorimetryRecord', + op.create_table('calorimetry_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -137,14 +137,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('CollectionMethod', + op.create_table('collection_method', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('CompositionalRecord', + op.create_table('compositional_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -162,7 +162,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Contact', + op.create_table('contact', sa.Column('id', sa.Integer(), nullable=False), sa.Column('first_name', sa.Text(), nullable=True), sa.Column('last_name', sa.Text(), nullable=True), @@ -170,7 +170,7 @@ def upgrade() -> None: sa.Column('affiliation', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('DataSource', + op.create_table('data_source', sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), @@ -187,7 +187,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('DataSourceType', + op.create_table('data_source_type', sa.Column('source_type_id', sa.Integer(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), sa.Column('created_at', sa.DateTime(), nullable=True), @@ -196,7 +196,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Dataset', + op.create_table('dataset', sa.Column('name', sa.Text(), nullable=True), sa.Column('record_type', sa.Text(), nullable=True), sa.Column('source_id', sa.Integer(), nullable=True), @@ -210,14 +210,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('DimensionType', + op.create_table('dimension_type', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('EntityLineage', + op.create_table('entity_lineage', sa.Column('id', sa.Integer(), nullable=False), sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.Column('source_table', sa.Text(), nullable=True), @@ -225,7 +225,7 @@ def upgrade() -> None: sa.Column('note', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Equipment', + op.create_table('equipment', sa.Column('equipment_location_id', sa.Integer(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), @@ -233,7 +233,7 @@ def upgrade() -> None: sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('EtlRun', + op.create_table('etl_run', sa.Column('id', sa.Integer(), nullable=False), sa.Column('started_at', sa.DateTime(), nullable=True), sa.Column('completed_at', sa.DateTime(), nullable=True), @@ -243,7 +243,7 @@ def upgrade() -> None: sa.Column('note', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Experiment', + op.create_table('experiment', sa.Column('analyst_id', sa.Integer(), nullable=True), sa.Column('exper_start_date', sa.Date(), nullable=True), sa.Column('exper_duration', sa.Numeric(), nullable=True), @@ -257,31 +257,31 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ExperimentAnalysis', + op.create_table('experiment_analysis', sa.Column('id', sa.Integer(), nullable=False), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('analysis_type_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ExperimentEquipment', + op.create_table('experiment_equipment', sa.Column('id', sa.Integer(), nullable=False), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('equipment_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ExperimentMethod', + op.create_table('experiment_method', sa.Column('id', sa.Integer(), nullable=False), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('method_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ExperimentPreparedSample', + op.create_table('experiment_prepared_sample', sa.Column('id', sa.Integer(), nullable=False), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('prepared_sample_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FermentationRecord', + op.create_table('fermentation_record', sa.Column('strain_id', sa.Integer(), nullable=True), sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), sa.Column('eh_method_id', sa.Integer(), nullable=True), @@ -308,7 +308,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FieldSample', + op.create_table('field_sample', sa.Column('name', sa.Text(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('provider_id', sa.Integer(), nullable=True), @@ -334,7 +334,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FieldSampleCondition', + op.create_table('field_sample_condition', sa.Column('field_sample_id', sa.Integer(), nullable=True), sa.Column('ag_treatment_id', sa.Integer(), nullable=True), sa.Column('last_application_date', sa.Date(), nullable=True), @@ -347,14 +347,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FieldStorageMethod', + op.create_table('field_storage_method', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FileObjectMetadata', + op.create_table('file_object_metadata', sa.Column('data_source_id', sa.Integer(), nullable=True), sa.Column('bucket_path', sa.Text(), nullable=True), sa.Column('file_format', sa.Text(), nullable=True), @@ -368,7 +368,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FtnirRecord', + op.create_table('ftnir_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -386,7 +386,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('GasificationRecord', + op.create_table('gasification_record', sa.Column('feedstock_mass', sa.Numeric(), nullable=True), sa.Column('bed_temperature', sa.Numeric(), nullable=True), sa.Column('gas_flow_rate', sa.Numeric(), nullable=True), @@ -407,7 +407,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Geography', + op.create_table('geography', sa.Column('geoid', sa.Text(), nullable=False), sa.Column('state_name', sa.Text(), nullable=True), sa.Column('state_fips', sa.Text(), nullable=True), @@ -417,14 +417,14 @@ def upgrade() -> None: sa.Column('agg_level_desc', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('geoid') ) - op.create_table('HarvestMethod', + op.create_table('harvest_method', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('IcpRecord', + op.create_table('icp_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -442,7 +442,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LandiqRecord', + op.create_table('landiq_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('polygon_id', sa.Integer(), nullable=True), sa.Column('main_crop', sa.Integer(), nullable=True), @@ -454,6 +454,7 @@ def upgrade() -> None: sa.Column('acres', sa.Float(), nullable=True), sa.Column('version', sa.Text(), nullable=True), sa.Column('note', sa.Text(), nullable=True), + sa.Column('test', sa.Text(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), sa.Column('created_at', sa.DateTime(), nullable=True), sa.Column('updated_at', sa.DateTime(), nullable=True), @@ -461,13 +462,13 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LineageGroup', + op.create_table('lineage_group', sa.Column('id', sa.Integer(), nullable=False), sa.Column('etl_run_id', sa.Text(), nullable=True), sa.Column('note', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LocationAddress', + op.create_table('location_address', sa.Column('geography_id', sa.Text(), nullable=True), sa.Column('address_line1', sa.Text(), nullable=True), sa.Column('address_line2', sa.Text(), nullable=True), @@ -483,14 +484,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LocationResolution', + op.create_table('location_resolution', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LocationSoilType', + op.create_table('location_soil_type', sa.Column('location_id', sa.Integer(), nullable=True), sa.Column('soil_type_id', sa.Integer(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), @@ -500,14 +501,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LookupBase', + op.create_table('lookup_base', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Method', + op.create_table('method', sa.Column('name', sa.Text(), nullable=True), sa.Column('method_abbrev_id', sa.Integer(), nullable=True), sa.Column('method_category_id', sa.Integer(), nullable=True), @@ -522,28 +523,28 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('MethodAbbrev', + op.create_table('method_abbrev', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('MethodCategory', + op.create_table('method_category', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('MethodStandard', + op.create_table('method_standard', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Observation', + op.create_table('observation', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('record_type', sa.Text(), nullable=True), sa.Column('record_id', sa.Integer(), nullable=True), @@ -561,7 +562,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Parameter', + op.create_table('parameter', sa.Column('name', sa.Text(), nullable=True), sa.Column('standard_unit_id', sa.Integer(), nullable=True), sa.Column('calculated', sa.Boolean(), nullable=True), @@ -573,26 +574,26 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ParameterCategory', + op.create_table('parameter_category', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ParameterCategoryParameter', + op.create_table('parameter_category_parameter', sa.Column('id', sa.Integer(), nullable=False), sa.Column('parameter_id', sa.Integer(), nullable=True), sa.Column('parameter_category_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ParameterUnit', + op.create_table('parameter_unit', sa.Column('id', sa.Integer(), nullable=False), sa.Column('parameter_id', sa.Integer(), nullable=True), sa.Column('alternate_unit_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PhysicalCharacteristic', + op.create_table('physical_characteristic', sa.Column('field_sample_id', sa.Integer(), nullable=True), sa.Column('particle_length', sa.Numeric(), nullable=True), sa.Column('particle_width', sa.Numeric(), nullable=True), @@ -605,13 +606,13 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Polygon', + op.create_table('polygon', sa.Column('id', sa.Integer(), nullable=False), sa.Column('geoid', sa.Text(), nullable=True), sa.Column('geom', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PreparationMethod', + op.create_table('preparation_method', sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('prep_method_abbrev_id', sa.Integer(), nullable=True), @@ -625,14 +626,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PreparationMethodAbbreviation', + op.create_table('preparation_method_abbreviation', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PreparedSample', + op.create_table('prepared_sample', sa.Column('name', sa.Text(), nullable=True), sa.Column('field_sample_id', sa.Integer(), nullable=True), sa.Column('prep_method_id', sa.Integer(), nullable=True), @@ -646,7 +647,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PretreatmentRecord', + op.create_table('pretreatment_record', sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), sa.Column('eh_method_id', sa.Integer(), nullable=True), sa.Column('reaction_block_id', sa.Integer(), nullable=True), @@ -670,7 +671,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PrimaryCrop', + op.create_table('primary_crop', sa.Column('note', sa.Text(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), @@ -678,19 +679,19 @@ def upgrade() -> None: sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ProcessingMethod', + op.create_table('processing_method', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Provider', + op.create_table('provider', sa.Column('id', sa.Integer(), nullable=False), sa.Column('codename', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ProximateRecord', + op.create_table('proximate_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -708,7 +709,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Resource', + op.create_table('resource', sa.Column('name', sa.Text(), nullable=True), sa.Column('primary_crop_id', sa.Integer(), nullable=True), sa.Column('resource_class_id', sa.Integer(), nullable=True), @@ -721,7 +722,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceAvailability', + op.create_table('resource_availability', sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('geoid', sa.Text(), nullable=True), sa.Column('from_month', sa.Integer(), nullable=True), @@ -735,14 +736,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceClass', + op.create_table('resource_class', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceCounterfactual', + op.create_table('resource_counterfactual', sa.Column('geoid', sa.Text(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('counterfactual_description', sa.Text(), nullable=True), @@ -767,20 +768,20 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceMorphology', + op.create_table('resource_morphology', sa.Column('id', sa.Integer(), nullable=False), sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('morphology_uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceSubclass', + op.create_table('resource_subclass', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceUsdaCommodityMap', + op.create_table('resource_usda_commodity_map', sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('primary_crop_id', sa.Integer(), nullable=True), sa.Column('usda_commodity_id', sa.Integer(), nullable=True), @@ -793,7 +794,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('RgbRecord', + op.create_table('rgb_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -811,21 +812,21 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('SoilType', + op.create_table('soil_type', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('SourceType', + op.create_table('source_type', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Strain', + op.create_table('strain', sa.Column('parent_strain_id', sa.Integer(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), @@ -833,7 +834,7 @@ def upgrade() -> None: sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UltimateRecord', + op.create_table('ultimate_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -851,14 +852,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Unit', + op.create_table('unit', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaCensusRecord', + op.create_table('usda_census_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('geoid', sa.Text(), nullable=True), sa.Column('commodity_code', sa.Integer(), nullable=True), @@ -872,7 +873,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaCommodity', + op.create_table('usda_commodity', sa.Column('usda_source', sa.Text(), nullable=True), sa.Column('usda_code', sa.Text(), nullable=True), sa.Column('parent_commodity_id', sa.Integer(), nullable=True), @@ -882,14 +883,14 @@ def upgrade() -> None: sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaDomain', + op.create_table('usda_domain', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaMarketRecord', + op.create_table('usda_market_record', sa.Column('report_id', sa.Integer(), nullable=True), sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('report_begin_date', sa.DateTime(), nullable=True), @@ -917,7 +918,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaMarketReport', + op.create_table('usda_market_report', sa.Column('slug_id', sa.Integer(), nullable=True), sa.Column('slug_name', sa.Text(), nullable=True), sa.Column('report_series_title', sa.Text(), nullable=True), @@ -933,21 +934,21 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaStatisticCategory', + op.create_table('usda_statistic_category', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaSurveyProgram', + op.create_table('usda_survey_program', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaSurveyRecord', + op.create_table('usda_survey_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('geoid', sa.Text(), nullable=True), sa.Column('commodity_code', sa.Integer(), nullable=True), @@ -964,7 +965,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaTermMap', + op.create_table('usda_term_map', sa.Column('source_system', sa.Text(), nullable=True), sa.Column('source_context', sa.Text(), nullable=True), sa.Column('raw_term', sa.Text(), nullable=True), @@ -978,7 +979,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('XrdRecord', + op.create_table('xrd_record', sa.Column('maybe_scan_low_nm', sa.Integer(), nullable=True), sa.Column('maybe_scan_high_nm', sa.Integer(), nullable=True), sa.Column('dataset_id', sa.Integer(), nullable=True), @@ -998,7 +999,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('XrfRecord', + op.create_table('xrf_record', sa.Column('maybe_wavelength_nm', sa.Numeric(), nullable=True), sa.Column('maybe_intensity', sa.Numeric(), nullable=True), sa.Column('maybe_energy_slope', sa.Numeric(), nullable=True), @@ -1026,86 +1027,86 @@ def upgrade() -> None: def downgrade() -> None: """Downgrade schema.""" # ### commands auto generated by Alembic - please adjust! ### - op.drop_table('XrfRecord') - op.drop_table('XrdRecord') - op.drop_table('UsdaTermMap') - op.drop_table('UsdaSurveyRecord') - op.drop_table('UsdaSurveyProgram') - op.drop_table('UsdaStatisticCategory') - op.drop_table('UsdaMarketReport') - op.drop_table('UsdaMarketRecord') - op.drop_table('UsdaDomain') - op.drop_table('UsdaCommodity') - op.drop_table('UsdaCensusRecord') - op.drop_table('Unit') - op.drop_table('UltimateRecord') - op.drop_table('Strain') - op.drop_table('SourceType') - op.drop_table('SoilType') - op.drop_table('RgbRecord') - op.drop_table('ResourceUsdaCommodityMap') - op.drop_table('ResourceSubclass') - op.drop_table('ResourceMorphology') - op.drop_table('ResourceCounterfactual') - op.drop_table('ResourceClass') - op.drop_table('ResourceAvailability') - op.drop_table('Resource') - op.drop_table('ProximateRecord') - op.drop_table('Provider') - op.drop_table('ProcessingMethod') - op.drop_table('PrimaryCrop') - op.drop_table('PretreatmentRecord') - op.drop_table('PreparedSample') - op.drop_table('PreparationMethodAbbreviation') - op.drop_table('PreparationMethod') - op.drop_table('Polygon') - op.drop_table('PhysicalCharacteristic') - op.drop_table('ParameterUnit') - op.drop_table('ParameterCategoryParameter') - op.drop_table('ParameterCategory') - op.drop_table('Parameter') - op.drop_table('Observation') - op.drop_table('MethodStandard') - op.drop_table('MethodCategory') - op.drop_table('MethodAbbrev') - op.drop_table('Method') - op.drop_table('LookupBase') - op.drop_table('LocationSoilType') - op.drop_table('LocationResolution') - op.drop_table('LocationAddress') - op.drop_table('LineageGroup') - op.drop_table('LandiqRecord') - op.drop_table('IcpRecord') - op.drop_table('HarvestMethod') - op.drop_table('Geography') - op.drop_table('GasificationRecord') - op.drop_table('FtnirRecord') - op.drop_table('FileObjectMetadata') - op.drop_table('FieldStorageMethod') - op.drop_table('FieldSampleCondition') - op.drop_table('FieldSample') - op.drop_table('FermentationRecord') - op.drop_table('ExperimentPreparedSample') - op.drop_table('ExperimentMethod') - op.drop_table('ExperimentEquipment') - op.drop_table('ExperimentAnalysis') - op.drop_table('Experiment') - op.drop_table('EtlRun') - op.drop_table('Equipment') - op.drop_table('EntityLineage') - op.drop_table('DimensionType') - op.drop_table('Dataset') - op.drop_table('DataSourceType') - op.drop_table('DataSource') - op.drop_table('Contact') - op.drop_table('CompositionalRecord') - op.drop_table('CollectionMethod') - op.drop_table('CalorimetryRecord') - op.drop_table('BillionTon2023Record') - op.drop_table('BaseEntity') - op.drop_table('AutoclaveRecord') - op.drop_table('AnalysisType') - op.drop_table('Aim2RecordBase') - op.drop_table('Aim1RecordBase') - op.drop_table('AgTreatment') + op.drop_table('xrf_record') + op.drop_table('xrd_record') + op.drop_table('usda_term_map') + op.drop_table('usda_survey_record') + op.drop_table('usda_survey_program') + op.drop_table('usda_statistic_category') + op.drop_table('usda_market_report') + op.drop_table('usda_market_record') + op.drop_table('usda_domain') + op.drop_table('usda_commodity') + op.drop_table('usda_census_record') + op.drop_table('unit') + op.drop_table('ultimate_record') + op.drop_table('strain') + op.drop_table('source_type') + op.drop_table('soil_type') + op.drop_table('rgb_record') + op.drop_table('resource_usda_commodity_map') + op.drop_table('resource_subclass') + op.drop_table('resource_morphology') + op.drop_table('resource_counterfactual') + op.drop_table('resource_class') + op.drop_table('resource_availability') + op.drop_table('resource') + op.drop_table('proximate_record') + op.drop_table('provider') + op.drop_table('processing_method') + op.drop_table('primary_crop') + op.drop_table('pretreatment_record') + op.drop_table('prepared_sample') + op.drop_table('preparation_method_abbreviation') + op.drop_table('preparation_method') + op.drop_table('polygon') + op.drop_table('physical_characteristic') + op.drop_table('parameter_unit') + op.drop_table('parameter_category_parameter') + op.drop_table('parameter_category') + op.drop_table('parameter') + op.drop_table('observation') + op.drop_table('method_standard') + op.drop_table('method_category') + op.drop_table('method_abbrev') + op.drop_table('method') + op.drop_table('lookup_base') + op.drop_table('location_soil_type') + op.drop_table('location_resolution') + op.drop_table('location_address') + op.drop_table('lineage_group') + op.drop_table('landiq_record') + op.drop_table('icp_record') + op.drop_table('harvest_method') + op.drop_table('geography') + op.drop_table('gasification_record') + op.drop_table('ftnir_record') + op.drop_table('file_object_metadata') + op.drop_table('field_storage_method') + op.drop_table('field_sample_condition') + op.drop_table('field_sample') + op.drop_table('fermentation_record') + op.drop_table('experiment_prepared_sample') + op.drop_table('experiment_method') + op.drop_table('experiment_equipment') + op.drop_table('experiment_analysis') + op.drop_table('experiment') + op.drop_table('etl_run') + op.drop_table('equipment') + op.drop_table('entity_lineage') + op.drop_table('dimension_type') + op.drop_table('dataset') + op.drop_table('data_source_type') + op.drop_table('data_source') + op.drop_table('contact') + op.drop_table('compositional_record') + op.drop_table('collection_method') + op.drop_table('calorimetry_record') + op.drop_table('billion_ton2023_record') + op.drop_table('base_entity') + op.drop_table('autoclave_record') + op.drop_table('analysis_type') + op.drop_table('aim2_record_base') + op.drop_table('aim1_record_base') + op.drop_table('ag_treatment') # ### end Alembic commands ### diff --git a/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py b/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py deleted file mode 100644 index 22464c6b..00000000 --- a/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py +++ /dev/null @@ -1,2192 +0,0 @@ -"""rename_tables_to_snake_case - -Revision ID: 42618fe6b09b -Revises: e22149be0d9c -Create Date: 2025-12-08 21:37:30.253589 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa -from sqlalchemy.dialects import postgresql - -# revision identifiers, used by Alembic. -revision: str = '42618fe6b09b' -down_revision: Union[str, Sequence[str], None] = 'e22149be0d9c' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.create_table('ag_treatment', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('aim1_record_base', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('aim2_record_base', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('analysis_type', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('autoclave_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('base_entity', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('billion_ton2023_record', - sa.Column('subclass_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('county_square_miles', sa.Float(), nullable=True), - sa.Column('model_name', sa.Text(), nullable=True), - sa.Column('scenario_name', sa.Text(), nullable=True), - sa.Column('price_offered_usd', sa.Numeric(), nullable=True), - sa.Column('production', sa.Integer(), nullable=True), - sa.Column('production_unit_id', sa.Integer(), nullable=True), - sa.Column('btu_ton', sa.Integer(), nullable=True), - sa.Column('production_energy_content', sa.Integer(), nullable=True), - sa.Column('energy_content_unit_id', sa.Integer(), nullable=True), - sa.Column('product_density_dtpersqmi', sa.Numeric(), nullable=True), - sa.Column('land_source', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('calorimetry_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('collection_method', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('compositional_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('contact', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('first_name', sa.Text(), nullable=True), - sa.Column('last_name', sa.Text(), nullable=True), - sa.Column('email', sa.Text(), nullable=True), - sa.Column('affiliation', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('data_source', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.Column('publication_date', sa.Date(), nullable=True), - sa.Column('version', sa.Text(), nullable=True), - sa.Column('publisher', sa.Text(), nullable=True), - sa.Column('author', sa.Text(), nullable=True), - sa.Column('license', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('data_source_type', - sa.Column('source_type_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('dataset', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('record_type', sa.Text(), nullable=True), - sa.Column('source_id', sa.Integer(), nullable=True), - sa.Column('start_date', sa.Date(), nullable=True), - sa.Column('end_date', sa.Date(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('dimension_type', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('entity_lineage', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.Column('source_table', sa.Text(), nullable=True), - sa.Column('source_row_id', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('equipment', - sa.Column('equipment_location_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('etl_run', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('started_at', sa.DateTime(), nullable=True), - sa.Column('completed_at', sa.DateTime(), nullable=True), - sa.Column('pipeline_name', sa.Text(), nullable=True), - sa.Column('status', sa.Text(), nullable=True), - sa.Column('records_ingested', sa.Integer(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('experiment', - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('exper_start_date', sa.Date(), nullable=True), - sa.Column('exper_duration', sa.Numeric(), nullable=True), - sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('exper_location_id', sa.Integer(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('experiment_analysis', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('experiment_equipment', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('equipment_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('experiment_method', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('experiment_prepared_sample', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('prepared_sample_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('fermentation_record', - sa.Column('strain_id', sa.Integer(), nullable=True), - sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), - sa.Column('eh_method_id', sa.Integer(), nullable=True), - sa.Column('replicate_no', sa.Integer(), nullable=True), - sa.Column('well_position', sa.Text(), nullable=True), - sa.Column('temperature', sa.Numeric(), nullable=True), - sa.Column('agitation_rpm', sa.Numeric(), nullable=True), - sa.Column('vessel_id', sa.Integer(), nullable=True), - sa.Column('analyte_detection_equipment_id', sa.Integer(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('field_sample', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('provider_id', sa.Integer(), nullable=True), - sa.Column('collector_id', sa.Integer(), nullable=True), - sa.Column('sample_collection_source', sa.Text(), nullable=True), - sa.Column('amount_collected', sa.Numeric(), nullable=True), - sa.Column('amount_collected_unit_id', sa.Integer(), nullable=True), - sa.Column('sampling_location_id', sa.Integer(), nullable=True), - sa.Column('field_storage_method_id', sa.Integer(), nullable=True), - sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), - sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('field_storage_location_id', sa.Integer(), nullable=True), - sa.Column('collection_timestamp', sa.DateTime(), nullable=True), - sa.Column('collection_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_date', sa.Date(), nullable=True), - sa.Column('field_sample_storage_location_id', sa.Integer(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('field_sample_condition', - sa.Column('field_sample_id', sa.Integer(), nullable=True), - sa.Column('ag_treatment_id', sa.Integer(), nullable=True), - sa.Column('last_application_date', sa.Date(), nullable=True), - sa.Column('treatment_amount_per_acre', sa.Float(), nullable=True), - sa.Column('processing_method_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('field_storage_method', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('file_object_metadata', - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('bucket_path', sa.Text(), nullable=True), - sa.Column('file_format', sa.Text(), nullable=True), - sa.Column('file_size', sa.Integer(), nullable=True), - sa.Column('checksum_md5', sa.Text(), nullable=True), - sa.Column('checksum_sha256', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('ftnir_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('gasification_record', - sa.Column('feedstock_mass', sa.Numeric(), nullable=True), - sa.Column('bed_temperature', sa.Numeric(), nullable=True), - sa.Column('gas_flow_rate', sa.Numeric(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('geography', - sa.Column('geoid', sa.Text(), nullable=False), - sa.Column('state_name', sa.Text(), nullable=True), - sa.Column('state_fips', sa.Text(), nullable=True), - sa.Column('county_name', sa.Text(), nullable=True), - sa.Column('county_fips', sa.Text(), nullable=True), - sa.Column('region_name', sa.Text(), nullable=True), - sa.Column('agg_level_desc', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('geoid') - ) - op.create_table('harvest_method', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('icp_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('landiq_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('polygon_id', sa.Integer(), nullable=True), - sa.Column('main_crop', sa.Integer(), nullable=True), - sa.Column('secondary_crop', sa.Integer(), nullable=True), - sa.Column('tertiary_crop', sa.Integer(), nullable=True), - sa.Column('quaternary_crop', sa.Integer(), nullable=True), - sa.Column('confidence', sa.Integer(), nullable=True), - sa.Column('irrigated', sa.Boolean(), nullable=True), - sa.Column('acres', sa.Float(), nullable=True), - sa.Column('version', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('lineage_group', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('location_address', - sa.Column('geography_id', sa.Text(), nullable=True), - sa.Column('address_line1', sa.Text(), nullable=True), - sa.Column('address_line2', sa.Text(), nullable=True), - sa.Column('city', sa.Text(), nullable=True), - sa.Column('zip', sa.Text(), nullable=True), - sa.Column('lat', sa.Float(), nullable=True), - sa.Column('lon', sa.Float(), nullable=True), - sa.Column('is_anonymous', sa.Boolean(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('location_resolution', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('location_soil_type', - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('soil_type_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('lookup_base', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('method', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('method_category_id', sa.Integer(), nullable=True), - sa.Column('method_standard_id', sa.Integer(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('detection_limits', sa.Text(), nullable=True), - sa.Column('source_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('method_abbrev', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('method_category', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('method_standard', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('observation', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('record_type', sa.Text(), nullable=True), - sa.Column('record_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('dimension_type_id', sa.Integer(), nullable=True), - sa.Column('dimension_value', sa.Numeric(), nullable=True), - sa.Column('dimension_unit_id', sa.Integer(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('parameter', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('standard_unit_id', sa.Integer(), nullable=True), - sa.Column('calculated', sa.Boolean(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('parameter_category', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('parameter_category_parameter', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_category_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('parameter_unit', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('alternate_unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('physical_characteristic', - sa.Column('field_sample_id', sa.Integer(), nullable=True), - sa.Column('particle_length', sa.Numeric(), nullable=True), - sa.Column('particle_width', sa.Numeric(), nullable=True), - sa.Column('particle_height', sa.Numeric(), nullable=True), - sa.Column('particle_unit_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('polygon', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('geom', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('preparation_method', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('prep_method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('prep_temp_c', sa.Numeric(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.Column('drying_step', sa.Boolean(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('preparation_method_abbreviation', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('prepared_sample', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('field_sample_id', sa.Integer(), nullable=True), - sa.Column('prep_method_id', sa.Integer(), nullable=True), - sa.Column('prep_date', sa.Date(), nullable=True), - sa.Column('preparer_id', sa.Integer(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('pretreatment_record', - sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), - sa.Column('eh_method_id', sa.Integer(), nullable=True), - sa.Column('reaction_block_id', sa.Integer(), nullable=True), - sa.Column('block_position', sa.Text(), nullable=True), - sa.Column('temperature', sa.Numeric(), nullable=True), - sa.Column('replicate_no', sa.Integer(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('primary_crop', - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('processing_method', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('provider', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('codename', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('proximate_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('primary_crop_id', sa.Integer(), nullable=True), - sa.Column('resource_class_id', sa.Integer(), nullable=True), - sa.Column('resource_subclass_id', sa.Integer(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_availability', - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('from_month', sa.Integer(), nullable=True), - sa.Column('to_month', sa.Integer(), nullable=True), - sa.Column('year_round', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_class', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_counterfactual', - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('counterfactual_description', sa.Text(), nullable=True), - sa.Column('animal_bedding_percent', sa.Numeric(), nullable=True), - sa.Column('animal_bedding_source_id', sa.Integer(), nullable=True), - sa.Column('animal_feed_percent', sa.Numeric(), nullable=True), - sa.Column('animal_feed_source_id', sa.Integer(), nullable=True), - sa.Column('bioelectricty_percent', sa.Numeric(), nullable=True), - sa.Column('bioelectricty_source_id', sa.Integer(), nullable=True), - sa.Column('burn_percent', sa.Numeric(), nullable=True), - sa.Column('burn_source_id', sa.Integer(), nullable=True), - sa.Column('compost_percent', sa.Numeric(), nullable=True), - sa.Column('compost_source_id', sa.Integer(), nullable=True), - sa.Column('landfill_percent', sa.Numeric(), nullable=True), - sa.Column('landfill_source_id', sa.Integer(), nullable=True), - sa.Column('counterfactual_date', sa.Date(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_morphology', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('morphology_uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_subclass', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_usda_commodity_map', - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('primary_crop_id', sa.Integer(), nullable=True), - sa.Column('usda_commodity_id', sa.Integer(), nullable=True), - sa.Column('match_tier', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('rgb_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('soil_type', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('source_type', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('strain', - sa.Column('parent_strain_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('ultimate_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('unit', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_census_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('commodity_code', sa.Integer(), nullable=True), - sa.Column('year', sa.Integer(), nullable=True), - sa.Column('source_reference', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_commodity', - sa.Column('usda_source', sa.Text(), nullable=True), - sa.Column('usda_code', sa.Text(), nullable=True), - sa.Column('parent_commodity_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_domain', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_market_record', - sa.Column('report_id', sa.Integer(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('report_begin_date', sa.DateTime(), nullable=True), - sa.Column('report_end_date', sa.DateTime(), nullable=True), - sa.Column('report_date', sa.DateTime(), nullable=True), - sa.Column('commodity_id', sa.Integer(), nullable=True), - sa.Column('market_type_id', sa.Integer(), nullable=True), - sa.Column('market_type_catagory', sa.Text(), nullable=True), - sa.Column('grp', sa.Text(), nullable=True), - sa.Column('market_catagory_id', sa.Integer(), nullable=True), - sa.Column('class_', sa.Text(), nullable=True), - sa.Column('grade', sa.Text(), nullable=True), - sa.Column('variety', sa.Text(), nullable=True), - sa.Column('protein_pct', sa.Numeric(), nullable=True), - sa.Column('application', sa.Text(), nullable=True), - sa.Column('pkg', sa.Text(), nullable=True), - sa.Column('sale_type', sa.Text(), nullable=True), - sa.Column('price_unit_id', sa.Integer(), nullable=True), - sa.Column('freight', sa.Text(), nullable=True), - sa.Column('trans_mode', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_market_report', - sa.Column('slug_id', sa.Integer(), nullable=True), - sa.Column('slug_name', sa.Text(), nullable=True), - sa.Column('report_series_title', sa.Text(), nullable=True), - sa.Column('frequency', sa.Text(), nullable=True), - sa.Column('office_name', sa.Text(), nullable=True), - sa.Column('office_city_id', sa.Integer(), nullable=True), - sa.Column('office_state_fips', sa.Text(), nullable=True), - sa.Column('source_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_statistic_category', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_survey_program', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_survey_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('commodity_code', sa.Integer(), nullable=True), - sa.Column('year', sa.Integer(), nullable=True), - sa.Column('survey_program_id', sa.Integer(), nullable=True), - sa.Column('survey_period', sa.Text(), nullable=True), - sa.Column('reference_month', sa.Text(), nullable=True), - sa.Column('seasonal_flag', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_term_map', - sa.Column('source_system', sa.Text(), nullable=True), - sa.Column('source_context', sa.Text(), nullable=True), - sa.Column('raw_term', sa.Text(), nullable=True), - sa.Column('usda_commodity_id', sa.Integer(), nullable=True), - sa.Column('is_verified', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('xrd_record', - sa.Column('maybe_scan_low_nm', sa.Integer(), nullable=True), - sa.Column('maybe_scan_high_nm', sa.Integer(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('xrf_record', - sa.Column('maybe_wavelength_nm', sa.Numeric(), nullable=True), - sa.Column('maybe_intensity', sa.Numeric(), nullable=True), - sa.Column('maybe_energy_slope', sa.Numeric(), nullable=True), - sa.Column('maybe_energy_offset', sa.Numeric(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.drop_table('UsdaMarketRecord') - op.drop_table('ResourceAvailability') - op.drop_table('PreparedSample') - op.drop_table('UsdaStatisticCategory') - op.drop_table('PrimaryCrop') - op.drop_table('BaseEntity') - op.drop_table('ResourceCounterfactual') - op.drop_table('UltimateRecord') - op.drop_table('SourceType') - op.drop_table('Contact') - op.drop_table('DataSourceType') - op.drop_table('ParameterUnit') - op.drop_table('Parameter') - op.drop_table('UsdaTermMap') - op.drop_table('Experiment') - op.drop_table('ParameterCategory') - op.drop_table('ExperimentEquipment') - op.drop_table('Aim1RecordBase') - op.drop_table('Geography') - op.drop_table('Method') - op.drop_table('LineageGroup') - op.drop_table('RgbRecord') - op.drop_table('MethodStandard') - op.drop_table('PretreatmentRecord') - op.drop_table('ResourceSubclass') - op.drop_table('UsdaMarketReport') - op.drop_table('Polygon') - op.drop_table('LocationResolution') - op.drop_table('ResourceMorphology') - op.drop_table('AutoclaveRecord') - op.drop_table('DimensionType') - op.drop_table('CompositionalRecord') - op.drop_table('PhysicalCharacteristic') - op.drop_table('Aim2RecordBase') - op.drop_table('UsdaCensusRecord') - op.drop_table('ResourceUsdaCommodityMap') - op.drop_table('AnalysisType') - op.drop_table('ParameterCategoryParameter') - op.drop_table('ExperimentAnalysis') - op.drop_table('UsdaDomain') - op.drop_table('HarvestMethod') - op.drop_table('LookupBase') - op.drop_table('FtnirRecord') - op.drop_table('Resource') - op.drop_table('Equipment') - op.drop_table('DataSource') - op.drop_table('ResourceClass') - op.drop_table('LocationAddress') - op.drop_table('UsdaSurveyRecord') - op.drop_table('FermentationRecord') - op.drop_table('XrdRecord') - op.drop_table('AgTreatment') - op.drop_table('ExperimentMethod') - op.drop_table('Dataset') - op.drop_table('LocationSoilType') - op.drop_table('FieldSampleCondition') - op.drop_table('XrfRecord') - op.drop_table('MethodAbbrev') - op.drop_table('Provider') - op.drop_table('LandiqRecord') - op.drop_table('EntityLineage') - op.drop_table('Unit') - op.drop_table('CalorimetryRecord') - op.drop_table('ExperimentPreparedSample') - op.drop_table('CollectionMethod') - op.drop_table('IcpRecord') - op.drop_table('PreparationMethodAbbreviation') - op.drop_table('BillionTon2023Record') - op.drop_table('ProcessingMethod') - op.drop_table('EtlRun') - op.drop_table('FileObjectMetadata') - op.drop_table('MethodCategory') - op.drop_table('GasificationRecord') - op.drop_table('UsdaCommodity') - op.drop_table('PreparationMethod') - op.drop_table('Observation') - op.drop_table('SoilType') - op.drop_table('FieldSample') - op.drop_table('FieldStorageMethod') - op.drop_table('Strain') - op.drop_table('ProximateRecord') - op.drop_table('UsdaSurveyProgram') - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.create_table('UsdaSurveyProgram', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaSurveyProgram_pkey')) - ) - op.create_table('ProximateRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ProximateRecord_pkey')) - ) - op.create_table('Strain', - sa.Column('parent_strain_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Strain_pkey')) - ) - op.create_table('FieldStorageMethod', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FieldStorageMethod_pkey')) - ) - op.create_table('FieldSample', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('provider_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('collector_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_collection_source', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('amount_collected', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('amount_collected_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sampling_location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('field_storage_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('field_storage_duration_value', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('field_storage_duration_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('field_storage_location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('collection_timestamp', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('collection_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('harvest_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('harvest_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('field_sample_storage_location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FieldSample_pkey')) - ) - op.create_table('SoilType', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('SoilType_pkey')) - ) - op.create_table('Observation', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('record_type', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('record_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('value', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dimension_type_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dimension_value', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('dimension_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Observation_pkey')) - ) - op.create_table('PreparationMethod', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('prep_method_abbrev_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('prep_temp_c', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('drying_step', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PreparationMethod_pkey')) - ) - op.create_table('UsdaCommodity', - sa.Column('usda_source', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('usda_code', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('parent_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaCommodity_pkey')) - ) - op.create_table('GasificationRecord', - sa.Column('feedstock_mass', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('bed_temperature', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('gas_flow_rate', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('GasificationRecord_pkey')) - ) - op.create_table('MethodCategory', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('MethodCategory_pkey')) - ) - op.create_table('FileObjectMetadata', - sa.Column('data_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('bucket_path', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('file_format', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('file_size', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('checksum_md5', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('checksum_sha256', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FileObjectMetadata_pkey')) - ) - op.create_table('EtlRun', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('started_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('completed_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('pipeline_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('records_ingested', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('EtlRun_pkey')) - ) - op.create_table('ProcessingMethod', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ProcessingMethod_pkey')) - ) - op.create_table('BillionTon2023Record', - sa.Column('subclass_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('county_square_miles', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), - sa.Column('model_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('scenario_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('price_offered_usd', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('production', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('production_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('btu_ton', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('production_energy_content', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('energy_content_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('product_density_dtpersqmi', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('land_source', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('BillionTon2023Record_pkey')) - ) - op.create_table('PreparationMethodAbbreviation', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PreparationMethodAbbreviation_pkey')) - ) - op.create_table('IcpRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('IcpRecord_pkey')) - ) - op.create_table('CollectionMethod', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('CollectionMethod_pkey')) - ) - op.create_table('ExperimentPreparedSample', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('prepared_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ExperimentPreparedSample_pkey')) - ) - op.create_table('CalorimetryRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('CalorimetryRecord_pkey')) - ) - op.create_table('Unit', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Unit_pkey')) - ) - op.create_table('EntityLineage', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('source_table', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('source_row_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('EntityLineage_pkey')) - ) - op.create_table('LandiqRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('polygon_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('main_crop', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('secondary_crop', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('tertiary_crop', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('quaternary_crop', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('confidence', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('irrigated', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('acres', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), - sa.Column('version', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LandiqRecord_pkey')) - ) - op.create_table('Provider', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('codename', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Provider_pkey')) - ) - op.create_table('MethodAbbrev', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('MethodAbbrev_pkey')) - ) - op.create_table('XrfRecord', - sa.Column('maybe_wavelength_nm', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('maybe_intensity', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('maybe_energy_slope', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('maybe_energy_offset', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('XrfRecord_pkey')) - ) - op.create_table('FieldSampleCondition', - sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('ag_treatment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('last_application_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('treatment_amount_per_acre', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), - sa.Column('processing_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FieldSampleCondition_pkey')) - ) - op.create_table('LocationSoilType', - sa.Column('location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('soil_type_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LocationSoilType_pkey')) - ) - op.create_table('Dataset', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('record_type', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('start_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('end_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Dataset_pkey')) - ) - op.create_table('ExperimentMethod', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ExperimentMethod_pkey')) - ) - op.create_table('AgTreatment', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('AgTreatment_pkey')) - ) - op.create_table('XrdRecord', - sa.Column('maybe_scan_low_nm', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('maybe_scan_high_nm', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('XrdRecord_pkey')) - ) - op.create_table('FermentationRecord', - sa.Column('strain_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('pretreatment_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('eh_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('well_position', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('temperature', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('agitation_rpm', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('vessel_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyte_detection_equipment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FermentationRecord_pkey')) - ) - op.create_table('UsdaSurveyRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('commodity_code', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('year', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('survey_program_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('survey_period', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('reference_month', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('seasonal_flag', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaSurveyRecord_pkey')) - ) - op.create_table('LocationAddress', - sa.Column('geography_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('address_line1', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('address_line2', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('zip', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lat', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), - sa.Column('lon', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), - sa.Column('is_anonymous', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LocationAddress_pkey')) - ) - op.create_table('ResourceClass', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceClass_pkey')) - ) - op.create_table('DataSource', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('publication_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('version', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('publisher', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('author', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('license', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('DataSource_pkey')) - ) - op.create_table('Equipment', - sa.Column('equipment_location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Equipment_pkey')) - ) - op.create_table('Resource', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('primary_crop_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_class_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_subclass_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Resource_pkey')) - ) - op.create_table('FtnirRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FtnirRecord_pkey')) - ) - op.create_table('LookupBase', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LookupBase_pkey')) - ) - op.create_table('HarvestMethod', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('HarvestMethod_pkey')) - ) - op.create_table('UsdaDomain', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaDomain_pkey')) - ) - op.create_table('ExperimentAnalysis', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analysis_type_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ExperimentAnalysis_pkey')) - ) - op.create_table('ParameterCategoryParameter', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('parameter_category_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ParameterCategoryParameter_pkey')) - ) - op.create_table('AnalysisType', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('AnalysisType_pkey')) - ) - op.create_table('ResourceUsdaCommodityMap', - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('primary_crop_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('usda_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('match_tier', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceUsdaCommodityMap_pkey')) - ) - op.create_table('UsdaCensusRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('commodity_code', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('year', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('source_reference', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaCensusRecord_pkey')) - ) - op.create_table('Aim2RecordBase', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Aim2RecordBase_pkey')) - ) - op.create_table('PhysicalCharacteristic', - sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('particle_length', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('particle_width', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('particle_height', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('particle_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PhysicalCharacteristic_pkey')) - ) - op.create_table('CompositionalRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('CompositionalRecord_pkey')) - ) - op.create_table('DimensionType', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('DimensionType_pkey')) - ) - op.create_table('AutoclaveRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('AutoclaveRecord_pkey')) - ) - op.create_table('ResourceMorphology', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('morphology_uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceMorphology_pkey')) - ) - op.create_table('LocationResolution', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LocationResolution_pkey')) - ) - op.create_table('Polygon', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('geom', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Polygon_pkey')) - ) - op.create_table('UsdaMarketReport', - sa.Column('slug_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('slug_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('report_series_title', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('frequency', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('office_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('office_city_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('office_state_fips', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaMarketReport_pkey')) - ) - op.create_table('ResourceSubclass', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceSubclass_pkey')) - ) - op.create_table('PretreatmentRecord', - sa.Column('pretreatment_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('eh_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('reaction_block_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('block_position', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('temperature', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PretreatmentRecord_pkey')) - ) - op.create_table('MethodStandard', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('MethodStandard_pkey')) - ) - op.create_table('RgbRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('RgbRecord_pkey')) - ) - op.create_table('LineageGroup', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LineageGroup_pkey')) - ) - op.create_table('Method', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('method_abbrev_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_category_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_standard_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('detection_limits', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Method_pkey')) - ) - op.create_table('Geography', - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=False), - sa.Column('state_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('state_fips', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('county_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('county_fips', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('region_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('agg_level_desc', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('geoid', name=op.f('Geography_pkey')) - ) - op.create_table('Aim1RecordBase', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Aim1RecordBase_pkey')) - ) - op.create_table('ExperimentEquipment', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('equipment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ExperimentEquipment_pkey')) - ) - op.create_table('ParameterCategory', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ParameterCategory_pkey')) - ) - op.create_table('Experiment', - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('exper_start_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('exper_duration', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('exper_duration_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('exper_location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Experiment_pkey')) - ) - op.create_table('UsdaTermMap', - sa.Column('source_system', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('source_context', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('raw_term', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('usda_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('is_verified', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaTermMap_pkey')) - ) - op.create_table('Parameter', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('standard_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('calculated', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Parameter_pkey')) - ) - op.create_table('ParameterUnit', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('alternate_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ParameterUnit_pkey')) - ) - op.create_table('DataSourceType', - sa.Column('source_type_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('DataSourceType_pkey')) - ) - op.create_table('Contact', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('first_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('last_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('email', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('affiliation', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Contact_pkey')) - ) - op.create_table('SourceType', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('SourceType_pkey')) - ) - op.create_table('UltimateRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UltimateRecord_pkey')) - ) - op.create_table('ResourceCounterfactual', - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('counterfactual_description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('animal_bedding_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('animal_bedding_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('animal_feed_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('animal_feed_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('bioelectricty_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('bioelectricty_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('burn_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('burn_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('compost_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('compost_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('landfill_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('landfill_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('counterfactual_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceCounterfactual_pkey')) - ) - op.create_table('BaseEntity', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('BaseEntity_pkey')) - ) - op.create_table('PrimaryCrop', - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PrimaryCrop_pkey')) - ) - op.create_table('UsdaStatisticCategory', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaStatisticCategory_pkey')) - ) - op.create_table('PreparedSample', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('prep_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('prep_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('preparer_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PreparedSample_pkey')) - ) - op.create_table('ResourceAvailability', - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('from_month', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('to_month', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('year_round', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceAvailability_pkey')) - ) - op.create_table('UsdaMarketRecord', - sa.Column('report_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('report_begin_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('report_end_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('report_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('market_type_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('market_type_catagory', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('grp', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('market_catagory_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('class_', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('grade', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('variety', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('protein_pct', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('application', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('pkg', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('sale_type', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('price_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('freight', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('trans_mode', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaMarketRecord_pkey')) - ) - op.drop_table('xrf_record') - op.drop_table('xrd_record') - op.drop_table('usda_term_map') - op.drop_table('usda_survey_record') - op.drop_table('usda_survey_program') - op.drop_table('usda_statistic_category') - op.drop_table('usda_market_report') - op.drop_table('usda_market_record') - op.drop_table('usda_domain') - op.drop_table('usda_commodity') - op.drop_table('usda_census_record') - op.drop_table('unit') - op.drop_table('ultimate_record') - op.drop_table('strain') - op.drop_table('source_type') - op.drop_table('soil_type') - op.drop_table('rgb_record') - op.drop_table('resource_usda_commodity_map') - op.drop_table('resource_subclass') - op.drop_table('resource_morphology') - op.drop_table('resource_counterfactual') - op.drop_table('resource_class') - op.drop_table('resource_availability') - op.drop_table('resource') - op.drop_table('proximate_record') - op.drop_table('provider') - op.drop_table('processing_method') - op.drop_table('primary_crop') - op.drop_table('pretreatment_record') - op.drop_table('prepared_sample') - op.drop_table('preparation_method_abbreviation') - op.drop_table('preparation_method') - op.drop_table('polygon') - op.drop_table('physical_characteristic') - op.drop_table('parameter_unit') - op.drop_table('parameter_category_parameter') - op.drop_table('parameter_category') - op.drop_table('parameter') - op.drop_table('observation') - op.drop_table('method_standard') - op.drop_table('method_category') - op.drop_table('method_abbrev') - op.drop_table('method') - op.drop_table('lookup_base') - op.drop_table('location_soil_type') - op.drop_table('location_resolution') - op.drop_table('location_address') - op.drop_table('lineage_group') - op.drop_table('landiq_record') - op.drop_table('icp_record') - op.drop_table('harvest_method') - op.drop_table('geography') - op.drop_table('gasification_record') - op.drop_table('ftnir_record') - op.drop_table('file_object_metadata') - op.drop_table('field_storage_method') - op.drop_table('field_sample_condition') - op.drop_table('field_sample') - op.drop_table('fermentation_record') - op.drop_table('experiment_prepared_sample') - op.drop_table('experiment_method') - op.drop_table('experiment_equipment') - op.drop_table('experiment_analysis') - op.drop_table('experiment') - op.drop_table('etl_run') - op.drop_table('equipment') - op.drop_table('entity_lineage') - op.drop_table('dimension_type') - op.drop_table('dataset') - op.drop_table('data_source_type') - op.drop_table('data_source') - op.drop_table('contact') - op.drop_table('compositional_record') - op.drop_table('collection_method') - op.drop_table('calorimetry_record') - op.drop_table('billion_ton2023_record') - op.drop_table('base_entity') - op.drop_table('autoclave_record') - op.drop_table('analysis_type') - op.drop_table('aim2_record_base') - op.drop_table('aim1_record_base') - op.drop_table('ag_treatment') - # ### end Alembic commands ### diff --git a/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py b/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py deleted file mode 100644 index c1db3ff6..00000000 --- a/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py +++ /dev/null @@ -1,32 +0,0 @@ -"""adding a test to landiqrecord - -Revision ID: b838c837616b -Revises: 42618fe6b09b -Create Date: 2025-12-08 22:33:34.608783 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = 'b838c837616b' -down_revision: Union[str, Sequence[str], None] = '42618fe6b09b' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.add_column('landiq_record', sa.Column('test', sa.Text(), nullable=True)) - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.drop_column('landiq_record', 'test') - # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/biomass.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/biomass.py deleted file mode 100644 index 03d4bfb1..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/biomass.py +++ /dev/null @@ -1,306 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - - -# ------------------------------------------------------------ -# SQLModel classes generated from the DBdiagram schema -# ------------------------------------------------------------ - - - -# If you later want to add real FK constraints you can uncomment the import below -# from sqlalchemy import Column, Numeric, DateTime, func - - -# ---------------------------------------------------------------------- -# Table: field_samples -# ---------------------------------------------------------------------- -class FieldSample(SQLModel, table=True): - """Sample metadata collected in the field.""" - __tablename__ = "field_samples" - - sample_id: Optional[int] = Field( - default=None, - primary_key=True, - description="Unique identifier for each sample", - ) - biomass_id: int = Field( - default=None, - index=True, - description="Reference to biomass" - # foreign_key="biomass.biomass_id" - ) - sample_name: str = Field( - default=None, - description='e.g., "Ene‑WaHu018"', - ) - source_codename_id: Optional[int] = Field( - default=None, - index=True, - description="Anonymized source identifier", - ) - data_source_id: Optional[int] = Field( - default=None, - description="Reference to data source" - # foreign_key="data_sources.source_id" - ) - location_id: Optional[int] = Field( - default=None, - description="Reference to geographic location (may be null)" - # foreign_key="geographic_locations.location_id" - ) - field_storage_id: Optional[int] = Field( - default=None, - description="Reference to field storage" - # foreign_key="field_storage.field_storage_id" - ) - field_storage_duration_value: Optional[Decimal] = Field( - default=None, - description="Duration value for field storage", - ) - field_storage_duration_unit_id: Optional[int] = Field( - default=None, - description="Reference to unit of storage duration" - # foreign_key="units.unit_id" - ) - collection_timestamp: Optional[datetime] = Field(default=None) - collection_method_id: Optional[int] = Field( - default=None, - description="Reference to collection method" - # foreign_key="collection_methods.collection_method_id" - ) - harvest_method_id: Optional[int] = Field( - default=None, - description="Reference to harvest method" - # foreign_key="harvest_methods.harvest_method_id" - ) - harvest_date: Optional[date] = Field(default=None) - amount_collected_kg: Optional[Decimal] = Field(default=None) - provider_id: Optional[int] = Field( - default=None, - description="Reference to provider (anonymized)" - # foreign_key="providers.provider_id" - ) - collector_id: Optional[int] = Field( - default=None, - description="Reference to collector" - # foreign_key="collectors.collector_id" - ) - basic_sample_info_note: Optional[str] = Field(default=None) - created_at: datetime = Field( - default_factory=datetime.utcnow, - description="Timestamp when the record was created", - ) - - -# ---------------------------------------------------------------------- -# Table: biomass -# ---------------------------------------------------------------------- -class Biomass(SQLModel, table=True): - """Core biomass entity.""" - __tablename__ = "biomass" - - biomass_id: Optional[int] = Field(default=None, primary_key=True) - biomass_name: str = Field(default=None, index=True) - primary_product_id: Optional[int] = Field( - default=None, - description="Reference to primary product" - # foreign_key="primary_product.primary_product_id" - ) - taxonomy_id: Optional[int] = Field( - default=None, - description="Reference to taxonomy" - # foreign_key="taxonomy.taxonomy_id" - ) - biomass_type_id: Optional[int] = Field( - default=None, - index=True, - description="Reference to biomass type" - # foreign_key="biomass_type.biomass_type_id" - ) - biomass_notes: Optional[str] = Field(default=None) - - -# ---------------------------------------------------------------------- -# Table: biomass_test -# ---------------------------------------------------------------------- - -class BiomassTest(SQLModel, table=True): - """Testing Table""" - __tablename__ = "biomass_test" - - biomass_test_id: Optional[int] = Field(default=None, primary_key=True) - biomass_test_name: str = Field(default=None, index=True) - biomass_test_notes: Optional[str] = Field(default=None) - - - -# ---------------------------------------------------------------------- -# Table: biomass_type -# ---------------------------------------------------------------------- -class BiomassType(SQLModel, table=True): - """Lookup table for biomass type (e.g., crop by‑product, wood residue).""" - __tablename__ = "biomass_type" - - biomass_type_id: Optional[int] = Field(default=None, primary_key=True) - biomass_type: str = Field( - default=None, - unique=True, - description="Crop by‑product, Wood residue, etc.", - ) - - -# ---------------------------------------------------------------------- -# Table: primary_product -# ---------------------------------------------------------------------- -class PrimaryProduct(SQLModel, table=True): - """Lookup table for primary products derived from biomass.""" - __tablename__ = "primary_product" - - primary_product_id: Optional[int] = Field(default=None, primary_key=True) - primary_product_name: str = Field(default=None, unique=True) - - -# ---------------------------------------------------------------------- -# Table: biomass_availability -# ---------------------------------------------------------------------- -class BiomassAvailability(SQLModel, table=True): - """Seasonal and quantitative availability of a biomass.""" - __tablename__ = "biomass_availability" - - availability_id: Optional[int] = Field(default=None, primary_key=True) - biomass_id: int = Field( - default=None, - index=True, - description="Reference to biomass" - # foreign_key="biomass.biomass_id" - ) - location_id: Optional[int] = Field( - default=None, - description="Reference to geographic location" - # foreign_key="geographic_locations.location_id" - ) - primary_product_id: Optional[int] = Field( - default=None, - description="Reference to primary product" - # foreign_key="primary_product.primary_product_id" - ) - from_month: Optional[Decimal] = Field( - default=None, - description="Start month (e.g. 1 = Jan, 6.5 = mid‑June)", - ) - to_month: Optional[Decimal] = Field( - default=None, - description="End month (e.g. 12 = Dec)", - ) - kg_low: Optional[Decimal] = Field(default=None, description="Annual low estimate (kg)") - kg_avg: Optional[Decimal] = Field(default=None, description="Annual average estimate (kg)") - kg_high: Optional[Decimal] = Field(default=None, description="Annual high estimate (kg)") - bdt_low: Optional[Decimal] = Field(default=None, description="Bone‑dry tons low estimate") - bdt_avg: Optional[Decimal] = Field(default=None, description="Bone‑dry tons average") - bdt_high: Optional[Decimal] = Field(default=None, description="Bone‑dry tons high estimate") - data_source: Optional[int] = Field( - default=None, - description="Reference to data source" - # foreign_key="data_sources.source_id" - ) - availability_notes: Optional[str] = Field(default=None) - - -# ---------------------------------------------------------------------- -# Table: biomass_quality -# ---------------------------------------------------------------------- -class BiomassQuality(SQLModel, table=True): - """Qualitative attributes of a biomass.""" - __tablename__ = "biomass_quality" - - quality_id: Optional[int] = Field(default=None, primary_key=True) - biomass_id: int = Field( - default=None, - index=True, - description="Reference to biomass" - # foreign_key="biomass.biomass_id" - ) - expected_quality: Optional[str] = Field(default=None) - output_feedstocks: Optional[str] = Field( - default=None, - description="(Optional) Output feedstocks – may be moved to another table", - ) - convertibility: Optional[str] = Field(default=None) - disposal_challenges: Optional[str] = Field( - default=None, - description="Nondisposability issues", - ) - existing_markets: Optional[str] = Field( - default=None, - description="Substitutability information", - ) - substitute_materials: Optional[str] = Field(default=None) - regulatory_issues: Optional[str] = Field(default=None) - quality_data_sources: Optional[int] = Field( - default=None, - description="Reference to data source" - # foreign_key="data_sources.source_id" - ) - notes: Optional[str] = Field(default=None) - - -# ---------------------------------------------------------------------- -# Table: biomass_price -# ---------------------------------------------------------------------- -class BiomassPrice(SQLModel, table=True): - """Pricing information for a biomass.""" - __tablename__ = "biomass_price" - - price_id: Optional[int] = Field(default=None, primary_key=True) - biomass_id: int = Field( - default=None, - index=True, - description="Reference to biomass" - # foreign_key="biomass.biomass_id" - ) - price_per_kg_low: Optional[Decimal] = Field(default=None) - price_per_kg_avg: Optional[Decimal] = Field(default=None) - price_per_kg_high: Optional[Decimal] = Field(default=None) - price_data_sources: Optional[int] = Field( - default=None, - description="Reference to data source" - # foreign_key="data_sources.source_id" - ) - notes: Optional[str] = Field(default=None) - -# ---------------------------------------------------------------------- -# Table: harvest_methods -# ---------------------------------------------------------------------- -class HarvestMethod(SQLModel, table=True): - """Lookup table for harvest methods.""" - __tablename__ = "harvest_methods" - - harvest_method_id: Optional[int] = Field(default=None, primary_key=True) - harvest_method_name: str = Field(default=None, unique=True) - -# ---------------------------------------------------------------------- -# Table: collection_methods -# ---------------------------------------------------------------------- -class CollectionMethod(SQLModel, table=True): - """Lookup table for collection methods.""" - __tablename__ = "collection_methods" - - collection_method_id: Optional[int] = Field(default=None, primary_key=True) - collection_method_name: str = Field(default=None, unique=True) - -# ---------------------------------------------------------------------- -# Table: field_storage -# ---------------------------------------------------------------------- -class FieldStorage(SQLModel, table=True): - """Lookup table for field storage methods.""" - __tablename__ = "field_storage" - - field_storage_id: Optional[int] = Field(default=None, primary_key=True) - storage_method: str = Field(default=None, unique=True) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/config.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/config.py deleted file mode 100644 index 40f4f9da..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/config.py +++ /dev/null @@ -1,37 +0,0 @@ -"""Configuration for CA Biositing data models. - -This module provides configuration management for database models using Pydantic Settings. -""" - -from __future__ import annotations - -from typing import Optional - -from pydantic_settings import BaseSettings, SettingsConfigDict - - -class ModelConfig(BaseSettings): - """Configuration for database models. - - Attributes: - database_url: PostgreSQL database connection URL - echo_sql: Whether to echo SQL statements (for debugging) - pool_size: Database connection pool size - max_overflow: Maximum number of connections that can be created beyond pool_size - """ - - model_config = SettingsConfigDict( - env_file=".env", - env_file_encoding="utf-8", - case_sensitive=False, - extra="ignore", - ) - - database_url: str = "postgresql://user:password@localhost:5432/ca_biositing" - echo_sql: bool = False - pool_size: int = 5 - max_overflow: int = 10 - - -# Global configuration instance -config = ModelConfig() diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/data_and_references.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/data_and_references.py deleted file mode 100644 index 0634e482..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/data_and_references.py +++ /dev/null @@ -1,85 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - - -# ---------------------------------------------------------------------- -# Data source / reference tables -# ---------------------------------------------------------------------- - - -class DataSource(SQLModel, table=True): - """Source of data (internal / external).""" - __tablename__ = "data_sources" - - source_id: Optional[int] = Field(default=None, primary_key=True) - source_name_id: Optional[int] = Field(default=None, - description="Reference to source_names.source_name_id") - # foreign_key="source_names.source_name_id") - source_type_id: Optional[int] = Field(default=None, - description="Reference to source_types.source_type_id") - # foreign_key="source_types.source_type_id") - data_resolution_id: Optional[int] = Field(default=None, - description="Reference to location_resolutions.location_resolution_id") - # foreign_key="location_resolutions.location_resolution_id") - description: Optional[str] = Field(default=None) - url_id: Optional[int] = Field(default=None, - description="Reference to url.url_id") - # foreign_key="url.url_id") - import_timestamp: Optional[datetime] = Field(default=None) - - __table_args__ = (Index("idx_data_sources_source_name_id", "source_name_id"),) - - -class SourceName(SQLModel, table=True): - """Human‑readable name for a data source.""" - __tablename__ = "source_names" - - source_name_id: Optional[int] = Field(default=None, primary_key=True) - source_name: str = Field(..., unique=True, description="Not null") - - -class SourceType(SQLModel, table=True): - """Type of source (e.g., internal, external).""" - __tablename__ = "source_types" - - source_type_id: Optional[int] = Field(default=None, primary_key=True) - source_type: str = Field(..., unique=True, description="Not null") - - -class Reference(SQLModel, table=True): - """Bibliographic reference.""" - __tablename__ = "references" - - reference_id: Optional[int] = Field(default=None, primary_key=True) - reference_title: Optional[str] = Field(default=None) - reference_author: Optional[str] = Field(default=None) - reference_publication: Optional[str] = Field(default=None) - reference_date: Optional[date] = Field(default=None) - reference_doi_id: Optional[int] = Field(default=None, - description="Reference to DOI.doi_id") - # foreign_key="doi.doi_id") - url_id: Optional[int] = Field(default=None, - description="Reference to url.url_id") - # foreign_key="url.url_id") - - -class DOI(SQLModel, table=True): - """Digital Object Identifier.""" - __tablename__ = "doi" - - doi_id: Optional[int] = Field(default=None, primary_key=True) - doi: Optional[str] = Field(default=None) - - -class URL(SQLModel, table=True): - """Unique URL.""" - __tablename__ = "url" - - url_id: Optional[int] = Field(default=None, primary_key=True) - url: Optional[str] = Field(default=None, unique=True) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py deleted file mode 100644 index 77e970af..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py +++ /dev/null @@ -1,27 +0,0 @@ -"""Database connection and session management for CA Biositing data models.""" - -from __future__ import annotations - -from typing import Generator - -from sqlmodel import Session, create_engine - -from ca_biositing.datamodels.config import config - -# Create database engine -engine = create_engine( - config.database_url, - echo=config.echo_sql, - pool_size=config.pool_size, - max_overflow=config.max_overflow, -) - - -def get_session() -> Generator[Session, None, None]: - """Get a database session. - - Yields: - Session: SQLModel database session - """ - with Session(engine) as session: - yield session diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/experiments_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/experiments_analysis.py deleted file mode 100644 index ff68ecbb..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/experiments_analysis.py +++ /dev/null @@ -1,296 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# Experiments & analyses -# ---------------------------------------------------------------------- - - -class Experiment(SQLModel, table=True): - """Experiment definition.""" - __tablename__ = "experiments" - - experiment_id: Optional[int] = Field(default=None, primary_key=True) - exper_uuid: Optional[str] = Field(default=None, unique=True) - gsheet_exper_id: Optional[int] = Field(default=None, unique=True, - description="e.g., Ex05") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id",) - # foreign_key="analysis_types.analysis_type_id") - analysis_abbrev_id: Optional[int] = Field(default=None, - description="Reference to analysis_abbreviations.analysis_abbreviations_id",) - # foreign_key="analysis_abbreviations.analysis_abbreviations_id") - exper_start_date: Optional[date] = Field(default=None) - exper_duration: Optional[Decimal] = Field(default=None) - exper_duration_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id",) - # foreign_key="units.unit_id") - exper_location_id: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id",) - # foreign_key="geographic_locations.location_id") - exper_description: Optional[str] = Field(default=None) - - __table_args__ = (Index("idx_experiments_analysis_type_id", "analysis_type_id"),) - - -class ExperimentMethod(SQLModel, table=True): - """Link table for many‑to‑many relationship between experiments and methods.""" - __tablename__ = "experiment_methods" - - experiment_method_id: Optional[int] = Field(default=None, primary_key=True) - experiment_id: Optional[int] = Field(default=None, - description="Reference to experiments.experiment_id",) - # foreign_key="experiments.experiment_id") - method_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id",) - # foreign_key="methods.method_id") - - __table_args__ = ( - Index("idx_experiment_methods_method_id", "method_id"), - Index("idx_experiment_methods_experiment_id", "experiment_id"), - ) - - -class AnalysisType(SQLModel, table=True): - """Type of analysis (e.g., XRF, proximate).""" - __tablename__ = "analysis_types" - - analysis_type_id: Optional[int] = Field(default=None, primary_key=True) - analysis_name: Optional[str] = Field(default=None, unique=True, - description="X‑Ray Fluorescence analysis, Proximate analysis, Chemical Composition, Fermentation Profile, etc.") - - -class AnalysisAbbreviation(SQLModel, table=True): - """Abbreviation for an analysis type.""" - __tablename__ = "analysis_abbreviations" - - analysis_abbreviations_id: Optional[int] = Field(default=None, primary_key=True) - analysis_abbreviation: Optional[str] = Field(default=None, unique=True, - description="XRF, Prox, Comp, etc.") - - -class AnalysisResult(SQLModel, table=True): - """Result of a single analysis measurement.""" - __tablename__ = "analysis_results" - - result_id: Optional[int] = Field(default=None, primary_key=True) - anlaysis_sample: Optional[int] = Field(default=None, - description="Reference to preprocessed_samples.prepro_material_id",) - # foreign_key="preprocessed_samples.prepro_material_id") - experiment_id: Optional[int] = Field(default=None, - description="Reference to experiments.experiment_id",) - # foreign_key="experiments.experiment_id") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id",) - # foreign_key="analysis_types.analysis_type_id") - replicate_no: Optional[int] = Field(default=None) - analysis_timestamp: Optional[datetime] = Field(default=None) - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id",) - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id",) - # foreign_key="units.unit_id") - qc_result_id: Optional[int] = Field(default=None, - description="Reference to qc_results.qc_result_id",) - # foreign_key="qc_results.qc_result_id") - measurement_equipment_id: Optional[int] = Field(default=None, - description="Reference to equipment.equipment_id",) - # foreign_key="equipment.equipment_id") - raw_data_url_id: Optional[int] = Field(default=None, - description="Reference to url.url_id",) - # foreign_key="url.url_id") - analyst_id: Optional[int] = Field(default=None, - description="Reference to analyst_contact.analyst_id",) - # foreign_key="analyst_contact.analyst_id") - analysis_note: Optional[str] = Field(default=None) - - __table_args__ = ( - Index("idx_analysis_results_parameter_id", "parameter_id"), - Index("uq_analysis_results_experiment_parameter_replicate", - "experiment_id", "parameter_id", "replicate_no", unique=True), - ) - - -class QCResult(SQLModel, table=True): - """Quality‑control result (Pass/Fail).""" - __tablename__ = "qc_results" - - qc_result_id: Optional[int] = Field(default=None, primary_key=True) - qc_result: Optional[str] = Field(default=None, unique=True, - description="Pass/Fail") - - -class Unit(SQLModel, table=True): - """Unit of measurement.""" - __tablename__ = "units" - - unit_id: Optional[int] = Field(default=None, primary_key=True) - unit: Optional[str] = Field(default=None, unique=True, - description="% total weight, % dry weight, ppm, %") - - -class ParameterMethod(SQLModel, table=True): - """Bridge table linking parameters to the methods that generate them.""" - __tablename__ = "parameter_methods" - - param_method_id: Optional[int] = Field(default=None, primary_key=True) - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id",) - # foreign_key="parameters.parameter_id") - method_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id",) - # foreign_key="methods.method_id") - - -class Method(SQLModel, table=True): - """Analytical method definition.""" - __tablename__ = "methods" - - method_id: Optional[int] = Field(default=None, primary_key=True) - method_name: Optional[str] = Field(default=None, unique=True) - method_abbrev_id: Optional[int] = Field(default=None, - description="Reference to method_abbrevs.method_abbrev_id",) - # foreign_key="method_abbrevs.method_abbrev_id") - method_category_id: Optional[int] = Field(default=None, - description="Reference to method_categories.method_category_id",) - # foreign_key="method_categories.method_category_id") - method_standard_id: Optional[int] = Field(default=None, - description="Reference to method_standards.method_standard_id",) - # foreign_key="method_standards.method_standard_id") - description: Optional[str] = Field(default=None) - detection_limits: Optional[str] = Field(default=None) - procedure_reference_id: Optional[int] = Field(default=None, - description="Reference to references.reference_id",) - # foreign_key="references.reference_id") - method_url_id: Optional[int] = Field(default=None, - description="Reference to url.url_id",) - # foreign_key="url.url_id") - - __table_args__ = (Index("idx_methods_method_name", "method_name"),) - - -class MethodAbbreviation(SQLModel, table=True): - """Abbreviation for a method (e.g., NREL, ASTM).""" - __tablename__ = "method_abbrevs" - - method_abbrev_id: Optional[int] = Field(default=None, primary_key=True) - method_abbrev: str = Field(..., unique=True, - description="NREL, ASTM") - - -class MethodCategory(SQLModel, table=True): - """Category of a method (e.g., ICP, dry, wet).""" - __tablename__ = "method_categories" - - method_category_id: Optional[int] = Field(default=None, primary_key=True) - method_category: str = Field(..., unique=True, - description="ICP method, CompAna method, dry, wet") - - -class MethodStandard(SQLModel, table=True): - """Standard associated with a method (e.g., AOAC 997.02).""" - __tablename__ = "method_standards" - - method_standard_id: Optional[int] = Field(default=None, primary_key=True) - method_standard: str = Field(..., unique=True) - - -class Equipment(SQLModel, table=True): - """Laboratory or field equipment.""" - __tablename__ = "equipment" - - equipment_id: Optional[int] = Field(default=None, primary_key=True) - equipment_name: str = Field(..., unique=True, - description="Not null") - equipment_room_id: Optional[int] = Field(default=None, - description="Reference to rooms.room_id",) - # foreign_key="rooms.room_id") - description: Optional[str] = Field(default=None) - - -class MethodEquipment(SQLModel, table=True): - """Many‑to‑many link between methods and equipment.""" - __tablename__ = "method_equipment" - - method_equipment_id: Optional[int] = Field(default=None, primary_key=True) - method_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id",) - # foreign_key="methods.method_id") - equipment_id: Optional[int] = Field(default=None, - description="Reference to equipment.equipment_id",) - # foreign_key="equipment.equipment_id") - - __table_args__ = ( - Index("idx_method_equipment_method_id", "method_id"), - Index("idx_method_equipment_equipment_id", "equipment_id"), - ) - - -class Parameter(SQLModel, table=True): - """Parameter that can be measured or calculated.""" - __tablename__ = "parameters" - - parameter_id: Optional[int] = Field(default=None, primary_key=True) - parameter_name: Optional[str] = Field(default=None, unique=True) - parameter_category_id: Optional[int] = Field(default=None, - description="Reference to parameter_catagories.parameter_catagory_id",) - # foreign_key="parameter_catagories.parameter_catagory_id") - standard_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id",) - # foreign_key="units.unit_id") - calculated: Optional[bool] = Field(default=None, - description="If not calculated then it is measured directly. E.g. glucose vs glucan") - description: Optional[str] = Field(default=None) - typical_range_min: Optional[Decimal] = Field(default=None) - typical_range_max: Optional[Decimal] = Field(default=None) - - -class ParameterCategory(SQLModel, table=True): - """Category of a parameter (e.g., Fermentation, Minerals).""" - __tablename__ = "parameter_catagories" - - parameter_catagory_id: Optional[int] = Field(default=None, primary_key=True) - parameter_catagory: Optional[str] = Field(default=None, - description="Fermentation, Minerals, Elements, Compositional Analysis, etc") - - -class ParameterUnit(SQLModel, table=True): - """Bridge table linking parameters to alternative units.""" - __tablename__ = "parameter_units" - - parameter_unit_id: Optional[int] = Field(default=None, primary_key=True) - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id",) - # foreign_key="parameters.parameter_id") - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id",) - # foreign_key="units.unit_id") - - __table_args__ = ( - Index("idx_parameter_units_parameter_id", "parameter_id"), - Index("idx_parameter_units_unit_id", "unit_id"), - ) - - -class ImportLog(SQLModel, table=True): - """Log of data‑import operations.""" - __tablename__ = "import_log" - - import_id: Optional[int] = Field(default=None, primary_key=True) - import_timestamp: Optional[datetime] = Field(default=None) - destination: Optional[str] = Field(default=None) - source_file: Optional[str] = Field(default=None) - source_type: Optional[str] = Field(default=None, - description="CSV, Excel, PDF extraction") - records_imported: Optional[int] = Field(default=None) - import_status: Optional[str] = Field(default=None) - error_log: Optional[str] = Field(default=None) - import_user: Optional[str] = Field(default=None) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/external_datasets.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/external_datasets.py deleted file mode 100644 index ad33d397..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/external_datasets.py +++ /dev/null @@ -1,295 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# External / third‑party data tables -# ---------------------------------------------------------------------- - - -class ExternalDairyOne(SQLModel, table=True): - """External data from the Dairy‑One dataset.""" - __tablename__ = "external_dairy_one" - - dairy_one_id: Optional[int] = Field(default=None, primary_key=True) - data_source_id: Optional[int] = Field(default=None, - description="Reference to data_sources.source_id") - # foreign_key="data_sources.source_id") - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id") - # foreign_key="analysis_types.analysis_type_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - parameter_method_id: Optional[int] = Field(default=None, - description="Reference to parameter_methods.param_method_id") - # foreign_key="parameter_methods.param_method_id") - samples_count: Optional[int] = Field(default=None) - mean_value: Optional[Decimal] = Field(default=None) - std_dev: Optional[Decimal] = Field(default=None) - min_value: Optional[Decimal] = Field(default=None) - max_value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - methodology_reference_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id") - # foreign_key="methods.method_id") - accumulated_years_from: Optional[date] = Field(default=None) - accumulated_years_to: Optional[date] = Field(default=None) - import_date: Optional[date] = Field(default=None) - - __table_args__ = ( - Index("idx_external_dairy_one_biomass_id", "biomass_id"), - Index("idx_external_dairy_one_parameter_id", "parameter_id"), - ) - - -class ExternalINLBiofeedstockLibrary(SQLModel, table=True): - """INL Bio‑Feedstock Library external data.""" - __tablename__ = "external_inl_biofeedstock_library" - - bfl_id: Optional[int] = Field(default=None, primary_key=True) - data_source_id: Optional[int] = Field(default=None, - description="Reference to data_sources.source_id") - # foreign_key="data_sources.source_id") - sample_id: Optional[int] = Field(default=None, - description="Reference to field_samples.sample_id") - # foreign_key="field_samples.sample_id") - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id") - # foreign_key="analysis_types.analysis_type_id") - state_id: Optional[int] = Field(default=None, - description="Reference to states.state_id") - # foreign_key="states.state_id") - affiliations_id: Optional[int] = Field(default=None, - description="Reference to affiliations.affiliation_id") - # foreign_key="affiliations.affiliation_id") - harvest_method_id: Optional[int] = Field(default=None, - description="Reference to harvest_methods.harvest_method_id") - # foreign_key="harvest_methods.harvest_method_id") - collection_method_id: Optional[int] = Field(default=None, - description="Reference to collection_methods.collection_method_id") - # foreign_key="collection_methods.collection_method_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - parameter_method_id: Optional[int] = Field(default=None, - description="Reference to parameter_methods.param_method_id") - # foreign_key="parameter_methods.param_method_id") - mean_value: Optional[Decimal] = Field(default=None) - std_dev: Optional[Decimal] = Field(default=None) - min_value: Optional[Decimal] = Field(default=None) - max_value: Optional[Decimal] = Field(default=None) - sample_count: Optional[int] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - methodology_reference_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id") - # foreign_key="methods.method_id") - accumulated_years_from: Optional[date] = Field(default=None) - accumulated_years_to: Optional[date] = Field(default=None) - import_date: Optional[date] = Field(default=None) - - __table_args__ = ( - Index("idx_external_inl_biofeedstock_library_biomass_id", "biomass_id"), - ) - - -class ExternalPhyllis2(SQLModel, table=True): - """External literature data (Phyllis2).""" - __tablename__ = "external_phyllis2" - - phyllis_id: Optional[int] = Field(default=None, primary_key=True) - data_source_id: Optional[int] = Field(default=None, - description="Reference to data_sources.source_id") - # foreign_key="data_sources.source_id") - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id") - # foreign_key="analysis_types.analysis_type_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - parameter_method_id: Optional[int] = Field(default=None, - description="Reference to parameter_methods.param_method_id") - # foreign_key="parameter_methods.param_method_id") - mean_value: Optional[Decimal] = Field(default=None) - std_dev: Optional[Decimal] = Field(default=None) - max_value: Optional[Decimal] = Field(default=None) - sample_count: Optional[int] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - methodology_reference_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id") - # foreign_key="methods.method_id") - import_date: Optional[date] = Field(default=None) - - __table_args__ = ( - Index("idx_external_phyllis2_biomass_id", "biomass_id"), - Index("idx_external_phyllis2_analysis_type_id", "analysis_type_id"), - ) - - -class ExternalEBMUD(SQLModel, table=True): - """External EBMUD dataset.""" - __tablename__ = "external_ebmud" - - ebmud_id: Optional[int] = Field(default=None, primary_key=True) - data_source_id: Optional[int] = Field(default=None, - description="Reference to data_sources.source_id") - # foreign_key="data_sources.source_id") - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id") - # foreign_key="analysis_types.analysis_type_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - parameter_method_id: Optional[int] = Field(default=None, - description="Reference to parameter_methods.param_method_id") - # foreign_key="parameter_methods.param_method_id") - mean_value: Optional[Decimal] = Field(default=None) - std_dev: Optional[Decimal] = Field(default=None) - min_value: Optional[Decimal] = Field(default=None) - max_value: Optional[Decimal] = Field(default=None) - sample_count: Optional[int] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - import_date: Optional[date] = Field(default=None) - - -class VectorizedRasterPolygon(SQLModel, table=True): - """Polygon derived from a raster (PostGIS geometry).""" - __tablename__ = "vectorized_raster_polygons" - - vectorized_ID: Optional[int] = Field(default=None, primary_key=True) - geometry: Optional[str] = Field(default=None, - description="Polygon geometry (PostGIS), use appropriate SRID") - raster_id: Optional[int] = Field(default=None, - description="Optional foreign key to raster_metadata.id") - # foreign_key="raster_metadata.id") - class_: Optional[str] = Field(default=None, - description="Classification label or category (e.g., land use type)", - alias="class") - value: Optional[float] = Field(default=None, - description="Raw pixel value this polygon was derived from") - mean_value: Optional[float] = Field(default=None, - description="Mean raster value within the polygon") - std_dev: Optional[float] = Field(default=None, - description="Standard deviation of raster values in the polygon") - area_m2: Optional[float] = Field(default=None, - description="Area of the polygon in square meters") - date_acquired: Optional[date] = Field(default=None, - description="Date the source raster was collected") - source: Optional[str] = Field(default=None, - description="Source of the raster (e.g., Sentinel‑2)") - notes: Optional[str] = Field(default=None, - description="Additional optional metadata or remarks") - - -class RasterMetadata(SQLModel, table=True): - """Metadata for raster layers.""" - __tablename__ = "raster_metadata" - - id: Optional[int] = Field(default=None, primary_key=True) - source: Optional[str] = Field(default=None, - description="Data source name or provider") - resolution: Optional[float] = Field(default=None, - description="Raster resolution in meters") - srid: Optional[int] = Field(default=None, - description="Spatial reference ID used in raster") - acquisition_date: Optional[date] = Field(default=None, - description="Date of raster acquisition") - notes: Optional[str] = Field(default=None, - description="Any additional metadata") - - -class ExternalATIP(SQLModel, table=True): - """ATIP external geospatial data.""" - __tablename__ = "external_atip" - - atip_ID: Optional[int] = Field(default=None, primary_key=True) - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - location_id: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id") - # foreign_key="geographic_locations.location_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - geometry_id: Optional[int] = Field(default=None) - geometry: Optional[str] = Field(default=None, - description="Geometry (PostGIS geom type)") - import_date: Optional[date] = Field(default=None) - - -class ExternalLandIQ(SQLModel, table=True): - """Land‑IQ external geospatial data.""" - __tablename__ = "external_land_id" - - land_id: Optional[int] = Field(default=None, primary_key=True) # renamed from land_id_id - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - location_id: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id") - # foreign_key="geographic_locations.location_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - geometry_id: Optional[int] = Field(default=None) - geometry: Optional[str] = Field(default=None, - description="Geometry (PostGIS geom type)") - import_date: Optional[date] = Field(default=None) - - -class ExternalUSDA(SQLModel, table=True): - """USDA external geospatial data.""" - __tablename__ = "external_usda" - - usda_id: Optional[int] = Field(default=None, primary_key=True) - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - location_id: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id") - # foreign_key="geographic_locations.location_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - geometry_id: Optional[int] = Field(default=None) - geometry: Optional[str] = Field(default=None, - description="Geometry (PostGIS geom type)") - import_date: Optional[date] = Field(default=None) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/geographic_locations.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/geographic_locations.py deleted file mode 100644 index 84e6e21e..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/geographic_locations.py +++ /dev/null @@ -1,113 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# Geographic / Location tables -# ---------------------------------------------------------------------- - - -class GeographicLocation(SQLModel, table=True): - """Geographic location (can be anonymised).""" - __tablename__ = "geographic_locations" - - location_id: Optional[int] = Field(default=None, primary_key=True) - street_address_id: Optional[int] = Field(default=None, - description="Reference to street_addresses.street_address_id") - # foreign_key="street_addresses.street_address_id") - city_id: Optional[int] = Field(default=None, - description="Reference to cities.city_id") - # foreign_key="cities.city_id") - zip_id: Optional[int] = Field(default=None, - description="Reference to zips.zip_id") - # foreign_key="zips.zip_id") - county_id: Optional[int] = Field(default=None, - description="Reference to counties.county_id") - # foreign_key="counties.county_id") - state_id: Optional[int] = Field(default=None, - description="Reference to states.state_id") - # foreign_key="states.state_id") - region_id: Optional[int] = Field(default=None, - description="Reference to regions.region_id") - # foreign_key="regions.region_id") - fips_id: Optional[int] = Field(default=None, - description="Reference to fips.fips_id") - # foreign_key="fips.fips_id") - latitude: Optional[Decimal] = Field(default=None, - description="Can be null or generalized") - longitude: Optional[Decimal] = Field(default=None, - description="Can be null or generalized") - location_resolution_id: Optional[int] = Field(default=None, - description="Reference to location_resolutions.location_resolution_id") - # foreign_key="location_resolutions.location_resolution_id") - is_anonymous: Optional[bool] = Field(default=None) - - -class StreetAddress(SQLModel, table=True): - """Street address (may be null for privacy).""" - __tablename__ = "street_addresses" - - street_address_id: Optional[int] = Field(default=None, primary_key=True) - street_address: str = Field(..., description="Not null") - - -class City(SQLModel, table=True): - """City lookup.""" - __tablename__ = "cities" - - city_id: Optional[int] = Field(default=None, primary_key=True) - city_name: str = Field(..., unique=True, description="Not null") - - -class Zip(SQLModel, table=True): - """ZIP code lookup.""" - __tablename__ = "zips" - - zip_id: Optional[int] = Field(default=None, primary_key=True) - zip_code: str = Field(..., unique=True, description="Not null") - - -class County(SQLModel, table=True): - """County lookup.""" - __tablename__ = "counties" - - county_id: Optional[int] = Field(default=None, primary_key=True) - county_name: str = Field(..., unique=True, description="Not null") - - -class FIPS(SQLModel, table=True): - """FIPS code (preserve leading zeros).""" - __tablename__ = "fips" - - fips_id: Optional[int] = Field(default=None, primary_key=True) - fips_description: Optional[str] = Field(default=None) - - -class State(SQLModel, table=True): - """State lookup.""" - __tablename__ = "states" - - state_id: Optional[int] = Field(default=None, primary_key=True) - state_name: str = Field(..., unique=True, description="Not null") - - -class Region(SQLModel, table=True): - """Region lookup.""" - __tablename__ = "regions" - - region_id: Optional[int] = Field(default=None, primary_key=True) - region_name: str = Field(..., unique=True, description="Not null") - - -class LocationResolution(SQLModel, table=True): - """Resolution of a location (e.g., GPS, county, state).""" - __tablename__ = "location_resolutions" - - location_resolution_id: Optional[int] = Field(default=None, primary_key=True) - resolution_type: str = Field(..., unique=True, - description="region, state, city, county, etc") diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml index f3d26ede..2cc58cf0 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml @@ -38,8 +38,6 @@ classes: PrimaryCrop: is_a: LookupBase description: Primary crop definition. - slots: - - note ResourceAvailability: is_a: BaseEntity diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/metadata_samples.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/metadata_samples.py deleted file mode 100644 index 7ab750e7..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/metadata_samples.py +++ /dev/null @@ -1,79 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - - -class Metadata(SQLModel, table=True): - """Additional metadata linked to a field sample.""" - __tablename__ = "metadata" - - metadata_id: Optional[int] = Field(default=None, primary_key=True) - sample_id: Optional[int] = Field(default=None, - description="Reference to field_samples.sample_id") - # foreign_key="field_samples.sample_id") - ag_treatment_id: Optional[int] = Field(default=None, - description="Reference to ag_treatments.ag_treatment_id") - # foreign_key="ag_treatments.ag_treatment_id") - last_application_date: Optional[date] = Field(default=None, - description="if applicable") - treatment_amount_per_acre: Optional[Decimal] = Field(default=None, - description="if applicable") - soil_type: Optional[int] = Field(default=None, - description="Reference to soil_type.soil_type_id") - # foreign_key="soil_type.soil_type_id") - - -class ParticleSize(SQLModel, table=True): - """Particle‑size measurements for a sample.""" - __tablename__ = "particle_size" - - particle_size_id: Optional[int] = Field(default=None, primary_key=True) - sample_id: Optional[int] = Field(default=None, - description="Reference to field_samples.sample_id") - # foreign_key="field_samples.sample_id") - particle_length: Optional[int] = Field(default=None) - particle_width: Optional[int] = Field(default=None) - particle_height: Optional[int] = Field(default=None) - particle_units: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - - -class SoilType(SQLModel, table=True): - """Soil classification.""" - __tablename__ = "soil_type" - - soil_type_id: Optional[int] = Field(default=None, primary_key=True) - soil_type: Optional[str] = Field(default=None, unique=True) - soil_location: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id") - # foreign_key="geographic_locations.location_id") - - -class AgTreatment(SQLModel, table=True): - """Agricultural treatment (e.g., pesticide, herbicide).""" - __tablename__ = "ag_treatments" - - ag_treatment_id: Optional[int] = Field(default=None, primary_key=True) - ag_treatment_name: Optional[str] = Field(default=None, - description="pesticide, herbicade") - - -class Taxonomy(SQLModel, table=True): - """Taxonomic hierarchy for a biomass.""" - __tablename__ = "taxonomy" - - taxonomy_id: Optional[int] = Field(default=None, primary_key=True) - kingdom: Optional[str] = Field(default=None) - phylum: Optional[str] = Field(default=None) - class_: Optional[str] = Field(default=None, alias="class") - order: Optional[str] = Field(default=None) - family: Optional[str] = Field(default=None) - genus: Optional[str] = Field(default=None) - species: Optional[str] = Field(default=None) - variety_subspecies_cultivar: Optional[str] = Field(default=None) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/organizations.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/organizations.py deleted file mode 100644 index 2db06cbb..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/organizations.py +++ /dev/null @@ -1,46 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - - -# ---------------------------------------------------------------------- -# Organizational tables -# ---------------------------------------------------------------------- - - -class Affiliation(SQLModel, table=True): - """Affiliation (e.g., university, company).""" - __tablename__ = "affiliations" - - affiliation_id: Optional[int] = Field(default=None, primary_key=True) - affiliation_name: str = Field(..., unique=True, description="Not null") - - -class Building(SQLModel, table=True): - """Building that can house rooms / equipment.""" - __tablename__ = "buildings" - - building_id: Optional[int] = Field(default=None, primary_key=True) - building_name: Optional[str] = Field(default=None, unique=True) - location_id: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id") - # foreign_key="geographic_locations.location_id") - affiliation_id: Optional[int] = Field(default=None, - description="Reference to affiliations.affiliation_id") - # foreign_key="affiliations.affiliation_id") - - -class Room(SQLModel, table=True): - """Room inside a building.""" - __tablename__ = "rooms" - - room_id: Optional[int] = Field(default=None, primary_key=True) - room_number: Optional[str] = Field(default=None, unique=True) - building_id: Optional[int] = Field(default=None, - description="Reference to buildings.building_id") - # foreign_key="buildings.building_id") diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/people_contacts.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/people_contacts.py deleted file mode 100644 index 9775edf0..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/people_contacts.py +++ /dev/null @@ -1,59 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# People / contacts -# ---------------------------------------------------------------------- - - -class AnalystContact(SQLModel, table=True): - """Analyst or data‑entry contact.""" - __tablename__ = "analyst_contact" - - analyst_id: Optional[int] = Field(default=None, primary_key=True) - analyst_first_name: Optional[str] = Field(default=None) - analyst_last_name: Optional[str] = Field(default=None) - analyst_email: Optional[str] = Field(default=None) - analyst_affiliation: Optional[int] = Field(default=None, - description="Reference to affiliations.affiliation_id") - # foreign_key="affiliations.affiliation_id") - - -class Provider(SQLModel, table=True): - """Provider of samples / data.""" - __tablename__ = "providers" - - provider_id: Optional[int] = Field(default=None, primary_key=True) - provider_name: str = Field(..., unique=True, description="Not null") - provider_affiliation: Optional[int] = Field(default=None, - description="Reference to affiliations.affiliation_id") - # foreign_key="affiliations.affiliation_id") - provider_type_id: Optional[int] = Field(default=None, - description="Reference to provider_types.provider_type_id") - # foreign_key="provider_types.provider_type_id") - anonymous: Optional[bool] = Field(default=None) - - -class ProviderType(SQLModel, table=True): - """Category of provider (facility, farm, processor, etc.).""" - __tablename__ = "provider_types" - - provider_type_id: Optional[int] = Field(default=None, primary_key=True) - provider_type: Optional[str] = Field(default=None) - - -class Collector(SQLModel, table=True): - """Collector of field samples.""" - __tablename__ = "collectors" - - collector_id: Optional[int] = Field(default=None, primary_key=True) - collector_name: str = Field(..., unique=True, description="Not null") - collector_affiliation: Optional[int] = Field(default=None, - description="Reference to affiliations.affiliation_id") - # foreign_key="affiliations.affiliation_id") diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/sample_preprocessing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/sample_preprocessing.py deleted file mode 100644 index 769001f6..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/sample_preprocessing.py +++ /dev/null @@ -1,68 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# Sample preprocessing / processing -# ---------------------------------------------------------------------- - - -class PreprocessingMethod(SQLModel, table=True): - """Method used to pre‑process a sample.""" - __tablename__ = "preprocessing_methods" - - prepro_method_id: Optional[int] = Field(default=None, primary_key=True) - prepro_method: Optional[str] = Field(default=None, - description="As Is, Knife Mill (2mm), Oven Dry") - prepro_method_abbrev_id: Optional[int] = Field(default=None, - description="Reference to preprocessing_methods_abbreviations.prepro_methods_abbrev_id",) - # foreign_key="preprocessing_methods_abbreviations.prepro_methods_abbrev_id") - prepro_temp_c: Optional[Decimal] = Field(default=None) - drying_step: Optional[bool] = Field(default=None) - method_ref_id: Optional[int] = Field(default=None, - description="Reference to references.reference_id",) - # foreign_key="references.reference_id") - - -class PreprocessingMethodAbbreviation(SQLModel, table=True): - """Abbreviation for a preprocessing method.""" - __tablename__ = "preprocessing_methods_abbreviations" - - prepro_methods_abbrev_id: Optional[int] = Field(default=None, primary_key=True) - prepro_method_abbrev: Optional[str] = Field(default=None, unique=True) - - -class PreprocessedSample(SQLModel, table=True): - """Result of a preprocessing step.""" - __tablename__ = "preprocessed_samples" - - prepro_material_id: Optional[int] = Field(default=None, primary_key=True) - prepro_material_name: Optional[str] = Field(default=None) - biomass_sample_id: Optional[int] = Field(default=None, - description="Reference to field_samples.sample_id",) - # foreign_key="field_samples.sample_id") - prepro_method_id: Optional[int] = Field(default=None, - description="Reference to preprocessing_methods.prepro_method_id",) - # foreign_key="preprocessing_methods.prepro_method_id") - amount_before_drying_g: Optional[Decimal] = Field(default=None) - amount_after_drying: Optional[Decimal] = Field(default=None) - processing_date: Optional[date] = Field(default=None) - storage_building: Optional[int] = Field(default=None, - description="Reference to buildings.building_id",) - # foreign_key="buildings.building_id") - amount_remaining_g: Optional[Decimal] = Field(default=None) - amount_as_of_date: Optional[date] = Field(default=None) - prepro_analyst_id: Optional[int] = Field(default=None, - description="Reference to analyst_contact.analyst_id",) - # foreign_key="analyst_contact.analyst_id") - prepro_note: Optional[str] = Field(default=None) - - __table_args__ = ( - Index("idx_preprocessed_samples_biomass_sample_id", "biomass_sample_id"), - Index("idx_preprocessed_samples_prepro_method_id", "prepro_method_id"), - ) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/specific_aalysis_results.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/specific_aalysis_results.py deleted file mode 100644 index f416bdf2..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/specific_aalysis_results.py +++ /dev/null @@ -1,199 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# Specific analysis result tables -# ---------------------------------------------------------------------- - - -class ProximateAnalysis(SQLModel, table=True): - """Proximate analysis results (e.g., moisture, ash).""" - __tablename__ = "proximate_analysis" - - prox_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - notes: Optional[str] = Field(default=None) - - -class ICPAnalysis(SQLModel, table=True): - """ICP (Inductively Coupled Plasma) analysis.""" - __tablename__ = "icp_analysis" - - icp_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - concentration_calculation_url_id: Optional[int] = Field(default=None, - description="Reference to url.url_id") - # foreign_key="url.url_id") - result_wavelength: Optional[Decimal] = Field(default=None) - raw_url: Optional[str] = Field(default=None) - notes: Optional[str] = Field(default=None) - - -class CompositionalAnalysis(SQLModel, table=True): - """Compositional analysis (derived parameters).""" - __tablename__ = "compositional_analysis" - - cmp_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - calculated_parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - calculated_parameter_value: Optional[Decimal] = Field(default=None) - calculated_parameter_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - notes: Optional[str] = Field(default=None) - - -class XRFAnalysis(SQLModel, table=True): - """X‑Ray Fluorescence analysis.""" - __tablename__ = "xrf_analysis" - - xrf_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - notes: Optional[str] = Field(default=None) - - -class FermentationProfile(SQLModel, table=True): - """Fermentation profile results.""" - __tablename__ = "fermentation_profile" - - fp_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - organism_id: Optional[int] = Field(default=None, - description="Reference to organisms.organism_id") - # foreign_key="organisms.organism_id") - product_type_id: Optional[int] = Field(default=None, - description="Reference to product_type.product_type_id") - # foreign_key="product_type.product_type_id") - product_value: Optional[Decimal] = Field(default=None) - product_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - notes: Optional[str] = Field(default=None) - - -class Organism(SQLModel, table=True): - """Organism used in a fermentation.""" - __tablename__ = "organisms" - - organism_id: Optional[int] = Field(default=None, primary_key=True) - organism_name: Optional[str] = Field(default=None) - organism_strain_id: Optional[int] = Field(default=None) - notes: Optional[str] = Field(default=None) - - -class GasificationProfile(SQLModel, table=True): - """Gasification profile results.""" - __tablename__ = "gasification_profile" - - gasification_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - notes: Optional[str] = Field(default=None) - product_type_id: Optional[int] = Field(default=None, - description="Reference to product_type.product_type_id") - # foreign_key="product_type.product_type_id") - product_value: Optional[Decimal] = Field(default=None) - product_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - - -class AutoclaveProfile(SQLModel, table=True): - """Autoclave experiment results.""" - __tablename__ = "autoclave_profile" - - autoclave_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - product_type_id: Optional[int] = Field(default=None, - description="Reference to product_type.product_type_id") - # foreign_key="product_type.product_type_id") - product_value: Optional[Decimal] = Field(default=None) - product_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - - -class AnalysisReplicate(SQLModel, table=True): - """Link between a result and its replicate UUID (used for G‑Sheet tracking).""" - __tablename__ = "analysis_replicate_id" - - analysis_replicate_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - analysis_types_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id") - # foreign_key="analysis_types.analysis_type_id") - analysis_replicate_uuid: Optional[str] = Field(default=None) - - -class ProductType(SQLModel, table=True): - """Product type produced in a process (e.g., Butyric, Biochar).""" - __tablename__ = "product_type" - - product_type_id: Optional[int] = Field(default=None, primary_key=True) - product: Optional[str] = Field(default=None, - description="e.g., Butyric, Iso‑Butyric, Propionic, Hydrogen, Syngas, Biochar, Indigoidine, 3HP, etc") diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/user.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/user.py deleted file mode 100644 index 7864a64c..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/user.py +++ /dev/null @@ -1,13 +0,0 @@ -from typing import Optional -from sqlmodel import SQLModel, Field - -class User(SQLModel, table=True): - __tablename__ = 'testusers2' - - id: Optional[int] = Field(default=None, primary_key=True) - name: Optional[str] = Field(default=None) - fullname: Optional[str] = Field(default=None) - nickname: Optional[str] = Field(default=None) - - def __repr__(self): - return f"" From 6e2a1c93955ff8c1d8b1597e558094dcb4a6f6ab Mon Sep 17 00:00:00 2001 From: mglbleta Date: Fri, 12 Dec 2025 12:32:57 -0800 Subject: [PATCH 24/81] changes to pixi.toml and some comments on linkml schema --- docs/README.md | 2 +- docs/datamodels/README.md | 2 +- docs/deployment/README.md | 2 +- docs/pipeline/README.md | 2 +- docs/resources/README.md | 2 +- docs/webservice/README.md | 2 +- pixi.toml | 2 +- .../linkml/modules/aim1_records.yaml | 3 ++ .../datamodels/linkml/modules/core.yaml | 6 +++ .../linkml/modules/data_sources_metadata.yaml | 18 ++++++++- .../linkml/modules/field_sampling.yaml | 40 +++++++++---------- 11 files changed, 53 insertions(+), 28 deletions(-) diff --git a/docs/README.md b/docs/README.md index 32d46ee8..94389aee 120000 --- a/docs/README.md +++ b/docs/README.md @@ -1 +1 @@ -../README.md \ No newline at end of file +../README.md diff --git a/docs/datamodels/README.md b/docs/datamodels/README.md index b62101ad..f3c7aa23 120000 --- a/docs/datamodels/README.md +++ b/docs/datamodels/README.md @@ -1 +1 @@ -../../src/ca_biositing/datamodels/README.md \ No newline at end of file +../../src/ca_biositing/datamodels/README.md diff --git a/docs/deployment/README.md b/docs/deployment/README.md index d5c46ad4..5159bcfe 120000 --- a/docs/deployment/README.md +++ b/docs/deployment/README.md @@ -1 +1 @@ -../../deployment/README.md \ No newline at end of file +../../deployment/README.md diff --git a/docs/pipeline/README.md b/docs/pipeline/README.md index 82a8c831..544d50b1 120000 --- a/docs/pipeline/README.md +++ b/docs/pipeline/README.md @@ -1 +1 @@ -../../src/ca_biositing/pipeline/README.md \ No newline at end of file +../../src/ca_biositing/pipeline/README.md diff --git a/docs/resources/README.md b/docs/resources/README.md index 9f21ec35..ea34ca59 120000 --- a/docs/resources/README.md +++ b/docs/resources/README.md @@ -1 +1 @@ -../../resources/README.md \ No newline at end of file +../../resources/README.md diff --git a/docs/webservice/README.md b/docs/webservice/README.md index 749a635e..24ea2883 120000 --- a/docs/webservice/README.md +++ b/docs/webservice/README.md @@ -1 +1 @@ -../../src/ca_biositing/webservice/README.md \ No newline at end of file +../../src/ca_biositing/webservice/README.md diff --git a/pixi.toml b/pixi.toml index bfb9ea0e..712f7d30 100644 --- a/pixi.toml +++ b/pixi.toml @@ -254,7 +254,7 @@ args = [ { "arg" = "env_file", "default" = "../docker/.env" }, ] cwd = "resources/prefect" -cmd = "./deploy.py --env-file {{ env_file }} {{ deployment_name }}" +cmd = ["python", "deploy.py", "--env-file", "{{ env_file }}", "{{ deployment_name }}"] description = "Deploy the ETL pipeline to Prefect." depends-on = [{ task = "start-services" }] diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml index fc2ae1ff..c3d5aae7 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml @@ -125,3 +125,6 @@ slots: sample_id: range: integer description: Reference to PreparedSample. +#How are slots above determined? I see the 6 slots that were defined outside of the Aim1RecordBase class, +#but I don't see why the other slots listed (technical_replicate_no, technical_replicate_total, qc_pass, raw_data_id, sample_id) are highlighted. +#Should the remaining slots in the base class be included in these slots as well? diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml index 234b9b4f..eec6318b 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml @@ -35,6 +35,8 @@ classes: - uri slots: + ##Slots from BaseEntity + id: identifier: true range: integer @@ -56,6 +58,8 @@ slots: range: integer description: Reference to the lineage group. + ##Slots from LookupBase + name: range: string description: Name of the entity. @@ -68,6 +72,8 @@ slots: range: uri description: URI for the entity. + ##Slots for other ETL related fields + note: range: string description: Additional notes. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index cc20fe83..ce6e04be 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -31,6 +31,22 @@ classes: - license - note + #missing fields compared to DBdiagram. Was this a purposeful paring down of fields? + #data_source_type_id + #full_title + #creator + #subject + #publisher + #date + #types + #biocirv + #format + #language + #relation + #temporal_coverage + #location_coverage + #rights + FileObjectMetadata: is_a: BaseEntity description: Metadata for a file object. @@ -44,7 +60,7 @@ classes: DataSourceType: is_a: BaseEntity - description: Type of data source. + description: Type of data source (e.g. database, literature). slots: - source_type_id diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml index 9eaedfd7..74ab00d6 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml @@ -43,6 +43,26 @@ classes: - field_sample_storage_location_id - note + PhysicalCharacteristic: + is_a: BaseEntity + description: Physical characteristics of a sample. + slots: + - field_sample_id + - particle_length + - particle_width + - particle_height + - particle_unit_id + + FieldSampleCondition: + is_a: BaseEntity + description: Condition of the field sample. + slots: + - field_sample_id + - ag_treatment_id + - last_application_date + - treatment_amount_per_acre + - processing_method_id + FieldStorageMethod: is_a: LookupBase description: Method of field storage. @@ -59,16 +79,6 @@ classes: is_a: LookupBase description: Method of processing. - PhysicalCharacteristic: - is_a: BaseEntity - description: Physical characteristics of a sample. - slots: - - field_sample_id - - particle_length - - particle_width - - particle_height - - particle_unit_id - SoilType: is_a: LookupBase description: Type of soil. @@ -77,16 +87,6 @@ classes: is_a: LookupBase description: Agricultural treatment. - FieldSampleCondition: - is_a: BaseEntity - description: Condition of the field sample. - slots: - - field_sample_id - - ag_treatment_id - - last_application_date - - treatment_amount_per_acre - - processing_method_id - LocationSoilType: is_a: BaseEntity description: Soil type at a location. From 2fcbf18f470f0226976c9bc08f1487684dfa8d4f Mon Sep 17 00:00:00 2001 From: mglbleta Date: Fri, 12 Dec 2025 18:30:11 -0800 Subject: [PATCH 25/81] added some comments to organize and ask questions --- .../linkml/modules/aim1_records.yaml | 22 +++-- .../linkml/modules/aim2_records.yaml | 8 +- .../datamodels/linkml/modules/analysis.yaml | 4 + .../linkml/modules/data_sources_metadata.yaml | 2 +- .../linkml/modules/external_data.yaml | 87 ++++++++++--------- .../linkml/modules/general_analysis.yaml | 4 + .../datamodels/linkml/modules/geography.yaml | 11 --- .../modules/methods_parameters_units.yaml | 8 ++ .../linkml/modules/resource_information.yaml | 6 ++ 9 files changed, 89 insertions(+), 63 deletions(-) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml index c3d5aae7..85028218 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml @@ -82,6 +82,19 @@ classes: description: RGB analysis record. slots: + #Slots imported + #dataset_id: from general_analysis.yaml + #experiment_id: from experiments.yaml + #resource_id: from resource_information.yaml + #method_id: from experiments.yaml + #note: from core.yaml + + #New slots defined in Aim1RecordBase class + + sample_id: + range: integer + description: Reference to PreparedSample. + technical_replicate_no: range: integer description: Replicate number. @@ -98,6 +111,8 @@ slots: range: boolean description: Whether the record passed QC. + #Potential slots for XrfRecord and XrdRecords + maybe_wavelength_nm: range: decimal description: Wavelength in nm. @@ -121,10 +136,3 @@ slots: maybe_scan_high_nm: range: integer description: High scan range in nm. - - sample_id: - range: integer - description: Reference to PreparedSample. -#How are slots above determined? I see the 6 slots that were defined outside of the Aim1RecordBase class, -#but I don't see why the other slots listed (technical_replicate_no, technical_replicate_total, qc_pass, raw_data_id, sample_id) are highlighted. -#Should the remaining slots in the base class be included in these slots as well? diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml index 8eabaa1f..2fdcda17 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml @@ -31,12 +31,12 @@ classes: - experiment_id - resource_id - sample_id + - technical_replicate_total + - technical_replicate_no - analyst_id - raw_data_id - qc_pass - note - - technical_replicate_total - - technical_replicate_no PretreatmentRecord: is_a: Aim2RecordBase @@ -47,7 +47,7 @@ classes: - reaction_block_id - block_position - temperature - - replicate_no + - replicate_no #delete bc redundancy with technical_replicate_no in aim2recordbase entity? FermentationRecord: is_a: Aim2RecordBase @@ -56,7 +56,7 @@ classes: - strain_id - pretreatment_method_id - eh_method_id - - replicate_no + - replicate_no #delete bc redundancy with technical_replicate_no in aim2recordbase entity? - well_position - temperature - agitation_rpm diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml index 456b876d..83292024 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml @@ -60,6 +60,10 @@ classes: description: Type of analysis. slots: + #Slots imported + #parameter_id: from methods.yaml + #note: from core.yaml + dataset_id: range: integer description: Reference to Dataset. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index ce6e04be..5710afd3 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -31,7 +31,7 @@ classes: - license - note - #missing fields compared to DBdiagram. Was this a purposeful paring down of fields? + #missing fields compared to DBdiagram. #data_source_type_id #full_title #creator diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml index cfca5168..4f80ac2d 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml @@ -33,6 +33,33 @@ classes: is_a: LookupBase description: USDA survey program. + UsdaCensusRecord: + is_a: BaseEntity + description: USDA census record. + slots: + - dataset_id + - geoid + - commodity_code + - year + - source_reference + - note + + UsdaSurveyRecord: + is_a: BaseEntity + description: USDA survey record. + slots: + - dataset_id + - geoid + - commodity_code + - year + - survey_program_id + - survey_period + - reference_month + - seasonal_flag + - note + + #RESOURCE ONTOLOGY MAPPING + UsdaCommodity: is_a: LookupBase description: USDA commodity. @@ -62,30 +89,7 @@ classes: - match_tier - note - UsdaCensusRecord: - is_a: BaseEntity - description: USDA census record. - slots: - - dataset_id - - geoid - - commodity_code - - year - - source_reference - - note - - UsdaSurveyRecord: - is_a: BaseEntity - description: USDA survey record. - slots: - - dataset_id - - geoid - - commodity_code - - year - - survey_program_id - - survey_period - - reference_month - - seasonal_flag - - note + #USDA MARKET DATA UsdaMarketReport: is_a: BaseEntity @@ -111,9 +115,9 @@ classes: - report_date - commodity_id - market_type_id - - market_type_catagory + - market_type_category - grp - - market_catagory_id + - market_category_id - class_ - grade - variety @@ -125,6 +129,8 @@ classes: - freight - trans_mode + #LANDIQ DATA + LandiqRecord: is_a: BaseEntity description: LandIQ record. @@ -140,7 +146,19 @@ classes: - acres - version - note - - test + + Polygon: + description: Geospatial polygon. + slots: + - id + - geoid + - geom + slot_usage: + id: + identifier: true + range: integer + + #BILLION TON DATA BillionTon2023Record: is_a: BaseEntity @@ -161,17 +179,6 @@ classes: - product_density_dtpersqmi - land_source - Polygon: - description: Geospatial polygon. - slots: - - id - - geoid - - geom - slot_usage: - id: - identifier: true - range: integer - slots: usda_source: range: string @@ -289,7 +296,7 @@ slots: range: integer description: ID of the market type. - market_type_catagory: + market_type_category: range: string description: Category of the market type. @@ -297,7 +304,7 @@ slots: range: string description: Group. - market_catagory_id: + market_category_id: range: integer description: ID of the market category. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml index cc8a195a..6f9db701 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml @@ -53,6 +53,10 @@ classes: - note slots: + #Slots imported + #parameter_id: from methods.yaml + #note: from core.yaml + record_type: range: string description: Type of record. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml index 32a8a880..0b6ec0eb 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml @@ -43,17 +43,6 @@ classes: - lon - is_anonymous - Polygon: - description: Geospatial polygon definition. - slots: - - id - - geoid - - geom - slot_usage: - id: - identifier: true - range: integer - slots: geoid: range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml index 1f4b0c5d..579609c2 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml @@ -81,6 +81,8 @@ classes: range: integer slots: + #Method slots + method_abbrev_id: range: integer description: Reference to MethodAbbrev. @@ -101,6 +103,8 @@ slots: range: integer description: Reference to DataSource. + #Parameter slots + standard_unit_id: range: integer description: Reference to Unit. @@ -109,6 +113,8 @@ slots: range: boolean description: Whether the parameter is calculated. + #ParameterCategoryParameter slots + parameter_id: range: integer description: Reference to Parameter. @@ -117,6 +123,8 @@ slots: range: integer description: Reference to ParameterCategory. + #ParameterUnit slots + alternate_unit_id: range: integer description: Reference to Unit. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml index 28d31e47..eb2ca5ed 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml @@ -86,6 +86,8 @@ classes: range: integer slots: + #Resource slots + primary_crop_id: range: integer description: Reference to PrimaryCrop. @@ -98,6 +100,8 @@ slots: range: integer description: Reference to ResourceSubclass. + #ResourceAvailability slots + resource_id: range: integer description: Reference to Resource. @@ -118,6 +122,8 @@ slots: range: boolean description: Whether available year-round. + #ResourceCounterfactual slots + counterfactual_description: range: string description: Description of counterfactual scenario. From 7558f39abe088c04a1ac36e7137d02c17b8a2336 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Mon, 15 Dec 2025 18:35:32 -0800 Subject: [PATCH 26/81] Add and edit revisions to schema (untested) --- .../linkml/modules/aim1_records.yaml | 6 +- .../linkml/modules/aim2_records.yaml | 3 +- .../datamodels/linkml/modules/core.yaml | 30 +---- .../linkml/modules/data_sources_metadata.yaml | 121 ++++++++++++------ .../linkml/modules/external_data.yaml | 4 + .../datamodels/linkml/modules/lineage.yaml | 33 +++++ 6 files changed, 126 insertions(+), 71 deletions(-) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml index 85028218..8328faec 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml @@ -33,6 +33,7 @@ classes: - technical_replicate_no - technical_replicate_total - method_id + - analyst_id - raw_data_id - qc_pass - note @@ -84,9 +85,10 @@ classes: slots: #Slots imported #dataset_id: from general_analysis.yaml - #experiment_id: from experiments.yaml + #experiment_id: from experiments_equipment.yaml + #analyst_id: from experiments_equipment.yaml #resource_id: from resource_information.yaml - #method_id: from experiments.yaml + #method_id: from experiments_equipment.yaml #note: from core.yaml #New slots defined in Aim1RecordBase class diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml index 2fdcda17..670c40b4 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml @@ -33,7 +33,8 @@ classes: - sample_id - technical_replicate_total - technical_replicate_no - - analyst_id + - calc_method_id #differentiated from method in the experiment, optional + - calc_analyst_id #differentiated from analyst in the experiment, optional - raw_data_id - qc_pass - note diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml index eec6318b..870eb513 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml @@ -72,36 +72,8 @@ slots: range: uri description: URI for the entity. - ##Slots for other ETL related fields + ##Slots for other basic fields used across the schema note: range: string description: Additional notes. - - source_table: - range: string - description: Source table name. - - source_row_id: - range: string - description: Source row identifier. - - started_at: - range: datetime - description: Start time of the ETL run. - - completed_at: - range: datetime - description: Completion time of the ETL run. - - pipeline_name: - range: string - description: Name of the pipeline. - - status: - range: string - description: Status of the ETL run. - - records_ingested: - range: integer - description: Number of records ingested. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index 5710afd3..32ae773d 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -23,30 +23,25 @@ classes: slots: - name - description - - uri - - publication_date - - version + - data_source_type_id + - full_title + - creator + - subject - publisher - - author + - contributor + - date + - type + - biocirv + - format + - language + - relation + - temporal_coverage + - location_coverage + - rights - license + - uri - note - #missing fields compared to DBdiagram. - #data_source_type_id - #full_title - #creator - #subject - #publisher - #date - #types - #biocirv - #format - #language - #relation - #temporal_coverage - #location_coverage - #rights - FileObjectMetadata: is_a: BaseEntity description: Metadata for a file object. @@ -73,25 +68,7 @@ classes: description: Type of source (e.g. database, literature). slots: - publication_date: - range: date - description: Date of publication. - - version: - range: string - description: Version of the data source. - - publisher: - range: string - description: Publisher of the data source. - - author: - range: string - description: Author of the data source. - - license: - range: string - description: License of the data source. + #FileObjectMetadata slots data_source_id: range: integer @@ -117,6 +94,72 @@ slots: range: string description: SHA256 checksum of the file. + #DataSourceType slots + source_type_id: range: integer description: Reference to SourceType. + + #DataSource slots + + data_source_type_id: + range: integer + description: Reference to DataSourceType. + + full_title: + range: string + description: Full title of the data source. + + creator: + range: string + description: Entity primarily responsible for making the resource. + + subject: + range: string + description: The topic of the resource. + + publisher: + range: string + description: Publisher of the data source. + + contributor: + range: string + description: Entity responsible for making contributions to the resource. + + date: + range: datetime + description: + Point or period of time associated with an event in the lifecycle of the + resource. + + type: + range: string + description: The nature or genre of the resource. + + biocirv: + range: boolean + description: Internal data flag (FALSE=External, TRUE=Internal). + + format: + range: string + description: File format, physical medium, or dimensions of the resource. + + language: + range: string + description: A language of the resource. + + relation: + range: string + description: A related resource. + + temporal_coverage: + range: string + description: The temporal topic of the resource (Daterange). + + location_coverage_id: + range: integer + description: Reference to LocationResolution. + + rights: + range: string + description: Information about rights held in and over the resource. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml index 4f80ac2d..3321a2f4 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml @@ -380,6 +380,10 @@ slots: range: float description: Number of acres. + version: + range: string + description: Version of the data source. + subclass_id: range: integer description: Reference to ResourceSubclass. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml index 6d0fd301..ed0d6c99 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml @@ -53,3 +53,36 @@ classes: slot_usage: id: identifier: true + +slots: + #Slots for EntityLineage class + + source_table: + range: string + description: Source table name. + + source_row_id: + range: string + description: Source row identifier. + + #Slots for EtlRun class + + started_at: + range: datetime + description: Start time of the ETL run. + + completed_at: + range: datetime + description: Completion time of the ETL run. + + pipeline_name: + range: string + description: Name of the pipeline. + + status: + range: string + description: Status of the ETL run. + + records_ingested: + range: integer + description: Number of records ingested. From d5ea8e14c31618994e2d35741487ca6fd7c8b9b8 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Mon, 15 Dec 2025 18:48:10 -0800 Subject: [PATCH 27/81] Making people group full of base entity --- .../ca_biositing/datamodels/linkml/modules/people.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml index 818bce18..94f0f42e 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml @@ -16,6 +16,7 @@ imports: classes: Contact: + is_a: BaseEntity description: Contact information for a person. slots: - id @@ -29,6 +30,7 @@ classes: range: integer Provider: + is_a: BaseEntity description: Provider information. slots: - id From 21baf816f4bb8d8afba4fbebadfc946c5f236f73 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Mon, 15 Dec 2025 21:47:39 -0800 Subject: [PATCH 28/81] made changes to try to make an alembic migration to represent the changes in the database. think there was an issue with the LinkML --> alembic --- .../27a733f8f5fb_sync_linkml_changes.py | 32 + .../5632747ee5fe_initial_migration.py | 32 + .../linkml/modules/aim2_records.yaml | 12 +- .../linkml/modules/data_sources_metadata.yaml | 6 +- .../schemas/generated/aim1_records.py | 227 +- .../schemas/generated/aim2_records.py | 242 +- .../schemas/generated/analysis_records.py | 118 +- .../schemas/generated/ca_biositing.py | 2404 ----------------- .../generated/data_sources_metadata.py | 231 +- .../schemas/generated/experiment_equipment.py | 197 +- .../schemas/generated/experiments.py | 118 +- .../schemas/generated/external_data.py | 346 +-- .../schemas/generated/field_sampling.py | 221 +- .../schemas/generated/general_analysis.py | 231 +- .../datamodels/schemas/generated/geography.py | 19 - .../schemas/generated/infrastructure.py | 231 +- .../generated/methods_parameters_units.py | 231 +- .../datamodels/schemas/generated/people.py | 44 - .../datamodels/schemas/generated/places.py | 106 - .../schemas/generated/resource_information.py | 307 --- .../datamodels/schemas/generated/resources.py | 326 --- .../schemas/generated/sample_preparation.py | 1089 -------- .../datamodels/schemas/generated/sampling.py | 964 ------- 23 files changed, 1411 insertions(+), 6323 deletions(-) create mode 100644 alembic/versions/27a733f8f5fb_sync_linkml_changes.py create mode 100644 alembic/versions/5632747ee5fe_initial_migration.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py diff --git a/alembic/versions/27a733f8f5fb_sync_linkml_changes.py b/alembic/versions/27a733f8f5fb_sync_linkml_changes.py new file mode 100644 index 00000000..18492f4a --- /dev/null +++ b/alembic/versions/27a733f8f5fb_sync_linkml_changes.py @@ -0,0 +1,32 @@ +"""Sync LinkML changes + +Revision ID: 27a733f8f5fb +Revises: 5632747ee5fe +Create Date: 2025-12-16 05:25:21.214170 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '27a733f8f5fb' +down_revision: Union[str, Sequence[str], None] = '5632747ee5fe' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/alembic/versions/5632747ee5fe_initial_migration.py b/alembic/versions/5632747ee5fe_initial_migration.py new file mode 100644 index 00000000..043c57bb --- /dev/null +++ b/alembic/versions/5632747ee5fe_initial_migration.py @@ -0,0 +1,32 @@ +"""Initial migration + +Revision ID: 5632747ee5fe +Revises: 1e9784d75e62 +Create Date: 2025-12-16 04:39:20.946195 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '5632747ee5fe' +down_revision: Union[str, Sequence[str], None] = '1e9784d75e62' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column('landiq_record', 'test') + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('landiq_record', sa.Column('test', sa.TEXT(), autoincrement=False, nullable=True)) + # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml index 670c40b4..8e20f1c9 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml @@ -33,8 +33,8 @@ classes: - sample_id - technical_replicate_total - technical_replicate_no - - calc_method_id #differentiated from method in the experiment, optional - - calc_analyst_id #differentiated from analyst in the experiment, optional + - calc_method_id + - calc_analyst_id - raw_data_id - qc_pass - note @@ -158,5 +158,13 @@ slots: range: integer description: Replicate number. + calc_method_id: + range: integer + description: Reference to Method used in calculation. + + calc_analyst_id: + range: integer + description: Reference to Analyst who performed calculation. + technical_replicate_total: range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index 32ae773d..1eeb2f53 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -36,7 +36,7 @@ classes: - language - relation - temporal_coverage - - location_coverage + - location_coverage_id - rights - license - uri @@ -163,3 +163,7 @@ slots: rights: range: string description: Information about rights held in and over the resource. + + license: + range: string + description: License of the resource. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py index 6a5fd758..834aaa45 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py @@ -206,45 +206,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class Aim1RecordBase(BaseEntity): """ @@ -258,6 +219,7 @@ class Aim1RecordBase(BaseEntity): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -269,7 +231,7 @@ class Aim1RecordBase(BaseEntity): def __repr__(self): - return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -718,12 +680,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -733,7 +706,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -779,7 +752,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -1138,6 +1111,68 @@ def __repr__(self): +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class FieldStorageMethod(LookupBase): """ Method of field storage. @@ -1238,26 +1273,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class SoilType(LookupBase): """ - Physical characteristics of a sample. + Type of soil. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'soil_type' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1269,11 +1298,11 @@ def __repr__(self): -class SoilType(LookupBase): +class AgTreatment(LookupBase): """ - Type of soil. + Agricultural treatment. """ - __tablename__ = 'soil_type' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1282,7 +1311,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1294,20 +1323,23 @@ def __repr__(self): -class AgTreatment(LookupBase): +class LocationSoilType(BaseEntity): """ - Agricultural treatment. + Soil type at a location. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'location_soil_type' + location_id = Column(Integer()) + soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1319,18 +1351,17 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class Contact(BaseEntity): """ - Condition of the field sample. + Contact information for a person. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'contact' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1338,7 +1369,7 @@ class FieldSampleCondition(BaseEntity): def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1350,15 +1381,14 @@ def __repr__(self): -class LocationSoilType(BaseEntity): +class Provider(BaseEntity): """ - Soil type at a location. + Provider information. """ - __tablename__ = 'location_soil_type' + __tablename__ = 'provider' - location_id = Column(Integer()) - soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1366,7 +1396,7 @@ class LocationSoilType(BaseEntity): def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1391,6 +1421,7 @@ class ProximateRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1402,7 +1433,7 @@ class ProximateRecord(Aim1RecordBase): def __repr__(self): - return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1427,6 +1458,7 @@ class UltimateRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1438,7 +1470,7 @@ class UltimateRecord(Aim1RecordBase): def __repr__(self): - return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1463,6 +1495,7 @@ class CompositionalRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1474,7 +1507,7 @@ class CompositionalRecord(Aim1RecordBase): def __repr__(self): - return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1499,6 +1532,7 @@ class IcpRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1510,7 +1544,7 @@ class IcpRecord(Aim1RecordBase): def __repr__(self): - return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1539,6 +1573,7 @@ class XrfRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1550,7 +1585,7 @@ class XrfRecord(Aim1RecordBase): def __repr__(self): - return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1577,6 +1612,7 @@ class XrdRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1588,7 +1624,7 @@ class XrdRecord(Aim1RecordBase): def __repr__(self): - return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1613,6 +1649,7 @@ class CalorimetryRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1624,7 +1661,7 @@ class CalorimetryRecord(Aim1RecordBase): def __repr__(self): - return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1649,6 +1686,7 @@ class FtnirRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1660,7 +1698,7 @@ class FtnirRecord(Aim1RecordBase): def __repr__(self): - return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1685,6 +1723,7 @@ class RgbRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1696,7 +1735,7 @@ class RgbRecord(Aim1RecordBase): def __repr__(self): - return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py index b282c9da..9315f884 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py @@ -206,45 +206,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class Aim2RecordBase(BaseEntity): """ @@ -255,12 +216,13 @@ class Aim2RecordBase(BaseEntity): experiment_id = Column(Integer()) resource_id = Column(Integer()) sample_id = Column(Integer()) - analyst_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -269,7 +231,7 @@ class Aim2RecordBase(BaseEntity): def __repr__(self): - return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -744,12 +706,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -759,7 +732,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -805,7 +778,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -1164,6 +1137,68 @@ def __repr__(self): +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class FieldStorageMethod(LookupBase): """ Method of field storage. @@ -1264,26 +1299,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class SoilType(LookupBase): """ - Physical characteristics of a sample. + Type of soil. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'soil_type' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1295,11 +1324,11 @@ def __repr__(self): -class SoilType(LookupBase): +class AgTreatment(LookupBase): """ - Type of soil. + Agricultural treatment. """ - __tablename__ = 'soil_type' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1308,7 +1337,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1320,20 +1349,23 @@ def __repr__(self): -class AgTreatment(LookupBase): +class LocationSoilType(BaseEntity): """ - Agricultural treatment. + Soil type at a location. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'location_soil_type' + location_id = Column(Integer()) + soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1345,18 +1377,17 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class Contact(BaseEntity): """ - Condition of the field sample. + Contact information for a person. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'contact' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1364,7 +1395,7 @@ class FieldSampleCondition(BaseEntity): def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1376,15 +1407,14 @@ def __repr__(self): -class LocationSoilType(BaseEntity): +class Provider(BaseEntity): """ - Soil type at a location. + Provider information. """ - __tablename__ = 'location_soil_type' + __tablename__ = 'provider' - location_id = Column(Integer()) - soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1392,7 +1422,7 @@ class LocationSoilType(BaseEntity): def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1420,12 +1450,13 @@ class PretreatmentRecord(Aim2RecordBase): experiment_id = Column(Integer()) resource_id = Column(Integer()) sample_id = Column(Integer()) - analyst_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1434,7 +1465,7 @@ class PretreatmentRecord(Aim2RecordBase): def __repr__(self): - return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1465,12 +1496,13 @@ class FermentationRecord(Aim2RecordBase): experiment_id = Column(Integer()) resource_id = Column(Integer()) sample_id = Column(Integer()) - analyst_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1479,7 +1511,7 @@ class FermentationRecord(Aim2RecordBase): def __repr__(self): - return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1504,12 +1536,13 @@ class GasificationRecord(Aim2RecordBase): experiment_id = Column(Integer()) resource_id = Column(Integer()) sample_id = Column(Integer()) - analyst_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1518,7 +1551,7 @@ class GasificationRecord(Aim2RecordBase): def __repr__(self): - return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1540,12 +1573,13 @@ class AutoclaveRecord(Aim2RecordBase): experiment_id = Column(Integer()) resource_id = Column(Integer()) sample_id = Column(Integer()) - analyst_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1554,7 +1588,7 @@ class AutoclaveRecord(Aim2RecordBase): def __repr__(self): - return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py index b8968702..35158f30 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py @@ -150,64 +150,6 @@ def __repr__(self): -class Polygon(Base): - """ - Geospatial polygon definition. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ParameterCategoryParameter(Base): """ Link between parameter and category. @@ -869,6 +811,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Unit(LookupBase): """ Unit of measurement. @@ -1601,7 +1600,6 @@ class PrimaryCrop(LookupBase): """ __tablename__ = 'primary_crop' - note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) description = Column(Text()) @@ -1609,7 +1607,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py deleted file mode 100644 index 87fb054a..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py +++ /dev/null @@ -1,2404 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - -class LineageGroup(Base): - """ - Grouping for lineage information. - """ - __tablename__ = 'lineage_group' - - id = Column(Integer(), primary_key=True, nullable=False ) - etl_run_id = Column(Text()) - note = Column(Text()) - - - def __repr__(self): - return f"LineageGroup(id={self.id},etl_run_id={self.etl_run_id},note={self.note},)" - - - - - - -class EntityLineage(Base): - """ - Lineage information for a specific entity. - """ - __tablename__ = 'entity_lineage' - - id = Column(Integer(), primary_key=True, nullable=False ) - lineage_group_id = Column(Integer()) - source_table = Column(Text()) - source_row_id = Column(Text()) - note = Column(Text()) - - - def __repr__(self): - return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" - - - - - - -class EtlRun(Base): - """ - Information about an ETL run. - """ - __tablename__ = 'etl_run' - - id = Column(Integer(), primary_key=True, nullable=False ) - started_at = Column(DateTime()) - completed_at = Column(DateTime()) - pipeline_name = Column(Text()) - status = Column(Text()) - records_ingested = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class ExperimentMethod(Base): - """ - Link between Experiment and Method. - """ - __tablename__ = 'experiment_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - method_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" - - - - - - -class ExperimentEquipment(Base): - """ - Link between Experiment and Equipment. - """ - __tablename__ = 'experiment_equipment' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - equipment_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" - - - - - - -class ExperimentAnalysis(Base): - """ - Link between Experiment and AnalysisType. - """ - __tablename__ = 'experiment_analysis' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - analysis_type_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" - - - - - - -class ExperimentPreparedSample(Base): - """ - Link between Experiment and PreparedSample. - """ - __tablename__ = 'experiment_prepared_sample' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - prepared_sample_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" - - - - - - -class Polygon(Base): - """ - Geospatial polygon. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) - publisher = Column(Text()) - author = Column(Text()) - license = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source. - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample that has been prepared. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Experiment(BaseEntity): - """ - Experiment definition. - """ - __tablename__ = 'experiment' - - analyst_id = Column(Integer()) - exper_start_date = Column(Date()) - exper_duration = Column(Numeric()) - exper_duration_unit_id = Column(Integer()) - exper_location_id = Column(Integer()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Equipment(LookupBase): - """ - Equipment used in experiments. - """ - __tablename__ = 'equipment' - - equipment_location_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Dataset(BaseEntity): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(Date()) - end_date = Column(Date()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension. - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Observation(BaseEntity): - """ - Observation data. - """ - __tablename__ = 'observation' - - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Aim1RecordBase(BaseEntity): - """ - - """ - __tablename__ = 'aim1_record_base' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Aim2RecordBase(BaseEntity): - """ - - """ - __tablename__ = 'aim2_record_base' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Strain(LookupBase): - """ - Strain used in fermentation. - """ - __tablename__ = 'strain' - - parent_strain_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaDomain(LookupBase): - """ - USDA domain. - """ - __tablename__ = 'usda_domain' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaDomain(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaStatisticCategory(LookupBase): - """ - USDA statistic category. - """ - __tablename__ = 'usda_statistic_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaStatisticCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaSurveyProgram(LookupBase): - """ - USDA survey program. - """ - __tablename__ = 'usda_survey_program' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaSurveyProgram(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaCommodity(LookupBase): - """ - USDA commodity. - """ - __tablename__ = 'usda_commodity' - - usda_source = Column(Text()) - usda_code = Column(Text()) - parent_commodity_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaTermMap(BaseEntity): - """ - Mapping of raw terms to USDA commodities. - """ - __tablename__ = 'usda_term_map' - - source_system = Column(Text()) - source_context = Column(Text()) - raw_term = Column(Text()) - usda_commodity_id = Column(Integer()) - is_verified = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceUsdaCommodityMap(BaseEntity): - """ - Mapping between resources/crops and USDA commodities. - """ - __tablename__ = 'resource_usda_commodity_map' - - resource_id = Column(Integer()) - primary_crop_id = Column(Integer()) - usda_commodity_id = Column(Integer()) - match_tier = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaCensusRecord(BaseEntity): - """ - USDA census record. - """ - __tablename__ = 'usda_census_record' - - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - source_reference = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaSurveyRecord(BaseEntity): - """ - USDA survey record. - """ - __tablename__ = 'usda_survey_record' - - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - survey_program_id = Column(Integer()) - survey_period = Column(Text()) - reference_month = Column(Text()) - seasonal_flag = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaMarketReport(BaseEntity): - """ - USDA market report. - """ - __tablename__ = 'usda_market_report' - - slug_id = Column(Integer()) - slug_name = Column(Text()) - report_series_title = Column(Text()) - frequency = Column(Text()) - office_name = Column(Text()) - office_city_id = Column(Integer()) - office_state_fips = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaMarketReport(slug_id={self.slug_id},slug_name={self.slug_name},report_series_title={self.report_series_title},frequency={self.frequency},office_name={self.office_name},office_city_id={self.office_city_id},office_state_fips={self.office_state_fips},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaMarketRecord(BaseEntity): - """ - USDA market record. - """ - __tablename__ = 'usda_market_record' - - report_id = Column(Integer()) - dataset_id = Column(Integer()) - report_begin_date = Column(DateTime()) - report_end_date = Column(DateTime()) - report_date = Column(DateTime()) - commodity_id = Column(Integer()) - market_type_id = Column(Integer()) - market_type_catagory = Column(Text()) - grp = Column(Text()) - market_catagory_id = Column(Integer()) - class_ = Column(Text()) - grade = Column(Text()) - variety = Column(Text()) - protein_pct = Column(Numeric()) - application = Column(Text()) - pkg = Column(Text()) - sale_type = Column(Text()) - price_unit_id = Column(Integer()) - freight = Column(Text()) - trans_mode = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_catagory={self.market_type_catagory},grp={self.grp},market_catagory_id={self.market_catagory_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LandiqRecord(BaseEntity): - """ - LandIQ record. - """ - __tablename__ = 'landiq_record' - - dataset_id = Column(Integer()) - polygon_id = Column(Integer()) - main_crop = Column(Integer()) - secondary_crop = Column(Integer()) - tertiary_crop = Column(Integer()) - quaternary_crop = Column(Integer()) - confidence = Column(Integer()) - irrigated = Column(Boolean()) - acres = Column(Float()) - version = Column(Text()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class BillionTon2023Record(BaseEntity): - """ - Billion Ton 2023 record. - """ - __tablename__ = 'billion_ton2023_record' - - subclass_id = Column(Integer()) - resource_id = Column(Integer()) - geoid = Column(Text()) - county_square_miles = Column(Float()) - model_name = Column(Text()) - scenario_name = Column(Text()) - price_offered_usd = Column(Numeric()) - production = Column(Integer()) - production_unit_id = Column(Integer()) - btu_ton = Column(Integer()) - production_energy_content = Column(Integer()) - energy_content_unit_id = Column(Integer()) - product_density_dtpersqmi = Column(Numeric()) - land_source = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BillionTon2023Record(subclass_id={self.subclass_id},resource_id={self.resource_id},geoid={self.geoid},county_square_miles={self.county_square_miles},model_name={self.model_name},scenario_name={self.scenario_name},price_offered_usd={self.price_offered_usd},production={self.production},production_unit_id={self.production_unit_id},btu_ton={self.btu_ton},production_energy_content={self.production_energy_content},energy_content_unit_id={self.energy_content_unit_id},product_density_dtpersqmi={self.product_density_dtpersqmi},land_source={self.land_source},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProximateRecord(Aim1RecordBase): - """ - Proximate analysis record. - """ - __tablename__ = 'proximate_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UltimateRecord(Aim1RecordBase): - """ - Ultimate analysis record. - """ - __tablename__ = 'ultimate_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CompositionalRecord(Aim1RecordBase): - """ - Compositional analysis record. - """ - __tablename__ = 'compositional_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class IcpRecord(Aim1RecordBase): - """ - ICP analysis record. - """ - __tablename__ = 'icp_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class XrfRecord(Aim1RecordBase): - """ - XRF analysis record. - """ - __tablename__ = 'xrf_record' - - maybe_wavelength_nm = Column(Numeric()) - maybe_intensity = Column(Numeric()) - maybe_energy_slope = Column(Numeric()) - maybe_energy_offset = Column(Numeric()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class XrdRecord(Aim1RecordBase): - """ - XRD analysis record. - """ - __tablename__ = 'xrd_record' - - maybe_scan_low_nm = Column(Integer()) - maybe_scan_high_nm = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CalorimetryRecord(Aim1RecordBase): - """ - Calorimetry analysis record. - """ - __tablename__ = 'calorimetry_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FtnirRecord(Aim1RecordBase): - """ - FT-NIR analysis record. - """ - __tablename__ = 'ftnir_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class RgbRecord(Aim1RecordBase): - """ - RGB analysis record. - """ - __tablename__ = 'rgb_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PretreatmentRecord(Aim2RecordBase): - """ - Pretreatment record. - """ - __tablename__ = 'pretreatment_record' - - pretreatment_method_id = Column(Integer()) - eh_method_id = Column(Integer()) - reaction_block_id = Column(Integer()) - block_position = Column(Text()) - temperature = Column(Numeric()) - replicate_no = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FermentationRecord(Aim2RecordBase): - """ - Fermentation record. - """ - __tablename__ = 'fermentation_record' - - strain_id = Column(Integer()) - pretreatment_method_id = Column(Integer()) - eh_method_id = Column(Integer()) - replicate_no = Column(Integer()) - well_position = Column(Text()) - temperature = Column(Numeric()) - agitation_rpm = Column(Numeric()) - vessel_id = Column(Integer()) - analyte_detection_equipment_id = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class GasificationRecord(Aim2RecordBase): - """ - Gasification record. - """ - __tablename__ = 'gasification_record' - - feedstock_mass = Column(Numeric()) - bed_temperature = Column(Numeric()) - gas_flow_rate = Column(Numeric()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AutoclaveRecord(Aim2RecordBase): - """ - Autoclave record. - """ - __tablename__ = 'autoclave_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py index 48fe18d7..964a4575 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py @@ -73,45 +73,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -177,12 +138,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -192,7 +164,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -238,7 +210,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -347,6 +319,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Resource(BaseEntity): """ Biomass resource definition. @@ -761,20 +790,26 @@ def __repr__(self): -class FieldStorageMethod(LookupBase): +class PhysicalCharacteristic(BaseEntity): """ - Method of field storage. + Physical characteristics of a sample. """ - __tablename__ = 'field_storage_method' + __tablename__ = 'physical_characteristic' + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -786,20 +821,26 @@ def __repr__(self): -class CollectionMethod(LookupBase): +class FieldSampleCondition(BaseEntity): """ - Method of collection. + Condition of the field sample. """ - __tablename__ = 'collection_method' + __tablename__ = 'field_sample_condition' + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -811,11 +852,11 @@ def __repr__(self): -class HarvestMethod(LookupBase): +class FieldStorageMethod(LookupBase): """ - Method of harvest. + Method of field storage. """ - __tablename__ = 'harvest_method' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -824,7 +865,7 @@ class HarvestMethod(LookupBase): def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -836,11 +877,11 @@ def __repr__(self): -class ProcessingMethod(LookupBase): +class CollectionMethod(LookupBase): """ - Method of processing. + Method of collection. """ - __tablename__ = 'processing_method' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -849,7 +890,7 @@ class ProcessingMethod(LookupBase): def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -861,26 +902,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class HarvestMethod(LookupBase): """ - Physical characteristics of a sample. + Method of harvest. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'harvest_method' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -892,11 +927,11 @@ def __repr__(self): -class SoilType(LookupBase): +class ProcessingMethod(LookupBase): """ - Type of soil. + Method of processing. """ - __tablename__ = 'soil_type' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -905,7 +940,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -917,11 +952,11 @@ def __repr__(self): -class AgTreatment(LookupBase): +class SoilType(LookupBase): """ - Agricultural treatment. + Type of soil. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -930,7 +965,7 @@ class AgTreatment(LookupBase): def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -942,26 +977,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class AgTreatment(LookupBase): """ - Condition of the field sample. + Agricultural treatment. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'ag_treatment' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py index 3f2ab322..7f0bdd34 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py @@ -187,45 +187,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -569,6 +530,68 @@ def __repr__(self): +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class FieldStorageMethod(LookupBase): """ Method of field storage. @@ -669,26 +692,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class SoilType(LookupBase): """ - Physical characteristics of a sample. + Type of soil. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'soil_type' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -700,11 +717,11 @@ def __repr__(self): -class SoilType(LookupBase): +class AgTreatment(LookupBase): """ - Type of soil. + Agricultural treatment. """ - __tablename__ = 'soil_type' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -713,7 +730,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -725,20 +742,23 @@ def __repr__(self): -class AgTreatment(LookupBase): +class LocationSoilType(BaseEntity): """ - Agricultural treatment. + Soil type at a location. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'location_soil_type' + location_id = Column(Integer()) + soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -750,18 +770,17 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class Contact(BaseEntity): """ - Condition of the field sample. + Contact information for a person. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'contact' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -769,7 +788,7 @@ class FieldSampleCondition(BaseEntity): def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -781,15 +800,14 @@ def __repr__(self): -class LocationSoilType(BaseEntity): +class Provider(BaseEntity): """ - Soil type at a location. + Provider information. """ - __tablename__ = 'location_soil_type' + __tablename__ = 'provider' - location_id = Column(Integer()) - soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -797,7 +815,7 @@ class LocationSoilType(BaseEntity): def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -906,12 +924,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -921,7 +950,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -967,7 +996,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py index 4d5b8097..bc022794 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py @@ -149,64 +149,6 @@ def __repr__(self): -class Polygon(Base): - """ - Geospatial polygon definition. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ParameterCategoryParameter(Base): """ Link between parameter and category. @@ -432,6 +374,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Unit(LookupBase): """ Unit of measurement. @@ -707,7 +706,6 @@ class PrimaryCrop(LookupBase): """ __tablename__ = 'primary_crop' - note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) description = Column(Text()) @@ -715,7 +713,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py index c1e3bad5..2c6e1121 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py @@ -149,45 +149,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class UsdaDomain(LookupBase): """ USDA domain. @@ -263,23 +224,27 @@ def __repr__(self): -class UsdaCommodity(LookupBase): +class UsdaCensusRecord(BaseEntity): """ - USDA commodity. + USDA census record. """ - __tablename__ = 'usda_commodity' + __tablename__ = 'usda_census_record' - usda_source = Column(Text()) - usda_code = Column(Text()) - parent_commodity_id = Column(Integer()) + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + source_reference = Column(Text()) + note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -291,17 +256,20 @@ def __repr__(self): -class UsdaTermMap(BaseEntity): +class UsdaSurveyRecord(BaseEntity): """ - Mapping of raw terms to USDA commodities. + USDA survey record. """ - __tablename__ = 'usda_term_map' + __tablename__ = 'usda_survey_record' - source_system = Column(Text()) - source_context = Column(Text()) - raw_term = Column(Text()) - usda_commodity_id = Column(Integer()) - is_verified = Column(Boolean()) + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + survey_program_id = Column(Integer()) + survey_period = Column(Text()) + reference_month = Column(Text()) + seasonal_flag = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -311,7 +279,7 @@ class UsdaTermMap(BaseEntity): def __repr__(self): - return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -323,26 +291,23 @@ def __repr__(self): -class ResourceUsdaCommodityMap(BaseEntity): +class UsdaCommodity(LookupBase): """ - Mapping between resources/crops and USDA commodities. + USDA commodity. """ - __tablename__ = 'resource_usda_commodity_map' + __tablename__ = 'usda_commodity' - resource_id = Column(Integer()) - primary_crop_id = Column(Integer()) - usda_commodity_id = Column(Integer()) - match_tier = Column(Text()) - note = Column(Text()) + usda_source = Column(Text()) + usda_code = Column(Text()) + parent_commodity_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -354,17 +319,17 @@ def __repr__(self): -class UsdaCensusRecord(BaseEntity): +class UsdaTermMap(BaseEntity): """ - USDA census record. + Mapping of raw terms to USDA commodities. """ - __tablename__ = 'usda_census_record' + __tablename__ = 'usda_term_map' - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - source_reference = Column(Text()) + source_system = Column(Text()) + source_context = Column(Text()) + raw_term = Column(Text()) + usda_commodity_id = Column(Integer()) + is_verified = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -374,7 +339,7 @@ class UsdaCensusRecord(BaseEntity): def __repr__(self): - return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -386,20 +351,16 @@ def __repr__(self): -class UsdaSurveyRecord(BaseEntity): +class ResourceUsdaCommodityMap(BaseEntity): """ - USDA survey record. + Mapping between resources/crops and USDA commodities. """ - __tablename__ = 'usda_survey_record' + __tablename__ = 'resource_usda_commodity_map' - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - survey_program_id = Column(Integer()) - survey_period = Column(Text()) - reference_month = Column(Text()) - seasonal_flag = Column(Boolean()) + resource_id = Column(Integer()) + primary_crop_id = Column(Integer()) + usda_commodity_id = Column(Integer()) + match_tier = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -409,7 +370,7 @@ class UsdaSurveyRecord(BaseEntity): def __repr__(self): - return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -468,9 +429,9 @@ class UsdaMarketRecord(BaseEntity): report_date = Column(DateTime()) commodity_id = Column(Integer()) market_type_id = Column(Integer()) - market_type_catagory = Column(Text()) + market_type_category = Column(Text()) grp = Column(Text()) - market_catagory_id = Column(Integer()) + market_category_id = Column(Integer()) class_ = Column(Text()) grade = Column(Text()) variety = Column(Text()) @@ -489,7 +450,7 @@ class UsdaMarketRecord(BaseEntity): def __repr__(self): - return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_catagory={self.market_type_catagory},grp={self.grp},market_catagory_id={self.market_catagory_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_category={self.market_type_category},grp={self.grp},market_category_id={self.market_category_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -518,7 +479,6 @@ class LandiqRecord(BaseEntity): acres = Column(Float()) version = Column(Text()) note = Column(Text()) - test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -527,7 +487,7 @@ class LandiqRecord(BaseEntity): def __repr__(self): - return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -587,12 +547,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -602,7 +573,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -648,7 +619,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -1245,6 +1216,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class FieldSample(BaseEntity): """ Sample collected from the field. @@ -1289,20 +1317,26 @@ def __repr__(self): -class FieldStorageMethod(LookupBase): +class PhysicalCharacteristic(BaseEntity): """ - Method of field storage. + Physical characteristics of a sample. """ - __tablename__ = 'field_storage_method' + __tablename__ = 'physical_characteristic' + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1314,20 +1348,26 @@ def __repr__(self): -class CollectionMethod(LookupBase): +class FieldSampleCondition(BaseEntity): """ - Method of collection. + Condition of the field sample. """ - __tablename__ = 'collection_method' + __tablename__ = 'field_sample_condition' + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1339,11 +1379,11 @@ def __repr__(self): -class HarvestMethod(LookupBase): +class FieldStorageMethod(LookupBase): """ - Method of harvest. + Method of field storage. """ - __tablename__ = 'harvest_method' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1352,7 +1392,7 @@ class HarvestMethod(LookupBase): def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1364,11 +1404,11 @@ def __repr__(self): -class ProcessingMethod(LookupBase): +class CollectionMethod(LookupBase): """ - Method of processing. + Method of collection. """ - __tablename__ = 'processing_method' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1377,7 +1417,7 @@ class ProcessingMethod(LookupBase): def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1389,26 +1429,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class HarvestMethod(LookupBase): """ - Physical characteristics of a sample. + Method of harvest. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'harvest_method' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1420,11 +1454,11 @@ def __repr__(self): -class SoilType(LookupBase): +class ProcessingMethod(LookupBase): """ - Type of soil. + Method of processing. """ - __tablename__ = 'soil_type' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1433,7 +1467,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1445,11 +1479,11 @@ def __repr__(self): -class AgTreatment(LookupBase): +class SoilType(LookupBase): """ - Agricultural treatment. + Type of soil. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1458,7 +1492,7 @@ class AgTreatment(LookupBase): def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1470,26 +1504,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class AgTreatment(LookupBase): """ - Condition of the field sample. + Agricultural treatment. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'ag_treatment' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py index 6fed28ad..0f1b410a 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py @@ -73,45 +73,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -213,6 +174,68 @@ def __repr__(self): +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class FieldStorageMethod(LookupBase): """ Method of field storage. @@ -313,26 +336,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class SoilType(LookupBase): """ - Physical characteristics of a sample. + Type of soil. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'soil_type' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -344,11 +361,11 @@ def __repr__(self): -class SoilType(LookupBase): +class AgTreatment(LookupBase): """ - Type of soil. + Agricultural treatment. """ - __tablename__ = 'soil_type' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -357,7 +374,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -369,20 +386,23 @@ def __repr__(self): -class AgTreatment(LookupBase): +class LocationSoilType(BaseEntity): """ - Agricultural treatment. + Soil type at a location. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'location_soil_type' + location_id = Column(Integer()) + soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -394,17 +414,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class LocationAddress(BaseEntity): """ - Condition of the field sample. + Physical address. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'location_address' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -413,7 +436,7 @@ class FieldSampleCondition(BaseEntity): def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -425,15 +448,17 @@ def __repr__(self): -class LocationSoilType(BaseEntity): +class Contact(BaseEntity): """ - Soil type at a location. + Contact information for a person. """ - __tablename__ = 'location_soil_type' + __tablename__ = 'contact' - location_id = Column(Integer()) - soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -441,7 +466,7 @@ class LocationSoilType(BaseEntity): def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -453,21 +478,14 @@ def __repr__(self): -class LocationAddress(BaseEntity): +class Provider(BaseEntity): """ - Physical address. + Provider information. """ - __tablename__ = 'location_address' + __tablename__ = 'provider' - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -475,7 +493,7 @@ class LocationAddress(BaseEntity): def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -677,12 +695,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -692,7 +721,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -738,7 +767,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py index 5b4bbd8c..69cd6452 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py @@ -73,45 +73,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -295,12 +256,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -310,7 +282,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -356,7 +328,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -465,6 +437,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Resource(BaseEntity): """ Biomass resource definition. @@ -879,20 +908,26 @@ def __repr__(self): -class FieldStorageMethod(LookupBase): +class PhysicalCharacteristic(BaseEntity): """ - Method of field storage. + Physical characteristics of a sample. """ - __tablename__ = 'field_storage_method' + __tablename__ = 'physical_characteristic' + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -904,20 +939,26 @@ def __repr__(self): -class CollectionMethod(LookupBase): +class FieldSampleCondition(BaseEntity): """ - Method of collection. + Condition of the field sample. """ - __tablename__ = 'collection_method' + __tablename__ = 'field_sample_condition' + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -929,11 +970,11 @@ def __repr__(self): -class HarvestMethod(LookupBase): +class FieldStorageMethod(LookupBase): """ - Method of harvest. + Method of field storage. """ - __tablename__ = 'harvest_method' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -942,7 +983,7 @@ class HarvestMethod(LookupBase): def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -954,11 +995,11 @@ def __repr__(self): -class ProcessingMethod(LookupBase): +class CollectionMethod(LookupBase): """ - Method of processing. + Method of collection. """ - __tablename__ = 'processing_method' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -967,7 +1008,7 @@ class ProcessingMethod(LookupBase): def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -979,26 +1020,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class HarvestMethod(LookupBase): """ - Physical characteristics of a sample. + Method of harvest. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'harvest_method' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1010,11 +1045,11 @@ def __repr__(self): -class SoilType(LookupBase): +class ProcessingMethod(LookupBase): """ - Type of soil. + Method of processing. """ - __tablename__ = 'soil_type' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1023,7 +1058,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1035,11 +1070,11 @@ def __repr__(self): -class AgTreatment(LookupBase): +class SoilType(LookupBase): """ - Agricultural treatment. + Type of soil. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1048,7 +1083,7 @@ class AgTreatment(LookupBase): def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1060,26 +1095,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class AgTreatment(LookupBase): """ - Condition of the field sample. + Agricultural treatment. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'ag_treatment' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py index 2de38d94..349885b9 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py @@ -32,25 +32,6 @@ def __repr__(self): -class Polygon(Base): - """ - Geospatial polygon definition. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - class BaseEntity(Base): """ Base entity included in all main entity tables. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py index 20dfafc8..87a37dab 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py @@ -516,45 +516,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -654,12 +615,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -669,7 +641,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -715,7 +687,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -824,6 +796,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Resource(BaseEntity): """ Biomass resource definition. @@ -1238,20 +1267,26 @@ def __repr__(self): -class FieldStorageMethod(LookupBase): +class PhysicalCharacteristic(BaseEntity): """ - Method of field storage. + Physical characteristics of a sample. """ - __tablename__ = 'field_storage_method' + __tablename__ = 'physical_characteristic' + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1263,20 +1298,26 @@ def __repr__(self): -class CollectionMethod(LookupBase): +class FieldSampleCondition(BaseEntity): """ - Method of collection. + Condition of the field sample. """ - __tablename__ = 'collection_method' + __tablename__ = 'field_sample_condition' + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1288,11 +1329,11 @@ def __repr__(self): -class HarvestMethod(LookupBase): +class FieldStorageMethod(LookupBase): """ - Method of harvest. + Method of field storage. """ - __tablename__ = 'harvest_method' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1301,7 +1342,7 @@ class HarvestMethod(LookupBase): def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1313,11 +1354,11 @@ def __repr__(self): -class ProcessingMethod(LookupBase): +class CollectionMethod(LookupBase): """ - Method of processing. + Method of collection. """ - __tablename__ = 'processing_method' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1326,7 +1367,7 @@ class ProcessingMethod(LookupBase): def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1338,26 +1379,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class HarvestMethod(LookupBase): """ - Physical characteristics of a sample. + Method of harvest. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'harvest_method' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1369,11 +1404,11 @@ def __repr__(self): -class SoilType(LookupBase): +class ProcessingMethod(LookupBase): """ - Type of soil. + Method of processing. """ - __tablename__ = 'soil_type' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1382,7 +1417,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1394,11 +1429,11 @@ def __repr__(self): -class AgTreatment(LookupBase): +class SoilType(LookupBase): """ - Agricultural treatment. + Type of soil. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1407,7 +1442,7 @@ class AgTreatment(LookupBase): def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1419,26 +1454,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class AgTreatment(LookupBase): """ - Condition of the field sample. + Agricultural treatment. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'ag_treatment' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py index 4e50f484..781ff528 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py @@ -111,45 +111,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -391,6 +352,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Resource(BaseEntity): """ Biomass resource definition. @@ -617,20 +635,26 @@ def __repr__(self): -class FieldStorageMethod(LookupBase): +class PhysicalCharacteristic(BaseEntity): """ - Method of field storage. + Physical characteristics of a sample. """ - __tablename__ = 'field_storage_method' + __tablename__ = 'physical_characteristic' + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -642,20 +666,26 @@ def __repr__(self): -class CollectionMethod(LookupBase): +class FieldSampleCondition(BaseEntity): """ - Method of collection. + Condition of the field sample. """ - __tablename__ = 'collection_method' + __tablename__ = 'field_sample_condition' + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -667,11 +697,11 @@ def __repr__(self): -class HarvestMethod(LookupBase): +class FieldStorageMethod(LookupBase): """ - Method of harvest. + Method of field storage. """ - __tablename__ = 'harvest_method' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -680,7 +710,7 @@ class HarvestMethod(LookupBase): def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -692,11 +722,11 @@ def __repr__(self): -class ProcessingMethod(LookupBase): +class CollectionMethod(LookupBase): """ - Method of processing. + Method of collection. """ - __tablename__ = 'processing_method' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -705,7 +735,7 @@ class ProcessingMethod(LookupBase): def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -717,26 +747,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class HarvestMethod(LookupBase): """ - Physical characteristics of a sample. + Method of harvest. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'harvest_method' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -748,11 +772,11 @@ def __repr__(self): -class SoilType(LookupBase): +class ProcessingMethod(LookupBase): """ - Type of soil. + Method of processing. """ - __tablename__ = 'soil_type' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -761,7 +785,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -773,11 +797,11 @@ def __repr__(self): -class AgTreatment(LookupBase): +class SoilType(LookupBase): """ - Agricultural treatment. + Type of soil. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -786,7 +810,7 @@ class AgTreatment(LookupBase): def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -798,26 +822,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class AgTreatment(LookupBase): """ - Condition of the field sample. + Agricultural treatment. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'ag_treatment' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -865,12 +883,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -880,7 +909,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -926,7 +955,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py index 7eacc534..e69de29b 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py @@ -1,44 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py deleted file mode 100644 index 4eccd8ac..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py +++ /dev/null @@ -1,106 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py deleted file mode 100644 index b1d3d70e..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py +++ /dev/null @@ -1,307 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py deleted file mode 100644 index bec06909..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py +++ /dev/null @@ -1,326 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Polygon(Base): - """ - Geospatial polygon definition. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py deleted file mode 100644 index a3da8a03..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py +++ /dev/null @@ -1,1089 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample that has been prepared. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) - publisher = Column(Text()) - author = Column(Text()) - license = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source. - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py deleted file mode 100644 index 63f68798..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py +++ /dev/null @@ -1,964 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Polygon(Base): - """ - Geospatial polygon definition. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample prepared for analysis. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } From 10ff5c0d10f84499b12036386f5ab0ef8c7f7c2c Mon Sep 17 00:00:00 2001 From: mglbleta Date: Tue, 16 Dec 2025 16:26:50 -0800 Subject: [PATCH 29/81] hallucinations removed working update --- .../bfa07351a507_remove_hallucinations.py | 138 + .../d82910ff757e_initial_migration.py | 32 + .../datamodels/linkml/modules/people.yaml | 8 +- .../schemas/generated/aim1_records.py | 8 +- .../schemas/generated/aim2_records.py | 8 +- .../schemas/generated/analysis_records.py | 8 +- .../schemas/generated/ca_biositing.py | 2447 +++++++++++++++++ .../generated/data_sources_metadata.py | 8 +- .../schemas/generated/experiment_equipment.py | 8 +- .../schemas/generated/experiments.py | 8 +- .../schemas/generated/external_data.py | 8 +- .../schemas/generated/field_sampling.py | 8 +- .../schemas/generated/general_analysis.py | 8 +- .../schemas/generated/infrastructure.py | 8 +- .../generated/methods_parameters_units.py | 8 +- .../datamodels/schemas/generated/people.py | 106 + .../datamodels/schemas/generated/places.py | 106 + .../schemas/generated/resource_information.py | 307 +++ .../datamodels/schemas/generated/resources.py | 306 +++ .../schemas/generated/sample_preparation.py | 1118 ++++++++ .../datamodels/schemas/generated/sampling.py | 962 +++++++ 21 files changed, 5567 insertions(+), 51 deletions(-) create mode 100644 alembic/versions/bfa07351a507_remove_hallucinations.py create mode 100644 alembic/versions/d82910ff757e_initial_migration.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py diff --git a/alembic/versions/bfa07351a507_remove_hallucinations.py b/alembic/versions/bfa07351a507_remove_hallucinations.py new file mode 100644 index 00000000..6ac8caa9 --- /dev/null +++ b/alembic/versions/bfa07351a507_remove_hallucinations.py @@ -0,0 +1,138 @@ +"""Remove hallucinations\ + +Revision ID: bfa07351a507 +Revises: d82910ff757e +Create Date: 2025-12-17 00:05:46.750313 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'bfa07351a507' +down_revision: Union[str, Sequence[str], None] = 'd82910ff757e' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('aim1_record_base', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('aim2_record_base', sa.Column('calc_method_id', sa.Integer(), nullable=True)) + op.add_column('aim2_record_base', sa.Column('calc_analyst_id', sa.Integer(), nullable=True)) + op.drop_column('aim2_record_base', 'analyst_id') + op.add_column('autoclave_record', sa.Column('calc_method_id', sa.Integer(), nullable=True)) + op.add_column('autoclave_record', sa.Column('calc_analyst_id', sa.Integer(), nullable=True)) + op.drop_column('autoclave_record', 'analyst_id') + op.add_column('calorimetry_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('compositional_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('contact', sa.Column('created_at', sa.DateTime(), nullable=True)) + op.add_column('contact', sa.Column('updated_at', sa.DateTime(), nullable=True)) + op.add_column('contact', sa.Column('etl_run_id', sa.Text(), nullable=True)) + op.add_column('contact', sa.Column('lineage_group_id', sa.Integer(), nullable=True)) + op.add_column('data_source', sa.Column('data_source_type_id', sa.Integer(), nullable=True)) + op.add_column('data_source', sa.Column('full_title', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('creator', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('subject', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('contributor', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('date', sa.DateTime(), nullable=True)) + op.add_column('data_source', sa.Column('type', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('biocirv', sa.Boolean(), nullable=True)) + op.add_column('data_source', sa.Column('format', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('language', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('relation', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('temporal_coverage', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('location_coverage_id', sa.Integer(), nullable=True)) + op.add_column('data_source', sa.Column('rights', sa.Text(), nullable=True)) + op.drop_column('data_source', 'publication_date') + op.drop_column('data_source', 'version') + op.drop_column('data_source', 'author') + op.add_column('fermentation_record', sa.Column('calc_method_id', sa.Integer(), nullable=True)) + op.add_column('fermentation_record', sa.Column('calc_analyst_id', sa.Integer(), nullable=True)) + op.drop_column('fermentation_record', 'analyst_id') + op.add_column('ftnir_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('gasification_record', sa.Column('calc_method_id', sa.Integer(), nullable=True)) + op.add_column('gasification_record', sa.Column('calc_analyst_id', sa.Integer(), nullable=True)) + op.drop_column('gasification_record', 'analyst_id') + op.add_column('icp_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('pretreatment_record', sa.Column('calc_method_id', sa.Integer(), nullable=True)) + op.add_column('pretreatment_record', sa.Column('calc_analyst_id', sa.Integer(), nullable=True)) + op.drop_column('pretreatment_record', 'analyst_id') + op.add_column('provider', sa.Column('created_at', sa.DateTime(), nullable=True)) + op.add_column('provider', sa.Column('updated_at', sa.DateTime(), nullable=True)) + op.add_column('provider', sa.Column('etl_run_id', sa.Text(), nullable=True)) + op.add_column('provider', sa.Column('lineage_group_id', sa.Integer(), nullable=True)) + op.add_column('proximate_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('rgb_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('ultimate_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('usda_market_record', sa.Column('market_type_category', sa.Text(), nullable=True)) + op.add_column('usda_market_record', sa.Column('market_category_id', sa.Integer(), nullable=True)) + op.drop_column('usda_market_record', 'market_type_catagory') + op.drop_column('usda_market_record', 'market_catagory_id') + op.add_column('xrd_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('xrf_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column('xrf_record', 'analyst_id') + op.drop_column('xrd_record', 'analyst_id') + op.add_column('usda_market_record', sa.Column('market_catagory_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.add_column('usda_market_record', sa.Column('market_type_catagory', sa.TEXT(), autoincrement=False, nullable=True)) + op.drop_column('usda_market_record', 'market_category_id') + op.drop_column('usda_market_record', 'market_type_category') + op.drop_column('ultimate_record', 'analyst_id') + op.drop_column('rgb_record', 'analyst_id') + op.drop_column('proximate_record', 'analyst_id') + op.drop_column('provider', 'lineage_group_id') + op.drop_column('provider', 'etl_run_id') + op.drop_column('provider', 'updated_at') + op.drop_column('provider', 'created_at') + op.add_column('pretreatment_record', sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('pretreatment_record', 'calc_analyst_id') + op.drop_column('pretreatment_record', 'calc_method_id') + op.drop_column('icp_record', 'analyst_id') + op.add_column('gasification_record', sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('gasification_record', 'calc_analyst_id') + op.drop_column('gasification_record', 'calc_method_id') + op.drop_column('ftnir_record', 'analyst_id') + op.add_column('fermentation_record', sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('fermentation_record', 'calc_analyst_id') + op.drop_column('fermentation_record', 'calc_method_id') + op.add_column('data_source', sa.Column('author', sa.TEXT(), autoincrement=False, nullable=True)) + op.add_column('data_source', sa.Column('version', sa.TEXT(), autoincrement=False, nullable=True)) + op.add_column('data_source', sa.Column('publication_date', sa.DATE(), autoincrement=False, nullable=True)) + op.drop_column('data_source', 'rights') + op.drop_column('data_source', 'location_coverage_id') + op.drop_column('data_source', 'temporal_coverage') + op.drop_column('data_source', 'relation') + op.drop_column('data_source', 'language') + op.drop_column('data_source', 'format') + op.drop_column('data_source', 'biocirv') + op.drop_column('data_source', 'type') + op.drop_column('data_source', 'date') + op.drop_column('data_source', 'contributor') + op.drop_column('data_source', 'subject') + op.drop_column('data_source', 'creator') + op.drop_column('data_source', 'full_title') + op.drop_column('data_source', 'data_source_type_id') + op.drop_column('contact', 'lineage_group_id') + op.drop_column('contact', 'etl_run_id') + op.drop_column('contact', 'updated_at') + op.drop_column('contact', 'created_at') + op.drop_column('compositional_record', 'analyst_id') + op.drop_column('calorimetry_record', 'analyst_id') + op.add_column('autoclave_record', sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('autoclave_record', 'calc_analyst_id') + op.drop_column('autoclave_record', 'calc_method_id') + op.add_column('aim2_record_base', sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('aim2_record_base', 'calc_analyst_id') + op.drop_column('aim2_record_base', 'calc_method_id') + op.drop_column('aim1_record_base', 'analyst_id') + # ### end Alembic commands ### diff --git a/alembic/versions/d82910ff757e_initial_migration.py b/alembic/versions/d82910ff757e_initial_migration.py new file mode 100644 index 00000000..d1550e08 --- /dev/null +++ b/alembic/versions/d82910ff757e_initial_migration.py @@ -0,0 +1,32 @@ +"""Initial migration + +Revision ID: d82910ff757e +Revises: 27a733f8f5fb +Create Date: 2025-12-16 22:48:03.561768 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'd82910ff757e' +down_revision: Union[str, Sequence[str], None] = '27a733f8f5fb' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml index 94f0f42e..5f5c59f5 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml @@ -13,13 +13,13 @@ default_range: string imports: - linkml:types + - core classes: Contact: is_a: BaseEntity description: Contact information for a person. slots: - - id - first_name - last_name - email @@ -33,7 +33,6 @@ classes: is_a: BaseEntity description: Provider information. slots: - - id - codename slot_usage: id: @@ -41,11 +40,6 @@ classes: range: integer slots: - id: - identifier: true - range: integer - description: Unique identifier. - first_name: range: string description: First name. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py index 834aaa45..ef08780e 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py @@ -1357,11 +1357,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1369,7 +1369,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1387,8 +1387,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1396,7 +1396,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py index 9315f884..db37c954 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py @@ -1383,11 +1383,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1395,7 +1395,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1413,8 +1413,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1422,7 +1422,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py index 35158f30..53befe22 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py @@ -817,11 +817,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -829,7 +829,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -847,8 +847,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -856,7 +856,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py new file mode 100644 index 00000000..7cdc3fb0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py @@ -0,0 +1,2447 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class LineageGroup(Base): + """ + Grouping for lineage information. + """ + __tablename__ = 'lineage_group' + + id = Column(Integer(), primary_key=True, nullable=False ) + etl_run_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"LineageGroup(id={self.id},etl_run_id={self.etl_run_id},note={self.note},)" + + + + + + +class EntityLineage(Base): + """ + Lineage information for a specific entity. + """ + __tablename__ = 'entity_lineage' + + id = Column(Integer(), primary_key=True, nullable=False ) + lineage_group_id = Column(Integer()) + source_table = Column(Text()) + source_row_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" + + + + + + +class EtlRun(Base): + """ + Information about an ETL run. + """ + __tablename__ = 'etl_run' + + id = Column(Integer(), primary_key=True, nullable=False ) + started_at = Column(DateTime()) + completed_at = Column(DateTime()) + pipeline_name = Column(Text()) + status = Column(Text()) + records_ingested = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'parameter_category_parameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'parameter_unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between Experiment and Method. + """ + __tablename__ = 'experiment_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between Experiment and Equipment. + """ + __tablename__ = 'experiment_equipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between Experiment and AnalysisType. + """ + __tablename__ = 'experiment_analysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between Experiment and PreparedSample. + """ + __tablename__ = 'experiment_prepared_sample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon. + """ + __tablename__ = 'polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'primary_crop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'field_sample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'field_storage_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'collection_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'harvest_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'processing_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'soil_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'ag_treatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'location_soil_type' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'data_source' + + name = Column(Text()) + description = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) + publisher = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) + license = Column(Text()) + uri = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'file_object_metadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source (e.g. database, literature). + """ + __tablename__ = 'data_source_type' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'location_resolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'source_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'preparation_method' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'preparation_method_abbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'prepared_sample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'method_abbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'method_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'method_standard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'parameter_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'analysis_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'dimension_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Aim1RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'aim1_record_base' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Aim2RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'aim2_record_base' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Strain(LookupBase): + """ + Strain used in fermentation. + """ + __tablename__ = 'strain' + + parent_strain_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaDomain(LookupBase): + """ + USDA domain. + """ + __tablename__ = 'usda_domain' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaDomain(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaStatisticCategory(LookupBase): + """ + USDA statistic category. + """ + __tablename__ = 'usda_statistic_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaStatisticCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyProgram(LookupBase): + """ + USDA survey program. + """ + __tablename__ = 'usda_survey_program' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaSurveyProgram(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCensusRecord(BaseEntity): + """ + USDA census record. + """ + __tablename__ = 'usda_census_record' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + source_reference = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyRecord(BaseEntity): + """ + USDA survey record. + """ + __tablename__ = 'usda_survey_record' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + survey_program_id = Column(Integer()) + survey_period = Column(Text()) + reference_month = Column(Text()) + seasonal_flag = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCommodity(LookupBase): + """ + USDA commodity. + """ + __tablename__ = 'usda_commodity' + + usda_source = Column(Text()) + usda_code = Column(Text()) + parent_commodity_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaTermMap(BaseEntity): + """ + Mapping of raw terms to USDA commodities. + """ + __tablename__ = 'usda_term_map' + + source_system = Column(Text()) + source_context = Column(Text()) + raw_term = Column(Text()) + usda_commodity_id = Column(Integer()) + is_verified = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceUsdaCommodityMap(BaseEntity): + """ + Mapping between resources/crops and USDA commodities. + """ + __tablename__ = 'resource_usda_commodity_map' + + resource_id = Column(Integer()) + primary_crop_id = Column(Integer()) + usda_commodity_id = Column(Integer()) + match_tier = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketReport(BaseEntity): + """ + USDA market report. + """ + __tablename__ = 'usda_market_report' + + slug_id = Column(Integer()) + slug_name = Column(Text()) + report_series_title = Column(Text()) + frequency = Column(Text()) + office_name = Column(Text()) + office_city_id = Column(Integer()) + office_state_fips = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketReport(slug_id={self.slug_id},slug_name={self.slug_name},report_series_title={self.report_series_title},frequency={self.frequency},office_name={self.office_name},office_city_id={self.office_city_id},office_state_fips={self.office_state_fips},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketRecord(BaseEntity): + """ + USDA market record. + """ + __tablename__ = 'usda_market_record' + + report_id = Column(Integer()) + dataset_id = Column(Integer()) + report_begin_date = Column(DateTime()) + report_end_date = Column(DateTime()) + report_date = Column(DateTime()) + commodity_id = Column(Integer()) + market_type_id = Column(Integer()) + market_type_category = Column(Text()) + grp = Column(Text()) + market_category_id = Column(Integer()) + class_ = Column(Text()) + grade = Column(Text()) + variety = Column(Text()) + protein_pct = Column(Numeric()) + application = Column(Text()) + pkg = Column(Text()) + sale_type = Column(Text()) + price_unit_id = Column(Integer()) + freight = Column(Text()) + trans_mode = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_category={self.market_type_category},grp={self.grp},market_category_id={self.market_category_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LandiqRecord(BaseEntity): + """ + LandIQ record. + """ + __tablename__ = 'landiq_record' + + dataset_id = Column(Integer()) + polygon_id = Column(Integer()) + main_crop = Column(Integer()) + secondary_crop = Column(Integer()) + tertiary_crop = Column(Integer()) + quaternary_crop = Column(Integer()) + confidence = Column(Integer()) + irrigated = Column(Boolean()) + acres = Column(Float()) + version = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class BillionTon2023Record(BaseEntity): + """ + Billion Ton 2023 record. + """ + __tablename__ = 'billion_ton2023_record' + + subclass_id = Column(Integer()) + resource_id = Column(Integer()) + geoid = Column(Text()) + county_square_miles = Column(Float()) + model_name = Column(Text()) + scenario_name = Column(Text()) + price_offered_usd = Column(Numeric()) + production = Column(Integer()) + production_unit_id = Column(Integer()) + btu_ton = Column(Integer()) + production_energy_content = Column(Integer()) + energy_content_unit_id = Column(Integer()) + product_density_dtpersqmi = Column(Numeric()) + land_source = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BillionTon2023Record(subclass_id={self.subclass_id},resource_id={self.resource_id},geoid={self.geoid},county_square_miles={self.county_square_miles},model_name={self.model_name},scenario_name={self.scenario_name},price_offered_usd={self.price_offered_usd},production={self.production},production_unit_id={self.production_unit_id},btu_ton={self.btu_ton},production_energy_content={self.production_energy_content},energy_content_unit_id={self.energy_content_unit_id},product_density_dtpersqmi={self.product_density_dtpersqmi},land_source={self.land_source},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProximateRecord(Aim1RecordBase): + """ + Proximate analysis record. + """ + __tablename__ = 'proximate_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UltimateRecord(Aim1RecordBase): + """ + Ultimate analysis record. + """ + __tablename__ = 'ultimate_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CompositionalRecord(Aim1RecordBase): + """ + Compositional analysis record. + """ + __tablename__ = 'compositional_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class IcpRecord(Aim1RecordBase): + """ + ICP analysis record. + """ + __tablename__ = 'icp_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrfRecord(Aim1RecordBase): + """ + XRF analysis record. + """ + __tablename__ = 'xrf_record' + + maybe_wavelength_nm = Column(Numeric()) + maybe_intensity = Column(Numeric()) + maybe_energy_slope = Column(Numeric()) + maybe_energy_offset = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrdRecord(Aim1RecordBase): + """ + XRD analysis record. + """ + __tablename__ = 'xrd_record' + + maybe_scan_low_nm = Column(Integer()) + maybe_scan_high_nm = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CalorimetryRecord(Aim1RecordBase): + """ + Calorimetry analysis record. + """ + __tablename__ = 'calorimetry_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FtnirRecord(Aim1RecordBase): + """ + FT-NIR analysis record. + """ + __tablename__ = 'ftnir_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class RgbRecord(Aim1RecordBase): + """ + RGB analysis record. + """ + __tablename__ = 'rgb_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PretreatmentRecord(Aim2RecordBase): + """ + Pretreatment record. + """ + __tablename__ = 'pretreatment_record' + + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + reaction_block_id = Column(Integer()) + block_position = Column(Text()) + temperature = Column(Numeric()) + replicate_no = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FermentationRecord(Aim2RecordBase): + """ + Fermentation record. + """ + __tablename__ = 'fermentation_record' + + strain_id = Column(Integer()) + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + replicate_no = Column(Integer()) + well_position = Column(Text()) + temperature = Column(Numeric()) + agitation_rpm = Column(Numeric()) + vessel_id = Column(Integer()) + analyte_detection_equipment_id = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class GasificationRecord(Aim2RecordBase): + """ + Gasification record. + """ + __tablename__ = 'gasification_record' + + feedstock_mass = Column(Numeric()) + bed_temperature = Column(Numeric()) + gas_flow_rate = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AutoclaveRecord(Aim2RecordBase): + """ + Autoclave record. + """ + __tablename__ = 'autoclave_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py index 964a4575..975b6bd5 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py @@ -325,11 +325,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -337,7 +337,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -355,8 +355,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -364,7 +364,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py index 7f0bdd34..b93abd1f 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py @@ -776,11 +776,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -788,7 +788,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -806,8 +806,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -815,7 +815,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py index bc022794..c953a83a 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py @@ -380,11 +380,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -392,7 +392,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -410,8 +410,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -419,7 +419,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py index 2c6e1121..d86817b3 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py @@ -1222,11 +1222,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1234,7 +1234,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1252,8 +1252,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1261,7 +1261,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py index 0f1b410a..f699dc79 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py @@ -454,11 +454,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -466,7 +466,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -484,8 +484,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -493,7 +493,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py index 69cd6452..88195134 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py @@ -443,11 +443,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -455,7 +455,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -473,8 +473,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -482,7 +482,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py index 87a37dab..833b7951 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py @@ -802,11 +802,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -814,7 +814,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -832,8 +832,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -841,7 +841,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py index 781ff528..61f06d91 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py @@ -358,11 +358,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -370,7 +370,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -388,8 +388,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -397,7 +397,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py index e69de29b..8219be89 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py @@ -0,0 +1,106 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py new file mode 100644 index 00000000..4eccd8ac --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py @@ -0,0 +1,106 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py new file mode 100644 index 00000000..b1d3d70e --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py @@ -0,0 +1,307 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'primary_crop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py new file mode 100644 index 00000000..41d9b229 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py @@ -0,0 +1,306 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'primary_crop' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py new file mode 100644 index 00000000..db5d6386 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py @@ -0,0 +1,1118 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'parameter_category_parameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'parameter_unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'preparation_method' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'preparation_method_abbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'prepared_sample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'primary_crop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'field_sample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'field_storage_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'collection_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'harvest_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'processing_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'soil_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'ag_treatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'location_soil_type' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'data_source' + + name = Column(Text()) + description = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) + publisher = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) + license = Column(Text()) + uri = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'file_object_metadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source (e.g. database, literature). + """ + __tablename__ = 'data_source_type' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'location_resolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'source_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'method_abbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'method_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'method_standard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'parameter_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py new file mode 100644 index 00000000..78c99d62 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py @@ -0,0 +1,962 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'parameter_category_parameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'parameter_unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'field_sample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'field_storage_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'collection_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'harvest_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'processing_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'soil_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'ag_treatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'location_soil_type' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'preparation_method' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'preparation_method_abbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample prepared for analysis. + """ + __tablename__ = 'prepared_sample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'primary_crop' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'method_abbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'method_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'method_standard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'parameter_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } From 032cf1e8d010b5bbf263c96c973435e81f6885f1 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Tue, 16 Dec 2025 17:14:22 -0800 Subject: [PATCH 30/81] removed useless alembic versions and fixed the revision path --- .../27a733f8f5fb_sync_linkml_changes.py | 32 ------------------- .../5632747ee5fe_initial_migration.py | 32 ------------------- .../bfa07351a507_remove_hallucinations.py | 2 +- .../d82910ff757e_initial_migration.py | 32 ------------------- 4 files changed, 1 insertion(+), 97 deletions(-) delete mode 100644 alembic/versions/27a733f8f5fb_sync_linkml_changes.py delete mode 100644 alembic/versions/5632747ee5fe_initial_migration.py delete mode 100644 alembic/versions/d82910ff757e_initial_migration.py diff --git a/alembic/versions/27a733f8f5fb_sync_linkml_changes.py b/alembic/versions/27a733f8f5fb_sync_linkml_changes.py deleted file mode 100644 index 18492f4a..00000000 --- a/alembic/versions/27a733f8f5fb_sync_linkml_changes.py +++ /dev/null @@ -1,32 +0,0 @@ -"""Sync LinkML changes - -Revision ID: 27a733f8f5fb -Revises: 5632747ee5fe -Create Date: 2025-12-16 05:25:21.214170 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '27a733f8f5fb' -down_revision: Union[str, Sequence[str], None] = '5632747ee5fe' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### diff --git a/alembic/versions/5632747ee5fe_initial_migration.py b/alembic/versions/5632747ee5fe_initial_migration.py deleted file mode 100644 index 043c57bb..00000000 --- a/alembic/versions/5632747ee5fe_initial_migration.py +++ /dev/null @@ -1,32 +0,0 @@ -"""Initial migration - -Revision ID: 5632747ee5fe -Revises: 1e9784d75e62 -Create Date: 2025-12-16 04:39:20.946195 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '5632747ee5fe' -down_revision: Union[str, Sequence[str], None] = '1e9784d75e62' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.drop_column('landiq_record', 'test') - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.add_column('landiq_record', sa.Column('test', sa.TEXT(), autoincrement=False, nullable=True)) - # ### end Alembic commands ### diff --git a/alembic/versions/bfa07351a507_remove_hallucinations.py b/alembic/versions/bfa07351a507_remove_hallucinations.py index 6ac8caa9..68d853dd 100644 --- a/alembic/versions/bfa07351a507_remove_hallucinations.py +++ b/alembic/versions/bfa07351a507_remove_hallucinations.py @@ -13,7 +13,7 @@ # revision identifiers, used by Alembic. revision: str = 'bfa07351a507' -down_revision: Union[str, Sequence[str], None] = 'd82910ff757e' +down_revision: Union[str, Sequence[str], None] = '1e9784d75e62' branch_labels: Union[str, Sequence[str], None] = None depends_on: Union[str, Sequence[str], None] = None diff --git a/alembic/versions/d82910ff757e_initial_migration.py b/alembic/versions/d82910ff757e_initial_migration.py deleted file mode 100644 index d1550e08..00000000 --- a/alembic/versions/d82910ff757e_initial_migration.py +++ /dev/null @@ -1,32 +0,0 @@ -"""Initial migration - -Revision ID: d82910ff757e -Revises: 27a733f8f5fb -Create Date: 2025-12-16 22:48:03.561768 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = 'd82910ff757e' -down_revision: Union[str, Sequence[str], None] = '27a733f8f5fb' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### From 2915797a02d38f334f89f73faa8e388232ec117a Mon Sep 17 00:00:00 2001 From: mglbleta Date: Wed, 17 Dec 2025 11:20:52 -0800 Subject: [PATCH 31/81] removed duplicate .yaml files --- ...4417c6d044_deleted_duplicate_yaml_files.py | 32 + .../datamodels/linkml/modules/analysis.yaml | 109 -- .../linkml/modules/analysis_records.yaml | 233 --- .../linkml/modules/experiments.yaml | 138 -- .../datamodels/linkml/modules/methods.yaml | 120 -- .../datamodels/linkml/modules/resources.yaml | 176 -- .../datamodels/linkml/modules/sampling.yaml | 250 --- .../datamodels/schemas/generated/analysis.py | 375 ---- .../schemas/generated/analysis_records.py | 1693 ----------------- .../schemas/generated/experiments.py | 1222 ------------ .../datamodels/schemas/generated/methods.py | 275 --- .../datamodels/schemas/generated/resources.py | 306 --- .../datamodels/schemas/generated/sampling.py | 962 ---------- 13 files changed, 32 insertions(+), 5859 deletions(-) create mode 100644 alembic/versions/184417c6d044_deleted_duplicate_yaml_files.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py diff --git a/alembic/versions/184417c6d044_deleted_duplicate_yaml_files.py b/alembic/versions/184417c6d044_deleted_duplicate_yaml_files.py new file mode 100644 index 00000000..1afa0f71 --- /dev/null +++ b/alembic/versions/184417c6d044_deleted_duplicate_yaml_files.py @@ -0,0 +1,32 @@ +"""Deleted duplicate .yaml files + +Revision ID: 184417c6d044 +Revises: bfa07351a507 +Create Date: 2025-12-17 19:03:32.278635 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '184417c6d044' +down_revision: Union[str, Sequence[str], None] = 'bfa07351a507' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml deleted file mode 100644 index 83292024..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml +++ /dev/null @@ -1,109 +0,0 @@ -id: https://w3id.org/ca_biositing/analysis -name: analysis -title: Analysis Definitions -description: Datasets and observations. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - methods - -classes: - Dataset: - description: Dataset definition. - slots: - - id - - name - - record_type - - source_id - - start_date - - end_date - - description - slot_usage: - id: - identifier: true - range: integer - - Observation: - description: Observation data. - slots: - - id - - dataset_id - - record_type - - record_id - - parameter_id - - value - - unit_id - - dimension_type_id - - dimension_value - - dimension_unit_id - - note - slot_usage: - id: - identifier: true - range: integer - - DimensionType: - is_a: LookupBase - description: Type of dimension (e.g. timepoint, wavelength). - - AnalysisType: - is_a: LookupBase - description: Type of analysis. - -slots: - #Slots imported - #parameter_id: from methods.yaml - #note: from core.yaml - - dataset_id: - range: integer - description: Reference to Dataset. - - record_type: - range: string - description: Type of record. - - record_id: - range: integer - description: ID of the record. - - value: - range: decimal - description: Value of the observation. - - unit_id: - range: integer - description: Reference to Unit. - - dimension_type_id: - range: integer - description: Reference to DimensionType. - - dimension_value: - range: decimal - description: Value of the dimension. - - dimension_unit_id: - range: integer - description: Reference to Unit (dimension). - - source_id: - range: integer - description: Reference to Source. - - start_date: - range: datetime - description: Start date of the dataset. - - end_date: - range: datetime - description: End date of the dataset. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml deleted file mode 100644 index 4ec92ee7..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml +++ /dev/null @@ -1,233 +0,0 @@ -id: https://w3id.org/ca_biositing/analysis_records -name: analysis_records -title: Analysis Records -description: Specific analysis record types. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - analysis - - experiments - - methods - - sampling - - resources - -classes: - # Base Record Class (Mixin) - RecordBase: - mixin: true - slots: - - id - - dataset_id - - experiment_id - - resource_id - - sample_id - - technical_replicate_no - - technical_replicate_total - - method_id - - raw_data_id - - qc_pass - - note - slot_usage: - id: - identifier: true - range: integer - - ProximateRecord: - is_a: RecordBase - description: Proximate analysis record. - - UltimateRecord: - is_a: RecordBase - description: Ultimate analysis record. - - CompositionalRecord: - is_a: RecordBase - description: Compositional analysis record. - - IcpRecord: - is_a: RecordBase - description: ICP analysis record. - - XrfRecord: - is_a: RecordBase - description: XRF analysis record. - slots: - - maybe_wavelength_nm - - maybe_intensity - - maybe_energy_slope - - maybe_energy_offset - - XrdRecord: - is_a: RecordBase - description: XRD analysis record. - slots: - - maybe_scan_low_nm - - maybe_scan_high_nm - - CalorimetryRecord: - is_a: RecordBase - description: Calorimetry analysis record. - - FtnirRecord: - is_a: RecordBase - description: FT-NIR analysis record. - - RgbRecord: - is_a: RecordBase - description: RGB analysis record. - - PretreatmentRecord: - is_a: RecordBase - description: Pretreatment record. - slots: - - pretreatment_method - - eh_method_id - - reaction_block_id - - block_position - - temperature - - replicate_no - - analyst_id - - FermentationRecord: - is_a: RecordBase - description: Fermentation record. - slots: - - strain_id - - pretreatement_method_id - - eh_method_id - - replicate_no - - well_position - - temperature - - agitation_rpm - - vessel_id - - analyte_detection_equipment_id - - analyst_id - - GasificationRecord: - is_a: RecordBase - description: Gasification record. - slots: - - feedstock_mass - - bed_temperature - - gas_flow_rate - - analyst_id - - AutoclaveRecord: - is_a: RecordBase - description: Autoclave record. - slots: - - analyst_id - -slots: - technical_replicate_no: - range: integer - description: Technical replicate number. - - technical_replicate_total: - range: integer - description: Total technical replicates. - - raw_data_id: - range: integer - description: Reference to FileObjectMetadata. - - qc_pass: - range: boolean - description: Whether QC passed. - - maybe_wavelength_nm: - range: decimal - description: Wavelength in nm. - - maybe_intensity: - range: decimal - description: Intensity. - - maybe_energy_slope: - range: decimal - description: Energy slope. - - maybe_energy_offset: - range: decimal - description: Energy offset. - - maybe_scan_low_nm: - range: integer - description: Scan low nm. - - maybe_scan_high_nm: - range: integer - description: Scan high nm. - - pretreatment_method: - range: integer - description: Reference to Method (pretreatment). - - eh_method_id: - range: integer - description: Reference to Method (enzymatic hydrolysis). - - reaction_block_id: - range: integer - description: Reaction block ID. - - block_position: - range: string - description: Position in block. - - temperature: - range: decimal - description: Temperature. - - replicate_no: - range: integer - description: Replicate number. - - strain_id: - range: integer - description: Reference to Strain. - - pretreatement_method_id: - range: integer - description: Reference to Method (pretreatment). - - well_position: - range: string - description: Well position. - - agitation_rpm: - range: decimal - description: Agitation RPM. - - vessel_id: - range: integer - description: Reference to Equipment (vessel). - - analyte_detection_equipment_id: - range: integer - description: Reference to Equipment (detection). - - feedstock_mass: - range: decimal - description: Feedstock mass. - - bed_temperature: - range: decimal - description: Bed temperature. - - gas_flow_rate: - range: decimal - description: Gas flow rate. - - sample_id: - range: integer - description: Reference to Sample. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml deleted file mode 100644 index 56bf5322..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml +++ /dev/null @@ -1,138 +0,0 @@ -id: https://w3id.org/ca_biositing/experiments -name: experiments -title: Experiment Definitions -description: Experiments, equipment, and analysis. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - geography - - people - - methods - - sampling - - analysis - -classes: - Experiment: - is_a: BaseEntity - description: Experiment definition. - slots: - - analyst_id - - exper_start_date - - exper_duration - - exper_duration_unit_id - - exper_location_id - - description - - Equipment: - is_a: LookupBase - description: Equipment used in experiments. - slots: - - equipment_location_id - - ExperimentEquipment: - description: Link between experiment and equipment. - slots: - - id - - experiment_id - - equipment_id - slot_usage: - id: - identifier: true - range: integer - - ExperimentAnalysis: - description: Link between experiment and analysis type. - slots: - - id - - experiment_id - - analysis_type_id - slot_usage: - id: - identifier: true - range: integer - - ExperimentPreparedSample: - description: Link between experiment and prepared sample. - slots: - - id - - experiment_id - - prepared_sample_id - slot_usage: - id: - identifier: true - range: integer - - ExperimentMethod: - description: Link between experiment and method. - slots: - - id - - experiment_id - - method_id - slot_usage: - id: - identifier: true - range: integer - - Strain: - is_a: LookupBase - description: Strain of organism. - slots: - - parent_strain_id - -slots: - analyst_id: - range: integer - description: Reference to Contact (analyst). - - exper_start_date: - range: date - description: Start date of experiment. - - exper_duration: - range: decimal - description: Duration of experiment. - - exper_duration_unit_id: - range: integer - description: Reference to Unit. - - exper_location_id: - range: integer - description: Reference to LocationAddress. - - equipment_location_id: - range: integer - description: Reference to LocationAddress. - - experiment_id: - range: integer - description: Reference to Experiment. - - equipment_id: - range: integer - description: Reference to Equipment. - - analysis_type_id: - range: integer - description: Reference to AnalysisType. - - prepared_sample_id: - range: integer - description: Reference to PreparedSample. - - method_id: - range: integer - description: Reference to Method. - - parent_strain_id: - range: integer - description: Reference to Strain (parent). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml deleted file mode 100644 index d370f253..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml +++ /dev/null @@ -1,120 +0,0 @@ -id: https://w3id.org/ca_biositing/methods -name: methods -title: Methods and Parameters -description: Methods, parameters, and units. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - -classes: - Unit: - is_a: LookupBase - description: Unit of measurement. - - Method: - is_a: BaseEntity - description: Analytical method. - slots: - - name - - method_abbrev_id - - method_category_id - - method_standard_id - - description - - detection_limits - - source_id - - MethodAbbrev: - is_a: LookupBase - description: Abbreviation for a method. - - MethodCategory: - is_a: LookupBase - description: Category of a method. - - MethodStandard: - is_a: LookupBase - description: Standard associated with a method. - - Parameter: - is_a: BaseEntity - description: Parameter measured. - slots: - - name - - standard_unit_id - - calculated - - description - - ParameterCategory: - is_a: LookupBase - description: Category of a parameter. - - ParameterCategoryParameter: - description: Link between parameter and category. - slots: - - id - - parameter_id - - parameter_category_id - slot_usage: - id: - identifier: true - range: integer - - ParameterUnit: - description: Link between parameter and alternate units. - slots: - - id - - parameter_id - - alternate_unit_id - slot_usage: - id: - identifier: true - range: integer - -slots: - method_abbrev_id: - range: integer - description: Reference to MethodAbbrev. - - method_category_id: - range: integer - description: Reference to MethodCategory. - - method_standard_id: - range: integer - description: Reference to MethodStandard. - - detection_limits: - range: string - description: Detection limits of the method. - - source_id: - range: integer - description: Reference to DataSource. - - standard_unit_id: - range: integer - description: Reference to Unit (standard). - - calculated: - range: boolean - description: Whether the parameter is calculated. - - parameter_id: - range: integer - description: Reference to Parameter. - - parameter_category_id: - range: integer - description: Reference to ParameterCategory. - - alternate_unit_id: - range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml deleted file mode 100644 index 2cc58cf0..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml +++ /dev/null @@ -1,176 +0,0 @@ -id: https://w3id.org/ca_biositing/resources -name: resources -title: Resource Definitions -description: Biomass resources and their classifications. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - geography - -classes: - Resource: - is_a: BaseEntity - description: Biomass resource definition. - slots: - - name - - primary_crop_id - - resource_class_id - - resource_subclass_id - - note - - ResourceClass: - is_a: LookupBase - description: Classification of resources. - - ResourceSubclass: - is_a: LookupBase - description: Sub-classification of resources. - - PrimaryCrop: - is_a: LookupBase - description: Primary crop definition. - - ResourceAvailability: - is_a: BaseEntity - description: Availability of a resource in a location. - slots: - - resource_id - - geoid - - from_month - - to_month - - year_round - - note - - ResourceCounterfactual: - is_a: BaseEntity - description: Counterfactual uses of a resource. - slots: - - geoid - - resource_id - - counterfactual_description - - animal_bedding_percent - - animal_bedding_source_id - - animal_feed_percent - - animal_feed_source_id - - bioelectricty_percent - - bioelectricty_source_id - - burn_percent - - burn_source_id - - compost_percent - - compost_source_id - - landfill_percent - - landfill_source_id - - counterfactual_date - - note - - ResourceMorphology: - description: Morphology of a resource. - slots: - - id - - resource_id - - morphology_uri - slot_usage: - id: - identifier: true - range: integer - -slots: - primary_crop_id: - range: integer - description: Reference to PrimaryCrop. - - resource_class_id: - range: integer - description: Reference to ResourceClass. - - resource_subclass_id: - range: integer - description: Reference to ResourceSubclass. - - resource_id: - range: integer - description: Reference to Resource. - - geoid: - range: string - description: Reference to Geography. - - from_month: - range: integer - description: Start month of availability. - - to_month: - range: integer - description: End month of availability. - - year_round: - range: boolean - description: Whether available year-round. - - counterfactual_description: - range: string - description: Description of counterfactual scenario. - - animal_bedding_percent: - range: decimal - description: Percentage used for animal bedding. - - animal_bedding_source_id: - range: integer - description: Source for animal bedding data. - - animal_feed_percent: - range: decimal - description: Percentage used for animal feed. - - animal_feed_source_id: - range: integer - description: Source for animal feed data. - - bioelectricty_percent: - range: decimal - description: Percentage used for bioelectricity. - - bioelectricty_source_id: - range: integer - description: Source for bioelectricity data. - - burn_percent: - range: decimal - description: Percentage burned. - - burn_source_id: - range: integer - description: Source for burn data. - - compost_percent: - range: decimal - description: Percentage composted. - - compost_source_id: - range: integer - description: Source for compost data. - - landfill_percent: - range: decimal - description: Percentage landfilled. - - landfill_source_id: - range: integer - description: Source for landfill data. - - counterfactual_date: - range: date - description: Date of counterfactual data. - - morphology_uri: - range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml deleted file mode 100644 index 9b449f57..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml +++ /dev/null @@ -1,250 +0,0 @@ -id: https://w3id.org/ca_biositing/sampling -name: sampling -title: Sampling Definitions -description: Field sampling and preparation. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - geography - - people - - resources - - methods - -classes: - FieldSample: - is_a: BaseEntity - description: Sample collected from the field. - slots: - - name - - resource_id - - provider_id - - collector_id - - sample_collection_source - - amount_collected - - amount_collected_unit_id - - sampling_location_id - - field_storage_method_id - - field_storage_duration_value - - field_storage_duration_unit_id - - field_storage_location_id - - collection_timestamp - - collection_method_id - - harvest_method_id - - harvest_date - - field_sample_storage_location_id - - note - - FieldStorageMethod: - is_a: LookupBase - description: Method of field storage. - - CollectionMethod: - is_a: LookupBase - description: Method of collection. - - HarvestMethod: - is_a: LookupBase - description: Method of harvest. - - ProcessingMethod: - is_a: LookupBase - description: Method of processing. - - PhysicalCharacteristic: - is_a: BaseEntity - description: Physical characteristics of a sample. - slots: - - field_sample_id - - particle_length - - particle_width - - particle_height - - particle_unit_id - - SoilType: - is_a: LookupBase - description: Type of soil. - - AgTreatment: - is_a: LookupBase - description: Agricultural treatment. - - FieldSampleCondition: - is_a: BaseEntity - description: Condition of the field sample. - slots: - - field_sample_id - - ag_treatment_id - - last_application_date - - treatment_amount_per_acre - - processing_method_id - - LocationSoilType: - is_a: BaseEntity - description: Soil type at a location. - slots: - - location_id - - soil_type_id - - PreparationMethod: - is_a: BaseEntity - description: Method of sample preparation. - slots: - - name - - description - - prep_method_abbrev_id - - prep_temp_c - - uri - - drying_step - - PreparationMethodAbbreviation: - is_a: LookupBase - description: Abbreviation for preparation method. - - PreparedSample: - is_a: BaseEntity - description: Sample prepared for analysis. - slots: - - name - - field_sample_id - - prep_method_id - - prep_date - - preparer_id - - note - -slots: - provider_id: - range: integer - description: Reference to Provider. - - collector_id: - range: integer - description: Reference to Contact (collector). - - sample_collection_source: - range: string - description: Source of sample collection. - - amount_collected: - range: decimal - description: Amount collected. - - amount_collected_unit_id: - range: integer - description: Reference to Unit. - - sampling_location_id: - range: integer - description: Reference to LocationAddress. - - field_storage_method_id: - range: integer - description: Reference to FieldStorageMethod. - - field_storage_duration_value: - range: decimal - description: Duration of field storage. - - field_storage_duration_unit_id: - range: integer - description: Reference to Unit. - - field_storage_location_id: - range: integer - description: Reference to LocationAddress. - - collection_timestamp: - range: datetime - description: Timestamp of collection. - - collection_method_id: - range: integer - description: Reference to CollectionMethod. - - harvest_method_id: - range: integer - description: Reference to HarvestMethod. - - harvest_date: - range: date - description: Date of harvest. - - field_sample_storage_location_id: - range: integer - description: Reference to LocationAddress. - - field_sample_id: - range: integer - description: Reference to FieldSample. - - particle_length: - range: decimal - description: Length of particle. - - particle_width: - range: decimal - description: Width of particle. - - particle_height: - range: decimal - description: Height of particle. - - particle_unit_id: - range: integer - description: Reference to Unit. - - ag_treatment_id: - range: integer - description: Reference to AgTreatment. - - last_application_date: - range: date - description: Date of last application. - - treatment_amount_per_acre: - range: float - description: Amount of treatment per acre. - - processing_method_id: - range: integer - description: Reference to ProcessingMethod. - - location_id: - range: integer - description: Reference to LocationAddress. - - soil_type_id: - range: integer - description: Reference to SoilType. - - prep_method_abbrev_id: - range: integer - description: Reference to PreparationMethodAbbreviation. - - prep_temp_c: - range: decimal - description: Preparation temperature in Celsius. - - drying_step: - range: boolean - description: Whether drying step was included. - - prep_method_id: - range: integer - description: Reference to PreparationMethod. - - prep_date: - range: date - description: Date of preparation. - - preparer_id: - range: integer - description: Reference to Contact (preparer). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py deleted file mode 100644 index f860432f..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py +++ /dev/null @@ -1,375 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class Dataset(Base): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(DateTime()) - end_date = Column(DateTime()) - description = Column(Text()) - - - def __repr__(self): - return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" - - - - - - -class Observation(Base): - """ - Observation data. - """ - __tablename__ = 'observation' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class DimensionType(LookupBase): - """ - Type of dimension (e.g. timepoint, wavelength). - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py deleted file mode 100644 index 53befe22..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py +++ /dev/null @@ -1,1693 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class RecordBase(Base): - """ - - """ - __tablename__ = 'record_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"RecordBase(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Dataset(Base): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(DateTime()) - end_date = Column(DateTime()) - description = Column(Text()) - - - def __repr__(self): - return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" - - - - - - -class Observation(Base): - """ - Observation data. - """ - __tablename__ = 'observation' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class ExperimentEquipment(Base): - """ - Link between experiment and equipment. - """ - __tablename__ = 'experiment_equipment' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - equipment_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" - - - - - - -class ExperimentAnalysis(Base): - """ - Link between experiment and analysis type. - """ - __tablename__ = 'experiment_analysis' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - analysis_type_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" - - - - - - -class ExperimentPreparedSample(Base): - """ - Link between experiment and prepared sample. - """ - __tablename__ = 'experiment_prepared_sample' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - prepared_sample_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" - - - - - - -class ExperimentMethod(Base): - """ - Link between experiment and method. - """ - __tablename__ = 'experiment_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - method_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ProximateRecord(RecordBase): - """ - Proximate analysis record. - """ - __tablename__ = 'proximate_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"ProximateRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UltimateRecord(RecordBase): - """ - Ultimate analysis record. - """ - __tablename__ = 'ultimate_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"UltimateRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CompositionalRecord(RecordBase): - """ - Compositional analysis record. - """ - __tablename__ = 'compositional_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"CompositionalRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class IcpRecord(RecordBase): - """ - ICP analysis record. - """ - __tablename__ = 'icp_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"IcpRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class XrfRecord(RecordBase): - """ - XRF analysis record. - """ - __tablename__ = 'xrf_record' - - maybe_wavelength_nm = Column(Numeric()) - maybe_intensity = Column(Numeric()) - maybe_energy_slope = Column(Numeric()) - maybe_energy_offset = Column(Numeric()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class XrdRecord(RecordBase): - """ - XRD analysis record. - """ - __tablename__ = 'xrd_record' - - maybe_scan_low_nm = Column(Integer()) - maybe_scan_high_nm = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CalorimetryRecord(RecordBase): - """ - Calorimetry analysis record. - """ - __tablename__ = 'calorimetry_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"CalorimetryRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FtnirRecord(RecordBase): - """ - FT-NIR analysis record. - """ - __tablename__ = 'ftnir_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"FtnirRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class RgbRecord(RecordBase): - """ - RGB analysis record. - """ - __tablename__ = 'rgb_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"RgbRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PretreatmentRecord(RecordBase): - """ - Pretreatment record. - """ - __tablename__ = 'pretreatment_record' - - pretreatment_method = Column(Integer()) - eh_method_id = Column(Integer()) - reaction_block_id = Column(Integer()) - block_position = Column(Text()) - temperature = Column(Numeric()) - replicate_no = Column(Integer()) - analyst_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"PretreatmentRecord(pretreatment_method={self.pretreatment_method},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FermentationRecord(RecordBase): - """ - Fermentation record. - """ - __tablename__ = 'fermentation_record' - - strain_id = Column(Integer()) - pretreatement_method_id = Column(Integer()) - eh_method_id = Column(Integer()) - replicate_no = Column(Integer()) - well_position = Column(Text()) - temperature = Column(Numeric()) - agitation_rpm = Column(Numeric()) - vessel_id = Column(Integer()) - analyte_detection_equipment_id = Column(Integer()) - analyst_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"FermentationRecord(strain_id={self.strain_id},pretreatement_method_id={self.pretreatement_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class GasificationRecord(RecordBase): - """ - Gasification record. - """ - __tablename__ = 'gasification_record' - - feedstock_mass = Column(Numeric()) - bed_temperature = Column(Numeric()) - gas_flow_rate = Column(Numeric()) - analyst_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AutoclaveRecord(RecordBase): - """ - Autoclave record. - """ - __tablename__ = 'autoclave_record' - - analyst_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"AutoclaveRecord(analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension (e.g. timepoint, wavelength). - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample prepared for analysis. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Experiment(BaseEntity): - """ - Experiment definition. - """ - __tablename__ = 'experiment' - - analyst_id = Column(Integer()) - exper_start_date = Column(Date()) - exper_duration = Column(Numeric()) - exper_duration_unit_id = Column(Integer()) - exper_location_id = Column(Integer()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Equipment(LookupBase): - """ - Equipment used in experiments. - """ - __tablename__ = 'equipment' - - equipment_location_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Strain(LookupBase): - """ - Strain of organism. - """ - __tablename__ = 'strain' - - parent_strain_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py deleted file mode 100644 index c953a83a..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py +++ /dev/null @@ -1,1222 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ExperimentEquipment(Base): - """ - Link between experiment and equipment. - """ - __tablename__ = 'experiment_equipment' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - equipment_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" - - - - - - -class ExperimentAnalysis(Base): - """ - Link between experiment and analysis type. - """ - __tablename__ = 'experiment_analysis' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - analysis_type_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" - - - - - - -class ExperimentPreparedSample(Base): - """ - Link between experiment and prepared sample. - """ - __tablename__ = 'experiment_prepared_sample' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - prepared_sample_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" - - - - - - -class ExperimentMethod(Base): - """ - Link between experiment and method. - """ - __tablename__ = 'experiment_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - method_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class Dataset(Base): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(DateTime()) - end_date = Column(DateTime()) - description = Column(Text()) - - - def __repr__(self): - return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" - - - - - - -class Observation(Base): - """ - Observation data. - """ - __tablename__ = 'observation' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" - - - - - - -class Experiment(BaseEntity): - """ - Experiment definition. - """ - __tablename__ = 'experiment' - - analyst_id = Column(Integer()) - exper_start_date = Column(Date()) - exper_duration = Column(Numeric()) - exper_duration_unit_id = Column(Integer()) - exper_location_id = Column(Integer()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Equipment(LookupBase): - """ - Equipment used in experiments. - """ - __tablename__ = 'equipment' - - equipment_location_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Strain(LookupBase): - """ - Strain of organism. - """ - __tablename__ = 'strain' - - parent_strain_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample prepared for analysis. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension (e.g. timepoint, wavelength). - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py deleted file mode 100644 index 5a5c33e9..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py +++ /dev/null @@ -1,275 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py deleted file mode 100644 index 41d9b229..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py +++ /dev/null @@ -1,306 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py deleted file mode 100644 index 78c99d62..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py +++ /dev/null @@ -1,962 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample prepared for analysis. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } From 2d5bc26be3eb30b1352bd15579df348d6e4136ad Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Fri, 19 Dec 2025 11:35:56 -0700 Subject: [PATCH 32/81] cleaning up a last few things before merge --- .../datamodels/utils/database_joins.ipynb | 570 ++++++++++++++++++ .../utils/query_landiq_observation.py | 22 + 2 files changed, 592 insertions(+) create mode 100644 src/ca_biositing/datamodels/utils/database_joins.ipynb create mode 100644 src/ca_biositing/datamodels/utils/query_landiq_observation.py diff --git a/src/ca_biositing/datamodels/utils/database_joins.ipynb b/src/ca_biositing/datamodels/utils/database_joins.ipynb new file mode 100644 index 00000000..dbb836f2 --- /dev/null +++ b/src/ca_biositing/datamodels/utils/database_joins.ipynb @@ -0,0 +1,570 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Database Joins and Denormalized Views\n", + "\n", + "This notebook demonstrates how to use SQLAlchemy to perform complex joins on the project's data models and create denormalized views suitable for API endpoints.\n", + "\n", + "It replaces the older `database_interaction.ipynb` and uses the new generated data models.\n", + "\n", + "**Note:** Ensure you are running this notebook in the project's Pixi environment where `ca-biositing-datamodels` is installed." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Python Executable: /Users/pjsmitty301/ca-biositing/.pixi/envs/default/bin/python\n", + "✅ You are running in a Pixi environment.\n" + ] + } + ], + "source": [ + "# Verify Kernel\n", + "import sys\n", + "print(f\"Python Executable: {sys.executable}\")\n", + "\n", + "# Check if we are in the pixi environment (path should contain .pixi)\n", + "if \".pixi\" in sys.executable:\n", + " print(\"✅ You are running in a Pixi environment.\")\n", + "else:\n", + " print(\"⚠️ You might be running in the wrong kernel. Please select the 'default' kernel created by Pixi.\")" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Libraries and models imported successfully.\n" + ] + } + ], + "source": [ + "import pandas as pd\n", + "from sqlalchemy import create_engine, select\n", + "from sqlalchemy.orm import Session\n", + "\n", + "# Import models from ca_biositing.py as the source of truth\n", + "from ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", + "\n", + "print(\"Libraries and models imported successfully.\")" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Connected to database.\n" + ] + } + ], + "source": [ + "# Database Connection\n", + "DATABASE_URL = \"postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db\"\n", + "engine = create_engine(DATABASE_URL)\n", + "print(f\"Connected to database.\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Join LandIQ Record and Observation\n", + "\n", + "We will join `LandiqRecord` and `Observation` tables on `observation.record_id = landiq_record.id`." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [ + { + "ename": "TypeError", + "evalue": " is not a generic class", + "output_type": "error", + "traceback": [ + "\u001b[31m---------------------------------------------------------------------------\u001b[39m", + "\u001b[31mTypeError\u001b[39m Traceback (most recent call last)", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[34]\u001b[39m\u001b[32m, line 2\u001b[39m\n\u001b[32m 1\u001b[39m stmt2 = select(LandiqRecord, PrimaryCrop).join(\n\u001b[32m----> \u001b[39m\u001b[32m2\u001b[39m \u001b[43mPrimaryCrop\u001b[49m\u001b[43m[\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mname\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m]\u001b[49m, \n\u001b[32m 3\u001b[39m LandiqRecord.main_crop == PrimaryCrop.id).limit(\u001b[32m10\u001b[39m)\n\u001b[32m 5\u001b[39m \u001b[38;5;28mprint\u001b[39m(stmt2)\n\u001b[32m 7\u001b[39m df2 = pd.read_sql(stmt2, engine)\n", + "\u001b[36mFile \u001b[39m\u001b[32m~/ca-biositing/.pixi/envs/default/lib/python3.12/typing.py:398\u001b[39m, in \u001b[36m_tp_cache..decorator..inner\u001b[39m\u001b[34m(*args, **kwds)\u001b[39m\n\u001b[32m 396\u001b[39m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m:\n\u001b[32m 397\u001b[39m \u001b[38;5;28;01mpass\u001b[39;00m \u001b[38;5;66;03m# All real errors (not unhashable args) are raised below.\u001b[39;00m\n\u001b[32m--> \u001b[39m\u001b[32m398\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[43m*\u001b[49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43m*\u001b[49m\u001b[43mkwds\u001b[49m\u001b[43m)\u001b[49m\n", + "\u001b[36mFile \u001b[39m\u001b[32m~/ca-biositing/.pixi/envs/default/lib/python3.12/typing.py:1110\u001b[39m, in \u001b[36m_generic_class_getitem\u001b[39m\u001b[34m(cls, params)\u001b[39m\n\u001b[32m 1108\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m prepare \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[32m 1109\u001b[39m params = prepare(\u001b[38;5;28mcls\u001b[39m, params)\n\u001b[32m-> \u001b[39m\u001b[32m1110\u001b[39m \u001b[43m_check_generic\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparams\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mlen\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m__parameters__\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 1112\u001b[39m new_args = []\n\u001b[32m 1113\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m param, new_arg \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mzip\u001b[39m(\u001b[38;5;28mcls\u001b[39m.__parameters__, params):\n", + "\u001b[36mFile \u001b[39m\u001b[32m~/ca-biositing/.pixi/envs/default/lib/python3.12/site-packages/typing_extensions.py:3111\u001b[39m, in \u001b[36m_check_generic\u001b[39m\u001b[34m(cls, parameters, elen)\u001b[39m\n\u001b[32m 3106\u001b[39m \u001b[38;5;250m\u001b[39m\u001b[33;03m\"\"\"Check correct count for parameters of a generic cls (internal helper).\u001b[39;00m\n\u001b[32m 3107\u001b[39m \n\u001b[32m 3108\u001b[39m \u001b[33;03mThis gives a nice error message in case of count mismatch.\u001b[39;00m\n\u001b[32m 3109\u001b[39m \u001b[33;03m\"\"\"\u001b[39;00m\n\u001b[32m 3110\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m elen:\n\u001b[32m-> \u001b[39m\u001b[32m3111\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(\u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mcls\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m is not a generic class\u001b[39m\u001b[33m\"\u001b[39m)\n\u001b[32m 3112\u001b[39m alen = \u001b[38;5;28mlen\u001b[39m(parameters)\n\u001b[32m 3113\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m alen != elen:\n", + "\u001b[31mTypeError\u001b[39m: is not a generic class" + ] + } + ], + "source": [ + "stmt2 = select(LandiqRecord, PrimaryCrop).join(\n", + " PrimaryCrop, \n", + " LandiqRecord.main_crop == PrimaryCrop.id).limit(10)\n", + "\n", + "print(stmt2)\n", + "\n", + "df2 = pd.read_sql(stmt2, engine)\n", + "\n", + "df2.columns\n" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "SQL Query:\n", + "SELECT landiq_record.dataset_id, landiq_record.polygon_id, landiq_record.main_crop, landiq_record.secondary_crop, landiq_record.tertiary_crop, landiq_record.quaternary_crop, landiq_record.confidence, landiq_record.irrigated, landiq_record.acres, landiq_record.version, landiq_record.note, landiq_record.test, landiq_record.id, landiq_record.created_at, landiq_record.updated_at, landiq_record.etl_run_id, landiq_record.lineage_group_id, observation.dataset_id AS dataset_id_1, observation.record_type, observation.record_id, observation.parameter_id, observation.value, observation.unit_id, observation.dimension_type_id, observation.dimension_value, observation.dimension_unit_id, observation.note AS note_1, observation.id AS id_1, observation.created_at AS created_at_1, observation.updated_at AS updated_at_1, observation.etl_run_id AS etl_run_id_1, observation.lineage_group_id AS lineage_group_id_1 \n", + "FROM landiq_record JOIN observation ON observation.record_id = landiq_record.id\n" + ] + } + ], + "source": [ + "# Create the join query\n", + "stmt = select(LandiqRecord, Observation).join(\n", + " Observation,\n", + " Observation.record_id == LandiqRecord.id\n", + ")\n", + "\n", + "print(\"SQL Query:\")\n", + "print(stmt)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loaded 0 rows.\n" + ] + }, + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "index", + "rawType": "int64", + "type": "integer" + }, + { + "name": "dataset_id", + "rawType": "object", + "type": "string" + }, + { + "name": "polygon_id", + "rawType": "object", + "type": "string" + }, + { + "name": "main_crop", + "rawType": "object", + "type": "string" + }, + { + "name": "secondary_crop", + "rawType": "object", + "type": "string" + }, + { + "name": "tertiary_crop", + "rawType": "object", + "type": "string" + }, + { + "name": "quaternary_crop", + "rawType": "object", + "type": "string" + }, + { + "name": "confidence", + 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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [dataset_id, polygon_id, main_crop, secondary_crop, tertiary_crop, quaternary_crop, confidence, irrigated, acres, version, note, test, id, created_at, updated_at, etl_run_id, lineage_group_id, dataset_id_1, record_type, record_id, parameter_id, value, unit_id, dimension_type_id, dimension_value, dimension_unit_id, note_1, id_1, created_at_1, updated_at_1, etl_run_id_1, lineage_group_id_1]\n", + "Index: []\n", + "\n", + "[0 rows x 32 columns]" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# Execute and load into DataFrame\n", + "try:\n", + " with Session(engine) as session:\n", + " # Using pandas read_sql to execute the statement and fetch results\n", + " # Note: Columns with same names (like 'id') might be duplicated or suffixed automatically by pandas.\n", + " df = pd.read_sql(stmt, session.bind)\n", + " \n", + " print(f\"Loaded {len(df)} rows.\")\n", + " display(df.head())\n", + "except Exception as e:\n", + " print(f\"Error executing query: {e}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "Index(['dataset_id', 'polygon_id', 'main_crop', 'secondary_crop',\n", + " 'tertiary_crop', 'quaternary_crop', 'confidence', 'irrigated', 'acres',\n", + " 'version', 'note', 'test', 'id', 'created_at', 'updated_at',\n", + " 'etl_run_id', 'lineage_group_id', 'dataset_id_1', 'record_type',\n", + " 'record_id', 'parameter_id', 'value', 'unit_id', 'dimension_type_id',\n", + " 'dimension_value', 'dimension_unit_id', 'note_1', 'id_1',\n", + " 'created_at_1', 'updated_at_1', 'etl_run_id_1', 'lineage_group_id_1'],\n", + " dtype='object')" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.columns" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "index", + "rawType": "int64", + "type": "integer" + }, + { + "name": "id", + "rawType": "object", + "type": "string" + }, + { + "name": "dataset_id", + "rawType": "object", + "type": "string" + }, + { + "name": "record_id", + "rawType": "object", + "type": "string" + }, + { + "name": "main_crop", + "rawType": "object", + "type": "string" + }, + { + "name": "parameter_id", + "rawType": "object", + "type": "string" + }, + { + "name": "value", + "rawType": "object", + "type": "string" + }, + { + "name": "unit_id", + "rawType": "object", + "type": "string" + } + ], + "ref": "5c95c323-56ec-4546-ad20-84e7b50c7748", + "rows": [], + "shape": { + "columns": 7, + "rows": 0 + } + }, + "text/html": [ + "
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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [id, dataset_id, record_id, main_crop, parameter_id, value, unit_id]\n", + "Index: []" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df[[\"id\", \"dataset_id\", \"record_id\", \"main_crop\", \"parameter_id\", \"value\", \"unit_id\"]]" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.0" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/src/ca_biositing/datamodels/utils/query_landiq_observation.py b/src/ca_biositing/datamodels/utils/query_landiq_observation.py new file mode 100644 index 00000000..6a7a0ee4 --- /dev/null +++ b/src/ca_biositing/datamodels/utils/query_landiq_observation.py @@ -0,0 +1,22 @@ +from sqlalchemy import select +from ca_biositing.datamodels.schemas.generated.ca_biositing import LandiqRecord, Observation + +def generate_query(): + """ + Generates a SQL query joining LandiqRecord and Observation tables. + """ + # Create the select statement + # We select from LandiqRecord and join Observation + # The join condition is explicitly specified as requested: + # observation.record_id = landiq_record.id + stmt = select(LandiqRecord, Observation).join( + Observation, + Observation.record_id == LandiqRecord.id + ) + + return stmt + +if __name__ == "__main__": + query = generate_query() + print("Generated SQL Query:") + print(query) From 536f209effdf2f3727ec701d38720c35e925bb6e Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Wed, 29 Oct 2025 11:33:41 -0600 Subject: [PATCH 33/81] adding USDA yaml schemas to test LinkML --- schemas/common/geography.yaml | 61 +++++++++++ schemas/common/locations_address.yml | 65 ++++++++++++ schemas/usda/census_survey.yaml | 153 +++++++++++++++++++++++++++ 3 files changed, 279 insertions(+) create mode 100644 schemas/common/geography.yaml create mode 100644 schemas/common/locations_address.yml create mode 100644 schemas/usda/census_survey.yaml diff --git a/schemas/common/geography.yaml b/schemas/common/geography.yaml new file mode 100644 index 00000000..41c9cf1c --- /dev/null +++ b/schemas/common/geography.yaml @@ -0,0 +1,61 @@ +id: geography +name: Geography +description: > + Common geographic identifiers used across multiple datasets. Includes states, + counties, FIPS codes, and optional regions. + +prefixes: + linkml: https://w3id.org/linkml/ + usda: https://schema.myorg.org/usda/ + agrovoc: https://agrovoc.fao.org/agrontology/en/page/ + +default_prefix: usda +imports: + - linkml:types + +classes: + Geography: + description: Reference table for U.S. geographic identifiers. + slots: + - state_name + - state_fips + - county_name + - county_fips + - geoid + - region_name + - agg_level_desc + +slots: + state_name: + range: string + description: U.S. state name. + exact_mappings: [] # TODO: map to AGROVOC/state concept + + state_fips: + range: string + pattern: "^[0-9]{2}$" + description: Two-digit FIPS code for the state. + + county_name: + range: string + description: U.S. county name. + exact_mappings: [] # TODO: map to AGROVOC/county concept + + county_fips: + range: string + pattern: "^[0-9]{3}$" + description: Three-digit county FIPS code. + + geoid: + range: string + pattern: "^[0-9]{5}$" + description: Combined state + county FIPS (e.g., 06019). + + region_name: + range: string + description: + Optional higher-level region grouping (e.g., San Joaquin Valley). + + agg_level_desc: + range: string + description: Aggregation level (e.g., COUNTY, STATE, NATIONAL). diff --git a/schemas/common/locations_address.yml b/schemas/common/locations_address.yml new file mode 100644 index 00000000..d36b769c --- /dev/null +++ b/schemas/common/locations_address.yml @@ -0,0 +1,65 @@ +id: location +name: Location +description: > + Specific address or farm location. Can be linked to a Geography row + (county-level). + +prefixes: + linkml: https://w3id.org/linkml/ + usda: https://schema.myorg.org/usda/ + agrovoc: https://agrovoc.fao.org/agrontology/en/page/ + +default_prefix: usda + +imports: + - ../common/geography.yaml + - linkml:types + +classes: + Location: + description: > + Represents a specific address or field location. References a parent + Geography (county-level). + slots: + - location_id + - geography # FK to Geography + - address_line1 + - address_line2 + - city + - zip + - lat + - lon + +slots: + location_id: + range: integer + description: Primary key for Location. + + geography: + range: Geography + description: Link to parent geography (county-level). + + address_line1: + range: string + description: Street address line 1. + + address_line2: + range: string + description: Street address line 2 (optional). + + city: + range: string + description: City name. + + zip: + range: string + pattern: "^[0-9]{5}$" + description: 5-digit ZIP code. + + lat: + range: float + description: Latitude in decimal degrees. + + lon: + range: float + description: Longitude in decimal degrees. diff --git a/schemas/usda/census_survey.yaml b/schemas/usda/census_survey.yaml new file mode 100644 index 00000000..9d91585a --- /dev/null +++ b/schemas/usda/census_survey.yaml @@ -0,0 +1,153 @@ +id: usda_data +name: USDA_Data +description: > + Schema for USDA Census and Survey data records accessed via the NASS Quick + Stats API, focusing on county-level data for key California crops. + +prefixes: + linkml: https://w3id.org/linkml/ + usda: https://schema.myorg.org/usda/ + agrovoc: https://agrovoc.fao.org/agrontology/en/page/ + ucum: http://unitsofmeasure.org/ucum.html + +default_prefix: usda +imports: + - linkml:types + - ../common/geography.yaml + +classes: + USDARecord: + description: Base class for USDA agricultural data records. + slots: + - year + - geography + - crop + - variable + - unit + - value + - bearing_status + - class_desc + - domain_desc + - source + - notes + slot_usage: + geography: + range: Geography + crop: + range: CropEnum + variable: + range: VariableEnum + unit: + range: UnitEnum + bearing_status: + range: BearingStatusEnum + + CensusRecord: + is_a: USDARecord + description: A USDA Census of Agriculture record (every 5 years). + + SurveyRecord: + is_a: USDARecord + description: A USDA Survey record (annual, seasonal, or periodic). + slots: + - period_desc + - freq_desc + - program_desc + +slots: + year: + range: integer + required: true + description: Census or survey year. + + geography: + range: Geography + description: Geographic information (state, county, FIPS). + + agg_level_desc: + range: string + description: Aggregation level (e.g., COUNTY, STATE, NATIONAL). + + crop: + description: Commodity or crop name. + exact_mappings: [] # TODO: map to AGROVOC crop concepts + + variable: + description: + Census or survey variable measured (e.g., Acreage, Yield, Production). + exact_mappings: [] # TODO: map to AGROVOC variable concepts + + unit: + description: Unit of measure (e.g., acres, tons, tons per acre). + exact_mappings: [] # TODO: map to UCUM or AGROVOC unit concepts + + value: + range: float + description: Reported numeric value. + + bearing_status: + description: Bearing or nonbearing acreage (if applicable). + + class_desc: + range: string + description: Class description (e.g., BEARING, NONBEARING). + + domain_desc: + range: string + description: Domain category (e.g., TOTAL, CHEMICAL, AREA HARVESTED). + + period_desc: + range: string + description: + For surveys, the time period of data collection (e.g., ANNUAL, MARCH). + + freq_desc: + range: string + description: + For surveys, the frequency of data collection (e.g., ANNUAL, MONTHLY). + + program_desc: + range: string + description: Survey program name (e.g., FRUIT & TREE NUTS, VEGETABLES). + + source: + range: string + description: Data source citation (e.g., USDA NASS Quick Stats API). + + notes: + range: string + description: Supplemental notes or flags (e.g., (D) data suppressed). + +enums: + CropEnum: + permissible_values: + Almond: + exact_mappings: [] # TODO: AGROVOC c_330 + Pistachio: + exact_mappings: [] # TODO: AGROVOC c_5733 + Tomato: + exact_mappings: [] # TODO: AGROVOC c_7824 + Olive: + exact_mappings: [] # TODO: AGROVOC c_5681 + + VariableEnum: + permissible_values: + ACREAGE_TOTAL: [] # TODO: AGROVOC mapping + ACREAGE_BEARING: [] # TODO: AGROVOC mapping + ACREAGE_NONBEARING: [] # TODO: AGROVOC mapping + YIELD: [] # TODO: AGROVOC mapping + PRODUCTION: [] # TODO: AGROVOC mapping + OPERATIONS: [] # TODO: AGROVOC mapping + + UnitEnum: + permissible_values: + ACRES: [] # TODO: UCUM mapping + TONS: [] # TODO: UCUM mapping + TONS_PER_ACRE: [] # TODO: UCUM mapping + OPERATIONS: [] # TODO: AGROVOC or UCUM mapping + + BearingStatusEnum: + permissible_values: + BEARING: [] # TODO: AGROVOC mapping + NONBEARING: [] # TODO: AGROVOC mapping + NA: [] # TODO: not applicable From 98af1b2ecb7cad30f4815fb57de3c8d90a963aa5 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Thu, 30 Oct 2025 11:16:15 -0600 Subject: [PATCH 34/81] feat:Adding linkml and modifying alembic .env to ensure compatiblity. Everything works I think. --- alembic/env.py | 26 ++ ...9_testing_linkml_created_python_object_.py | 32 ++ ...490235da5633_use_snake_case_table_names.py | 158 +++++++++ ...4_testing_linkml_created_python_object_.py | 96 ++++++ pixi.toml | 19 +- schemas/common/geography.yaml | 2 + schemas/generated/census_survey.py | 132 ++++++++ schemas/generated/geography.py | 29 ++ schemas/linkml_sqla_generation.md | 108 +++++++ schemas/pydantic/census_survey.py | 304 ++++++++++++++++++ schemas/pydantic/geography.py | 153 +++++++++ schemas/template.yaml | 45 +++ schemas/usda/census_survey.yaml | 65 ++-- .../pipeline/utils/test_lookup_utils.ipynb | 203 ++++++++++++ 14 files changed, 1342 insertions(+), 30 deletions(-) create mode 100644 alembic/versions/38398b232319_testing_linkml_created_python_object_.py create mode 100644 alembic/versions/490235da5633_use_snake_case_table_names.py create mode 100644 alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py create mode 100644 schemas/generated/census_survey.py create mode 100644 schemas/generated/geography.py create mode 100644 schemas/linkml_sqla_generation.md create mode 100644 schemas/pydantic/census_survey.py create mode 100644 schemas/pydantic/geography.py create mode 100644 schemas/template.yaml create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/test_lookup_utils.ipynb diff --git a/alembic/env.py b/alembic/env.py index 2d1671a0..8f072a32 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -25,6 +25,27 @@ from ca_biositing.datamodels.specific_aalysis_results import * from ca_biositing.datamodels.user import * from sqlmodel import SQLModel +import importlib.util +from pathlib import Path + +# --- Import generated models --- +# You can explicitly import your generated models here, or uncomment the +# code below to dynamically import them. +from schemas.generated.census_survey import * +from schemas.generated.geography import * + +# # --- Dynamically import generated models --- +# # This code will dynamically import all Python files from the +# # schemas/generated directory. This is a convenience so that you don't have +# # to add a new import statement every time you generate a new model from a +# # LinkML schema. +# generated_path = Path(__file__).resolve().parents[1] / "schemas" / "generated" +# for file in os.listdir(generated_path): +# if file.endswith(".py") and file != "__init__.py": +# module_name = file[:-3] +# spec = importlib.util.spec_from_file_location(module_name, generated_path / file) +# module = importlib.util.module_from_spec(spec) +# spec.loader.exec_module(module) # --- Alembic Config object, provides access to alembic.ini values --- config = context.config @@ -41,6 +62,11 @@ fileConfig(config.config_file_name) # --- Metadata from your models for autogenerate --- +# Combine metadata from all models +# See: https://alembic.sqlalchemy.org/en/latest/autogenerate.html#affecting-the-autogenerate-process +for table in SQLModel.metadata.tables.values(): + table.tometadata(SQLModel.metadata) + target_metadata = SQLModel.metadata diff --git a/alembic/versions/38398b232319_testing_linkml_created_python_object_.py b/alembic/versions/38398b232319_testing_linkml_created_python_object_.py new file mode 100644 index 00000000..fd2da614 --- /dev/null +++ b/alembic/versions/38398b232319_testing_linkml_created_python_object_.py @@ -0,0 +1,32 @@ +"""testing linkml created python object creation + +Revision ID: 38398b232319 +Revises: 8de419051d03 +Create Date: 2025-10-30 16:23:52.506268 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '38398b232319' +down_revision: Union[str, Sequence[str], None] = '8de419051d03' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/alembic/versions/490235da5633_use_snake_case_table_names.py b/alembic/versions/490235da5633_use_snake_case_table_names.py new file mode 100644 index 00000000..0a51c6d2 --- /dev/null +++ b/alembic/versions/490235da5633_use_snake_case_table_names.py @@ -0,0 +1,158 @@ +"""use snake_case table names + +Revision ID: 490235da5633 +Revises: 99af25a3b574 +Create Date: 2025-10-30 16:42:11.402363 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '490235da5633' +down_revision: Union[str, Sequence[str], None] = '99af25a3b574' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + op.drop_table('USDARecord') + op.drop_table('SurveyRecord') + op.drop_table('CensusRecord') + op.drop_table('Geography') + op.create_table('geography', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('state_name', sa.Text(), nullable=True), + sa.Column('state_fips', sa.Text(), nullable=True), + sa.Column('county_name', sa.Text(), nullable=True), + sa.Column('county_fips', sa.Text(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('region_name', sa.Text(), nullable=True), + sa.Column('agg_level_desc', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_record', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('census_record', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('survey_record', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('period_desc', sa.Text(), nullable=True), + sa.Column('freq_desc', sa.Text(), nullable=True), + sa.Column('program_desc', sa.Text(), nullable=True), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + + +def downgrade() -> None: + """Downgrade schema.""" + op.drop_table('survey_record') + op.drop_table('census_record') + op.drop_table('usda_record') + op.drop_table('geography') + op.create_table('USDARecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('SurveyRecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('period_desc', sa.Text(), nullable=True), + sa.Column('freq_desc', sa.Text(), nullable=True), + sa.Column('program_desc', sa.Text(), nullable=True), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('CensusRecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Geography', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('state_name', sa.Text(), nullable=True), + sa.Column('state_fips', sa.Text(), nullable=True), + sa.Column('county_name', sa.Text(), nullable=True), + sa.Column('county_fips', sa.Text(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('region_name', sa.Text(), nullable=True), + sa.Column('agg_level_desc', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) diff --git a/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py b/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py new file mode 100644 index 00000000..0d1fba2e --- /dev/null +++ b/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py @@ -0,0 +1,96 @@ +"""testing linkml created python object creation + +Revision ID: 99af25a3b574 +Revises: 38398b232319 +Create Date: 2025-10-30 16:38:00.752859 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '99af25a3b574' +down_revision: Union[str, Sequence[str], None] = '38398b232319' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('Geography', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('state_name', sa.Text(), nullable=True), + sa.Column('state_fips', sa.Text(), nullable=True), + sa.Column('county_name', sa.Text(), nullable=True), + sa.Column('county_fips', sa.Text(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('region_name', sa.Text(), nullable=True), + sa.Column('agg_level_desc', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('CensusRecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('SurveyRecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('period_desc', sa.Text(), nullable=True), + sa.Column('freq_desc', sa.Text(), nullable=True), + sa.Column('program_desc', sa.Text(), nullable=True), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('USDARecord', + sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), + sa.Column('year', sa.Integer(), nullable=False), + sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), + sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), + sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), + sa.Column('class_desc', sa.Text(), nullable=True), + sa.Column('domain_desc', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('geography_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), + sa.PrimaryKeyConstraint('id') + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('USDARecord') + op.drop_table('SurveyRecord') + op.drop_table('CensusRecord') + op.drop_table('Geography') + # ### end Alembic commands ### diff --git a/pixi.toml b/pixi.toml index 03900a02..e9b83a16 100644 --- a/pixi.toml +++ b/pixi.toml @@ -29,11 +29,20 @@ python = "~=3.12" pre-commit = ">=4.2.0,<5" pytest = ">=8.4.2,<9" pytest-cov = ">=7.0.0,<8" -pip = ">=25.2,<26" -docker-compose = ">=2.39.2,<3" -docker-cli = ">=28.3.1,<29" -testcontainers = ">=4.13.2,<5" -python-dotenv = ">=1.2.1,<2" +sqlmodel = ">=0.0.19,<0.1" +alembic = ">=1.13.2,<2" +psycopg2 = ">=2.9.9,<3" +python-dotenv = ">=1.0.1,<2" +pandas = ">=2.2.0,<3" +pyjanitor = "*" +gspread = "*" +gspread-dataframe = "*" +pydantic-settings = "*" +google-auth-oauthlib = "*" +prefect = "*" +uvicorn = ">=0.30.0,<1" +fastapi = ">=0.115.0,<1" +linkml = "*" [tasks] pre-commit-all = "pre-commit run --all-files" diff --git a/schemas/common/geography.yaml b/schemas/common/geography.yaml index 41c9cf1c..d5d6fda2 100644 --- a/schemas/common/geography.yaml +++ b/schemas/common/geography.yaml @@ -16,6 +16,8 @@ imports: classes: Geography: description: Reference table for U.S. geographic identifiers. + annotations: + __tablename__: geography slots: - state_name - state_fips diff --git a/schemas/generated/census_survey.py b/schemas/generated/census_survey.py new file mode 100644 index 00000000..158c32a4 --- /dev/null +++ b/schemas/generated/census_survey.py @@ -0,0 +1,132 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class USDARecord(Base): + """ + Base class for USDA agricultural data records. + """ + __tablename__ = 'USDARecord' + + id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) + year = Column(Integer(), nullable=False ) + crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) + variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) + unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) + value = Column(Float()) + bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) + class_desc = Column(Text()) + domain_desc = Column(Text()) + source = Column(Text()) + notes = Column(Text()) + geography_id = Column(Integer(), ForeignKey('Geography.id')) + geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) + + + def __repr__(self): + return f"USDARecord(id={self.id},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" + + + + + + +class Geography(Base): + """ + Reference table for U.S. geographic identifiers. + """ + __tablename__ = 'Geography' + + id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + geoid = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(id={self.id},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},geoid={self.geoid},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class CensusRecord(USDARecord): + """ + A USDA Census of Agriculture record (every 5 years). + """ + __tablename__ = 'CensusRecord' + + id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) + year = Column(Integer(), nullable=False ) + crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) + variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) + unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) + value = Column(Float()) + bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) + class_desc = Column(Text()) + domain_desc = Column(Text()) + source = Column(Text()) + notes = Column(Text()) + geography_id = Column(Integer(), ForeignKey('Geography.id')) + geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) + + + def __repr__(self): + return f"CensusRecord(id={self.id},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SurveyRecord(USDARecord): + """ + A USDA Survey record (annual, seasonal, or periodic). + """ + __tablename__ = 'SurveyRecord' + + id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) + period_desc = Column(Text()) + freq_desc = Column(Text()) + program_desc = Column(Text()) + year = Column(Integer(), nullable=False ) + crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) + variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) + unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) + value = Column(Float()) + bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) + class_desc = Column(Text()) + domain_desc = Column(Text()) + source = Column(Text()) + notes = Column(Text()) + geography_id = Column(Integer(), ForeignKey('Geography.id')) + geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) + + + def __repr__(self): + return f"SurveyRecord(id={self.id},period_desc={self.period_desc},freq_desc={self.freq_desc},program_desc={self.program_desc},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/schemas/generated/geography.py b/schemas/generated/geography.py new file mode 100644 index 00000000..dcc8a564 --- /dev/null +++ b/schemas/generated/geography.py @@ -0,0 +1,29 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Geography(Base): + """ + Reference table for U.S. geographic identifiers. + """ + __tablename__ = 'Geography' + + id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + geoid = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(id={self.id},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},geoid={self.geoid},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" diff --git a/schemas/linkml_sqla_generation.md b/schemas/linkml_sqla_generation.md new file mode 100644 index 00000000..7c3692cf --- /dev/null +++ b/schemas/linkml_sqla_generation.md @@ -0,0 +1,108 @@ +# Generating SQLAlchemy Models from LinkML Schemas + +This document outlines the process of generating SQLAlchemy (SQLA) models from +LinkML schemas and integrating them with Alembic for database migrations. + +## 1. Create a LinkML Schema + +Create a YAML file (e.g., `my_schema.yaml`) to define your data model. The +schema should include: + +- **`id`**: A unique identifier for the schema. +- **`name`**: A human-readable name for the schema. +- **`description`**: A brief description of the schema's purpose. +- **`prefixes`**: A mapping of prefixes to URIs for linked data. +- **`imports`**: A list of other LinkML schemas to import. +- **`classes`**: The main data structures of your model. +- **`slots`**: The properties of your classes. +- **`enums`**: Controlled vocabularies for your slots. + +## 2. Define Classes and Slots + +Define your classes and their corresponding slots. For SQLAlchemy model +generation, it's important to specify the table name using the `__tablename__` +annotation to ensure snake_case naming conventions. + +```yaml +classes: + MyClassName: + description: "A description of my class." + annotations: + __tablename__: my_snake_case_name + slots: + - my_slot_name +``` + +## 3. Generate SQLAlchemy Models + +Use the `linkml-sqla` generator to create SQLAlchemy models from your schema. +The following command will generate a Python file containing your models: + +```bash +linkml generate sqla my_schema.yaml > schemas/generated/my_model.py +``` + +If your schema imports other schemas, you may want to use the +`--no-mergeimports` flag to avoid including the imported models in the generated +file: + +```bash +linkml generate sqla --no-mergeimports my_schema.yaml > schemas/generated/my_model.py +``` + +## 4. Integrate with Alembic + +Once you have your generated models, you can use Alembic to create and apply +database migrations. + +### a. Configure Alembic + +Ensure your `alembic/env.py` is configured to use your generated models. You +will need to explicitly import your generated models and then merge their +metadata with your main `SQLModel` metadata. + +```python +# alembic/env.py +import os +import sys +from sqlmodel import SQLModel + +# Add the project root to the Python path +sys.path.append(str(Path(__file__).resolve().parents[1])) + +# Import your main models +from src.pipeline.etl.models import * + +# Import your generated models +from schemas.generated.my_model import * + +# Merge metadata +for table in SQLModel.metadata.tables.values(): + table.tometadata(SQLModel.metadata) + +target_metadata = SQLModel.metadata +``` + +Alternatively, you can uncomment the dynamic import code in `alembic/env.py` to +automatically import all generated models from the `schemas/generated` +directory. + +### b. Create a Migration + +Generate a new migration file using the `alembic revision` command: + +```bash +alembic revision --autogenerate -m "Add my_snake_case_name table" +``` + +### c. Apply the Migration + +Apply the migration to your database using the `alembic upgrade` command: + +```bash +alembic upgrade head +``` + +By following these steps, you can effectively use LinkML to define your data +models and generate SQLAlchemy models for your database, while maintaining a +clean and organized migration history with Alembic. diff --git a/schemas/pydantic/census_survey.py b/schemas/pydantic/census_survey.py new file mode 100644 index 00000000..c858fbaa --- /dev/null +++ b/schemas/pydantic/census_survey.py @@ -0,0 +1,304 @@ +from __future__ import annotations + +import re +import sys +from datetime import ( + date, + datetime, + time +) +from decimal import Decimal +from enum import Enum +from typing import ( + Any, + ClassVar, + Literal, + Optional, + Union +) + +from pydantic import ( + BaseModel, + ConfigDict, + Field, + RootModel, + SerializationInfo, + SerializerFunctionWrapHandler, + field_validator, + model_serializer +) + + +metamodel_version = "None" +version = "None" + + +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + serialize_by_alias = True, + validate_by_name = True, + validate_assignment = True, + validate_default = True, + extra = "forbid", + arbitrary_types_allowed = True, + use_enum_values = True, + strict = False, + ) + + @model_serializer(mode='wrap', when_used='unless-none') + def treat_empty_lists_as_none( + self, handler: SerializerFunctionWrapHandler, + info: SerializationInfo) -> dict[str, Any]: + if info.exclude_none: + _instance = self.model_copy() + for field, field_info in type(_instance).model_fields.items(): + if getattr(_instance, field) == [] and not( + field_info.is_required()): + setattr(_instance, field, None) + else: + _instance = self + return handler(_instance, info) + + + +class LinkMLMeta(RootModel): + root: dict[str, Any] = {} + model_config = ConfigDict(frozen=True) + + def __getattr__(self, key:str): + return getattr(self.root, key) + + def __getitem__(self, key:str): + return self.root[key] + + def __setitem__(self, key:str, value): + self.root[key] = value + + def __contains__(self, key:str) -> bool: + return key in self.root + + +linkml_meta = LinkMLMeta({'default_prefix': 'usda', + 'description': 'Schema for USDA Census and Survey data records accessed via ' + 'the NASS Quick Stats API, focusing on county-level data for ' + 'key California crops.\n', + 'id': 'usda_data', + 'imports': ['linkml:types', '../common/geography'], + 'name': 'USDA_Data', + 'prefixes': {'agrovoc': {'prefix_prefix': 'agrovoc', + 'prefix_reference': 'https://agrovoc.fao.org/agrontology/en/page/'}, + 'linkml': {'prefix_prefix': 'linkml', + 'prefix_reference': 'https://w3id.org/linkml/'}, + 'ucum': {'prefix_prefix': 'ucum', + 'prefix_reference': 'http://unitsofmeasure.org/ucum.html'}, + 'usda': {'prefix_prefix': 'usda', + 'prefix_reference': 'https://schema.myorg.org/usda/'}}, + 'source_file': 'schemas/usda/census_survey.yaml'} ) + +class CropEnum(str, Enum): + Almond = "Almond" + """ + TODO: AGROVOC c_330 + """ + Pistachio = "Pistachio" + """ + TODO: AGROVOC c_5733 + """ + Tomato = "Tomato" + """ + TODO: AGROVOC c_7824 + """ + Olive = "Olive" + """ + TODO: AGROVOC c_5681 + """ + + +class VariableEnum(str, Enum): + ACREAGE_TOTAL = "ACREAGE_TOTAL" + """ + TODO: AGROVOC mapping + """ + ACREAGE_BEARING = "ACREAGE_BEARING" + """ + TODO: AGROVOC mapping + """ + ACREAGE_NONBEARING = "ACREAGE_NONBEARING" + """ + TODO: AGROVOC mapping + """ + YIELD = "YIELD" + """ + TODO: AGROVOC mapping + """ + PRODUCTION = "PRODUCTION" + """ + TODO: AGROVOC mapping + """ + OPERATIONS = "OPERATIONS" + """ + TODO: AGROVOC mapping + """ + + +class UnitEnum(str, Enum): + ACRES = "ACRES" + """ + TODO: UCUM mapping + """ + TONS = "TONS" + """ + TODO: UCUM mapping + """ + TONS_PER_ACRE = "TONS_PER_ACRE" + """ + TODO: UCUM mapping + """ + OPERATIONS = "OPERATIONS" + """ + TODO: AGROVOC or UCUM mapping + """ + + +class BearingStatusEnum(str, Enum): + BEARING = "BEARING" + """ + TODO: AGROVOC mapping + """ + NONBEARING = "NONBEARING" + """ + TODO: AGROVOC mapping + """ + NA = "NA" + """ + TODO: not applicable + """ + + + +class Geography(ConfiguredBaseModel): + """ + Reference table for U.S. geographic identifiers. + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'geography'}) + + state_name: Optional[str] = Field(default=None, description="""U.S. state name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + state_fips: Optional[str] = Field(default=None, description="""Two-digit FIPS code for the state.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + county_name: Optional[str] = Field(default=None, description="""U.S. county name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + county_fips: Optional[str] = Field(default=None, description="""Three-digit county FIPS code.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + geoid: Optional[str] = Field(default=None, description="""Combined state + county FIPS (e.g., 06019).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + region_name: Optional[str] = Field(default=None, description="""Optional higher-level region grouping (e.g., San Joaquin Valley).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + agg_level_desc: Optional[str] = Field(default=None, description="""Aggregation level (e.g., COUNTY, STATE, NATIONAL).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + + @field_validator('state_fips') + def pattern_state_fips(cls, v): + pattern=re.compile(r"^[0-9]{2}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid state_fips format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid state_fips format: {v}" + raise ValueError(err_msg) + return v + + @field_validator('county_fips') + def pattern_county_fips(cls, v): + pattern=re.compile(r"^[0-9]{3}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid county_fips format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid county_fips format: {v}" + raise ValueError(err_msg) + return v + + @field_validator('geoid') + def pattern_geoid(cls, v): + pattern=re.compile(r"^[0-9]{5}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid geoid format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid geoid format: {v}" + raise ValueError(err_msg) + return v + + +class USDARecord(ConfiguredBaseModel): + """ + Base class for USDA agricultural data records. + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'usda_data', + 'slot_usage': {'bearing_status': {'name': 'bearing_status', + 'range': 'BearingStatusEnum'}, + 'crop': {'name': 'crop', 'range': 'CropEnum'}, + 'geography': {'name': 'geography', 'range': 'Geography'}, + 'unit': {'name': 'unit', 'range': 'UnitEnum'}, + 'variable': {'name': 'variable', 'range': 'VariableEnum'}}}) + + year: int = Field(default=..., description="""Census or survey year.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + geography: Optional[Geography] = Field(default=None, description="""Geographic information (state, county, FIPS).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + crop: Optional[CropEnum] = Field(default=None, description="""Commodity or crop name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + variable: Optional[VariableEnum] = Field(default=None, description="""Census or survey variable measured (e.g., Acreage, Yield, Production).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + unit: Optional[UnitEnum] = Field(default=None, description="""Unit of measure (e.g., acres, tons, tons per acre).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + value: Optional[float] = Field(default=None, description="""Reported numeric value.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + bearing_status: Optional[BearingStatusEnum] = Field(default=None, description="""Bearing or nonbearing acreage (if applicable).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + class_desc: Optional[str] = Field(default=None, description="""Class description (e.g., BEARING, NONBEARING).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + domain_desc: Optional[str] = Field(default=None, description="""Domain category (e.g., TOTAL, CHEMICAL, AREA HARVESTED).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + source: Optional[str] = Field(default=None, description="""Data source citation (e.g., USDA NASS Quick Stats API).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + notes: Optional[str] = Field(default=None, description="""Supplemental notes or flags (e.g., (D) data suppressed).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + + +class CensusRecord(USDARecord): + """ + A USDA Census of Agriculture record (every 5 years). + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'usda_data'}) + + year: int = Field(default=..., description="""Census or survey year.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + geography: Optional[Geography] = Field(default=None, description="""Geographic information (state, county, FIPS).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + crop: Optional[CropEnum] = Field(default=None, description="""Commodity or crop name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + variable: Optional[VariableEnum] = Field(default=None, description="""Census or survey variable measured (e.g., Acreage, Yield, Production).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + unit: Optional[UnitEnum] = Field(default=None, description="""Unit of measure (e.g., acres, tons, tons per acre).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + value: Optional[float] = Field(default=None, description="""Reported numeric value.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + bearing_status: Optional[BearingStatusEnum] = Field(default=None, description="""Bearing or nonbearing acreage (if applicable).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + class_desc: Optional[str] = Field(default=None, description="""Class description (e.g., BEARING, NONBEARING).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + domain_desc: Optional[str] = Field(default=None, description="""Domain category (e.g., TOTAL, CHEMICAL, AREA HARVESTED).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + source: Optional[str] = Field(default=None, description="""Data source citation (e.g., USDA NASS Quick Stats API).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + notes: Optional[str] = Field(default=None, description="""Supplemental notes or flags (e.g., (D) data suppressed).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + + +class SurveyRecord(USDARecord): + """ + A USDA Survey record (annual, seasonal, or periodic). + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'usda_data'}) + + period_desc: Optional[str] = Field(default=None, description="""For surveys, the time period of data collection (e.g., ANNUAL, MARCH).""", json_schema_extra = { "linkml_meta": {'domain_of': ['SurveyRecord']} }) + freq_desc: Optional[str] = Field(default=None, description="""For surveys, the frequency of data collection (e.g., ANNUAL, MONTHLY).""", json_schema_extra = { "linkml_meta": {'domain_of': ['SurveyRecord']} }) + program_desc: Optional[str] = Field(default=None, description="""Survey program name (e.g., FRUIT & TREE NUTS, VEGETABLES).""", json_schema_extra = { "linkml_meta": {'domain_of': ['SurveyRecord']} }) + year: int = Field(default=..., description="""Census or survey year.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + geography: Optional[Geography] = Field(default=None, description="""Geographic information (state, county, FIPS).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + crop: Optional[CropEnum] = Field(default=None, description="""Commodity or crop name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + variable: Optional[VariableEnum] = Field(default=None, description="""Census or survey variable measured (e.g., Acreage, Yield, Production).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + unit: Optional[UnitEnum] = Field(default=None, description="""Unit of measure (e.g., acres, tons, tons per acre).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + value: Optional[float] = Field(default=None, description="""Reported numeric value.""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + bearing_status: Optional[BearingStatusEnum] = Field(default=None, description="""Bearing or nonbearing acreage (if applicable).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + class_desc: Optional[str] = Field(default=None, description="""Class description (e.g., BEARING, NONBEARING).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + domain_desc: Optional[str] = Field(default=None, description="""Domain category (e.g., TOTAL, CHEMICAL, AREA HARVESTED).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + source: Optional[str] = Field(default=None, description="""Data source citation (e.g., USDA NASS Quick Stats API).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + notes: Optional[str] = Field(default=None, description="""Supplemental notes or flags (e.g., (D) data suppressed).""", json_schema_extra = { "linkml_meta": {'domain_of': ['USDARecord']} }) + + +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +Geography.model_rebuild() +USDARecord.model_rebuild() +CensusRecord.model_rebuild() +SurveyRecord.model_rebuild() diff --git a/schemas/pydantic/geography.py b/schemas/pydantic/geography.py new file mode 100644 index 00000000..7e0cdb4b --- /dev/null +++ b/schemas/pydantic/geography.py @@ -0,0 +1,153 @@ +from __future__ import annotations + +import re +import sys +from datetime import ( + date, + datetime, + time +) +from decimal import Decimal +from enum import Enum +from typing import ( + Any, + ClassVar, + Literal, + Optional, + Union +) + +from pydantic import ( + BaseModel, + ConfigDict, + Field, + RootModel, + SerializationInfo, + SerializerFunctionWrapHandler, + field_validator, + model_serializer +) + + +metamodel_version = "None" +version = "None" + + +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + serialize_by_alias = True, + validate_by_name = True, + validate_assignment = True, + validate_default = True, + extra = "forbid", + arbitrary_types_allowed = True, + use_enum_values = True, + strict = False, + ) + + @model_serializer(mode='wrap', when_used='unless-none') + def treat_empty_lists_as_none( + self, handler: SerializerFunctionWrapHandler, + info: SerializationInfo) -> dict[str, Any]: + if info.exclude_none: + _instance = self.model_copy() + for field, field_info in type(_instance).model_fields.items(): + if getattr(_instance, field) == [] and not( + field_info.is_required()): + setattr(_instance, field, None) + else: + _instance = self + return handler(_instance, info) + + + +class LinkMLMeta(RootModel): + root: dict[str, Any] = {} + model_config = ConfigDict(frozen=True) + + def __getattr__(self, key:str): + return getattr(self.root, key) + + def __getitem__(self, key:str): + return self.root[key] + + def __setitem__(self, key:str, value): + self.root[key] = value + + def __contains__(self, key:str) -> bool: + return key in self.root + + +linkml_meta = LinkMLMeta({'default_prefix': 'usda', + 'description': 'Common geographic identifiers used across multiple datasets. ' + 'Includes states, counties, FIPS codes, and optional ' + 'regions.\n', + 'id': 'geography', + 'imports': ['linkml:types'], + 'name': 'Geography', + 'prefixes': {'agrovoc': {'prefix_prefix': 'agrovoc', + 'prefix_reference': 'https://agrovoc.fao.org/agrontology/en/page/'}, + 'linkml': {'prefix_prefix': 'linkml', + 'prefix_reference': 'https://w3id.org/linkml/'}, + 'usda': {'prefix_prefix': 'usda', + 'prefix_reference': 'https://schema.myorg.org/usda/'}}, + 'source_file': 'schemas/common/geography.yaml'} ) + + +class Geography(ConfiguredBaseModel): + """ + Reference table for U.S. geographic identifiers. + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'geography'}) + + state_name: Optional[str] = Field(default=None, description="""U.S. state name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + state_fips: Optional[str] = Field(default=None, description="""Two-digit FIPS code for the state.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + county_name: Optional[str] = Field(default=None, description="""U.S. county name.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + county_fips: Optional[str] = Field(default=None, description="""Three-digit county FIPS code.""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + geoid: Optional[str] = Field(default=None, description="""Combined state + county FIPS (e.g., 06019).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + region_name: Optional[str] = Field(default=None, description="""Optional higher-level region grouping (e.g., San Joaquin Valley).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + agg_level_desc: Optional[str] = Field(default=None, description="""Aggregation level (e.g., COUNTY, STATE, NATIONAL).""", json_schema_extra = { "linkml_meta": {'domain_of': ['Geography']} }) + + @field_validator('state_fips') + def pattern_state_fips(cls, v): + pattern=re.compile(r"^[0-9]{2}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid state_fips format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid state_fips format: {v}" + raise ValueError(err_msg) + return v + + @field_validator('county_fips') + def pattern_county_fips(cls, v): + pattern=re.compile(r"^[0-9]{3}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid county_fips format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid county_fips format: {v}" + raise ValueError(err_msg) + return v + + @field_validator('geoid') + def pattern_geoid(cls, v): + pattern=re.compile(r"^[0-9]{5}$") + if isinstance(v, list): + for element in v: + if isinstance(element, str) and not pattern.match(element): + err_msg = f"Invalid geoid format: {element}" + raise ValueError(err_msg) + elif isinstance(v, str) and not pattern.match(v): + err_msg = f"Invalid geoid format: {v}" + raise ValueError(err_msg) + return v + + +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +Geography.model_rebuild() diff --git a/schemas/template.yaml b/schemas/template.yaml new file mode 100644 index 00000000..c1de51ef --- /dev/null +++ b/schemas/template.yaml @@ -0,0 +1,45 @@ +id: new_schema +name: NewSchema +description: > + A template for creating new LinkML schemas. + +prefixes: + linkml: https://w3id.org/linkml/ + schema: https://schema.org/ + skos: http://www.w3.org/2004/02/skos/core# + +default_prefix: schema +imports: + - linkml:types + +classes: + MyClass: + description: "A description of my class." + annotations: + __tablename__: my_class + slots: + - id + - name + - description + +slots: + id: + identifier: true + range: string + description: "A unique identifier for the instance." + + name: + range: string + description: "A human-readable name for the instance." + + description: + range: string + description: "A description of the instance." + +enums: + MyEnum: + permissible_values: + VALUE_1: + description: "The first value." + VALUE_2: + description: "The second value." diff --git a/schemas/usda/census_survey.yaml b/schemas/usda/census_survey.yaml index 9d91585a..6ab40f7f 100644 --- a/schemas/usda/census_survey.yaml +++ b/schemas/usda/census_survey.yaml @@ -13,11 +13,13 @@ prefixes: default_prefix: usda imports: - linkml:types - - ../common/geography.yaml + - ../common/geography classes: USDARecord: description: Base class for USDA agricultural data records. + annotations: + __tablename__: usda_record slots: - year - geography @@ -45,10 +47,14 @@ classes: CensusRecord: is_a: USDARecord description: A USDA Census of Agriculture record (every 5 years). + annotations: + __tablename__: census_record SurveyRecord: is_a: USDARecord description: A USDA Survey record (annual, seasonal, or periodic). + annotations: + __tablename__: survey_record slots: - period_desc - freq_desc @@ -64,22 +70,18 @@ slots: range: Geography description: Geographic information (state, county, FIPS). - agg_level_desc: - range: string - description: Aggregation level (e.g., COUNTY, STATE, NATIONAL). - crop: description: Commodity or crop name. - exact_mappings: [] # TODO: map to AGROVOC crop concepts + exact_mappings: # TODO: map to AGROVOC crop concepts variable: description: Census or survey variable measured (e.g., Acreage, Yield, Production). - exact_mappings: [] # TODO: map to AGROVOC variable concepts + exact_mappings: # TODO: map to AGROVOC variable concepts unit: description: Unit of measure (e.g., acres, tons, tons per acre). - exact_mappings: [] # TODO: map to UCUM or AGROVOC unit concepts + exact_mappings: # TODO: map to AGROVOC unit concepts value: range: float @@ -122,32 +124,45 @@ enums: CropEnum: permissible_values: Almond: - exact_mappings: [] # TODO: AGROVOC c_330 + description: "TODO: AGROVOC c_330" Pistachio: - exact_mappings: [] # TODO: AGROVOC c_5733 + description: "TODO: AGROVOC c_5733" Tomato: - exact_mappings: [] # TODO: AGROVOC c_7824 + description: "TODO: AGROVOC c_7824" Olive: - exact_mappings: [] # TODO: AGROVOC c_5681 + description: "TODO: AGROVOC c_5681" VariableEnum: permissible_values: - ACREAGE_TOTAL: [] # TODO: AGROVOC mapping - ACREAGE_BEARING: [] # TODO: AGROVOC mapping - ACREAGE_NONBEARING: [] # TODO: AGROVOC mapping - YIELD: [] # TODO: AGROVOC mapping - PRODUCTION: [] # TODO: AGROVOC mapping - OPERATIONS: [] # TODO: AGROVOC mapping + ACREAGE_TOTAL: + description: "TODO: AGROVOC mapping" + ACREAGE_BEARING: + description: "TODO: AGROVOC mapping" + ACREAGE_NONBEARING: + description: "TODO: AGROVOC mapping" + YIELD: + description: "TODO: AGROVOC mapping" + PRODUCTION: + description: "TODO: AGROVOC mapping" + OPERATIONS: + description: "TODO: AGROVOC mapping" UnitEnum: permissible_values: - ACRES: [] # TODO: UCUM mapping - TONS: [] # TODO: UCUM mapping - TONS_PER_ACRE: [] # TODO: UCUM mapping - OPERATIONS: [] # TODO: AGROVOC or UCUM mapping + ACRES: + description: "TODO: UCUM mapping" + TONS: + description: "TODO: UCUM mapping" + TONS_PER_ACRE: + description: "TODO: UCUM mapping" + OPERATIONS: + description: "TODO: AGROVOC or UCUM mapping" BearingStatusEnum: permissible_values: - BEARING: [] # TODO: AGROVOC mapping - NONBEARING: [] # TODO: AGROVOC mapping - NA: [] # TODO: not applicable + BEARING: + description: "TODO: AGROVOC mapping" + NONBEARING: + description: "TODO: AGROVOC mapping" + NA: + description: "TODO: not applicable" diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/test_lookup_utils.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/test_lookup_utils.ipynb new file mode 100644 index 00000000..5f7c94e0 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/test_lookup_utils.ipynb @@ -0,0 +1,203 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Test Notebook for Lookup Utils\n", + "\n", + "This notebook demonstrates how to use the utility functions in `lookup_utils.py` to swap foreign key IDs with names and vice-versa." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "from sqlmodel import Session, select\n", + "import sys\n", + "import os\n", + "\n", + "# Add the project root to the Python path to allow for module imports\n", + "project_root = os.path.abspath(os.path.join(os.getcwd(), '..'))\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + "\n", + "from src.database import engine\n", + "from src.models.biomass import Biomass, BiomassType\n", + "from src.utils.lookup_utils import replace_id_with_name_df, replace_name_with_id_df" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Create a Database Session\n", + "\n", + "First, we create a database session using the engine from our `database.py` module. This session is used to communicate with the database." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "db = Session(engine)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 2. Load Tables into Pandas DataFrames\n", + "\n", + "Next, we query the `Biomass` and `BiomassType` tables and load their contents into pandas DataFrames. This simulates the data you would be working with in a transformation script." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Load Biomass table\n", + "biomass_statement = select(Biomass)\n", + "biomass_records = db.exec(biomass_statement).all()\n", + "biomass_df = pd.DataFrame([record.dict() for record in biomass_records])\n", + "\n", + "print(\"Original Biomass DataFrame:\")\n", + "display(biomass_df.head())" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Load BiomassType table\n", + "biomass_type_statement = select(BiomassType)\n", + "biomass_type_records = db.exec(biomass_type_statement).all()\n", + "biomass_type_df = pd.DataFrame([record.dict() for record in biomass_type_records])\n", + "\n", + "print(\"Biomass Type Reference DataFrame:\")\n", + "display(biomass_type_df.head())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 3. Example Usage\n", + "\n", + "Now you can use the utility functions to transform the DataFrames. The cells below provide examples that you can run and modify." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Example 1: Replace `biomass_type_id` with `biomass_type` Name" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# To run this, uncomment the following lines:\n", + "# df_with_names = replace_id_with_name_df(\n", + "# db=db,\n", + "# df=biomass_df,\n", + "# ref_model=BiomassType,\n", + "# id_column_name=\"biomass_type_id\",\n", + "# name_column_name=\"biomass_type\"\n", + "# )\n", + "#\n", + "# print(\"DataFrame with Biomass Type Names:\")\n", + "# display(df_with_names.head())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Example 2: Replace `biomass_type` Name with `biomass_type_id`\n", + "\n", + "This example also demonstrates the 'get or create' functionality. Let's first add a new, non-existent biomass type to our DataFrame to see if the function correctly adds it to the database." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# Create a dummy DataFrame for this example\n", + "data = {'biomass_name': ['Test Biomass 1', 'Test Biomass 2'], 'biomass_type': ['ag_residue', 'new_test_type']}\n", + "name_df = pd.DataFrame(data)\n", + "\n", + "# To run this, uncomment the following lines:\n", + "# df_with_ids = replace_name_with_id_df(\n", + "# db=db,\n", + "# df=name_df,\n", + "# ref_model=BiomassType,\n", + "# name_column_name=\"biomass_type\",\n", + "# id_column_name=\"biomass_type_id\"\n", + "# )\n", + "#\n", + "# print(\"DataFrame with Biomass Type IDs:\")\n", + "# display(df_with_ids.head())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Verify New Type was Added\n", + "\n", + "If you ran the cell above, you can run this cell to query the `BiomassType` table again and see the new `new_test_type` entry." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# To run this, uncomment the following lines:\n", + "# updated_biomass_type_statement = select(BiomassType)\n", + "# updated_biomass_type_records = db.exec(updated_biomass_type_statement).all()\n", + "# updated_biomass_type_df = pd.DataFrame([record.dict() for record in updated_biomass_type_records])\n", + "#\n", + "# print(\"Updated Biomass Type Table:\")\n", + "# display(updated_biomass_type_df)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "default", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.11" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} From 5f84c4ed14c52c18ac187f20f7b00ca2a09df910 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Thu, 30 Oct 2025 12:54:10 -0600 Subject: [PATCH 35/81] adding win-64 to platforms in pixi toml --- pixi.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pixi.toml b/pixi.toml index e9b83a16..083ced6e 100644 --- a/pixi.toml +++ b/pixi.toml @@ -6,7 +6,7 @@ requires-pixi = ">=0.55,<1.0" authors = ["SSEC Team"] channels = ["conda-forge"] name = "ca-biositing" -platforms = ["osx-arm64", "osx-64", "linux-64", "linux-aarch64"] +platforms = ["osx-arm64", "osx-64", "linux-64", "linux-aarch64", "win-64"] version = "0.1.0" [environments] From 44417f0d010d11d48a8b008a7c465cde44b9d579 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Thu, 30 Oct 2025 14:38:13 -0700 Subject: [PATCH 36/81] total test --- test.txt | 1 + 1 file changed, 1 insertion(+) create mode 100644 test.txt diff --git a/test.txt b/test.txt new file mode 100644 index 00000000..b33c5606 --- /dev/null +++ b/test.txt @@ -0,0 +1 @@ +test test From 719fe29e4ef0dbe0faab45e6b24d9c5d4cf28c5a Mon Sep 17 00:00:00 2001 From: mglbleta Date: Thu, 30 Oct 2025 14:45:39 -0700 Subject: [PATCH 37/81] test is our commit message --- test.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test.txt b/test.txt index b33c5606..d49aab15 100644 --- a/test.txt +++ b/test.txt @@ -1 +1 @@ -test test +test test test From a00253f2d8da065a4c2c1a7d099b084846e1eed6 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Sun, 2 Nov 2025 15:30:23 -0800 Subject: [PATCH 38/81] Removing test file and revising docker setup instructions in README.md --- src/pipeline/README.md | 6 ++---- test.txt | 1 - 2 files changed, 2 insertions(+), 5 deletions(-) delete mode 100644 test.txt diff --git a/src/pipeline/README.md b/src/pipeline/README.md index fc01d1f0..f2db60b9 100644 --- a/src/pipeline/README.md +++ b/src/pipeline/README.md @@ -119,9 +119,7 @@ Follow these steps to set up and run the project for the first time. **3. Build the Docker Image:** -- From the project root directory, build the Docker image. You do not need to - activate the `pixi shell` for this, as the container manages its own - environment. +- From the project root directory, build the Docker image. ```bash docker-compose build @@ -143,7 +141,7 @@ Follow these steps to set up and run the project for the first time. migrations. ```bash - docker-compose exec app alembic upgrade head + docker-compose exec app pixi run alembic upgrade head ``` The environment is now fully set up and running. diff --git a/test.txt b/test.txt deleted file mode 100644 index d49aab15..00000000 --- a/test.txt +++ /dev/null @@ -1 +0,0 @@ -test test test From f307b999cca9ce315bcb35950355140be3265b86 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Sun, 2 Nov 2025 15:51:51 -0800 Subject: [PATCH 39/81] Adding notes to env.example which would've explained points I got confused on. --- src/ca_biositing/pipeline/.env.example | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/ca_biositing/pipeline/.env.example b/src/ca_biositing/pipeline/.env.example index 818cbf5a..1f839159 100644 --- a/src/ca_biositing/pipeline/.env.example +++ b/src/ca_biositing/pipeline/.env.example @@ -2,6 +2,8 @@ # --- # This file serves as an example. Copy it to a new file named .env # and replace the placeholder values with your actual development settings. +# These development settings are NOT found elsewhere and input here. You generate them in +# this document. # 1. Individual Connection Parameters # These are used by docker-compose to initialize the PostgreSQL container. @@ -17,7 +19,9 @@ POSTGRES_PORT=5432 # 3. Application Database URL # This is the full connection string used by the Python application (e.g., SQLAlchemy, Alembic) -# to connect to the database container. +# to connect to the database container. Make sure to replace the placeholders with the actual values. +# Do NOT use POSTGRES_USER, POSTGRES_PASSWORD, and POSTGRES_DB as variables here, type the +#actual username, password and database name from above in the DATABASE_URL string. # Note: # - It uses the service name 'db' as the host, which is how containers talk to each other. # - It uses the internal port '5432', not the host port. From 5e9fd3e5934e539a9ba2f7d46ac18edfab75f6ce Mon Sep 17 00:00:00 2001 From: mglbleta Date: Sun, 2 Nov 2025 15:53:28 -0800 Subject: [PATCH 40/81] potentially fixed whitespace --- src/ca_biositing/pipeline/.env.example | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ca_biositing/pipeline/.env.example b/src/ca_biositing/pipeline/.env.example index 1f839159..7c5efee0 100644 --- a/src/ca_biositing/pipeline/.env.example +++ b/src/ca_biositing/pipeline/.env.example @@ -21,7 +21,7 @@ POSTGRES_PORT=5432 # This is the full connection string used by the Python application (e.g., SQLAlchemy, Alembic) # to connect to the database container. Make sure to replace the placeholders with the actual values. # Do NOT use POSTGRES_USER, POSTGRES_PASSWORD, and POSTGRES_DB as variables here, type the -#actual username, password and database name from above in the DATABASE_URL string. +# actual username, password and database name from above in the DATABASE_URL string. # Note: # - It uses the service name 'db' as the host, which is how containers talk to each other. # - It uses the internal port '5432', not the host port. From 985278163bd3f35a9799341024d7285f643ef3d3 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Sun, 2 Nov 2025 16:16:12 -0800 Subject: [PATCH 41/81] Added explation for @task instruction --- docs/pipeline/ETL_WORKFLOW.md | 30 ++++++++++-------------------- 1 file changed, 10 insertions(+), 20 deletions(-) diff --git a/docs/pipeline/ETL_WORKFLOW.md b/docs/pipeline/ETL_WORKFLOW.md index b5279625..b6a13ff3 100644 --- a/docs/pipeline/ETL_WORKFLOW.md +++ b/docs/pipeline/ETL_WORKFLOW.md @@ -9,33 +9,16 @@ and how to use Prefect to execute it. The ETL pipeline is designed to extract data from Google Sheets, transform it into a structured format, and load it into the PostgreSQL database. The system -is built to be modular and extensible. The ETL pipeline is designed to extract -data from Google Sheets, transform it into a structured format, and load it into -the PostgreSQL database. The system is built to be modular and extensible. +is built to be modular and extensible. - **Structure:** The core logic is organized into three main packages within - `src/etl/`: + `src/pipeline/etl/`: - `extract`: Contains functions to pull raw data from sources (e.g., Google Sheets). - `transform`: Contains functions to clean, process, and structure the raw data. - `load`: Contains functions to insert the transformed data into the database. -- **Structure:** The core logic is organized into three main packages within - `src/etl/`: - - `extract`: Contains functions to pull raw data from sources (e.g., Google - Sheets). - - `transform`: Contains functions to clean, process, and structure the raw - data. - - `load`: Contains functions to insert the transformed data into the database. - -- **Hierarchical Pipelines:** To keep the project organized, individual - pipelines are nested within subdirectories that reflect the data they handle - (e.g., `products`, `analysis`). A complete pipeline for a single data type, - like `primary_product`, consists of three corresponding files: - - `src/etl/extract/products/primary_product.py` - - `src/etl/transform/products/primary_product.py` - - `src/etl/load/products/primary_product.py` - **Hierarchical Pipelines:** To keep the project organized, individual pipelines are nested within subdirectories that reflect the data they handle (e.g., `products`, `analysis`). A complete pipeline for a single data type, @@ -69,7 +52,14 @@ in the main `run_prefect_flow.py` script. **Step 1: Create the Task Files** Create the three Python files for your extract, transform, and load logic in the -appropriate subdirectories. Decorate each function with `@task`. +appropriate subdirectories. Decorate each function with `@task`, which is a +Prefect decorator that transforms a normal Python function into a managed Task. +Applying `@task` enables Prefect to: + +- Schedule and orchestrate the function as an individual Task within a flow. +- Track the Task’s execution state (pending, running, succeeded, failed). +- Automatically handle retries, timeouts, and result caching when configured. +- Collect logs and metrics for observability and debugging. - `src/etl/extract/samples/new_sample_type.py` - `src/etl/transform/samples/new_sample_type.py` From 719aa94ebc8df4316514850c96310998a623a778 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Fri, 14 Nov 2025 12:33:31 -0700 Subject: [PATCH 42/81] trying to commit again --- .../pipeline/utils/database_interaction.ipynb | 204 ++++++++++++++++++ 1 file changed, 204 insertions(+) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb new file mode 100644 index 00000000..41d5e443 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb @@ -0,0 +1,204 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Interactive Database Querying\n", + "\n", + "This notebook demonstrates how to connect to the project's PostgreSQL database from a local Jupyter environment to perform interactive queries and data analysis. It is intended as an educational tool and a template for data exploration." + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Step 1: Import Necessary Libraries\n", + "\n", + "We begin by importing the required libraries:\n", + "- `pandas` for data manipulation.\n", + "- `create_engine`, `Session`, and `select` from `sqlmodel` for database interaction.\n", + "- The specific SQLModel data models (`FieldSample`, `GeographicLocation`) we want to query." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "from sqlmodel import create_engine, Session, select\n", + "\n", + "try:\n", + " from ca_biositing.datamodels.biomass import FieldSample\n", + " from ca_biositing.datamodels.biomass import PrimaryProduct\n", + " from ca_biositing.datamodels.geographic_locations import GeographicLocation\n", + " print(\"Libraries and models imported successfully.\")\n", + "except ImportError as e:\n", + " print(f\"Error importing models: {e}\")\n", + " print(\"Please ensure the project is installed correctly by running 'pixi install' in your terminal.\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Step 2: Create the Database Engine\n", + "\n", + "Next, we create a SQLAlchemy engine to manage connections to the database. \n", + "\n", + "**Note:** We are hardcoding the database URL here to ensure the notebook runs reliably. It connects to `localhost:5432`, which is the default port mapped to the project's Dockerized database." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "DATABASE_URL = \"postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db\"\n", + "\n", + "try:\n", + " engine = create_engine(DATABASE_URL, echo=False)\n", + " print(f\"Database engine created. Ready to connect to: {DATABASE_URL.replace('biocirv_dev_password', '')}\")\n", + "except Exception as e:\n", + " print(f\"Error creating database engine: {e}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Step 3: Query the Tables\n", + "\n", + "Now we can use the engine to open a session and query our tables. We will query the `field_samples` and `geographic_locations` tables and load them into separate pandas DataFrames." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "field_samples_df = None\n", + "locations_df = None\n", + "primary_product_df = None\n", + "\n", + "try:\n", + " with Session(engine) as session:\n", + " # Query the field_samples table\n", + " statement_samples = select(FieldSample)\n", + " results_samples = session.exec(statement_samples).all()\n", + " field_samples_df = pd.DataFrame([sample.model_dump() for sample in results_samples])\n", + " print(f\"- Loaded {len(field_samples_df)} records from 'field_samples'.\")\n", + " \n", + " # Query the geographic_locations table\n", + " statement_locations = select(GeographicLocation)\n", + " results_locations = session.exec(statement_locations).all()\n", + " locations_df = pd.DataFrame([location.model_dump() for location in results_locations])\n", + " print(f\"- Loaded {len(locations_df)} records from 'geographic_locations'.\")\n", + "\n", + " # Query the primary_product table\n", + " statement_products = select(PrimaryProduct)\n", + " results_products = session.exec(statement_products).all()\n", + " primary_product_df = pd.DataFrame([product.model_dump() for product in results_products])\n", + " print(f\"- Loaded {len(primary_product_df)} records from 'primary_product'.\")\n", + "\n", + "except Exception as e:\n", + " print(f\"Error during database query: {e}\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "df2 = pd.read_sql(\"SELECT * FROM analysis_types\", engine)\n", + "df2 = df2.set_index(\"analysis_type_id\")\n", + "\n", + "df2.head()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Step 4: Join the DataFrames\n", + "\n", + "With our data loaded into DataFrames, we can now perform a standard `left` join using pandas to combine them on the `location_id` key. \n", + "\n", + "We include error handling to manage the case where the database is empty. If the DataFrames are empty, the join key might not exist, and the merge will fail. Our code will catch this and print a helpful message." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "merged_df = None\n", + "\n", + "try:\n", + " # Ensure dataframes are not None and not empty before merging\n", + " if field_samples_df is not None and not field_samples_df.empty:\n", + " merged_df = pd.merge(\n", + " left=field_samples_df, \n", + " right=locations_df, \n", + " how='left', \n", + " on='location_id'\n", + " )\n", + " print(\"Join complete.\")\n", + " else:\n", + " print(\"Skipping join because 'field_samples' table is empty.\")\n", + "except KeyError as e:\n", + " print(f\"Error during join: Could not find join key {e}. This can happen if the tables are empty.\")\n", + "except Exception as e:\n", + " print(f\"An unexpected error occurred during the join: {e}\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Step 5: Display Results\n", + "\n", + "Finally, we can display the head of the merged DataFrame to inspect the result." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "if merged_df is not None:\n", + " display(merged_df.head())\n", + "else:\n", + " print(\"No data to display.\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "default", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.14.0" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} From 883a01a0d4d5e52bc023d3780a8c8fa9388ad0ac Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Fri, 14 Nov 2025 14:02:33 -0700 Subject: [PATCH 43/81] feat: attempting to add schemas folder to datamodels module and import sqlalchemy via alembic --- alembic/env.py | 19 +- ...9_testing_linkml_created_python_object_.py | 32 - ...490235da5633_use_snake_case_table_names.py | 158 ---- .../523eedbcaf6e_initial_migration.py | 877 ++++++++++++++++++ ...4_testing_linkml_created_python_object_.py | 96 -- .../datamodels/schemas/__init__.py | 1 + .../datamodels/schemas}/common/geography.yaml | 0 .../schemas}/common/locations_address.yml | 0 .../datamodels/schemas/generated/__init__.py | 1 + .../schemas}/generated/census_survey.py | 0 .../schemas}/generated/geography.py | 0 .../schemas}/linkml_sqla_generation.md | 0 .../schemas}/pydantic/census_survey.py | 0 .../datamodels/schemas}/pydantic/geography.py | 0 .../datamodels/schemas}/template.yaml | 0 .../schemas}/usda/census_survey.yaml | 0 16 files changed, 881 insertions(+), 303 deletions(-) delete mode 100644 alembic/versions/38398b232319_testing_linkml_created_python_object_.py delete mode 100644 alembic/versions/490235da5633_use_snake_case_table_names.py create mode 100644 alembic/versions/523eedbcaf6e_initial_migration.py delete mode 100644 alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/common/geography.yaml (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/common/locations_address.yml (100%) create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/generated/census_survey.py (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/generated/geography.py (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/linkml_sqla_generation.md (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/pydantic/census_survey.py (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/pydantic/geography.py (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/template.yaml (100%) rename {schemas => src/ca_biositing/datamodels/ca_biositing/datamodels/schemas}/usda/census_survey.yaml (100%) diff --git a/alembic/env.py b/alembic/env.py index 8f072a32..4b372e23 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -29,23 +29,8 @@ from pathlib import Path # --- Import generated models --- -# You can explicitly import your generated models here, or uncomment the -# code below to dynamically import them. -from schemas.generated.census_survey import * -from schemas.generated.geography import * - -# # --- Dynamically import generated models --- -# # This code will dynamically import all Python files from the -# # schemas/generated directory. This is a convenience so that you don't have -# # to add a new import statement every time you generate a new model from a -# # LinkML schema. -# generated_path = Path(__file__).resolve().parents[1] / "schemas" / "generated" -# for file in os.listdir(generated_path): -# if file.endswith(".py") and file != "__init__.py": -# module_name = file[:-3] -# spec = importlib.util.spec_from_file_location(module_name, generated_path / file) -# module = importlib.util.module_from_spec(spec) -# spec.loader.exec_module(module) +from ca_biositing.datamodels.schemas.generated.census_survey import * +from ca_biositing.datamodels.schemas.generated.geography import * # --- Alembic Config object, provides access to alembic.ini values --- config = context.config diff --git a/alembic/versions/38398b232319_testing_linkml_created_python_object_.py b/alembic/versions/38398b232319_testing_linkml_created_python_object_.py deleted file mode 100644 index fd2da614..00000000 --- a/alembic/versions/38398b232319_testing_linkml_created_python_object_.py +++ /dev/null @@ -1,32 +0,0 @@ -"""testing linkml created python object creation - -Revision ID: 38398b232319 -Revises: 8de419051d03 -Create Date: 2025-10-30 16:23:52.506268 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '38398b232319' -down_revision: Union[str, Sequence[str], None] = '8de419051d03' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### diff --git a/alembic/versions/490235da5633_use_snake_case_table_names.py b/alembic/versions/490235da5633_use_snake_case_table_names.py deleted file mode 100644 index 0a51c6d2..00000000 --- a/alembic/versions/490235da5633_use_snake_case_table_names.py +++ /dev/null @@ -1,158 +0,0 @@ -"""use snake_case table names - -Revision ID: 490235da5633 -Revises: 99af25a3b574 -Create Date: 2025-10-30 16:42:11.402363 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '490235da5633' -down_revision: Union[str, Sequence[str], None] = '99af25a3b574' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - op.drop_table('USDARecord') - op.drop_table('SurveyRecord') - op.drop_table('CensusRecord') - op.drop_table('Geography') - op.create_table('geography', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('state_name', sa.Text(), nullable=True), - sa.Column('state_fips', sa.Text(), nullable=True), - sa.Column('county_name', sa.Text(), nullable=True), - sa.Column('county_fips', sa.Text(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('region_name', sa.Text(), nullable=True), - sa.Column('agg_level_desc', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_record', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('census_record', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('survey_record', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('period_desc', sa.Text(), nullable=True), - sa.Column('freq_desc', sa.Text(), nullable=True), - sa.Column('program_desc', sa.Text(), nullable=True), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - - -def downgrade() -> None: - """Downgrade schema.""" - op.drop_table('survey_record') - op.drop_table('census_record') - op.drop_table('usda_record') - op.drop_table('geography') - op.create_table('USDARecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('SurveyRecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('period_desc', sa.Text(), nullable=True), - sa.Column('freq_desc', sa.Text(), nullable=True), - sa.Column('program_desc', sa.Text(), nullable=True), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('CensusRecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('Geography', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('state_name', sa.Text(), nullable=True), - sa.Column('state_fips', sa.Text(), nullable=True), - sa.Column('county_name', sa.Text(), nullable=True), - sa.Column('county_fips', sa.Text(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('region_name', sa.Text(), nullable=True), - sa.Column('agg_level_desc', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) diff --git a/alembic/versions/523eedbcaf6e_initial_migration.py b/alembic/versions/523eedbcaf6e_initial_migration.py new file mode 100644 index 00000000..402bc49d --- /dev/null +++ b/alembic/versions/523eedbcaf6e_initial_migration.py @@ -0,0 +1,877 @@ +"""Initial migration + +Revision ID: 523eedbcaf6e +Revises: +Create Date: 2025-11-14 20:44:50.143083 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa +import sqlmodel + +# revision identifiers, used by Alembic. +revision: str = '523eedbcaf6e' +down_revision: Union[str, Sequence[str], None] = None +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('affiliations', + sa.Column('affiliation_id', sa.Integer(), nullable=False), + sa.Column('affiliation_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('affiliation_id'), + sa.UniqueConstraint('affiliation_name') + ) + op.create_table('ag_treatments', + sa.Column('ag_treatment_id', sa.Integer(), nullable=False), + sa.Column('ag_treatment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('ag_treatment_id') + ) + op.create_table('analysis_abbreviations', + sa.Column('analysis_abbreviations_id', sa.Integer(), nullable=False), + sa.Column('analysis_abbreviation', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_abbreviations_id'), + sa.UniqueConstraint('analysis_abbreviation') + ) + op.create_table('analysis_replicate_id', + sa.Column('analysis_replicate_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('analysis_types_id', sa.Integer(), nullable=True), + sa.Column('analysis_replicate_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_replicate_id') + ) + op.create_table('analysis_results', + sa.Column('result_id', sa.Integer(), nullable=False), + sa.Column('anlaysis_sample', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('analysis_timestamp', sa.DateTime(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('qc_result_id', sa.Integer(), nullable=True), + sa.Column('measurement_equipment_id', sa.Integer(), nullable=True), + sa.Column('raw_data_url_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('analysis_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('result_id') + ) + op.create_index('idx_analysis_results_parameter_id', 'analysis_results', ['parameter_id'], unique=False) + op.create_index('uq_analysis_results_experiment_parameter_replicate', 'analysis_results', ['experiment_id', 'parameter_id', 'replicate_no'], unique=True) + op.create_table('analysis_types', + sa.Column('analysis_type_id', sa.Integer(), nullable=False), + sa.Column('analysis_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_type_id'), + sa.UniqueConstraint('analysis_name') + ) + op.create_table('analyst_contact', + sa.Column('analyst_id', sa.Integer(), nullable=False), + sa.Column('analyst_first_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_last_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_email', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_affiliation', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('analyst_id') + ) + op.create_table('autoclave_profile', + sa.Column('autoclave_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('autoclave_id') + ) + op.create_table('biomass', + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('biomass_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('primary_product_id', sa.Integer(), nullable=True), + sa.Column('taxonomy_id', sa.Integer(), nullable=True), + sa.Column('biomass_type_id', sa.Integer(), nullable=True), + sa.Column('biomass_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('biomass_id') + ) + op.create_index(op.f('ix_biomass_biomass_name'), 'biomass', ['biomass_name'], unique=False) + op.create_index(op.f('ix_biomass_biomass_type_id'), 'biomass', ['biomass_type_id'], unique=False) + op.create_table('biomass_availability', + sa.Column('availability_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('primary_product_id', sa.Integer(), nullable=True), + sa.Column('from_month', sa.Numeric(), nullable=True), + sa.Column('to_month', sa.Numeric(), nullable=True), + sa.Column('kg_low', sa.Numeric(), nullable=True), + sa.Column('kg_avg', sa.Numeric(), nullable=True), + sa.Column('kg_high', sa.Numeric(), nullable=True), + sa.Column('bdt_low', sa.Numeric(), nullable=True), + sa.Column('bdt_avg', sa.Numeric(), nullable=True), + sa.Column('bdt_high', sa.Numeric(), nullable=True), + sa.Column('data_source', sa.Integer(), nullable=True), + sa.Column('availability_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('availability_id') + ) + op.create_index(op.f('ix_biomass_availability_biomass_id'), 'biomass_availability', ['biomass_id'], unique=False) + op.create_table('biomass_price', + sa.Column('price_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('price_per_kg_low', sa.Numeric(), nullable=True), + sa.Column('price_per_kg_avg', sa.Numeric(), nullable=True), + sa.Column('price_per_kg_high', sa.Numeric(), nullable=True), + sa.Column('price_data_sources', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('price_id') + ) + op.create_index(op.f('ix_biomass_price_biomass_id'), 'biomass_price', ['biomass_id'], unique=False) + op.create_table('biomass_quality', + sa.Column('quality_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('expected_quality', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('output_feedstocks', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('convertibility', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('disposal_challenges', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('existing_markets', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('substitute_materials', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('regulatory_issues', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('quality_data_sources', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('quality_id') + ) + op.create_index(op.f('ix_biomass_quality_biomass_id'), 'biomass_quality', ['biomass_id'], unique=False) + op.create_table('biomass_test', + sa.Column('biomass_test_id', sa.Integer(), nullable=False), + sa.Column('biomass_test_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('biomass_test_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('biomass_test_id') + ) + op.create_index(op.f('ix_biomass_test_biomass_test_name'), 'biomass_test', ['biomass_test_name'], unique=False) + op.create_table('biomass_type', + sa.Column('biomass_type_id', sa.Integer(), nullable=False), + sa.Column('biomass_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('biomass_type_id'), + sa.UniqueConstraint('biomass_type') + ) + op.create_table('buildings', + sa.Column('building_id', sa.Integer(), nullable=False), + sa.Column('building_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('affiliation_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('building_id'), + sa.UniqueConstraint('building_name') + ) + op.create_table('cities', + sa.Column('city_id', sa.Integer(), nullable=False), + sa.Column('city_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('city_id'), + sa.UniqueConstraint('city_name') + ) + op.create_table('collection_methods', + sa.Column('collection_method_id', sa.Integer(), nullable=False), + sa.Column('collection_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('collection_method_id'), + sa.UniqueConstraint('collection_method_name') + ) + op.create_table('collectors', + sa.Column('collector_id', sa.Integer(), nullable=False), + sa.Column('collector_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('collector_affiliation', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('collector_id'), + sa.UniqueConstraint('collector_name') + ) + op.create_table('compositional_analysis', + sa.Column('cmp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('calculated_parameter_id', sa.Integer(), nullable=True), + sa.Column('calculated_parameter_value', sa.Numeric(), nullable=True), + sa.Column('calculated_parameter_unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('cmp_id') + ) + op.create_table('counties', + sa.Column('county_id', sa.Integer(), nullable=False), + sa.Column('county_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('county_id'), + sa.UniqueConstraint('county_name') + ) + op.create_table('data_sources', + sa.Column('source_id', sa.Integer(), nullable=False), + sa.Column('source_name_id', sa.Integer(), nullable=True), + sa.Column('source_type_id', sa.Integer(), nullable=True), + sa.Column('data_resolution_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('url_id', sa.Integer(), nullable=True), + sa.Column('import_timestamp', sa.DateTime(), nullable=True), + sa.PrimaryKeyConstraint('source_id') + ) + op.create_index('idx_data_sources_source_name_id', 'data_sources', ['source_name_id'], unique=False) + op.create_table('doi', + sa.Column('doi_id', sa.Integer(), nullable=False), + sa.Column('doi', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('doi_id') + ) + op.create_table('equipment', + sa.Column('equipment_id', sa.Integer(), nullable=False), + sa.Column('equipment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('equipment_room_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('equipment_id'), + sa.UniqueConstraint('equipment_name') + ) + op.create_table('experiment_methods', + sa.Column('experiment_method_id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('experiment_method_id') + ) + op.create_index('idx_experiment_methods_experiment_id', 'experiment_methods', ['experiment_id'], unique=False) + op.create_index('idx_experiment_methods_method_id', 'experiment_methods', ['method_id'], unique=False) + op.create_table('experiments', + sa.Column('experiment_id', sa.Integer(), nullable=False), + sa.Column('exper_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('gsheet_exper_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('analysis_abbrev_id', sa.Integer(), nullable=True), + sa.Column('exper_start_date', sa.Date(), nullable=True), + sa.Column('exper_duration', sa.Numeric(), nullable=True), + sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('exper_location_id', sa.Integer(), nullable=True), + sa.Column('exper_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('experiment_id'), + sa.UniqueConstraint('exper_uuid'), + sa.UniqueConstraint('gsheet_exper_id') + ) + op.create_index('idx_experiments_analysis_type_id', 'experiments', ['analysis_type_id'], unique=False) + op.create_table('external_atip', + sa.Column('atip_ID', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('atip_ID') + ) + op.create_table('external_dairy_one', + sa.Column('dairy_one_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('samples_count', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('accumulated_years_from', sa.Date(), nullable=True), + sa.Column('accumulated_years_to', sa.Date(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('dairy_one_id') + ) + op.create_index('idx_external_dairy_one_biomass_id', 'external_dairy_one', ['biomass_id'], unique=False) + op.create_index('idx_external_dairy_one_parameter_id', 'external_dairy_one', ['parameter_id'], unique=False) + op.create_table('external_ebmud', + sa.Column('ebmud_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('ebmud_id') + ) + op.create_table('external_inl_biofeedstock_library', + sa.Column('bfl_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('state_id', sa.Integer(), nullable=True), + sa.Column('affiliations_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('accumulated_years_from', sa.Date(), nullable=True), + sa.Column('accumulated_years_to', sa.Date(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('bfl_id') + ) + op.create_index('idx_external_inl_biofeedstock_library_biomass_id', 'external_inl_biofeedstock_library', ['biomass_id'], unique=False) + op.create_table('external_land_id', + sa.Column('land_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('land_id') + ) + op.create_table('external_phyllis2', + sa.Column('phyllis_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('phyllis_id') + ) + op.create_index('idx_external_phyllis2_analysis_type_id', 'external_phyllis2', ['analysis_type_id'], unique=False) + op.create_index('idx_external_phyllis2_biomass_id', 'external_phyllis2', ['biomass_id'], unique=False) + op.create_table('external_usda', + sa.Column('usda_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('usda_id') + ) + op.create_table('fermentation_profile', + sa.Column('fp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('organism_id', sa.Integer(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('fp_id') + ) + op.create_table('field_samples', + sa.Column('sample_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('sample_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('source_codename_id', sa.Integer(), nullable=True), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('field_storage_id', sa.Integer(), nullable=True), + sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), + sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('collection_timestamp', sa.DateTime(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_date', sa.Date(), nullable=True), + sa.Column('amount_collected_kg', sa.Numeric(), nullable=True), + sa.Column('provider_id', sa.Integer(), nullable=True), + sa.Column('collector_id', sa.Integer(), nullable=True), + sa.Column('basic_sample_info_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.PrimaryKeyConstraint('sample_id') + ) + op.create_index(op.f('ix_field_samples_biomass_id'), 'field_samples', ['biomass_id'], unique=False) + op.create_index(op.f('ix_field_samples_source_codename_id'), 'field_samples', ['source_codename_id'], unique=False) + op.create_table('field_storage', + sa.Column('field_storage_id', sa.Integer(), nullable=False), + sa.Column('storage_method', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('field_storage_id'), + sa.UniqueConstraint('storage_method') + ) + op.create_table('fips', + sa.Column('fips_id', sa.Integer(), nullable=False), + sa.Column('fips_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('fips_id') + ) + op.create_table('gasification_profile', + sa.Column('gasification_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('gasification_id') + ) + op.create_table('geographic_locations', + sa.Column('location_id', sa.Integer(), nullable=False), + sa.Column('street_address_id', sa.Integer(), nullable=True), + sa.Column('city_id', sa.Integer(), nullable=True), + sa.Column('zip_id', sa.Integer(), nullable=True), + sa.Column('county_id', sa.Integer(), nullable=True), + sa.Column('state_id', sa.Integer(), nullable=True), + sa.Column('region_id', sa.Integer(), nullable=True), + sa.Column('fips_id', sa.Integer(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('location_resolution_id', sa.Integer(), nullable=True), + sa.Column('is_anonymous', sa.Boolean(), nullable=True), + sa.PrimaryKeyConstraint('location_id') + ) + op.create_table('harvest_methods', + sa.Column('harvest_method_id', sa.Integer(), nullable=False), + sa.Column('harvest_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('harvest_method_id'), + sa.UniqueConstraint('harvest_method_name') + ) + op.create_table('icp_analysis', + sa.Column('icp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('concentration_calculation_url_id', sa.Integer(), nullable=True), + sa.Column('result_wavelength', sa.Numeric(), nullable=True), + sa.Column('raw_url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('icp_id') + ) + op.create_table('import_log', + sa.Column('import_id', sa.Integer(), nullable=False), + sa.Column('import_timestamp', sa.DateTime(), nullable=True), + sa.Column('destination', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('source_file', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('records_imported', sa.Integer(), nullable=True), + sa.Column('import_status', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('error_log', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_user', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('import_id') + ) + op.create_table('location_resolutions', + sa.Column('location_resolution_id', sa.Integer(), nullable=False), + sa.Column('resolution_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('location_resolution_id'), + sa.UniqueConstraint('resolution_type') + ) + op.create_table('metadata', + sa.Column('metadata_id', sa.Integer(), nullable=False), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('ag_treatment_id', sa.Integer(), nullable=True), + sa.Column('last_application_date', sa.Date(), nullable=True), + sa.Column('treatment_amount_per_acre', sa.Numeric(), nullable=True), + sa.Column('soil_type', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('metadata_id') + ) + op.create_table('method_abbrevs', + sa.Column('method_abbrev_id', sa.Integer(), nullable=False), + sa.Column('method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_abbrev_id'), + sa.UniqueConstraint('method_abbrev') + ) + op.create_table('method_categories', + sa.Column('method_category_id', sa.Integer(), nullable=False), + sa.Column('method_category', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_category_id'), + sa.UniqueConstraint('method_category') + ) + op.create_table('method_equipment', + sa.Column('method_equipment_id', sa.Integer(), nullable=False), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('equipment_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('method_equipment_id') + ) + op.create_index('idx_method_equipment_equipment_id', 'method_equipment', ['equipment_id'], unique=False) + op.create_index('idx_method_equipment_method_id', 'method_equipment', ['method_id'], unique=False) + op.create_table('method_standards', + sa.Column('method_standard_id', sa.Integer(), nullable=False), + sa.Column('method_standard', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_standard_id'), + sa.UniqueConstraint('method_standard') + ) + op.create_table('methods', + sa.Column('method_id', sa.Integer(), nullable=False), + sa.Column('method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('method_category_id', sa.Integer(), nullable=True), + sa.Column('method_standard_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('detection_limits', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('procedure_reference_id', sa.Integer(), nullable=True), + sa.Column('method_url_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('method_id'), + sa.UniqueConstraint('method_name') + ) + op.create_index('idx_methods_method_name', 'methods', ['method_name'], unique=False) + op.create_table('organisms', + sa.Column('organism_id', sa.Integer(), nullable=False), + sa.Column('organism_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('organism_strain_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('organism_id') + ) + op.create_table('parameter_catagories', + sa.Column('parameter_catagory_id', sa.Integer(), nullable=False), + sa.Column('parameter_catagory', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('parameter_catagory_id') + ) + op.create_table('parameter_methods', + sa.Column('param_method_id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('param_method_id') + ) + op.create_table('parameter_units', + sa.Column('parameter_unit_id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('parameter_unit_id') + ) + op.create_index('idx_parameter_units_parameter_id', 'parameter_units', ['parameter_id'], unique=False) + op.create_index('idx_parameter_units_unit_id', 'parameter_units', ['unit_id'], unique=False) + op.create_table('parameters', + sa.Column('parameter_id', sa.Integer(), nullable=False), + sa.Column('parameter_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('parameter_category_id', sa.Integer(), nullable=True), + sa.Column('standard_unit_id', sa.Integer(), nullable=True), + sa.Column('calculated', sa.Boolean(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('typical_range_min', sa.Numeric(), nullable=True), + sa.Column('typical_range_max', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('parameter_id'), + sa.UniqueConstraint('parameter_name') + ) + op.create_table('particle_size', + sa.Column('particle_size_id', sa.Integer(), nullable=False), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('particle_length', sa.Integer(), nullable=True), + sa.Column('particle_width', sa.Integer(), nullable=True), + sa.Column('particle_height', sa.Integer(), nullable=True), + sa.Column('particle_units', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('particle_size_id') + ) + op.create_table('preprocessed_samples', + sa.Column('prepro_material_id', sa.Integer(), nullable=False), + sa.Column('prepro_material_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('biomass_sample_id', sa.Integer(), nullable=True), + sa.Column('prepro_method_id', sa.Integer(), nullable=True), + sa.Column('amount_before_drying_g', sa.Numeric(), nullable=True), + sa.Column('amount_after_drying', sa.Numeric(), nullable=True), + sa.Column('processing_date', sa.Date(), nullable=True), + sa.Column('storage_building', sa.Integer(), nullable=True), + sa.Column('amount_remaining_g', sa.Numeric(), nullable=True), + sa.Column('amount_as_of_date', sa.Date(), nullable=True), + sa.Column('prepro_analyst_id', sa.Integer(), nullable=True), + sa.Column('prepro_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prepro_material_id') + ) + op.create_index('idx_preprocessed_samples_biomass_sample_id', 'preprocessed_samples', ['biomass_sample_id'], unique=False) + op.create_index('idx_preprocessed_samples_prepro_method_id', 'preprocessed_samples', ['prepro_method_id'], unique=False) + op.create_table('preprocessing_methods', + sa.Column('prepro_method_id', sa.Integer(), nullable=False), + sa.Column('prepro_method', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('prepro_method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('prepro_temp_c', sa.Numeric(), nullable=True), + sa.Column('drying_step', sa.Boolean(), nullable=True), + sa.Column('method_ref_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('prepro_method_id') + ) + op.create_table('preprocessing_methods_abbreviations', + sa.Column('prepro_methods_abbrev_id', sa.Integer(), nullable=False), + sa.Column('prepro_method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prepro_methods_abbrev_id'), + sa.UniqueConstraint('prepro_method_abbrev') + ) + op.create_table('primary_product', + sa.Column('primary_product_id', sa.Integer(), nullable=False), + sa.Column('primary_product_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('primary_product_id'), + sa.UniqueConstraint('primary_product_name') + ) + op.create_table('product_type', + sa.Column('product_type_id', sa.Integer(), nullable=False), + sa.Column('product', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('product_type_id') + ) + op.create_table('provider_types', + sa.Column('provider_type_id', sa.Integer(), nullable=False), + sa.Column('provider_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('provider_type_id') + ) + op.create_table('providers', + sa.Column('provider_id', sa.Integer(), nullable=False), + sa.Column('provider_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('provider_affiliation', sa.Integer(), nullable=True), + sa.Column('provider_type_id', sa.Integer(), nullable=True), + sa.Column('anonymous', sa.Boolean(), nullable=True), + sa.PrimaryKeyConstraint('provider_id'), + sa.UniqueConstraint('provider_name') + ) + op.create_table('proximate_analysis', + sa.Column('prox_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prox_id') + ) + op.create_table('qc_results', + sa.Column('qc_result_id', sa.Integer(), nullable=False), + sa.Column('qc_result', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('qc_result_id'), + sa.UniqueConstraint('qc_result') + ) + op.create_table('raster_metadata', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('resolution', sa.Float(), nullable=True), + sa.Column('srid', sa.Integer(), nullable=True), + sa.Column('acquisition_date', sa.Date(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('references', + sa.Column('reference_id', sa.Integer(), nullable=False), + sa.Column('reference_title', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_author', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_publication', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_date', sa.Date(), nullable=True), + sa.Column('reference_doi_id', sa.Integer(), nullable=True), + sa.Column('url_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('reference_id') + ) + op.create_table('regions', + sa.Column('region_id', sa.Integer(), nullable=False), + sa.Column('region_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('region_id'), + sa.UniqueConstraint('region_name') + ) + op.create_table('rooms', + sa.Column('room_id', sa.Integer(), nullable=False), + sa.Column('room_number', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('building_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('room_id'), + sa.UniqueConstraint('room_number') + ) + op.create_table('soil_type', + sa.Column('soil_type_id', sa.Integer(), nullable=False), + sa.Column('soil_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('soil_location', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('soil_type_id'), + sa.UniqueConstraint('soil_type') + ) + op.create_table('source_names', + sa.Column('source_name_id', sa.Integer(), nullable=False), + sa.Column('source_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('source_name_id'), + sa.UniqueConstraint('source_name') + ) + op.create_table('source_types', + sa.Column('source_type_id', sa.Integer(), nullable=False), + sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('source_type_id'), + sa.UniqueConstraint('source_type') + ) + op.create_table('states', + sa.Column('state_id', sa.Integer(), nullable=False), + sa.Column('state_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('state_id'), + sa.UniqueConstraint('state_name') + ) + op.create_table('street_addresses', + sa.Column('street_address_id', sa.Integer(), nullable=False), + sa.Column('street_address', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('street_address_id') + ) + op.create_table('taxonomy', + sa.Column('taxonomy_id', sa.Integer(), nullable=False), + sa.Column('kingdom', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('phylum', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('order', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('family', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('genus', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('species', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('variety_subspecies_cultivar', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('taxonomy_id') + ) + op.create_table('testusers2', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('fullname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('nickname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('units', + sa.Column('unit_id', sa.Integer(), nullable=False), + sa.Column('unit', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('unit_id'), + sa.UniqueConstraint('unit') + ) + op.create_table('url', + sa.Column('url_id', sa.Integer(), nullable=False), + sa.Column('url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('url_id'), + sa.UniqueConstraint('url') + ) + op.create_table('vectorized_raster_polygons', + sa.Column('vectorized_ID', sa.Integer(), nullable=False), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('raster_id', sa.Integer(), nullable=True), + sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('mean_value', sa.Float(), nullable=True), + sa.Column('std_dev', sa.Float(), nullable=True), + sa.Column('area_m2', sa.Float(), nullable=True), + sa.Column('date_acquired', sa.Date(), nullable=True), + sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('vectorized_ID') + ) + op.create_table('xrf_analysis', + sa.Column('xrf_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('xrf_id') + ) + op.create_table('zips', + sa.Column('zip_id', sa.Integer(), nullable=False), + sa.Column('zip_code', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('zip_id'), + sa.UniqueConstraint('zip_code') + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('zips') + op.drop_table('xrf_analysis') + op.drop_table('vectorized_raster_polygons') + op.drop_table('url') + op.drop_table('units') + op.drop_table('testusers2') + op.drop_table('taxonomy') + op.drop_table('street_addresses') + op.drop_table('states') + op.drop_table('source_types') + op.drop_table('source_names') + op.drop_table('soil_type') + op.drop_table('rooms') + op.drop_table('regions') + op.drop_table('references') + op.drop_table('raster_metadata') + op.drop_table('qc_results') + op.drop_table('proximate_analysis') + op.drop_table('providers') + op.drop_table('provider_types') + op.drop_table('product_type') + op.drop_table('primary_product') + op.drop_table('preprocessing_methods_abbreviations') + op.drop_table('preprocessing_methods') + op.drop_index('idx_preprocessed_samples_prepro_method_id', table_name='preprocessed_samples') + op.drop_index('idx_preprocessed_samples_biomass_sample_id', table_name='preprocessed_samples') + op.drop_table('preprocessed_samples') + op.drop_table('particle_size') + op.drop_table('parameters') + op.drop_index('idx_parameter_units_unit_id', table_name='parameter_units') + op.drop_index('idx_parameter_units_parameter_id', table_name='parameter_units') + op.drop_table('parameter_units') + op.drop_table('parameter_methods') + op.drop_table('parameter_catagories') + op.drop_table('organisms') + op.drop_index('idx_methods_method_name', table_name='methods') + op.drop_table('methods') + op.drop_table('method_standards') + op.drop_index('idx_method_equipment_method_id', table_name='method_equipment') + op.drop_index('idx_method_equipment_equipment_id', table_name='method_equipment') + op.drop_table('method_equipment') + op.drop_table('method_categories') + op.drop_table('method_abbrevs') + op.drop_table('metadata') + op.drop_table('location_resolutions') + op.drop_table('import_log') + op.drop_table('icp_analysis') + op.drop_table('harvest_methods') + op.drop_table('geographic_locations') + op.drop_table('gasification_profile') + op.drop_table('fips') + op.drop_table('field_storage') + op.drop_index(op.f('ix_field_samples_source_codename_id'), table_name='field_samples') + op.drop_index(op.f('ix_field_samples_biomass_id'), table_name='field_samples') + op.drop_table('field_samples') + op.drop_table('fermentation_profile') + op.drop_table('external_usda') + op.drop_index('idx_external_phyllis2_biomass_id', table_name='external_phyllis2') + op.drop_index('idx_external_phyllis2_analysis_type_id', table_name='external_phyllis2') + op.drop_table('external_phyllis2') + op.drop_table('external_land_id') + op.drop_index('idx_external_inl_biofeedstock_library_biomass_id', table_name='external_inl_biofeedstock_library') + op.drop_table('external_inl_biofeedstock_library') + op.drop_table('external_ebmud') + op.drop_index('idx_external_dairy_one_parameter_id', table_name='external_dairy_one') + op.drop_index('idx_external_dairy_one_biomass_id', table_name='external_dairy_one') + op.drop_table('external_dairy_one') + op.drop_table('external_atip') + op.drop_index('idx_experiments_analysis_type_id', table_name='experiments') + op.drop_table('experiments') + op.drop_index('idx_experiment_methods_method_id', table_name='experiment_methods') + op.drop_index('idx_experiment_methods_experiment_id', table_name='experiment_methods') + op.drop_table('experiment_methods') + op.drop_table('equipment') + op.drop_table('doi') + op.drop_index('idx_data_sources_source_name_id', table_name='data_sources') + op.drop_table('data_sources') + op.drop_table('counties') + op.drop_table('compositional_analysis') + op.drop_table('collectors') + op.drop_table('collection_methods') + op.drop_table('cities') + op.drop_table('buildings') + op.drop_table('biomass_type') + op.drop_index(op.f('ix_biomass_test_biomass_test_name'), table_name='biomass_test') + op.drop_table('biomass_test') + op.drop_index(op.f('ix_biomass_quality_biomass_id'), table_name='biomass_quality') + op.drop_table('biomass_quality') + op.drop_index(op.f('ix_biomass_price_biomass_id'), table_name='biomass_price') + op.drop_table('biomass_price') + op.drop_index(op.f('ix_biomass_availability_biomass_id'), table_name='biomass_availability') + op.drop_table('biomass_availability') + op.drop_index(op.f('ix_biomass_biomass_type_id'), table_name='biomass') + op.drop_index(op.f('ix_biomass_biomass_name'), table_name='biomass') + op.drop_table('biomass') + op.drop_table('autoclave_profile') + op.drop_table('analyst_contact') + op.drop_table('analysis_types') + op.drop_index('uq_analysis_results_experiment_parameter_replicate', table_name='analysis_results') + op.drop_index('idx_analysis_results_parameter_id', table_name='analysis_results') + op.drop_table('analysis_results') + op.drop_table('analysis_replicate_id') + op.drop_table('analysis_abbreviations') + op.drop_table('ag_treatments') + op.drop_table('affiliations') + # ### end Alembic commands ### diff --git a/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py b/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py deleted file mode 100644 index 0d1fba2e..00000000 --- a/alembic/versions/99af25a3b574_testing_linkml_created_python_object_.py +++ /dev/null @@ -1,96 +0,0 @@ -"""testing linkml created python object creation - -Revision ID: 99af25a3b574 -Revises: 38398b232319 -Create Date: 2025-10-30 16:38:00.752859 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '99af25a3b574' -down_revision: Union[str, Sequence[str], None] = '38398b232319' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.create_table('Geography', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('state_name', sa.Text(), nullable=True), - sa.Column('state_fips', sa.Text(), nullable=True), - sa.Column('county_name', sa.Text(), nullable=True), - sa.Column('county_fips', sa.Text(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('region_name', sa.Text(), nullable=True), - sa.Column('agg_level_desc', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('CensusRecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('SurveyRecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('period_desc', sa.Text(), nullable=True), - sa.Column('freq_desc', sa.Text(), nullable=True), - sa.Column('program_desc', sa.Text(), nullable=True), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('USDARecord', - sa.Column('id', sa.Integer(), autoincrement=True, nullable=False), - sa.Column('year', sa.Integer(), nullable=False), - sa.Column('crop', sa.Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum'), nullable=True), - sa.Column('variable', sa.Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum'), nullable=True), - sa.Column('unit', sa.Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum'), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('bearing_status', sa.Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum'), nullable=True), - sa.Column('class_desc', sa.Text(), nullable=True), - sa.Column('domain_desc', sa.Text(), nullable=True), - sa.Column('source', sa.Text(), nullable=True), - sa.Column('notes', sa.Text(), nullable=True), - sa.Column('geography_id', sa.Integer(), nullable=True), - sa.ForeignKeyConstraint(['geography_id'], ['Geography.id'], ), - sa.PrimaryKeyConstraint('id') - ) - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.drop_table('USDARecord') - op.drop_table('SurveyRecord') - op.drop_table('CensusRecord') - op.drop_table('Geography') - # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py new file mode 100644 index 00000000..dbb70e85 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py @@ -0,0 +1 @@ +# This file makes this a Python package. diff --git a/schemas/common/geography.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/common/geography.yaml similarity index 100% rename from schemas/common/geography.yaml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/common/geography.yaml diff --git a/schemas/common/locations_address.yml b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/common/locations_address.yml similarity index 100% rename from schemas/common/locations_address.yml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/common/locations_address.yml diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py new file mode 100644 index 00000000..dbb70e85 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py @@ -0,0 +1 @@ +# This file makes this a Python package. diff --git a/schemas/generated/census_survey.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py similarity index 100% rename from schemas/generated/census_survey.py rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py diff --git a/schemas/generated/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py similarity index 100% rename from schemas/generated/geography.py rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py diff --git a/schemas/linkml_sqla_generation.md b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/linkml_sqla_generation.md similarity index 100% rename from schemas/linkml_sqla_generation.md rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/linkml_sqla_generation.md diff --git a/schemas/pydantic/census_survey.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/pydantic/census_survey.py similarity index 100% rename from schemas/pydantic/census_survey.py rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/pydantic/census_survey.py diff --git a/schemas/pydantic/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/pydantic/geography.py similarity index 100% rename from schemas/pydantic/geography.py rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/pydantic/geography.py diff --git a/schemas/template.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/template.yaml similarity index 100% rename from schemas/template.yaml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/template.yaml diff --git a/schemas/usda/census_survey.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/usda/census_survey.yaml similarity index 100% rename from schemas/usda/census_survey.yaml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/usda/census_survey.yaml From d53f226ab73a7479b48cebf601af56ada7912be1 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Fri, 14 Nov 2025 11:54:16 -0700 Subject: [PATCH 44/81] added a jupyter notebook for playing around with connecting to db --- ERD_VIEW.md | 61 ++ .../301006b4795f_initial_migration.py | 32 + .../e15bda744fef_initial_migration.py | 877 ++++++++++++++++++ census.survey.mmd | 53 ++ review_summary.txt | 76 ++ 5 files changed, 1099 insertions(+) create mode 100644 ERD_VIEW.md create mode 100644 alembic/versions/301006b4795f_initial_migration.py create mode 100644 alembic/versions/e15bda744fef_initial_migration.py create mode 100644 census.survey.mmd create mode 100644 review_summary.txt diff --git a/ERD_VIEW.md b/ERD_VIEW.md new file mode 100644 index 00000000..05b1930f --- /dev/null +++ b/ERD_VIEW.md @@ -0,0 +1,61 @@ +# ERD for USDA Census and Survey Data + +To view this diagram, open the Command Palette (`Cmd+Shift+P` on Mac or +`Ctrl+Shift+P` on Windows/Linux) and run **"Markdown: Open Preview to the +Side"**. + +```mermaid +erDiagram +CensusRecord { + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} +Geography { + string state_name + string state_fips + string county_name + string county_fips + string geoid + string region_name + string agg_level_desc +} +SurveyRecord { + string period_desc + string freq_desc + string program_desc + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} +UsdaRecord { + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} + +CensusRecord ||--|o Geography : "geography" +SurveyRecord ||--|o Geography : "geography" +UsdaRecord ||--|o Geography : "geography" +``` diff --git a/alembic/versions/301006b4795f_initial_migration.py b/alembic/versions/301006b4795f_initial_migration.py new file mode 100644 index 00000000..8e4f7afd --- /dev/null +++ b/alembic/versions/301006b4795f_initial_migration.py @@ -0,0 +1,32 @@ +"""Initial migration + +Revision ID: 301006b4795f +Revises: e15bda744fef +Create Date: 2025-11-12 20:54:01.573577 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '301006b4795f' +down_revision: Union[str, Sequence[str], None] = 'e15bda744fef' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/alembic/versions/e15bda744fef_initial_migration.py b/alembic/versions/e15bda744fef_initial_migration.py new file mode 100644 index 00000000..18517bc2 --- /dev/null +++ b/alembic/versions/e15bda744fef_initial_migration.py @@ -0,0 +1,877 @@ +"""Initial migration + +Revision ID: e15bda744fef +Revises: +Create Date: 2025-11-04 20:03:41.870493 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa +import sqlmodel + +# revision identifiers, used by Alembic. +revision: str = 'e15bda744fef' +down_revision: Union[str, Sequence[str], None] = None +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('affiliations', + sa.Column('affiliation_id', sa.Integer(), nullable=False), + sa.Column('affiliation_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('affiliation_id'), + sa.UniqueConstraint('affiliation_name') + ) + op.create_table('ag_treatments', + sa.Column('ag_treatment_id', sa.Integer(), nullable=False), + sa.Column('ag_treatment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('ag_treatment_id') + ) + op.create_table('analysis_abbreviations', + sa.Column('analysis_abbreviations_id', sa.Integer(), nullable=False), + sa.Column('analysis_abbreviation', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_abbreviations_id'), + sa.UniqueConstraint('analysis_abbreviation') + ) + op.create_table('analysis_replicate_id', + sa.Column('analysis_replicate_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('analysis_types_id', sa.Integer(), nullable=True), + sa.Column('analysis_replicate_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_replicate_id') + ) + op.create_table('analysis_results', + sa.Column('result_id', sa.Integer(), nullable=False), + sa.Column('anlaysis_sample', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('analysis_timestamp', sa.DateTime(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('qc_result_id', sa.Integer(), nullable=True), + sa.Column('measurement_equipment_id', sa.Integer(), nullable=True), + sa.Column('raw_data_url_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('analysis_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('result_id') + ) + op.create_index('idx_analysis_results_parameter_id', 'analysis_results', ['parameter_id'], unique=False) + op.create_index('uq_analysis_results_experiment_parameter_replicate', 'analysis_results', ['experiment_id', 'parameter_id', 'replicate_no'], unique=True) + op.create_table('analysis_types', + sa.Column('analysis_type_id', sa.Integer(), nullable=False), + sa.Column('analysis_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('analysis_type_id'), + sa.UniqueConstraint('analysis_name') + ) + op.create_table('analyst_contact', + sa.Column('analyst_id', sa.Integer(), nullable=False), + sa.Column('analyst_first_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_last_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_email', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('analyst_affiliation', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('analyst_id') + ) + op.create_table('autoclave_profile', + sa.Column('autoclave_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('autoclave_id') + ) + op.create_table('biomass', + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('biomass_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('primary_product_id', sa.Integer(), nullable=True), + sa.Column('taxonomy_id', sa.Integer(), nullable=True), + sa.Column('biomass_type_id', sa.Integer(), nullable=True), + sa.Column('biomass_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('biomass_id') + ) + op.create_index(op.f('ix_biomass_biomass_name'), 'biomass', ['biomass_name'], unique=False) + op.create_index(op.f('ix_biomass_biomass_type_id'), 'biomass', ['biomass_type_id'], unique=False) + op.create_table('biomass_availability', + sa.Column('availability_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('primary_product_id', sa.Integer(), nullable=True), + sa.Column('from_month', sa.Numeric(), nullable=True), + sa.Column('to_month', sa.Numeric(), nullable=True), + sa.Column('kg_low', sa.Numeric(), nullable=True), + sa.Column('kg_avg', sa.Numeric(), nullable=True), + sa.Column('kg_high', sa.Numeric(), nullable=True), + sa.Column('bdt_low', sa.Numeric(), nullable=True), + sa.Column('bdt_avg', sa.Numeric(), nullable=True), + sa.Column('bdt_high', sa.Numeric(), nullable=True), + sa.Column('data_source', sa.Integer(), nullable=True), + sa.Column('availability_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('availability_id') + ) + op.create_index(op.f('ix_biomass_availability_biomass_id'), 'biomass_availability', ['biomass_id'], unique=False) + op.create_table('biomass_price', + sa.Column('price_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('price_per_kg_low', sa.Numeric(), nullable=True), + sa.Column('price_per_kg_avg', sa.Numeric(), nullable=True), + sa.Column('price_per_kg_high', sa.Numeric(), nullable=True), + sa.Column('price_data_sources', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('price_id') + ) + op.create_index(op.f('ix_biomass_price_biomass_id'), 'biomass_price', ['biomass_id'], unique=False) + op.create_table('biomass_quality', + sa.Column('quality_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('expected_quality', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('output_feedstocks', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('convertibility', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('disposal_challenges', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('existing_markets', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('substitute_materials', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('regulatory_issues', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('quality_data_sources', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('quality_id') + ) + op.create_index(op.f('ix_biomass_quality_biomass_id'), 'biomass_quality', ['biomass_id'], unique=False) + op.create_table('biomass_test', + sa.Column('biomass_test_id', sa.Integer(), nullable=False), + sa.Column('biomass_test_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('biomass_test_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('biomass_test_id') + ) + op.create_index(op.f('ix_biomass_test_biomass_test_name'), 'biomass_test', ['biomass_test_name'], unique=False) + op.create_table('biomass_type', + sa.Column('biomass_type_id', sa.Integer(), nullable=False), + sa.Column('biomass_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('biomass_type_id'), + sa.UniqueConstraint('biomass_type') + ) + op.create_table('buildings', + sa.Column('building_id', sa.Integer(), nullable=False), + sa.Column('building_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('affiliation_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('building_id'), + sa.UniqueConstraint('building_name') + ) + op.create_table('cities', + sa.Column('city_id', sa.Integer(), nullable=False), + sa.Column('city_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('city_id'), + sa.UniqueConstraint('city_name') + ) + op.create_table('collection_methods', + sa.Column('collection_method_id', sa.Integer(), nullable=False), + sa.Column('collection_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('collection_method_id'), + sa.UniqueConstraint('collection_method_name') + ) + op.create_table('collectors', + sa.Column('collector_id', sa.Integer(), nullable=False), + sa.Column('collector_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('collector_affiliation', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('collector_id'), + sa.UniqueConstraint('collector_name') + ) + op.create_table('compositional_analysis', + sa.Column('cmp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('calculated_parameter_id', sa.Integer(), nullable=True), + sa.Column('calculated_parameter_value', sa.Numeric(), nullable=True), + sa.Column('calculated_parameter_unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('cmp_id') + ) + op.create_table('counties', + sa.Column('county_id', sa.Integer(), nullable=False), + sa.Column('county_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('county_id'), + sa.UniqueConstraint('county_name') + ) + op.create_table('data_sources', + sa.Column('source_id', sa.Integer(), nullable=False), + sa.Column('source_name_id', sa.Integer(), nullable=True), + sa.Column('source_type_id', sa.Integer(), nullable=True), + sa.Column('data_resolution_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('url_id', sa.Integer(), nullable=True), + sa.Column('import_timestamp', sa.DateTime(), nullable=True), + sa.PrimaryKeyConstraint('source_id') + ) + op.create_index('idx_data_sources_source_name_id', 'data_sources', ['source_name_id'], unique=False) + op.create_table('doi', + sa.Column('doi_id', sa.Integer(), nullable=False), + sa.Column('doi', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('doi_id') + ) + op.create_table('equipment', + sa.Column('equipment_id', sa.Integer(), nullable=False), + sa.Column('equipment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('equipment_room_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('equipment_id'), + sa.UniqueConstraint('equipment_name') + ) + op.create_table('experiment_methods', + sa.Column('experiment_method_id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('experiment_method_id') + ) + op.create_index('idx_experiment_methods_experiment_id', 'experiment_methods', ['experiment_id'], unique=False) + op.create_index('idx_experiment_methods_method_id', 'experiment_methods', ['method_id'], unique=False) + op.create_table('experiments', + sa.Column('experiment_id', sa.Integer(), nullable=False), + sa.Column('exper_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('gsheet_exper_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('analysis_abbrev_id', sa.Integer(), nullable=True), + sa.Column('exper_start_date', sa.Date(), nullable=True), + sa.Column('exper_duration', sa.Numeric(), nullable=True), + sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('exper_location_id', sa.Integer(), nullable=True), + sa.Column('exper_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('experiment_id'), + sa.UniqueConstraint('exper_uuid'), + sa.UniqueConstraint('gsheet_exper_id') + ) + op.create_index('idx_experiments_analysis_type_id', 'experiments', ['analysis_type_id'], unique=False) + op.create_table('external_atip', + sa.Column('atip_ID', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('atip_ID') + ) + op.create_table('external_dairy_one', + sa.Column('dairy_one_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('samples_count', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('accumulated_years_from', sa.Date(), nullable=True), + sa.Column('accumulated_years_to', sa.Date(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('dairy_one_id') + ) + op.create_index('idx_external_dairy_one_biomass_id', 'external_dairy_one', ['biomass_id'], unique=False) + op.create_index('idx_external_dairy_one_parameter_id', 'external_dairy_one', ['parameter_id'], unique=False) + op.create_table('external_ebmud', + sa.Column('ebmud_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('ebmud_id') + ) + op.create_table('external_inl_biofeedstock_library', + sa.Column('bfl_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('state_id', sa.Integer(), nullable=True), + sa.Column('affiliations_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('min_value', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('accumulated_years_from', sa.Date(), nullable=True), + sa.Column('accumulated_years_to', sa.Date(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('bfl_id') + ) + op.create_index('idx_external_inl_biofeedstock_library_biomass_id', 'external_inl_biofeedstock_library', ['biomass_id'], unique=False) + op.create_table('external_land_id', + sa.Column('land_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('land_id') + ) + op.create_table('external_phyllis2', + sa.Column('phyllis_id', sa.Integer(), nullable=False), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_method_id', sa.Integer(), nullable=True), + sa.Column('mean_value', sa.Numeric(), nullable=True), + sa.Column('std_dev', sa.Numeric(), nullable=True), + sa.Column('max_value', sa.Numeric(), nullable=True), + sa.Column('sample_count', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('methodology_reference_id', sa.Integer(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('phyllis_id') + ) + op.create_index('idx_external_phyllis2_analysis_type_id', 'external_phyllis2', ['analysis_type_id'], unique=False) + op.create_index('idx_external_phyllis2_biomass_id', 'external_phyllis2', ['biomass_id'], unique=False) + op.create_table('external_usda', + sa.Column('usda_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('geometry_id', sa.Integer(), nullable=True), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_date', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('usda_id') + ) + op.create_table('fermentation_profile', + sa.Column('fp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('organism_id', sa.Integer(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('fp_id') + ) + op.create_table('field_samples', + sa.Column('sample_id', sa.Integer(), nullable=False), + sa.Column('biomass_id', sa.Integer(), nullable=False), + sa.Column('sample_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('source_codename_id', sa.Integer(), nullable=True), + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('field_storage_id', sa.Integer(), nullable=True), + sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), + sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('collection_timestamp', sa.DateTime(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_date', sa.Date(), nullable=True), + sa.Column('amount_collected_kg', sa.Numeric(), nullable=True), + sa.Column('provider_id', sa.Integer(), nullable=True), + sa.Column('collector_id', sa.Integer(), nullable=True), + sa.Column('basic_sample_info_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('created_at', sa.DateTime(), nullable=False), + sa.PrimaryKeyConstraint('sample_id') + ) + op.create_index(op.f('ix_field_samples_biomass_id'), 'field_samples', ['biomass_id'], unique=False) + op.create_index(op.f('ix_field_samples_source_codename_id'), 'field_samples', ['source_codename_id'], unique=False) + op.create_table('field_storage', + sa.Column('field_storage_id', sa.Integer(), nullable=False), + sa.Column('storage_method', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('field_storage_id'), + sa.UniqueConstraint('storage_method') + ) + op.create_table('fips', + sa.Column('fips_id', sa.Integer(), nullable=False), + sa.Column('fips_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('fips_id') + ) + op.create_table('gasification_profile', + sa.Column('gasification_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('product_type_id', sa.Integer(), nullable=True), + sa.Column('product_value', sa.Numeric(), nullable=True), + sa.Column('product_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('gasification_id') + ) + op.create_table('geographic_locations', + sa.Column('location_id', sa.Integer(), nullable=False), + sa.Column('street_address_id', sa.Integer(), nullable=True), + sa.Column('city_id', sa.Integer(), nullable=True), + sa.Column('zip_id', sa.Integer(), nullable=True), + sa.Column('county_id', sa.Integer(), nullable=True), + sa.Column('state_id', sa.Integer(), nullable=True), + sa.Column('region_id', sa.Integer(), nullable=True), + sa.Column('fips_id', sa.Integer(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('location_resolution_id', sa.Integer(), nullable=True), + sa.Column('is_anonymous', sa.Boolean(), nullable=True), + sa.PrimaryKeyConstraint('location_id') + ) + op.create_table('harvest_methods', + sa.Column('harvest_method_id', sa.Integer(), nullable=False), + sa.Column('harvest_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('harvest_method_id'), + sa.UniqueConstraint('harvest_method_name') + ) + op.create_table('icp_analysis', + sa.Column('icp_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('concentration_calculation_url_id', sa.Integer(), nullable=True), + sa.Column('result_wavelength', sa.Numeric(), nullable=True), + sa.Column('raw_url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('icp_id') + ) + op.create_table('import_log', + sa.Column('import_id', sa.Integer(), nullable=False), + sa.Column('import_timestamp', sa.DateTime(), nullable=True), + sa.Column('destination', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('source_file', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('records_imported', sa.Integer(), nullable=True), + sa.Column('import_status', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('error_log', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('import_user', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('import_id') + ) + op.create_table('location_resolutions', + sa.Column('location_resolution_id', sa.Integer(), nullable=False), + sa.Column('resolution_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('location_resolution_id'), + sa.UniqueConstraint('resolution_type') + ) + op.create_table('metadata', + sa.Column('metadata_id', sa.Integer(), nullable=False), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('ag_treatment_id', sa.Integer(), nullable=True), + sa.Column('last_application_date', sa.Date(), nullable=True), + sa.Column('treatment_amount_per_acre', sa.Numeric(), nullable=True), + sa.Column('soil_type', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('metadata_id') + ) + op.create_table('method_abbrevs', + sa.Column('method_abbrev_id', sa.Integer(), nullable=False), + sa.Column('method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_abbrev_id'), + sa.UniqueConstraint('method_abbrev') + ) + op.create_table('method_categories', + sa.Column('method_category_id', sa.Integer(), nullable=False), + sa.Column('method_category', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_category_id'), + sa.UniqueConstraint('method_category') + ) + op.create_table('method_equipment', + sa.Column('method_equipment_id', sa.Integer(), nullable=False), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('equipment_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('method_equipment_id') + ) + op.create_index('idx_method_equipment_equipment_id', 'method_equipment', ['equipment_id'], unique=False) + op.create_index('idx_method_equipment_method_id', 'method_equipment', ['method_id'], unique=False) + op.create_table('method_standards', + sa.Column('method_standard_id', sa.Integer(), nullable=False), + sa.Column('method_standard', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('method_standard_id'), + sa.UniqueConstraint('method_standard') + ) + op.create_table('methods', + sa.Column('method_id', sa.Integer(), nullable=False), + sa.Column('method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('method_category_id', sa.Integer(), nullable=True), + sa.Column('method_standard_id', sa.Integer(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('detection_limits', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('procedure_reference_id', sa.Integer(), nullable=True), + sa.Column('method_url_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('method_id'), + sa.UniqueConstraint('method_name') + ) + op.create_index('idx_methods_method_name', 'methods', ['method_name'], unique=False) + op.create_table('organisms', + sa.Column('organism_id', sa.Integer(), nullable=False), + sa.Column('organism_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('organism_strain_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('organism_id') + ) + op.create_table('parameter_catagories', + sa.Column('parameter_catagory_id', sa.Integer(), nullable=False), + sa.Column('parameter_catagory', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('parameter_catagory_id') + ) + op.create_table('parameter_methods', + sa.Column('param_method_id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('param_method_id') + ) + op.create_table('parameter_units', + sa.Column('parameter_unit_id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('parameter_unit_id') + ) + op.create_index('idx_parameter_units_parameter_id', 'parameter_units', ['parameter_id'], unique=False) + op.create_index('idx_parameter_units_unit_id', 'parameter_units', ['unit_id'], unique=False) + op.create_table('parameters', + sa.Column('parameter_id', sa.Integer(), nullable=False), + sa.Column('parameter_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('parameter_category_id', sa.Integer(), nullable=True), + sa.Column('standard_unit_id', sa.Integer(), nullable=True), + sa.Column('calculated', sa.Boolean(), nullable=True), + sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('typical_range_min', sa.Numeric(), nullable=True), + sa.Column('typical_range_max', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('parameter_id'), + sa.UniqueConstraint('parameter_name') + ) + op.create_table('particle_size', + sa.Column('particle_size_id', sa.Integer(), nullable=False), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('particle_length', sa.Integer(), nullable=True), + sa.Column('particle_width', sa.Integer(), nullable=True), + sa.Column('particle_height', sa.Integer(), nullable=True), + sa.Column('particle_units', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('particle_size_id') + ) + op.create_table('preprocessed_samples', + sa.Column('prepro_material_id', sa.Integer(), nullable=False), + sa.Column('prepro_material_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('biomass_sample_id', sa.Integer(), nullable=True), + sa.Column('prepro_method_id', sa.Integer(), nullable=True), + sa.Column('amount_before_drying_g', sa.Numeric(), nullable=True), + sa.Column('amount_after_drying', sa.Numeric(), nullable=True), + sa.Column('processing_date', sa.Date(), nullable=True), + sa.Column('storage_building', sa.Integer(), nullable=True), + sa.Column('amount_remaining_g', sa.Numeric(), nullable=True), + sa.Column('amount_as_of_date', sa.Date(), nullable=True), + sa.Column('prepro_analyst_id', sa.Integer(), nullable=True), + sa.Column('prepro_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prepro_material_id') + ) + op.create_index('idx_preprocessed_samples_biomass_sample_id', 'preprocessed_samples', ['biomass_sample_id'], unique=False) + op.create_index('idx_preprocessed_samples_prepro_method_id', 'preprocessed_samples', ['prepro_method_id'], unique=False) + op.create_table('preprocessing_methods', + sa.Column('prepro_method_id', sa.Integer(), nullable=False), + sa.Column('prepro_method', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('prepro_method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('prepro_temp_c', sa.Numeric(), nullable=True), + sa.Column('drying_step', sa.Boolean(), nullable=True), + sa.Column('method_ref_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('prepro_method_id') + ) + op.create_table('preprocessing_methods_abbreviations', + sa.Column('prepro_methods_abbrev_id', sa.Integer(), nullable=False), + sa.Column('prepro_method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prepro_methods_abbrev_id'), + sa.UniqueConstraint('prepro_method_abbrev') + ) + op.create_table('primary_product', + sa.Column('primary_product_id', sa.Integer(), nullable=False), + sa.Column('primary_product_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('primary_product_id'), + sa.UniqueConstraint('primary_product_name') + ) + op.create_table('product_type', + sa.Column('product_type_id', sa.Integer(), nullable=False), + sa.Column('product', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('product_type_id') + ) + op.create_table('provider_types', + sa.Column('provider_type_id', sa.Integer(), nullable=False), + sa.Column('provider_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('provider_type_id') + ) + op.create_table('providers', + sa.Column('provider_id', sa.Integer(), nullable=False), + sa.Column('provider_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.Column('provider_affiliation', sa.Integer(), nullable=True), + sa.Column('provider_type_id', sa.Integer(), nullable=True), + sa.Column('anonymous', sa.Boolean(), nullable=True), + sa.PrimaryKeyConstraint('provider_id'), + sa.UniqueConstraint('provider_name') + ) + op.create_table('proximate_analysis', + sa.Column('prox_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('prox_id') + ) + op.create_table('qc_results', + sa.Column('qc_result_id', sa.Integer(), nullable=False), + sa.Column('qc_result', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('qc_result_id'), + sa.UniqueConstraint('qc_result') + ) + op.create_table('raster_metadata', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('resolution', sa.Float(), nullable=True), + sa.Column('srid', sa.Integer(), nullable=True), + sa.Column('acquisition_date', sa.Date(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('references', + sa.Column('reference_id', sa.Integer(), nullable=False), + sa.Column('reference_title', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_author', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_publication', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('reference_date', sa.Date(), nullable=True), + sa.Column('reference_doi_id', sa.Integer(), nullable=True), + sa.Column('url_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('reference_id') + ) + op.create_table('regions', + sa.Column('region_id', sa.Integer(), nullable=False), + sa.Column('region_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('region_id'), + sa.UniqueConstraint('region_name') + ) + op.create_table('rooms', + sa.Column('room_id', sa.Integer(), nullable=False), + sa.Column('room_number', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('building_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('room_id'), + sa.UniqueConstraint('room_number') + ) + op.create_table('soil_type', + sa.Column('soil_type_id', sa.Integer(), nullable=False), + sa.Column('soil_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('soil_location', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('soil_type_id'), + sa.UniqueConstraint('soil_type') + ) + op.create_table('source_names', + sa.Column('source_name_id', sa.Integer(), nullable=False), + sa.Column('source_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('source_name_id'), + sa.UniqueConstraint('source_name') + ) + op.create_table('source_types', + sa.Column('source_type_id', sa.Integer(), nullable=False), + sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('source_type_id'), + sa.UniqueConstraint('source_type') + ) + op.create_table('states', + sa.Column('state_id', sa.Integer(), nullable=False), + sa.Column('state_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('state_id'), + sa.UniqueConstraint('state_name') + ) + op.create_table('street_addresses', + sa.Column('street_address_id', sa.Integer(), nullable=False), + sa.Column('street_address', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('street_address_id') + ) + op.create_table('taxonomy', + sa.Column('taxonomy_id', sa.Integer(), nullable=False), + sa.Column('kingdom', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('phylum', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('order', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('family', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('genus', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('species', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('variety_subspecies_cultivar', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('taxonomy_id') + ) + op.create_table('testusers2', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('fullname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('nickname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('units', + sa.Column('unit_id', sa.Integer(), nullable=False), + sa.Column('unit', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('unit_id'), + sa.UniqueConstraint('unit') + ) + op.create_table('url', + sa.Column('url_id', sa.Integer(), nullable=False), + sa.Column('url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('url_id'), + sa.UniqueConstraint('url') + ) + op.create_table('vectorized_raster_polygons', + sa.Column('vectorized_ID', sa.Integer(), nullable=False), + sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('raster_id', sa.Integer(), nullable=True), + sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('value', sa.Float(), nullable=True), + sa.Column('mean_value', sa.Float(), nullable=True), + sa.Column('std_dev', sa.Float(), nullable=True), + sa.Column('area_m2', sa.Float(), nullable=True), + sa.Column('date_acquired', sa.Date(), nullable=True), + sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('vectorized_ID') + ) + op.create_table('xrf_analysis', + sa.Column('xrf_id', sa.Integer(), nullable=False), + sa.Column('result_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), + sa.PrimaryKeyConstraint('xrf_id') + ) + op.create_table('zips', + sa.Column('zip_id', sa.Integer(), nullable=False), + sa.Column('zip_code', sqlmodel.sql.sqltypes.AutoString(), nullable=False), + sa.PrimaryKeyConstraint('zip_id'), + sa.UniqueConstraint('zip_code') + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('zips') + op.drop_table('xrf_analysis') + op.drop_table('vectorized_raster_polygons') + op.drop_table('url') + op.drop_table('units') + op.drop_table('testusers2') + op.drop_table('taxonomy') + op.drop_table('street_addresses') + op.drop_table('states') + op.drop_table('source_types') + op.drop_table('source_names') + op.drop_table('soil_type') + op.drop_table('rooms') + op.drop_table('regions') + op.drop_table('references') + op.drop_table('raster_metadata') + op.drop_table('qc_results') + op.drop_table('proximate_analysis') + op.drop_table('providers') + op.drop_table('provider_types') + op.drop_table('product_type') + op.drop_table('primary_product') + op.drop_table('preprocessing_methods_abbreviations') + op.drop_table('preprocessing_methods') + op.drop_index('idx_preprocessed_samples_prepro_method_id', table_name='preprocessed_samples') + op.drop_index('idx_preprocessed_samples_biomass_sample_id', table_name='preprocessed_samples') + op.drop_table('preprocessed_samples') + op.drop_table('particle_size') + op.drop_table('parameters') + op.drop_index('idx_parameter_units_unit_id', table_name='parameter_units') + op.drop_index('idx_parameter_units_parameter_id', table_name='parameter_units') + op.drop_table('parameter_units') + op.drop_table('parameter_methods') + op.drop_table('parameter_catagories') + op.drop_table('organisms') + op.drop_index('idx_methods_method_name', table_name='methods') + op.drop_table('methods') + op.drop_table('method_standards') + op.drop_index('idx_method_equipment_method_id', table_name='method_equipment') + op.drop_index('idx_method_equipment_equipment_id', table_name='method_equipment') + op.drop_table('method_equipment') + op.drop_table('method_categories') + op.drop_table('method_abbrevs') + op.drop_table('metadata') + op.drop_table('location_resolutions') + op.drop_table('import_log') + op.drop_table('icp_analysis') + op.drop_table('harvest_methods') + op.drop_table('geographic_locations') + op.drop_table('gasification_profile') + op.drop_table('fips') + op.drop_table('field_storage') + op.drop_index(op.f('ix_field_samples_source_codename_id'), table_name='field_samples') + op.drop_index(op.f('ix_field_samples_biomass_id'), table_name='field_samples') + op.drop_table('field_samples') + op.drop_table('fermentation_profile') + op.drop_table('external_usda') + op.drop_index('idx_external_phyllis2_biomass_id', table_name='external_phyllis2') + op.drop_index('idx_external_phyllis2_analysis_type_id', table_name='external_phyllis2') + op.drop_table('external_phyllis2') + op.drop_table('external_land_id') + op.drop_index('idx_external_inl_biofeedstock_library_biomass_id', table_name='external_inl_biofeedstock_library') + op.drop_table('external_inl_biofeedstock_library') + op.drop_table('external_ebmud') + op.drop_index('idx_external_dairy_one_parameter_id', table_name='external_dairy_one') + op.drop_index('idx_external_dairy_one_biomass_id', table_name='external_dairy_one') + op.drop_table('external_dairy_one') + op.drop_table('external_atip') + op.drop_index('idx_experiments_analysis_type_id', table_name='experiments') + op.drop_table('experiments') + op.drop_index('idx_experiment_methods_method_id', table_name='experiment_methods') + op.drop_index('idx_experiment_methods_experiment_id', table_name='experiment_methods') + op.drop_table('experiment_methods') + op.drop_table('equipment') + op.drop_table('doi') + op.drop_index('idx_data_sources_source_name_id', table_name='data_sources') + op.drop_table('data_sources') + op.drop_table('counties') + op.drop_table('compositional_analysis') + op.drop_table('collectors') + op.drop_table('collection_methods') + op.drop_table('cities') + op.drop_table('buildings') + op.drop_table('biomass_type') + op.drop_index(op.f('ix_biomass_test_biomass_test_name'), table_name='biomass_test') + op.drop_table('biomass_test') + op.drop_index(op.f('ix_biomass_quality_biomass_id'), table_name='biomass_quality') + op.drop_table('biomass_quality') + op.drop_index(op.f('ix_biomass_price_biomass_id'), table_name='biomass_price') + op.drop_table('biomass_price') + op.drop_index(op.f('ix_biomass_availability_biomass_id'), table_name='biomass_availability') + op.drop_table('biomass_availability') + op.drop_index(op.f('ix_biomass_biomass_type_id'), table_name='biomass') + op.drop_index(op.f('ix_biomass_biomass_name'), table_name='biomass') + op.drop_table('biomass') + op.drop_table('autoclave_profile') + op.drop_table('analyst_contact') + op.drop_table('analysis_types') + op.drop_index('uq_analysis_results_experiment_parameter_replicate', table_name='analysis_results') + op.drop_index('idx_analysis_results_parameter_id', table_name='analysis_results') + op.drop_table('analysis_results') + op.drop_table('analysis_replicate_id') + op.drop_table('analysis_abbreviations') + op.drop_table('ag_treatments') + op.drop_table('affiliations') + # ### end Alembic commands ### diff --git a/census.survey.mmd b/census.survey.mmd new file mode 100644 index 00000000..8ff952c9 --- /dev/null +++ b/census.survey.mmd @@ -0,0 +1,53 @@ +erDiagram +CensusRecord { + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} +Geography { + string state_name + string state_fips + string county_name + string county_fips + string geoid + string region_name + string agg_level_desc +} +SurveyRecord { + string period_desc + string freq_desc + string program_desc + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} +UsdaRecord { + integer year + CropEnum crop + VariableEnum variable + UnitEnum unit + float value + BearingStatusEnum bearing_status + string class_desc + string domain_desc + string source + string notes +} + +CensusRecord ||--|o Geography : "geography" +SurveyRecord ||--|o Geography : "geography" +UsdaRecord ||--|o Geography : "geography" diff --git a/review_summary.txt b/review_summary.txt new file mode 100644 index 00000000..fcdf7f74 --- /dev/null +++ b/review_summary.txt @@ -0,0 +1,76 @@ +# Pull Request Review Summary + +This document summarizes key findings and documentation gaps discovered while setting up the project environment for testing. + +--- + +## 1. Environment Setup: `.env` File Creation + +**Finding:** The project requires a `.env` file to be created in the `resources/docker/` directory for the Docker services to function correctly. This step was not documented in the main `README.md`. + +**Recommendation:** Add the following instructions to the "ETL Pipeline (Prefect + Docker)" section of the main `README.md` to guide new users. + +**Added Documentation:** +```markdown +**Note**: Before starting the services for the first time, create the required environment file from the template: + +```bash +cp resources/docker/.env.example resources/docker/.env +``` +``` + +--- + +## 2. Database Migrations: Generating an Initial Migration + +**Finding:** The process for generating a new initial Alembic migration is not documented and was difficult to discover. The correct method involves using the dedicated `setup-db` service defined in `resources/docker/docker-compose.yml`, which was not mentioned in any high-level documentation. + +Initial attempts to run the `alembic` command inside the `prefect-worker` container failed because it does not have the necessary files or `PATH` configuration. + +**Correct Procedure for Initial Migration:** + +1. **Tear Down Services and Volumes:** Completely reset the database environment. + ```bash + pixi run teardown-services-volumes + ``` + +2. **Remove Old Migration Files:** Clear the existing migration history. + ```bash + rm alembic/versions/*.py + ``` + +3. **Generate New Migration:** Use the `setup-db` service to run the `alembic` command. This is the critical, undocumented step. + ```bash + docker-compose -f resources/docker/docker-compose.yml run --rm setup-db alembic revision --autogenerate -m "Initial migration" + ``` + +4. **Apply the Migration:** Start the services. The `setup-db` service will automatically apply the newly created migration upon startup. + ```bash + pixi run start-services + ``` + +**Recommendation:** This entire process should be clearly documented in a relevant location, such as the `ALEMBIC_WORKFLOW.md` or a new troubleshooting guide, to prevent confusion for future developers. The existence and purpose of the `setup-db` service is a key piece of information that is currently missing from the documentation. + +--- + +## 3. Accessing the Database + +**Finding:** The workflow for directly accessing the database to inspect data is not documented. It requires using the `psql` command inside the `db` container with the correct user and database name, which are defined in `resources/docker/.env.example`. + +**Correct Procedure for Listing Tables:** + +```bash +pixi run exec-db psql -U biocirv_user -d biocirv_db -c "\dt" +``` + +**Recommendation:** Add a section to the documentation explaining how to connect to the database for debugging and inspection purposes. + +--- + +## 4. Prefect API Connection + +**Finding:** When running a Prefect flow from the host machine (e.g., via `pixi run run-etl`), the client fails to connect to the Prefect server API. This is because the `PREFECT_API_URL` in the `.env` file is set to `http://0.0.0.0:4200/api`. This address is only valid for processes inside the same container, not for clients on the host. + +**Resolution:** The `PREFECT_API_URL` and `PREFECT_UI_API_URL` in `resources/docker/.env` were changed to `http://localhost:4200/api`. + +**Recommendation:** The `.env.example` file should be updated with the correct `localhost` address to prevent this issue for other developers. An explanation of the different network contexts (host vs. container) would also be beneficial in the documentation. From 3490faac7c5d49b573e4c79eafc84c6207c4b9c2 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Tue, 18 Nov 2025 09:48:13 -0700 Subject: [PATCH 45/81] fixing alembic migration issues. Commenting out all SQLalchemy stuff for now --- README.md | 177 +++++++++++++++++- alembic/env.py | 16 +- ...n.py => 2eaabfd71d17_initial_migration.py} | 6 +- pixi.toml | 17 +- resources/docker/docker-compose.yml | 2 + 5 files changed, 203 insertions(+), 15 deletions(-) rename alembic/versions/{523eedbcaf6e_initial_migration.py => 2eaabfd71d17_initial_migration.py} (99%) diff --git a/README.md b/README.md index a58ea18b..5dc89ccc 100644 --- a/README.md +++ b/README.md @@ -35,11 +35,180 @@ run QGIS using pixi with the following command: pixi run qgis ``` -This will launch QGIS in the `gis` environment with all necessary dependencies -installed. +**Note**: On macOS, you may see a Python faulthandler error - this is expected +and can be ignored. See +[QGIS Issue #52987](https://github.com/qgis/QGIS/issues/52987). -For MacOS, there will be a Python error about faulthandler, which is expected -and can be ignored, see https://github.com/qgis/QGIS/issues/52987. +## Development + +### Running Tests + +```bash +# Run all tests +pixi run test + +# Run tests with coverage +pixi run test-cov +``` + +### Code Quality + +```bash +# Run pre-commit checks on staged files +pixi run pre-commit + +# Run pre-commit on all files (before PR) +pixi run pre-commit-all +``` + +### Available Pixi Tasks + +View all available tasks: + +```bash +pixi task list +``` + +Key tasks: + +- **Service Management**: `start-services`, `teardown-services`, + `service-status` +- **ETL Operations**: `deploy`, `run-etl` +- **Development**: `test`, `test-cov`, `pre-commit`, `pre-commit-all` +- **Applications**: `start-webservice`, `qgis` +- **Database**: `access-db`, `check-db-health` + +## Architecture + +### Namespace Packages + +This project uses **PEP 420 namespace packages** to organize code into +independently installable components that share a common namespace: + +- Each component has its own `pyproject.toml` and can be installed separately +- Shared models in `datamodels` are used by both `pipeline` and `webservice` +- Clear separation of concerns while maintaining type consistency + +### ETL Pipeline + +The ETL pipeline uses: + +- **Prefect**: Workflow orchestration and monitoring +- **Docker**: Containerized execution environment +- **PostgreSQL**: Data persistence +- **Google Sheets API**: Primary data source + +Pipeline architecture: + +1. **Extract**: Pull data from Google Sheets +2. **Transform**: Clean and normalize data with pandas +3. **Load**: Insert/update records in PostgreSQL via SQLModel + +### Database Models + +SQLModel-based models provide: + +- Type-safe database operations +- Automatic schema generation (via Alembic) +- Shared models across ETL and API components +- Pydantic validation + +## Project Components + +### 1. Data Models (`ca_biositing.datamodels`) + +Database models for: + +- Biomass data (field samples, measurements) +- Geographic locations +- Experiments and analysis +- Metadata and samples +- Organizations and contacts + +**Documentation**: +[`src/ca_biositing/datamodels/README.md`](src/ca_biositing/datamodels/README.md) + +### 2. ETL Pipeline (`ca_biositing.pipeline`) + +Prefect-orchestrated workflows for: + +- Data extraction from Google Sheets +- Data transformation and validation +- Database loading and updates +- Lookup table management + +**Documentation**: +[`src/ca_biositing/pipeline/README.md`](src/ca_biositing/pipeline/README.md) + +**Guides**: + +- [Docker Workflow](src/ca_biositing/pipeline/docs/DOCKER_WORKFLOW.md) +- [Prefect Workflow](src/ca_biositing/pipeline/docs/PREFECT_WORKFLOW.md) +- [ETL Development](src/ca_biositing/pipeline/docs/ETL_WORKFLOW.md) +- [Database Migrations](src/ca_biositing/pipeline/docs/ALEMBIC_WORKFLOW.md) + +### 3. Web Service (`ca_biositing.webservice`) + +FastAPI REST API providing: + +- Read access to database records +- Interactive API documentation (Swagger/OpenAPI) +- Type-safe endpoints using Pydantic + +**Documentation**: +[`src/ca_biositing/webservice/README.md`](src/ca_biositing/webservice/README.md) + +### 4. Deployment Resources (`resources/`) + +Docker and Prefect configuration for: + +- Service orchestration (Docker Compose) +- Prefect deployments +- Database initialization + +**Documentation**: [`resources/README.md`](resources/README.md) + +## Adding Dependencies + +### For Local Development (Pixi) + +```bash +# Add conda package to default environment +pixi add + +# Add PyPI package to default environment +pixi add --pypi + +# Add to specific feature (e.g., pipeline) +pixi add --feature pipeline --pypi +``` + +### For ETL Pipeline (Docker) + +The pipeline dependencies are managed by Pixi's `etl` environment feature in +`pixi.toml`. When you add dependencies and rebuild Docker images, they are +automatically included: + +```bash +# Add dependency to pipeline feature +pixi add --feature pipeline --pypi + +# Rebuild Docker images +pixi run rebuild-services + +# Restart services +pixi run start-services +``` + +## Environment Management + +This project uses **Pixi environments** for different workflows: + +- **`default`**: General development, testing, pre-commit hooks +- **`gis`**: QGIS and geospatial analysis tools +- **`etl`**: ETL pipeline (used in Docker containers) +- **`webservice`**: FastAPI web service +- **`frontend`**: Node.js/npm for frontend development ## Frontend Integration diff --git a/alembic/env.py b/alembic/env.py index 4b372e23..cd3a09ea 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -28,9 +28,9 @@ import importlib.util from pathlib import Path -# --- Import generated models --- -from ca_biositing.datamodels.schemas.generated.census_survey import * -from ca_biositing.datamodels.schemas.generated.geography import * +# --- Import generated models and their metadata --- +# from ca_biositing.datamodels.schemas.generated.census_survey import metadata as census_metadata +# from ca_biositing.datamodels.schemas.generated.geography import metadata as geography_metadata # --- Alembic Config object, provides access to alembic.ini values --- config = context.config @@ -49,11 +49,17 @@ # --- Metadata from your models for autogenerate --- # Combine metadata from all models # See: https://alembic.sqlalchemy.org/en/latest/autogenerate.html#affecting-the-autogenerate-process -for table in SQLModel.metadata.tables.values(): - table.tometadata(SQLModel.metadata) +# Start with the default SQLModel metadata target_metadata = SQLModel.metadata +# Manually merge metadata from generated modules +# for table in census_metadata.tables.values(): +# table.tometadata(target_metadata) +# +# for table in geography_metadata.tables.values(): +# table.tometadata(target_metadata) + def render_item(type_, obj, autogen_context): """Add custom imports to the migration template.""" diff --git a/alembic/versions/523eedbcaf6e_initial_migration.py b/alembic/versions/2eaabfd71d17_initial_migration.py similarity index 99% rename from alembic/versions/523eedbcaf6e_initial_migration.py rename to alembic/versions/2eaabfd71d17_initial_migration.py index 402bc49d..3273b864 100644 --- a/alembic/versions/523eedbcaf6e_initial_migration.py +++ b/alembic/versions/2eaabfd71d17_initial_migration.py @@ -1,8 +1,8 @@ """Initial migration -Revision ID: 523eedbcaf6e +Revision ID: 2eaabfd71d17 Revises: -Create Date: 2025-11-14 20:44:50.143083 +Create Date: 2025-11-18 16:35:19.779152 """ from typing import Sequence, Union @@ -12,7 +12,7 @@ import sqlmodel # revision identifiers, used by Alembic. -revision: str = '523eedbcaf6e' +revision: str = '2eaabfd71d17' down_revision: Union[str, Sequence[str], None] = None branch_labels: Union[str, Sequence[str], None] = None depends_on: Union[str, Sequence[str], None] = None diff --git a/pixi.toml b/pixi.toml index 083ced6e..f742f613 100644 --- a/pixi.toml +++ b/pixi.toml @@ -68,9 +68,7 @@ start-services = { cmd = [ "resources/docker/docker-compose.yml", "up", "-d", -], description = "Start required services using Docker Compose.", depends-on = [ - "initial-migration", -] } +], description = "Start required services using Docker Compose." } teardown-services = { cmd = [ "docker-compose", "-f", @@ -180,6 +178,19 @@ restart-prefect-worker = { cmd = [ "prefect-worker", ], description = "Restart the Prefect worker service." } +migrate = { cmd = [ + "docker-compose", + "-f", + "resources/docker/docker-compose.yml", + "exec", + "prefect-worker", + "/bin/bash", + "-c", + "source /shell-hook.sh && alembic upgrade head", +], description = "Apply database migrations.", depends-on = [ + "start-services", +] } + [tasks.qgis] depends-on = [{ task = "run-qgis", environment = "gis" }] diff --git a/resources/docker/docker-compose.yml b/resources/docker/docker-compose.yml index 7328859f..8ad138b5 100644 --- a/resources/docker/docker-compose.yml +++ b/resources/docker/docker-compose.yml @@ -70,6 +70,8 @@ services: # Adding the flow code to the worker - ../prefect/run_prefect_flow.py:/app/run_prefect_flow.py - ../../credentials.json:/app/credentials.json + - ../../alembic:/app/alembic + - ../../alembic.ini:/app/alembic.ini depends_on: prefect-server: condition: service_healthy From 8458b18ec3660d0a8152c59470aaee35dde6acef Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Tue, 18 Nov 2025 10:02:48 -0700 Subject: [PATCH 46/81] needed to clear alembic migrations first --- .../2eaabfd71d17_initial_migration.py | 877 ------------------ .../e15bda744fef_initial_migration.py | 877 ------------------ 2 files changed, 1754 deletions(-) delete mode 100644 alembic/versions/2eaabfd71d17_initial_migration.py delete mode 100644 alembic/versions/e15bda744fef_initial_migration.py diff --git a/alembic/versions/2eaabfd71d17_initial_migration.py b/alembic/versions/2eaabfd71d17_initial_migration.py deleted file mode 100644 index 3273b864..00000000 --- a/alembic/versions/2eaabfd71d17_initial_migration.py +++ /dev/null @@ -1,877 +0,0 @@ -"""Initial migration - -Revision ID: 2eaabfd71d17 -Revises: -Create Date: 2025-11-18 16:35:19.779152 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa -import sqlmodel - -# revision identifiers, used by Alembic. -revision: str = '2eaabfd71d17' -down_revision: Union[str, Sequence[str], None] = None -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.create_table('affiliations', - sa.Column('affiliation_id', sa.Integer(), nullable=False), - sa.Column('affiliation_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('affiliation_id'), - sa.UniqueConstraint('affiliation_name') - ) - op.create_table('ag_treatments', - sa.Column('ag_treatment_id', sa.Integer(), nullable=False), - sa.Column('ag_treatment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('ag_treatment_id') - ) - op.create_table('analysis_abbreviations', - sa.Column('analysis_abbreviations_id', sa.Integer(), nullable=False), - sa.Column('analysis_abbreviation', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_abbreviations_id'), - sa.UniqueConstraint('analysis_abbreviation') - ) - op.create_table('analysis_replicate_id', - sa.Column('analysis_replicate_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('analysis_types_id', sa.Integer(), nullable=True), - sa.Column('analysis_replicate_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_replicate_id') - ) - op.create_table('analysis_results', - sa.Column('result_id', sa.Integer(), nullable=False), - sa.Column('anlaysis_sample', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('replicate_no', sa.Integer(), nullable=True), - sa.Column('analysis_timestamp', sa.DateTime(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('qc_result_id', sa.Integer(), nullable=True), - sa.Column('measurement_equipment_id', sa.Integer(), nullable=True), - sa.Column('raw_data_url_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('analysis_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('result_id') - ) - op.create_index('idx_analysis_results_parameter_id', 'analysis_results', ['parameter_id'], unique=False) - op.create_index('uq_analysis_results_experiment_parameter_replicate', 'analysis_results', ['experiment_id', 'parameter_id', 'replicate_no'], unique=True) - op.create_table('analysis_types', - sa.Column('analysis_type_id', sa.Integer(), nullable=False), - sa.Column('analysis_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_type_id'), - sa.UniqueConstraint('analysis_name') - ) - op.create_table('analyst_contact', - sa.Column('analyst_id', sa.Integer(), nullable=False), - sa.Column('analyst_first_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_last_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_email', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_affiliation', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('analyst_id') - ) - op.create_table('autoclave_profile', - sa.Column('autoclave_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('autoclave_id') - ) - op.create_table('biomass', - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('biomass_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('primary_product_id', sa.Integer(), nullable=True), - sa.Column('taxonomy_id', sa.Integer(), nullable=True), - sa.Column('biomass_type_id', sa.Integer(), nullable=True), - sa.Column('biomass_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('biomass_id') - ) - op.create_index(op.f('ix_biomass_biomass_name'), 'biomass', ['biomass_name'], unique=False) - op.create_index(op.f('ix_biomass_biomass_type_id'), 'biomass', ['biomass_type_id'], unique=False) - op.create_table('biomass_availability', - sa.Column('availability_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('primary_product_id', sa.Integer(), nullable=True), - sa.Column('from_month', sa.Numeric(), nullable=True), - sa.Column('to_month', sa.Numeric(), nullable=True), - sa.Column('kg_low', sa.Numeric(), nullable=True), - sa.Column('kg_avg', sa.Numeric(), nullable=True), - sa.Column('kg_high', sa.Numeric(), nullable=True), - sa.Column('bdt_low', sa.Numeric(), nullable=True), - sa.Column('bdt_avg', sa.Numeric(), nullable=True), - sa.Column('bdt_high', sa.Numeric(), nullable=True), - sa.Column('data_source', sa.Integer(), nullable=True), - sa.Column('availability_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('availability_id') - ) - op.create_index(op.f('ix_biomass_availability_biomass_id'), 'biomass_availability', ['biomass_id'], unique=False) - op.create_table('biomass_price', - sa.Column('price_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('price_per_kg_low', sa.Numeric(), nullable=True), - sa.Column('price_per_kg_avg', sa.Numeric(), nullable=True), - sa.Column('price_per_kg_high', sa.Numeric(), nullable=True), - sa.Column('price_data_sources', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('price_id') - ) - op.create_index(op.f('ix_biomass_price_biomass_id'), 'biomass_price', ['biomass_id'], unique=False) - op.create_table('biomass_quality', - sa.Column('quality_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('expected_quality', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('output_feedstocks', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('convertibility', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('disposal_challenges', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('existing_markets', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('substitute_materials', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('regulatory_issues', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('quality_data_sources', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('quality_id') - ) - op.create_index(op.f('ix_biomass_quality_biomass_id'), 'biomass_quality', ['biomass_id'], unique=False) - op.create_table('biomass_test', - sa.Column('biomass_test_id', sa.Integer(), nullable=False), - sa.Column('biomass_test_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('biomass_test_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('biomass_test_id') - ) - op.create_index(op.f('ix_biomass_test_biomass_test_name'), 'biomass_test', ['biomass_test_name'], unique=False) - op.create_table('biomass_type', - sa.Column('biomass_type_id', sa.Integer(), nullable=False), - sa.Column('biomass_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('biomass_type_id'), - sa.UniqueConstraint('biomass_type') - ) - op.create_table('buildings', - sa.Column('building_id', sa.Integer(), nullable=False), - sa.Column('building_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('affiliation_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('building_id'), - sa.UniqueConstraint('building_name') - ) - op.create_table('cities', - sa.Column('city_id', sa.Integer(), nullable=False), - sa.Column('city_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('city_id'), - sa.UniqueConstraint('city_name') - ) - op.create_table('collection_methods', - sa.Column('collection_method_id', sa.Integer(), nullable=False), - sa.Column('collection_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('collection_method_id'), - sa.UniqueConstraint('collection_method_name') - ) - op.create_table('collectors', - sa.Column('collector_id', sa.Integer(), nullable=False), - sa.Column('collector_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('collector_affiliation', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('collector_id'), - sa.UniqueConstraint('collector_name') - ) - op.create_table('compositional_analysis', - sa.Column('cmp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('calculated_parameter_id', sa.Integer(), nullable=True), - sa.Column('calculated_parameter_value', sa.Numeric(), nullable=True), - sa.Column('calculated_parameter_unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('cmp_id') - ) - op.create_table('counties', - sa.Column('county_id', sa.Integer(), nullable=False), - sa.Column('county_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('county_id'), - sa.UniqueConstraint('county_name') - ) - op.create_table('data_sources', - sa.Column('source_id', sa.Integer(), nullable=False), - sa.Column('source_name_id', sa.Integer(), nullable=True), - sa.Column('source_type_id', sa.Integer(), nullable=True), - sa.Column('data_resolution_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('url_id', sa.Integer(), nullable=True), - sa.Column('import_timestamp', sa.DateTime(), nullable=True), - sa.PrimaryKeyConstraint('source_id') - ) - op.create_index('idx_data_sources_source_name_id', 'data_sources', ['source_name_id'], unique=False) - op.create_table('doi', - sa.Column('doi_id', sa.Integer(), nullable=False), - sa.Column('doi', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('doi_id') - ) - op.create_table('equipment', - sa.Column('equipment_id', sa.Integer(), nullable=False), - sa.Column('equipment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('equipment_room_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('equipment_id'), - sa.UniqueConstraint('equipment_name') - ) - op.create_table('experiment_methods', - sa.Column('experiment_method_id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('experiment_method_id') - ) - op.create_index('idx_experiment_methods_experiment_id', 'experiment_methods', ['experiment_id'], unique=False) - op.create_index('idx_experiment_methods_method_id', 'experiment_methods', ['method_id'], unique=False) - op.create_table('experiments', - sa.Column('experiment_id', sa.Integer(), nullable=False), - sa.Column('exper_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('gsheet_exper_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('analysis_abbrev_id', sa.Integer(), nullable=True), - sa.Column('exper_start_date', sa.Date(), nullable=True), - sa.Column('exper_duration', sa.Numeric(), nullable=True), - sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('exper_location_id', sa.Integer(), nullable=True), - sa.Column('exper_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('experiment_id'), - sa.UniqueConstraint('exper_uuid'), - sa.UniqueConstraint('gsheet_exper_id') - ) - op.create_index('idx_experiments_analysis_type_id', 'experiments', ['analysis_type_id'], unique=False) - op.create_table('external_atip', - sa.Column('atip_ID', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('atip_ID') - ) - op.create_table('external_dairy_one', - sa.Column('dairy_one_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('samples_count', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('accumulated_years_from', sa.Date(), nullable=True), - sa.Column('accumulated_years_to', sa.Date(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('dairy_one_id') - ) - op.create_index('idx_external_dairy_one_biomass_id', 'external_dairy_one', ['biomass_id'], unique=False) - op.create_index('idx_external_dairy_one_parameter_id', 'external_dairy_one', ['parameter_id'], unique=False) - op.create_table('external_ebmud', - sa.Column('ebmud_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('ebmud_id') - ) - op.create_table('external_inl_biofeedstock_library', - sa.Column('bfl_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('state_id', sa.Integer(), nullable=True), - sa.Column('affiliations_id', sa.Integer(), nullable=True), - sa.Column('harvest_method_id', sa.Integer(), nullable=True), - sa.Column('collection_method_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('accumulated_years_from', sa.Date(), nullable=True), - sa.Column('accumulated_years_to', sa.Date(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('bfl_id') - ) - op.create_index('idx_external_inl_biofeedstock_library_biomass_id', 'external_inl_biofeedstock_library', ['biomass_id'], unique=False) - op.create_table('external_land_id', - sa.Column('land_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('land_id') - ) - op.create_table('external_phyllis2', - sa.Column('phyllis_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('phyllis_id') - ) - op.create_index('idx_external_phyllis2_analysis_type_id', 'external_phyllis2', ['analysis_type_id'], unique=False) - op.create_index('idx_external_phyllis2_biomass_id', 'external_phyllis2', ['biomass_id'], unique=False) - op.create_table('external_usda', - sa.Column('usda_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('usda_id') - ) - op.create_table('fermentation_profile', - sa.Column('fp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('organism_id', sa.Integer(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('fp_id') - ) - op.create_table('field_samples', - sa.Column('sample_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('sample_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('source_codename_id', sa.Integer(), nullable=True), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('field_storage_id', sa.Integer(), nullable=True), - sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), - sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('collection_timestamp', sa.DateTime(), nullable=True), - sa.Column('collection_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_date', sa.Date(), nullable=True), - sa.Column('amount_collected_kg', sa.Numeric(), nullable=True), - sa.Column('provider_id', sa.Integer(), nullable=True), - sa.Column('collector_id', sa.Integer(), nullable=True), - sa.Column('basic_sample_info_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('created_at', sa.DateTime(), nullable=False), - sa.PrimaryKeyConstraint('sample_id') - ) - op.create_index(op.f('ix_field_samples_biomass_id'), 'field_samples', ['biomass_id'], unique=False) - op.create_index(op.f('ix_field_samples_source_codename_id'), 'field_samples', ['source_codename_id'], unique=False) - op.create_table('field_storage', - sa.Column('field_storage_id', sa.Integer(), nullable=False), - sa.Column('storage_method', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('field_storage_id'), - sa.UniqueConstraint('storage_method') - ) - op.create_table('fips', - sa.Column('fips_id', sa.Integer(), nullable=False), - sa.Column('fips_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('fips_id') - ) - op.create_table('gasification_profile', - sa.Column('gasification_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('gasification_id') - ) - op.create_table('geographic_locations', - sa.Column('location_id', sa.Integer(), nullable=False), - sa.Column('street_address_id', sa.Integer(), nullable=True), - sa.Column('city_id', sa.Integer(), nullable=True), - sa.Column('zip_id', sa.Integer(), nullable=True), - sa.Column('county_id', sa.Integer(), nullable=True), - sa.Column('state_id', sa.Integer(), nullable=True), - sa.Column('region_id', sa.Integer(), nullable=True), - sa.Column('fips_id', sa.Integer(), nullable=True), - sa.Column('latitude', sa.Numeric(), nullable=True), - sa.Column('longitude', sa.Numeric(), nullable=True), - sa.Column('location_resolution_id', sa.Integer(), nullable=True), - sa.Column('is_anonymous', sa.Boolean(), nullable=True), - sa.PrimaryKeyConstraint('location_id') - ) - op.create_table('harvest_methods', - sa.Column('harvest_method_id', sa.Integer(), nullable=False), - sa.Column('harvest_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('harvest_method_id'), - sa.UniqueConstraint('harvest_method_name') - ) - op.create_table('icp_analysis', - sa.Column('icp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('concentration_calculation_url_id', sa.Integer(), nullable=True), - sa.Column('result_wavelength', sa.Numeric(), nullable=True), - sa.Column('raw_url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('icp_id') - ) - op.create_table('import_log', - sa.Column('import_id', sa.Integer(), nullable=False), - sa.Column('import_timestamp', sa.DateTime(), nullable=True), - sa.Column('destination', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('source_file', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('records_imported', sa.Integer(), nullable=True), - sa.Column('import_status', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('error_log', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_user', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('import_id') - ) - op.create_table('location_resolutions', - sa.Column('location_resolution_id', sa.Integer(), nullable=False), - sa.Column('resolution_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('location_resolution_id'), - sa.UniqueConstraint('resolution_type') - ) - op.create_table('metadata', - sa.Column('metadata_id', sa.Integer(), nullable=False), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('ag_treatment_id', sa.Integer(), nullable=True), - sa.Column('last_application_date', sa.Date(), nullable=True), - sa.Column('treatment_amount_per_acre', sa.Numeric(), nullable=True), - sa.Column('soil_type', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('metadata_id') - ) - op.create_table('method_abbrevs', - sa.Column('method_abbrev_id', sa.Integer(), nullable=False), - sa.Column('method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_abbrev_id'), - sa.UniqueConstraint('method_abbrev') - ) - op.create_table('method_categories', - sa.Column('method_category_id', sa.Integer(), nullable=False), - sa.Column('method_category', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_category_id'), - sa.UniqueConstraint('method_category') - ) - op.create_table('method_equipment', - sa.Column('method_equipment_id', sa.Integer(), nullable=False), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('equipment_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('method_equipment_id') - ) - op.create_index('idx_method_equipment_equipment_id', 'method_equipment', ['equipment_id'], unique=False) - op.create_index('idx_method_equipment_method_id', 'method_equipment', ['method_id'], unique=False) - op.create_table('method_standards', - sa.Column('method_standard_id', sa.Integer(), nullable=False), - sa.Column('method_standard', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_standard_id'), - sa.UniqueConstraint('method_standard') - ) - op.create_table('methods', - sa.Column('method_id', sa.Integer(), nullable=False), - sa.Column('method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('method_category_id', sa.Integer(), nullable=True), - sa.Column('method_standard_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('detection_limits', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('procedure_reference_id', sa.Integer(), nullable=True), - sa.Column('method_url_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('method_id'), - sa.UniqueConstraint('method_name') - ) - op.create_index('idx_methods_method_name', 'methods', ['method_name'], unique=False) - op.create_table('organisms', - sa.Column('organism_id', sa.Integer(), nullable=False), - sa.Column('organism_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('organism_strain_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('organism_id') - ) - op.create_table('parameter_catagories', - sa.Column('parameter_catagory_id', sa.Integer(), nullable=False), - sa.Column('parameter_catagory', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('parameter_catagory_id') - ) - op.create_table('parameter_methods', - sa.Column('param_method_id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('param_method_id') - ) - op.create_table('parameter_units', - sa.Column('parameter_unit_id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('parameter_unit_id') - ) - op.create_index('idx_parameter_units_parameter_id', 'parameter_units', ['parameter_id'], unique=False) - op.create_index('idx_parameter_units_unit_id', 'parameter_units', ['unit_id'], unique=False) - op.create_table('parameters', - sa.Column('parameter_id', sa.Integer(), nullable=False), - sa.Column('parameter_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('parameter_category_id', sa.Integer(), nullable=True), - sa.Column('standard_unit_id', sa.Integer(), nullable=True), - sa.Column('calculated', sa.Boolean(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('typical_range_min', sa.Numeric(), nullable=True), - sa.Column('typical_range_max', sa.Numeric(), nullable=True), - sa.PrimaryKeyConstraint('parameter_id'), - sa.UniqueConstraint('parameter_name') - ) - op.create_table('particle_size', - sa.Column('particle_size_id', sa.Integer(), nullable=False), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('particle_length', sa.Integer(), nullable=True), - sa.Column('particle_width', sa.Integer(), nullable=True), - sa.Column('particle_height', sa.Integer(), nullable=True), - sa.Column('particle_units', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('particle_size_id') - ) - op.create_table('preprocessed_samples', - sa.Column('prepro_material_id', sa.Integer(), nullable=False), - sa.Column('prepro_material_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('biomass_sample_id', sa.Integer(), nullable=True), - sa.Column('prepro_method_id', sa.Integer(), nullable=True), - sa.Column('amount_before_drying_g', sa.Numeric(), nullable=True), - sa.Column('amount_after_drying', sa.Numeric(), nullable=True), - sa.Column('processing_date', sa.Date(), nullable=True), - sa.Column('storage_building', sa.Integer(), nullable=True), - sa.Column('amount_remaining_g', sa.Numeric(), nullable=True), - sa.Column('amount_as_of_date', sa.Date(), nullable=True), - sa.Column('prepro_analyst_id', sa.Integer(), nullable=True), - sa.Column('prepro_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prepro_material_id') - ) - op.create_index('idx_preprocessed_samples_biomass_sample_id', 'preprocessed_samples', ['biomass_sample_id'], unique=False) - op.create_index('idx_preprocessed_samples_prepro_method_id', 'preprocessed_samples', ['prepro_method_id'], unique=False) - op.create_table('preprocessing_methods', - sa.Column('prepro_method_id', sa.Integer(), nullable=False), - sa.Column('prepro_method', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('prepro_method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('prepro_temp_c', sa.Numeric(), nullable=True), - sa.Column('drying_step', sa.Boolean(), nullable=True), - sa.Column('method_ref_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('prepro_method_id') - ) - op.create_table('preprocessing_methods_abbreviations', - sa.Column('prepro_methods_abbrev_id', sa.Integer(), nullable=False), - sa.Column('prepro_method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prepro_methods_abbrev_id'), - sa.UniqueConstraint('prepro_method_abbrev') - ) - op.create_table('primary_product', - sa.Column('primary_product_id', sa.Integer(), nullable=False), - sa.Column('primary_product_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('primary_product_id'), - sa.UniqueConstraint('primary_product_name') - ) - op.create_table('product_type', - sa.Column('product_type_id', sa.Integer(), nullable=False), - sa.Column('product', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('product_type_id') - ) - op.create_table('provider_types', - sa.Column('provider_type_id', sa.Integer(), nullable=False), - sa.Column('provider_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('provider_type_id') - ) - op.create_table('providers', - sa.Column('provider_id', sa.Integer(), nullable=False), - sa.Column('provider_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('provider_affiliation', sa.Integer(), nullable=True), - sa.Column('provider_type_id', sa.Integer(), nullable=True), - sa.Column('anonymous', sa.Boolean(), nullable=True), - sa.PrimaryKeyConstraint('provider_id'), - sa.UniqueConstraint('provider_name') - ) - op.create_table('proximate_analysis', - sa.Column('prox_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prox_id') - ) - op.create_table('qc_results', - sa.Column('qc_result_id', sa.Integer(), nullable=False), - sa.Column('qc_result', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('qc_result_id'), - sa.UniqueConstraint('qc_result') - ) - op.create_table('raster_metadata', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('resolution', sa.Float(), nullable=True), - sa.Column('srid', sa.Integer(), nullable=True), - sa.Column('acquisition_date', sa.Date(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('references', - sa.Column('reference_id', sa.Integer(), nullable=False), - sa.Column('reference_title', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_author', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_publication', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_date', sa.Date(), nullable=True), - sa.Column('reference_doi_id', sa.Integer(), nullable=True), - sa.Column('url_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('reference_id') - ) - op.create_table('regions', - sa.Column('region_id', sa.Integer(), nullable=False), - sa.Column('region_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('region_id'), - sa.UniqueConstraint('region_name') - ) - op.create_table('rooms', - sa.Column('room_id', sa.Integer(), nullable=False), - sa.Column('room_number', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('building_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('room_id'), - sa.UniqueConstraint('room_number') - ) - op.create_table('soil_type', - sa.Column('soil_type_id', sa.Integer(), nullable=False), - sa.Column('soil_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('soil_location', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('soil_type_id'), - sa.UniqueConstraint('soil_type') - ) - op.create_table('source_names', - sa.Column('source_name_id', sa.Integer(), nullable=False), - sa.Column('source_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('source_name_id'), - sa.UniqueConstraint('source_name') - ) - op.create_table('source_types', - sa.Column('source_type_id', sa.Integer(), nullable=False), - sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('source_type_id'), - sa.UniqueConstraint('source_type') - ) - op.create_table('states', - sa.Column('state_id', sa.Integer(), nullable=False), - sa.Column('state_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('state_id'), - sa.UniqueConstraint('state_name') - ) - op.create_table('street_addresses', - sa.Column('street_address_id', sa.Integer(), nullable=False), - sa.Column('street_address', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('street_address_id') - ) - op.create_table('taxonomy', - sa.Column('taxonomy_id', sa.Integer(), nullable=False), - sa.Column('kingdom', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('phylum', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('order', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('family', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('genus', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('species', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('variety_subspecies_cultivar', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('taxonomy_id') - ) - op.create_table('testusers2', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('fullname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('nickname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('units', - sa.Column('unit_id', sa.Integer(), nullable=False), - sa.Column('unit', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('unit_id'), - sa.UniqueConstraint('unit') - ) - op.create_table('url', - sa.Column('url_id', sa.Integer(), nullable=False), - sa.Column('url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('url_id'), - sa.UniqueConstraint('url') - ) - op.create_table('vectorized_raster_polygons', - sa.Column('vectorized_ID', sa.Integer(), nullable=False), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('raster_id', sa.Integer(), nullable=True), - sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('mean_value', sa.Float(), nullable=True), - sa.Column('std_dev', sa.Float(), nullable=True), - sa.Column('area_m2', sa.Float(), nullable=True), - sa.Column('date_acquired', sa.Date(), nullable=True), - sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('vectorized_ID') - ) - op.create_table('xrf_analysis', - sa.Column('xrf_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('xrf_id') - ) - op.create_table('zips', - sa.Column('zip_id', sa.Integer(), nullable=False), - sa.Column('zip_code', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('zip_id'), - sa.UniqueConstraint('zip_code') - ) - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.drop_table('zips') - op.drop_table('xrf_analysis') - op.drop_table('vectorized_raster_polygons') - op.drop_table('url') - op.drop_table('units') - op.drop_table('testusers2') - op.drop_table('taxonomy') - op.drop_table('street_addresses') - op.drop_table('states') - op.drop_table('source_types') - op.drop_table('source_names') - op.drop_table('soil_type') - op.drop_table('rooms') - op.drop_table('regions') - op.drop_table('references') - op.drop_table('raster_metadata') - op.drop_table('qc_results') - op.drop_table('proximate_analysis') - op.drop_table('providers') - op.drop_table('provider_types') - op.drop_table('product_type') - op.drop_table('primary_product') - op.drop_table('preprocessing_methods_abbreviations') - op.drop_table('preprocessing_methods') - op.drop_index('idx_preprocessed_samples_prepro_method_id', table_name='preprocessed_samples') - op.drop_index('idx_preprocessed_samples_biomass_sample_id', table_name='preprocessed_samples') - op.drop_table('preprocessed_samples') - op.drop_table('particle_size') - op.drop_table('parameters') - op.drop_index('idx_parameter_units_unit_id', table_name='parameter_units') - op.drop_index('idx_parameter_units_parameter_id', table_name='parameter_units') - op.drop_table('parameter_units') - op.drop_table('parameter_methods') - op.drop_table('parameter_catagories') - op.drop_table('organisms') - op.drop_index('idx_methods_method_name', table_name='methods') - op.drop_table('methods') - op.drop_table('method_standards') - op.drop_index('idx_method_equipment_method_id', table_name='method_equipment') - op.drop_index('idx_method_equipment_equipment_id', table_name='method_equipment') - op.drop_table('method_equipment') - op.drop_table('method_categories') - op.drop_table('method_abbrevs') - op.drop_table('metadata') - op.drop_table('location_resolutions') - op.drop_table('import_log') - op.drop_table('icp_analysis') - op.drop_table('harvest_methods') - op.drop_table('geographic_locations') - op.drop_table('gasification_profile') - op.drop_table('fips') - op.drop_table('field_storage') - op.drop_index(op.f('ix_field_samples_source_codename_id'), table_name='field_samples') - op.drop_index(op.f('ix_field_samples_biomass_id'), table_name='field_samples') - op.drop_table('field_samples') - op.drop_table('fermentation_profile') - op.drop_table('external_usda') - op.drop_index('idx_external_phyllis2_biomass_id', table_name='external_phyllis2') - op.drop_index('idx_external_phyllis2_analysis_type_id', table_name='external_phyllis2') - op.drop_table('external_phyllis2') - op.drop_table('external_land_id') - op.drop_index('idx_external_inl_biofeedstock_library_biomass_id', table_name='external_inl_biofeedstock_library') - op.drop_table('external_inl_biofeedstock_library') - op.drop_table('external_ebmud') - op.drop_index('idx_external_dairy_one_parameter_id', table_name='external_dairy_one') - op.drop_index('idx_external_dairy_one_biomass_id', table_name='external_dairy_one') - op.drop_table('external_dairy_one') - op.drop_table('external_atip') - op.drop_index('idx_experiments_analysis_type_id', table_name='experiments') - op.drop_table('experiments') - op.drop_index('idx_experiment_methods_method_id', table_name='experiment_methods') - op.drop_index('idx_experiment_methods_experiment_id', table_name='experiment_methods') - op.drop_table('experiment_methods') - op.drop_table('equipment') - op.drop_table('doi') - op.drop_index('idx_data_sources_source_name_id', table_name='data_sources') - op.drop_table('data_sources') - op.drop_table('counties') - op.drop_table('compositional_analysis') - op.drop_table('collectors') - op.drop_table('collection_methods') - op.drop_table('cities') - op.drop_table('buildings') - op.drop_table('biomass_type') - op.drop_index(op.f('ix_biomass_test_biomass_test_name'), table_name='biomass_test') - op.drop_table('biomass_test') - op.drop_index(op.f('ix_biomass_quality_biomass_id'), table_name='biomass_quality') - op.drop_table('biomass_quality') - op.drop_index(op.f('ix_biomass_price_biomass_id'), table_name='biomass_price') - op.drop_table('biomass_price') - op.drop_index(op.f('ix_biomass_availability_biomass_id'), table_name='biomass_availability') - op.drop_table('biomass_availability') - op.drop_index(op.f('ix_biomass_biomass_type_id'), table_name='biomass') - op.drop_index(op.f('ix_biomass_biomass_name'), table_name='biomass') - op.drop_table('biomass') - op.drop_table('autoclave_profile') - op.drop_table('analyst_contact') - op.drop_table('analysis_types') - op.drop_index('uq_analysis_results_experiment_parameter_replicate', table_name='analysis_results') - op.drop_index('idx_analysis_results_parameter_id', table_name='analysis_results') - op.drop_table('analysis_results') - op.drop_table('analysis_replicate_id') - op.drop_table('analysis_abbreviations') - op.drop_table('ag_treatments') - op.drop_table('affiliations') - # ### end Alembic commands ### diff --git a/alembic/versions/e15bda744fef_initial_migration.py b/alembic/versions/e15bda744fef_initial_migration.py deleted file mode 100644 index 18517bc2..00000000 --- a/alembic/versions/e15bda744fef_initial_migration.py +++ /dev/null @@ -1,877 +0,0 @@ -"""Initial migration - -Revision ID: e15bda744fef -Revises: -Create Date: 2025-11-04 20:03:41.870493 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa -import sqlmodel - -# revision identifiers, used by Alembic. -revision: str = 'e15bda744fef' -down_revision: Union[str, Sequence[str], None] = None -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.create_table('affiliations', - sa.Column('affiliation_id', sa.Integer(), nullable=False), - sa.Column('affiliation_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('affiliation_id'), - sa.UniqueConstraint('affiliation_name') - ) - op.create_table('ag_treatments', - sa.Column('ag_treatment_id', sa.Integer(), nullable=False), - sa.Column('ag_treatment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('ag_treatment_id') - ) - op.create_table('analysis_abbreviations', - sa.Column('analysis_abbreviations_id', sa.Integer(), nullable=False), - sa.Column('analysis_abbreviation', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_abbreviations_id'), - sa.UniqueConstraint('analysis_abbreviation') - ) - op.create_table('analysis_replicate_id', - sa.Column('analysis_replicate_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('analysis_types_id', sa.Integer(), nullable=True), - sa.Column('analysis_replicate_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_replicate_id') - ) - op.create_table('analysis_results', - sa.Column('result_id', sa.Integer(), nullable=False), - sa.Column('anlaysis_sample', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('replicate_no', sa.Integer(), nullable=True), - sa.Column('analysis_timestamp', sa.DateTime(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('qc_result_id', sa.Integer(), nullable=True), - sa.Column('measurement_equipment_id', sa.Integer(), nullable=True), - sa.Column('raw_data_url_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('analysis_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('result_id') - ) - op.create_index('idx_analysis_results_parameter_id', 'analysis_results', ['parameter_id'], unique=False) - op.create_index('uq_analysis_results_experiment_parameter_replicate', 'analysis_results', ['experiment_id', 'parameter_id', 'replicate_no'], unique=True) - op.create_table('analysis_types', - sa.Column('analysis_type_id', sa.Integer(), nullable=False), - sa.Column('analysis_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('analysis_type_id'), - sa.UniqueConstraint('analysis_name') - ) - op.create_table('analyst_contact', - sa.Column('analyst_id', sa.Integer(), nullable=False), - sa.Column('analyst_first_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_last_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_email', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('analyst_affiliation', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('analyst_id') - ) - op.create_table('autoclave_profile', - sa.Column('autoclave_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('autoclave_id') - ) - op.create_table('biomass', - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('biomass_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('primary_product_id', sa.Integer(), nullable=True), - sa.Column('taxonomy_id', sa.Integer(), nullable=True), - sa.Column('biomass_type_id', sa.Integer(), nullable=True), - sa.Column('biomass_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('biomass_id') - ) - op.create_index(op.f('ix_biomass_biomass_name'), 'biomass', ['biomass_name'], unique=False) - op.create_index(op.f('ix_biomass_biomass_type_id'), 'biomass', ['biomass_type_id'], unique=False) - op.create_table('biomass_availability', - sa.Column('availability_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('primary_product_id', sa.Integer(), nullable=True), - sa.Column('from_month', sa.Numeric(), nullable=True), - sa.Column('to_month', sa.Numeric(), nullable=True), - sa.Column('kg_low', sa.Numeric(), nullable=True), - sa.Column('kg_avg', sa.Numeric(), nullable=True), - sa.Column('kg_high', sa.Numeric(), nullable=True), - sa.Column('bdt_low', sa.Numeric(), nullable=True), - sa.Column('bdt_avg', sa.Numeric(), nullable=True), - sa.Column('bdt_high', sa.Numeric(), nullable=True), - sa.Column('data_source', sa.Integer(), nullable=True), - sa.Column('availability_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('availability_id') - ) - op.create_index(op.f('ix_biomass_availability_biomass_id'), 'biomass_availability', ['biomass_id'], unique=False) - op.create_table('biomass_price', - sa.Column('price_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('price_per_kg_low', sa.Numeric(), nullable=True), - sa.Column('price_per_kg_avg', sa.Numeric(), nullable=True), - sa.Column('price_per_kg_high', sa.Numeric(), nullable=True), - sa.Column('price_data_sources', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('price_id') - ) - op.create_index(op.f('ix_biomass_price_biomass_id'), 'biomass_price', ['biomass_id'], unique=False) - op.create_table('biomass_quality', - sa.Column('quality_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('expected_quality', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('output_feedstocks', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('convertibility', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('disposal_challenges', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('existing_markets', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('substitute_materials', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('regulatory_issues', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('quality_data_sources', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('quality_id') - ) - op.create_index(op.f('ix_biomass_quality_biomass_id'), 'biomass_quality', ['biomass_id'], unique=False) - op.create_table('biomass_test', - sa.Column('biomass_test_id', sa.Integer(), nullable=False), - sa.Column('biomass_test_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('biomass_test_notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('biomass_test_id') - ) - op.create_index(op.f('ix_biomass_test_biomass_test_name'), 'biomass_test', ['biomass_test_name'], unique=False) - op.create_table('biomass_type', - sa.Column('biomass_type_id', sa.Integer(), nullable=False), - sa.Column('biomass_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('biomass_type_id'), - sa.UniqueConstraint('biomass_type') - ) - op.create_table('buildings', - sa.Column('building_id', sa.Integer(), nullable=False), - sa.Column('building_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('affiliation_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('building_id'), - sa.UniqueConstraint('building_name') - ) - op.create_table('cities', - sa.Column('city_id', sa.Integer(), nullable=False), - sa.Column('city_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('city_id'), - sa.UniqueConstraint('city_name') - ) - op.create_table('collection_methods', - sa.Column('collection_method_id', sa.Integer(), nullable=False), - sa.Column('collection_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('collection_method_id'), - sa.UniqueConstraint('collection_method_name') - ) - op.create_table('collectors', - sa.Column('collector_id', sa.Integer(), nullable=False), - sa.Column('collector_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('collector_affiliation', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('collector_id'), - sa.UniqueConstraint('collector_name') - ) - op.create_table('compositional_analysis', - sa.Column('cmp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('calculated_parameter_id', sa.Integer(), nullable=True), - sa.Column('calculated_parameter_value', sa.Numeric(), nullable=True), - sa.Column('calculated_parameter_unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('cmp_id') - ) - op.create_table('counties', - sa.Column('county_id', sa.Integer(), nullable=False), - sa.Column('county_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('county_id'), - sa.UniqueConstraint('county_name') - ) - op.create_table('data_sources', - sa.Column('source_id', sa.Integer(), nullable=False), - sa.Column('source_name_id', sa.Integer(), nullable=True), - sa.Column('source_type_id', sa.Integer(), nullable=True), - sa.Column('data_resolution_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('url_id', sa.Integer(), nullable=True), - sa.Column('import_timestamp', sa.DateTime(), nullable=True), - sa.PrimaryKeyConstraint('source_id') - ) - op.create_index('idx_data_sources_source_name_id', 'data_sources', ['source_name_id'], unique=False) - op.create_table('doi', - sa.Column('doi_id', sa.Integer(), nullable=False), - sa.Column('doi', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('doi_id') - ) - op.create_table('equipment', - sa.Column('equipment_id', sa.Integer(), nullable=False), - sa.Column('equipment_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('equipment_room_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('equipment_id'), - sa.UniqueConstraint('equipment_name') - ) - op.create_table('experiment_methods', - sa.Column('experiment_method_id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('experiment_method_id') - ) - op.create_index('idx_experiment_methods_experiment_id', 'experiment_methods', ['experiment_id'], unique=False) - op.create_index('idx_experiment_methods_method_id', 'experiment_methods', ['method_id'], unique=False) - op.create_table('experiments', - sa.Column('experiment_id', sa.Integer(), nullable=False), - sa.Column('exper_uuid', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('gsheet_exper_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('analysis_abbrev_id', sa.Integer(), nullable=True), - sa.Column('exper_start_date', sa.Date(), nullable=True), - sa.Column('exper_duration', sa.Numeric(), nullable=True), - sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('exper_location_id', sa.Integer(), nullable=True), - sa.Column('exper_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('experiment_id'), - sa.UniqueConstraint('exper_uuid'), - sa.UniqueConstraint('gsheet_exper_id') - ) - op.create_index('idx_experiments_analysis_type_id', 'experiments', ['analysis_type_id'], unique=False) - op.create_table('external_atip', - sa.Column('atip_ID', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('atip_ID') - ) - op.create_table('external_dairy_one', - sa.Column('dairy_one_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('samples_count', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('accumulated_years_from', sa.Date(), nullable=True), - sa.Column('accumulated_years_to', sa.Date(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('dairy_one_id') - ) - op.create_index('idx_external_dairy_one_biomass_id', 'external_dairy_one', ['biomass_id'], unique=False) - op.create_index('idx_external_dairy_one_parameter_id', 'external_dairy_one', ['parameter_id'], unique=False) - op.create_table('external_ebmud', - sa.Column('ebmud_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('ebmud_id') - ) - op.create_table('external_inl_biofeedstock_library', - sa.Column('bfl_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('state_id', sa.Integer(), nullable=True), - sa.Column('affiliations_id', sa.Integer(), nullable=True), - sa.Column('harvest_method_id', sa.Integer(), nullable=True), - sa.Column('collection_method_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('min_value', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('accumulated_years_from', sa.Date(), nullable=True), - sa.Column('accumulated_years_to', sa.Date(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('bfl_id') - ) - op.create_index('idx_external_inl_biofeedstock_library_biomass_id', 'external_inl_biofeedstock_library', ['biomass_id'], unique=False) - op.create_table('external_land_id', - sa.Column('land_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('land_id') - ) - op.create_table('external_phyllis2', - sa.Column('phyllis_id', sa.Integer(), nullable=False), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_method_id', sa.Integer(), nullable=True), - sa.Column('mean_value', sa.Numeric(), nullable=True), - sa.Column('std_dev', sa.Numeric(), nullable=True), - sa.Column('max_value', sa.Numeric(), nullable=True), - sa.Column('sample_count', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('methodology_reference_id', sa.Integer(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('phyllis_id') - ) - op.create_index('idx_external_phyllis2_analysis_type_id', 'external_phyllis2', ['analysis_type_id'], unique=False) - op.create_index('idx_external_phyllis2_biomass_id', 'external_phyllis2', ['biomass_id'], unique=False) - op.create_table('external_usda', - sa.Column('usda_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('geometry_id', sa.Integer(), nullable=True), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_date', sa.Date(), nullable=True), - sa.PrimaryKeyConstraint('usda_id') - ) - op.create_table('fermentation_profile', - sa.Column('fp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('organism_id', sa.Integer(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('fp_id') - ) - op.create_table('field_samples', - sa.Column('sample_id', sa.Integer(), nullable=False), - sa.Column('biomass_id', sa.Integer(), nullable=False), - sa.Column('sample_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('source_codename_id', sa.Integer(), nullable=True), - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('field_storage_id', sa.Integer(), nullable=True), - sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), - sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('collection_timestamp', sa.DateTime(), nullable=True), - sa.Column('collection_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_date', sa.Date(), nullable=True), - sa.Column('amount_collected_kg', sa.Numeric(), nullable=True), - sa.Column('provider_id', sa.Integer(), nullable=True), - sa.Column('collector_id', sa.Integer(), nullable=True), - sa.Column('basic_sample_info_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('created_at', sa.DateTime(), nullable=False), - sa.PrimaryKeyConstraint('sample_id') - ) - op.create_index(op.f('ix_field_samples_biomass_id'), 'field_samples', ['biomass_id'], unique=False) - op.create_index(op.f('ix_field_samples_source_codename_id'), 'field_samples', ['source_codename_id'], unique=False) - op.create_table('field_storage', - sa.Column('field_storage_id', sa.Integer(), nullable=False), - sa.Column('storage_method', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('field_storage_id'), - sa.UniqueConstraint('storage_method') - ) - op.create_table('fips', - sa.Column('fips_id', sa.Integer(), nullable=False), - sa.Column('fips_description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('fips_id') - ) - op.create_table('gasification_profile', - sa.Column('gasification_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('product_type_id', sa.Integer(), nullable=True), - sa.Column('product_value', sa.Numeric(), nullable=True), - sa.Column('product_unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('gasification_id') - ) - op.create_table('geographic_locations', - sa.Column('location_id', sa.Integer(), nullable=False), - sa.Column('street_address_id', sa.Integer(), nullable=True), - sa.Column('city_id', sa.Integer(), nullable=True), - sa.Column('zip_id', sa.Integer(), nullable=True), - sa.Column('county_id', sa.Integer(), nullable=True), - sa.Column('state_id', sa.Integer(), nullable=True), - sa.Column('region_id', sa.Integer(), nullable=True), - sa.Column('fips_id', sa.Integer(), nullable=True), - sa.Column('latitude', sa.Numeric(), nullable=True), - sa.Column('longitude', sa.Numeric(), nullable=True), - sa.Column('location_resolution_id', sa.Integer(), nullable=True), - sa.Column('is_anonymous', sa.Boolean(), nullable=True), - sa.PrimaryKeyConstraint('location_id') - ) - op.create_table('harvest_methods', - sa.Column('harvest_method_id', sa.Integer(), nullable=False), - sa.Column('harvest_method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('harvest_method_id'), - sa.UniqueConstraint('harvest_method_name') - ) - op.create_table('icp_analysis', - sa.Column('icp_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('concentration_calculation_url_id', sa.Integer(), nullable=True), - sa.Column('result_wavelength', sa.Numeric(), nullable=True), - sa.Column('raw_url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('icp_id') - ) - op.create_table('import_log', - sa.Column('import_id', sa.Integer(), nullable=False), - sa.Column('import_timestamp', sa.DateTime(), nullable=True), - sa.Column('destination', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('source_file', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('records_imported', sa.Integer(), nullable=True), - sa.Column('import_status', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('error_log', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('import_user', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('import_id') - ) - op.create_table('location_resolutions', - sa.Column('location_resolution_id', sa.Integer(), nullable=False), - sa.Column('resolution_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('location_resolution_id'), - sa.UniqueConstraint('resolution_type') - ) - op.create_table('metadata', - sa.Column('metadata_id', sa.Integer(), nullable=False), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('ag_treatment_id', sa.Integer(), nullable=True), - sa.Column('last_application_date', sa.Date(), nullable=True), - sa.Column('treatment_amount_per_acre', sa.Numeric(), nullable=True), - sa.Column('soil_type', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('metadata_id') - ) - op.create_table('method_abbrevs', - sa.Column('method_abbrev_id', sa.Integer(), nullable=False), - sa.Column('method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_abbrev_id'), - sa.UniqueConstraint('method_abbrev') - ) - op.create_table('method_categories', - sa.Column('method_category_id', sa.Integer(), nullable=False), - sa.Column('method_category', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_category_id'), - sa.UniqueConstraint('method_category') - ) - op.create_table('method_equipment', - sa.Column('method_equipment_id', sa.Integer(), nullable=False), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('equipment_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('method_equipment_id') - ) - op.create_index('idx_method_equipment_equipment_id', 'method_equipment', ['equipment_id'], unique=False) - op.create_index('idx_method_equipment_method_id', 'method_equipment', ['method_id'], unique=False) - op.create_table('method_standards', - sa.Column('method_standard_id', sa.Integer(), nullable=False), - sa.Column('method_standard', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('method_standard_id'), - sa.UniqueConstraint('method_standard') - ) - op.create_table('methods', - sa.Column('method_id', sa.Integer(), nullable=False), - sa.Column('method_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('method_category_id', sa.Integer(), nullable=True), - sa.Column('method_standard_id', sa.Integer(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('detection_limits', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('procedure_reference_id', sa.Integer(), nullable=True), - sa.Column('method_url_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('method_id'), - sa.UniqueConstraint('method_name') - ) - op.create_index('idx_methods_method_name', 'methods', ['method_name'], unique=False) - op.create_table('organisms', - sa.Column('organism_id', sa.Integer(), nullable=False), - sa.Column('organism_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('organism_strain_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('organism_id') - ) - op.create_table('parameter_catagories', - sa.Column('parameter_catagory_id', sa.Integer(), nullable=False), - sa.Column('parameter_catagory', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('parameter_catagory_id') - ) - op.create_table('parameter_methods', - sa.Column('param_method_id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('param_method_id') - ) - op.create_table('parameter_units', - sa.Column('parameter_unit_id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('parameter_unit_id') - ) - op.create_index('idx_parameter_units_parameter_id', 'parameter_units', ['parameter_id'], unique=False) - op.create_index('idx_parameter_units_unit_id', 'parameter_units', ['unit_id'], unique=False) - op.create_table('parameters', - sa.Column('parameter_id', sa.Integer(), nullable=False), - sa.Column('parameter_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('parameter_category_id', sa.Integer(), nullable=True), - sa.Column('standard_unit_id', sa.Integer(), nullable=True), - sa.Column('calculated', sa.Boolean(), nullable=True), - sa.Column('description', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('typical_range_min', sa.Numeric(), nullable=True), - sa.Column('typical_range_max', sa.Numeric(), nullable=True), - sa.PrimaryKeyConstraint('parameter_id'), - sa.UniqueConstraint('parameter_name') - ) - op.create_table('particle_size', - sa.Column('particle_size_id', sa.Integer(), nullable=False), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('particle_length', sa.Integer(), nullable=True), - sa.Column('particle_width', sa.Integer(), nullable=True), - sa.Column('particle_height', sa.Integer(), nullable=True), - sa.Column('particle_units', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('particle_size_id') - ) - op.create_table('preprocessed_samples', - sa.Column('prepro_material_id', sa.Integer(), nullable=False), - sa.Column('prepro_material_name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('biomass_sample_id', sa.Integer(), nullable=True), - sa.Column('prepro_method_id', sa.Integer(), nullable=True), - sa.Column('amount_before_drying_g', sa.Numeric(), nullable=True), - sa.Column('amount_after_drying', sa.Numeric(), nullable=True), - sa.Column('processing_date', sa.Date(), nullable=True), - sa.Column('storage_building', sa.Integer(), nullable=True), - sa.Column('amount_remaining_g', sa.Numeric(), nullable=True), - sa.Column('amount_as_of_date', sa.Date(), nullable=True), - sa.Column('prepro_analyst_id', sa.Integer(), nullable=True), - sa.Column('prepro_note', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prepro_material_id') - ) - op.create_index('idx_preprocessed_samples_biomass_sample_id', 'preprocessed_samples', ['biomass_sample_id'], unique=False) - op.create_index('idx_preprocessed_samples_prepro_method_id', 'preprocessed_samples', ['prepro_method_id'], unique=False) - op.create_table('preprocessing_methods', - sa.Column('prepro_method_id', sa.Integer(), nullable=False), - sa.Column('prepro_method', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('prepro_method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('prepro_temp_c', sa.Numeric(), nullable=True), - sa.Column('drying_step', sa.Boolean(), nullable=True), - sa.Column('method_ref_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('prepro_method_id') - ) - op.create_table('preprocessing_methods_abbreviations', - sa.Column('prepro_methods_abbrev_id', sa.Integer(), nullable=False), - sa.Column('prepro_method_abbrev', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prepro_methods_abbrev_id'), - sa.UniqueConstraint('prepro_method_abbrev') - ) - op.create_table('primary_product', - sa.Column('primary_product_id', sa.Integer(), nullable=False), - sa.Column('primary_product_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('primary_product_id'), - sa.UniqueConstraint('primary_product_name') - ) - op.create_table('product_type', - sa.Column('product_type_id', sa.Integer(), nullable=False), - sa.Column('product', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('product_type_id') - ) - op.create_table('provider_types', - sa.Column('provider_type_id', sa.Integer(), nullable=False), - sa.Column('provider_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('provider_type_id') - ) - op.create_table('providers', - sa.Column('provider_id', sa.Integer(), nullable=False), - sa.Column('provider_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.Column('provider_affiliation', sa.Integer(), nullable=True), - sa.Column('provider_type_id', sa.Integer(), nullable=True), - sa.Column('anonymous', sa.Boolean(), nullable=True), - sa.PrimaryKeyConstraint('provider_id'), - sa.UniqueConstraint('provider_name') - ) - op.create_table('proximate_analysis', - sa.Column('prox_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('prox_id') - ) - op.create_table('qc_results', - sa.Column('qc_result_id', sa.Integer(), nullable=False), - sa.Column('qc_result', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('qc_result_id'), - sa.UniqueConstraint('qc_result') - ) - op.create_table('raster_metadata', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('resolution', sa.Float(), nullable=True), - sa.Column('srid', sa.Integer(), nullable=True), - sa.Column('acquisition_date', sa.Date(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('references', - sa.Column('reference_id', sa.Integer(), nullable=False), - sa.Column('reference_title', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_author', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_publication', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('reference_date', sa.Date(), nullable=True), - sa.Column('reference_doi_id', sa.Integer(), nullable=True), - sa.Column('url_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('reference_id') - ) - op.create_table('regions', - sa.Column('region_id', sa.Integer(), nullable=False), - sa.Column('region_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('region_id'), - sa.UniqueConstraint('region_name') - ) - op.create_table('rooms', - sa.Column('room_id', sa.Integer(), nullable=False), - sa.Column('room_number', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('building_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('room_id'), - sa.UniqueConstraint('room_number') - ) - op.create_table('soil_type', - sa.Column('soil_type_id', sa.Integer(), nullable=False), - sa.Column('soil_type', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('soil_location', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('soil_type_id'), - sa.UniqueConstraint('soil_type') - ) - op.create_table('source_names', - sa.Column('source_name_id', sa.Integer(), nullable=False), - sa.Column('source_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('source_name_id'), - sa.UniqueConstraint('source_name') - ) - op.create_table('source_types', - sa.Column('source_type_id', sa.Integer(), nullable=False), - sa.Column('source_type', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('source_type_id'), - sa.UniqueConstraint('source_type') - ) - op.create_table('states', - sa.Column('state_id', sa.Integer(), nullable=False), - sa.Column('state_name', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('state_id'), - sa.UniqueConstraint('state_name') - ) - op.create_table('street_addresses', - sa.Column('street_address_id', sa.Integer(), nullable=False), - sa.Column('street_address', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('street_address_id') - ) - op.create_table('taxonomy', - sa.Column('taxonomy_id', sa.Integer(), nullable=False), - sa.Column('kingdom', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('phylum', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('order', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('family', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('genus', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('species', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('variety_subspecies_cultivar', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('taxonomy_id') - ) - op.create_table('testusers2', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('fullname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('nickname', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('units', - sa.Column('unit_id', sa.Integer(), nullable=False), - sa.Column('unit', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('unit_id'), - sa.UniqueConstraint('unit') - ) - op.create_table('url', - sa.Column('url_id', sa.Integer(), nullable=False), - sa.Column('url', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('url_id'), - sa.UniqueConstraint('url') - ) - op.create_table('vectorized_raster_polygons', - sa.Column('vectorized_ID', sa.Integer(), nullable=False), - sa.Column('geometry', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('raster_id', sa.Integer(), nullable=True), - sa.Column('class_', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('value', sa.Float(), nullable=True), - sa.Column('mean_value', sa.Float(), nullable=True), - sa.Column('std_dev', sa.Float(), nullable=True), - sa.Column('area_m2', sa.Float(), nullable=True), - sa.Column('date_acquired', sa.Date(), nullable=True), - sa.Column('source', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('vectorized_ID') - ) - op.create_table('xrf_analysis', - sa.Column('xrf_id', sa.Integer(), nullable=False), - sa.Column('result_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('notes', sqlmodel.sql.sqltypes.AutoString(), nullable=True), - sa.PrimaryKeyConstraint('xrf_id') - ) - op.create_table('zips', - sa.Column('zip_id', sa.Integer(), nullable=False), - sa.Column('zip_code', sqlmodel.sql.sqltypes.AutoString(), nullable=False), - sa.PrimaryKeyConstraint('zip_id'), - sa.UniqueConstraint('zip_code') - ) - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.drop_table('zips') - op.drop_table('xrf_analysis') - op.drop_table('vectorized_raster_polygons') - op.drop_table('url') - op.drop_table('units') - op.drop_table('testusers2') - op.drop_table('taxonomy') - op.drop_table('street_addresses') - op.drop_table('states') - op.drop_table('source_types') - op.drop_table('source_names') - op.drop_table('soil_type') - op.drop_table('rooms') - op.drop_table('regions') - op.drop_table('references') - op.drop_table('raster_metadata') - op.drop_table('qc_results') - op.drop_table('proximate_analysis') - op.drop_table('providers') - op.drop_table('provider_types') - op.drop_table('product_type') - op.drop_table('primary_product') - op.drop_table('preprocessing_methods_abbreviations') - op.drop_table('preprocessing_methods') - op.drop_index('idx_preprocessed_samples_prepro_method_id', table_name='preprocessed_samples') - op.drop_index('idx_preprocessed_samples_biomass_sample_id', table_name='preprocessed_samples') - op.drop_table('preprocessed_samples') - op.drop_table('particle_size') - op.drop_table('parameters') - op.drop_index('idx_parameter_units_unit_id', table_name='parameter_units') - op.drop_index('idx_parameter_units_parameter_id', table_name='parameter_units') - op.drop_table('parameter_units') - op.drop_table('parameter_methods') - op.drop_table('parameter_catagories') - op.drop_table('organisms') - op.drop_index('idx_methods_method_name', table_name='methods') - op.drop_table('methods') - op.drop_table('method_standards') - op.drop_index('idx_method_equipment_method_id', table_name='method_equipment') - op.drop_index('idx_method_equipment_equipment_id', table_name='method_equipment') - op.drop_table('method_equipment') - op.drop_table('method_categories') - op.drop_table('method_abbrevs') - op.drop_table('metadata') - op.drop_table('location_resolutions') - op.drop_table('import_log') - op.drop_table('icp_analysis') - op.drop_table('harvest_methods') - op.drop_table('geographic_locations') - op.drop_table('gasification_profile') - op.drop_table('fips') - op.drop_table('field_storage') - op.drop_index(op.f('ix_field_samples_source_codename_id'), table_name='field_samples') - op.drop_index(op.f('ix_field_samples_biomass_id'), table_name='field_samples') - op.drop_table('field_samples') - op.drop_table('fermentation_profile') - op.drop_table('external_usda') - op.drop_index('idx_external_phyllis2_biomass_id', table_name='external_phyllis2') - op.drop_index('idx_external_phyllis2_analysis_type_id', table_name='external_phyllis2') - op.drop_table('external_phyllis2') - op.drop_table('external_land_id') - op.drop_index('idx_external_inl_biofeedstock_library_biomass_id', table_name='external_inl_biofeedstock_library') - op.drop_table('external_inl_biofeedstock_library') - op.drop_table('external_ebmud') - op.drop_index('idx_external_dairy_one_parameter_id', table_name='external_dairy_one') - op.drop_index('idx_external_dairy_one_biomass_id', table_name='external_dairy_one') - op.drop_table('external_dairy_one') - op.drop_table('external_atip') - op.drop_index('idx_experiments_analysis_type_id', table_name='experiments') - op.drop_table('experiments') - op.drop_index('idx_experiment_methods_method_id', table_name='experiment_methods') - op.drop_index('idx_experiment_methods_experiment_id', table_name='experiment_methods') - op.drop_table('experiment_methods') - op.drop_table('equipment') - op.drop_table('doi') - op.drop_index('idx_data_sources_source_name_id', table_name='data_sources') - op.drop_table('data_sources') - op.drop_table('counties') - op.drop_table('compositional_analysis') - op.drop_table('collectors') - op.drop_table('collection_methods') - op.drop_table('cities') - op.drop_table('buildings') - op.drop_table('biomass_type') - op.drop_index(op.f('ix_biomass_test_biomass_test_name'), table_name='biomass_test') - op.drop_table('biomass_test') - op.drop_index(op.f('ix_biomass_quality_biomass_id'), table_name='biomass_quality') - op.drop_table('biomass_quality') - op.drop_index(op.f('ix_biomass_price_biomass_id'), table_name='biomass_price') - op.drop_table('biomass_price') - op.drop_index(op.f('ix_biomass_availability_biomass_id'), table_name='biomass_availability') - op.drop_table('biomass_availability') - op.drop_index(op.f('ix_biomass_biomass_type_id'), table_name='biomass') - op.drop_index(op.f('ix_biomass_biomass_name'), table_name='biomass') - op.drop_table('biomass') - op.drop_table('autoclave_profile') - op.drop_table('analyst_contact') - op.drop_table('analysis_types') - op.drop_index('uq_analysis_results_experiment_parameter_replicate', table_name='analysis_results') - op.drop_index('idx_analysis_results_parameter_id', table_name='analysis_results') - op.drop_table('analysis_results') - op.drop_table('analysis_replicate_id') - op.drop_table('analysis_abbreviations') - op.drop_table('ag_treatments') - op.drop_table('affiliations') - # ### end Alembic commands ### From 47734049017a409ac730258e6a18761ce44864af Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Tue, 18 Nov 2025 11:07:32 -0700 Subject: [PATCH 47/81] alembic issue fixed. sqlalchemy commented out for now --- README.md | 117 ++++++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 96 insertions(+), 21 deletions(-) diff --git a/README.md b/README.md index 5dc89ccc..114d504c 100644 --- a/README.md +++ b/README.md @@ -1,35 +1,110 @@ # ca-biositing -Discussion of general issues related to the project and protyping or research +A geospatial bioeconomy project for biositing analysis in California. This +repository provides tools for ETL pipelines to process data from Google Sheets +into PostgreSQL databases, geospatial analysis using QGIS, and a REST API for +data access. + +## Project Structure + +This project uses a **PEP 420 namespace package** structure with three main +components: + +- **`ca_biositing.datamodels`**: Shared SQLModel database models and database + configuration +- **`ca_biositing.pipeline`**: ETL pipelines orchestrated with Prefect, deployed + via Docker +- **`ca_biositing.webservice`**: FastAPI REST API for data access + +### Directory Layout + +```text +ca-biositing/ +├── src/ca_biositing/ # Namespace package root +│ ├── datamodels/ # Database models (SQLModel) +│ ├── pipeline/ # ETL pipelines (Prefect) +│ └── webservice/ # REST API (FastAPI) +├── resources/ # Deployment resources +│ ├── docker/ # Docker Compose configuration +│ └── prefect/ # Prefect deployment files +├── tests/ # Integration tests +├── pixi.toml # Pixi dependencies and tasks +└── pixi.lock # Dependency lock file +``` + +## Quick Start + +### Prerequisites + +- **Pixi** (v0.55.0+): + [Installation Guide](https://pixi.sh/latest/#installation) +- **Docker**: For running the ETL pipeline +- **Google Cloud credentials**: For Google Sheets access (optional) + +### Installation + +```bash +# Clone the repository +git clone https://github.com/uw-ssec/ca-biositing.git +cd ca-biositing + +# Install dependencies with Pixi +pixi install + +# Install pre-commit hooks +pixi run pre-commit-install +``` + +### Running Components + +#### ETL Pipeline (Prefect + Docker) + +**Note**: Before starting the services for the first time, create the required +environment file from the template: -## Relevant Links for project documentations and context +```bash +cp resources/docker/.env.example resources/docker/.env +``` -- eScience Slack channel: 🔒 - [#ssec-ca-biositing](https://escience-institute.slack.com/archives/C098GJCTTFE) -- SSEC Sharepoint (**INTERNAL SSEC ONLY**): 🔒 - [Projects/GeospatialBioeconomy](https://uwnetid.sharepoint.com/:f:/r/sites/og_ssec_escience/Shared%20Documents/Projects/GeospatialBioeconomy?csf=1&web=1&e=VBUGQG) -- Shared Sharepoint Directory: 🔒 - [SSEC CA Biositing Shared Folder](https://uwnetid.sharepoint.com/:f:/r/sites/og_ssec_escience/Shared%20Documents/Projects/GeospatialBioeconomy/SSEC%20CA%20Biositing%20Shared%20Folder?csf=1&web=1&e=p5wBel) +Then start and use the services: -## General Discussions +```bash +# 1. Create the initial database migration script +# (This is only needed once for a new database) +pixi run initial-migration -For general discussion, ideas, and resources please use the -[GitHub Discussions](https://github.com/uw-ssec/ca-biositing/discussions). -However, if there's an internal discussion that need to happen, please use the -slack channel provided. +# 2. Start all services (PostgreSQL, Prefect server, worker) +# This will also automatically apply any pending database migrations. +pixi run start-services -- Meeting Notes in GitHub: - [discussions/meetings](https://github.com/uw-ssec/ca-biositing/discussions/categories/meetings) +# 3. Deploy flows to Prefect +pixi run deploy -## Questions +# Run the ETL pipeline +pixi run run-etl -If you have any questions about our process, or locations of SSEC resources, -please ask [Anshul Tambay](https://github.com/atambay37). +# Monitor via Prefect UI: http://localhost:4200 + +# To apply new migrations after the initial setup +pixi run migrate + +# Stop services +pixi run teardown-services +``` -## QGIS +See [`resources/README.md`](resources/README.md) for detailed pipeline +documentation. + +#### Web Service (FastAPI) + +```bash +# Start the web service +pixi run start-webservice + +# Access API docs: http://localhost:8000/docs +``` -This project includes QGIS for geospatial analysis and visualization. You can -run QGIS using pixi with the following command: +#### QGIS (Geospatial Analysis) ```bash pixi run qgis From 8048a0c8f6b28e56bbff0417b0902d95f498d93d Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Wed, 19 Nov 2025 16:24:37 -0700 Subject: [PATCH 48/81] adding asyncpg to root pixi.toml --- pixi.toml | 20 ++++++-------------- 1 file changed, 6 insertions(+), 14 deletions(-) diff --git a/pixi.toml b/pixi.toml index f742f613..a3887d3c 100644 --- a/pixi.toml +++ b/pixi.toml @@ -29,20 +29,12 @@ python = "~=3.12" pre-commit = ">=4.2.0,<5" pytest = ">=8.4.2,<9" pytest-cov = ">=7.0.0,<8" -sqlmodel = ">=0.0.19,<0.1" -alembic = ">=1.13.2,<2" -psycopg2 = ">=2.9.9,<3" -python-dotenv = ">=1.0.1,<2" -pandas = ">=2.2.0,<3" -pyjanitor = "*" -gspread = "*" -gspread-dataframe = "*" -pydantic-settings = "*" -google-auth-oauthlib = "*" -prefect = "*" -uvicorn = ">=0.30.0,<1" -fastapi = ">=0.115.0,<1" -linkml = "*" +pip = ">=25.2,<26" +docker-compose = ">=2.39.2,<3" +docker-cli = ">=28.3.1,<29" +testcontainers = ">=4.13.2,<5" +python-dotenv = ">=1.2.1,<2" +asyncpg = ">=0.29.0,<0.30" [tasks] pre-commit-all = "pre-commit run --all-files" From 3404501961c13b0f47d467ae0000cd1e1467b9a0 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Sun, 7 Dec 2025 20:24:49 -0700 Subject: [PATCH 49/81] rebasing to upstream main. 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cbafb470cf848d93b5d013e2ecb245d4aa1c8fd0504e863ccefa32445359d680 + requires_dist: + - pyyaml>=3.10 ; extra == 'watchmedo' + requires_python: '>=3.9' +- pypi: https://files.pythonhosted.org/packages/fe/c4/225c87bae08c8b9ec99030cd48ae9c4eca050a59bf5c2255853e18c87b50/watchdog-6.0.0-cp313-cp313-macosx_11_0_arm64.whl + name: watchdog + version: 6.0.0 + sha256: a175f755fc2279e0b7312c0035d52e27211a5bc39719dd529625b1930917345b + requires_dist: + - pyyaml>=3.10 ; extra == 'watchmedo' + requires_python: '>=3.9' - conda: https://conda.anaconda.org/conda-forge/linux-64/watchdog-6.0.0-py312h7900ff3_2.conda sha256: 0c0c7064908f7cf5d97e9fdf94f6892f05b3ba148ef8f5321ae6e7317720f05f md5: a5379513de9c827fb27935cefa3bf30d @@ -33641,6 +36143,11 @@ packages: - pkg:pypi/wcwidth?source=hash-mapping size: 33670 timestamp: 1758622418893 +- pypi: https://files.pythonhosted.org/packages/e2/cc/e097523dd85c9cf5d354f78310927f1656c422bd7b2613b2db3e3f9a0f2c/webcolors-25.10.0-py3-none-any.whl + name: webcolors + version: 25.10.0 + sha256: 032c727334856fc0b968f63daa252a1ac93d33db2f5267756623c210e57a4f1d + requires_python: '>=3.10' - conda: https://conda.anaconda.org/conda-forge/noarch/websocket-client-1.9.0-pyhd8ed1ab_0.conda sha256: 42a2b61e393e61cdf75ced1f5f324a64af25f347d16c60b14117393a98656397 md5: 2f1ed718fcd829c184a6d4f0f2e07409 diff --git a/pixi.toml b/pixi.toml index a3887d3c..bd7e5fdd 100644 --- a/pixi.toml +++ b/pixi.toml @@ -311,3 +311,7 @@ cwd = "deployment/cloud/gcp/infrastructure" [feature.cloud.tasks.cloud-destroy] cmd = "tofu destroy" cwd = "deployment/cloud/gcp/infrastructure" + +[pypi-dependencies] +linkml = ">=1.9.3, <2" +sqlalchemy = ">=2.0.44, <3" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml new file mode 100644 index 00000000..94d9f8d2 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml @@ -0,0 +1,32 @@ +id: https://w3id.org/ca_biositing +name: ca_biositing +title: CA Biositing Schema +description: >- + LinkML schema for the CA Biositing project, defining data models for + bioeconomy site selection, including resources, sampling, analysis, and + infrastructure. +license: https://creativecommons.org/publicdomain/zero/1.0/ +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + schema: http://schema.org/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - modules/core + - modules/resource_information + - modules/field_sampling + - modules/places + - modules/people + - modules/lineage + - modules/data_sources_metadata + - modules/sample_preparation + - modules/methods_parameters_units + - modules/experiment_equipment + - modules/general_analysis + - modules/aim1_records + - modules/aim2_records + - modules/external_data diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml new file mode 100644 index 00000000..179c4898 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml @@ -0,0 +1,123 @@ +id: https://w3id.org/ca_biositing/aim1_records +name: aim1_records +title: Aim 1 Records +description: Records for Aim 1 analysis. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - general_analysis + - experiment_equipment + - resource_information + - sample_preparation + - methods_parameters_units + - data_sources_metadata + +classes: + Aim1RecordBase: + is_a: BaseEntity + abstract: true + slots: + - dataset_id + - experiment_id + - resource_id + - sample_id + - technical_replicate_no + - technical_replicate_total + - method_id + - raw_data_id + - qc_pass + - note + + ProximateRecord: + is_a: Aim1RecordBase + description: Proximate analysis record. + + UltimateRecord: + is_a: Aim1RecordBase + description: Ultimate analysis record. + + CompositionalRecord: + is_a: Aim1RecordBase + description: Compositional analysis record. + + IcpRecord: + is_a: Aim1RecordBase + description: ICP analysis record. + + XrfRecord: + is_a: Aim1RecordBase + description: XRF analysis record. + slots: + - maybe_wavelength_nm + - maybe_intensity + - maybe_energy_slope + - maybe_energy_offset + + XrdRecord: + is_a: Aim1RecordBase + description: XRD analysis record. + slots: + - maybe_scan_low_nm + - maybe_scan_high_nm + + CalorimetryRecord: + is_a: Aim1RecordBase + description: Calorimetry analysis record. + + FtnirRecord: + is_a: Aim1RecordBase + description: FT-NIR analysis record. + + RgbRecord: + is_a: Aim1RecordBase + description: RGB analysis record. + +slots: + technical_replicate_no: + range: integer + description: Replicate number. + + technical_replicate_total: + range: integer + description: Total number of replicates. + + raw_data_id: + range: integer + description: Reference to FileObjectMetadata. + + qc_pass: + range: boolean + description: Whether the record passed QC. + + maybe_wavelength_nm: + range: decimal + description: Wavelength in nm. + + maybe_intensity: + range: decimal + description: Intensity. + + maybe_energy_slope: + range: decimal + description: Energy slope. + + maybe_energy_offset: + range: decimal + description: Energy offset. + + maybe_scan_low_nm: + range: integer + description: Low scan range in nm. + + maybe_scan_high_nm: + range: integer + description: High scan range in nm. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml new file mode 100644 index 00000000..416589b7 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml @@ -0,0 +1,143 @@ +id: https://w3id.org/ca_biositing/aim2_records +name: aim2_records +title: Aim 2 Records +description: Records for Aim 2 analysis. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - general_analysis + - experiment_equipment + - resource_information + - sample_preparation + - methods_parameters_units + - data_sources_metadata + - people + +classes: + Aim2RecordBase: + is_a: BaseEntity + abstract: true + slots: + - dataset_id + - experiment_id + - resource_id + - sample_id + - analyst_id + - raw_data_id + - qc_pass + - note + + PretreatmentRecord: + is_a: Aim2RecordBase + description: Pretreatment record. + slots: + - pretreatment_method_id + - eh_method_id + - reaction_block_id + - block_position + - temperature + - replicate_no + + FermentationRecord: + is_a: Aim2RecordBase + description: Fermentation record. + slots: + - strain_id + - pretreatment_method_id + - eh_method_id + - replicate_no + - well_position + - temperature + - agitation_rpm + - vessel_id + - analyte_detection_equipment_id + + GasificationRecord: + is_a: Aim2RecordBase + description: Gasification record. + slots: + - feedstock_mass + - bed_temperature + - gas_flow_rate + - technical_replicate_no + + AutoclaveRecord: + is_a: Aim2RecordBase + description: Autoclave record. + slots: + - technical_replicate_no + + Strain: + is_a: LookupBase + description: Strain used in fermentation. + slots: + - parent_strain_id + +slots: + pretreatment_method_id: + range: integer + description: Reference to Method (pretreatment). + + eh_method_id: + range: integer + description: Reference to Method (enzymatic hydrolysis). + + reaction_block_id: + range: integer + description: ID of the reaction block. + + block_position: + range: string + description: Position in the block. + + temperature: + range: decimal + description: Temperature. + + replicate_no: + range: integer + description: Replicate number. + + strain_id: + range: integer + description: Reference to Strain. + + well_position: + range: string + description: Position in the well. + + agitation_rpm: + range: decimal + description: Agitation in RPM. + + vessel_id: + range: integer + description: Reference to Equipment (vessel). + + analyte_detection_equipment_id: + range: integer + description: Reference to Equipment (detection). + + feedstock_mass: + range: decimal + description: Mass of feedstock. + + bed_temperature: + range: decimal + description: Bed temperature. + + gas_flow_rate: + range: decimal + description: Gas flow rate. + + parent_strain_id: + range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml new file mode 100644 index 00000000..987f0d1d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml @@ -0,0 +1,93 @@ +id: https://w3id.org/ca_biositing/analysis +name: analysis +title: Analysis Definitions +description: Datasets and observations. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - methods + +classes: + Dataset: + description: Dataset definition. + slots: + - id + - name + - record_type + - source_id + - start_date + - end_date + - description + slot_usage: + id: + identifier: true + range: integer + + Observation: + description: Observation data. + slots: + - id + - dataset_id + - record_type + - record_id + - parameter_id + - value + - unit_id + - dimension_type_id + - dimension_value + - dimension_unit_id + - note + slot_usage: + id: + identifier: true + range: integer + + DimensionType: + is_a: LookupBase + description: Type of dimension (e.g. timepoint, wavelength). + + AnalysisType: + is_a: LookupBase + description: Type of analysis. + +slots: + dataset_id: + range: integer + description: Reference to Dataset. + + record_type: + range: string + description: Type of record. + + record_id: + range: integer + description: ID of the record. + + value: + range: decimal + description: Value of the observation. + + unit_id: + range: integer + description: Reference to Unit. + + dimension_type_id: + range: integer + description: Reference to DimensionType. + + dimension_value: + range: decimal + description: Value of the dimension. + + dimension_unit_id: + range: integer + description: Reference to Unit (dimension). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml new file mode 100644 index 00000000..35cc271d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml @@ -0,0 +1,229 @@ +id: https://w3id.org/ca_biositing/analysis_records +name: analysis_records +title: Analysis Records +description: Specific analysis record types. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - analysis + - experiments + - methods + - sampling + - resources + +classes: + # Base Record Class (Mixin) + RecordBase: + mixin: true + slots: + - id + - dataset_id + - experiment_id + - resource_id + - sample_id + - technical_replicate_no + - technical_replicate_total + - method_id + - raw_data_id + - qc_pass + - note + slot_usage: + id: + identifier: true + range: integer + + ProximateRecord: + is_a: RecordBase + description: Proximate analysis record. + + UltimateRecord: + is_a: RecordBase + description: Ultimate analysis record. + + CompositionalRecord: + is_a: RecordBase + description: Compositional analysis record. + + IcpRecord: + is_a: RecordBase + description: ICP analysis record. + + XrfRecord: + is_a: RecordBase + description: XRF analysis record. + slots: + - maybe_wavelength_nm + - maybe_intensity + - maybe_energy_slope + - maybe_energy_offset + + XrdRecord: + is_a: RecordBase + description: XRD analysis record. + slots: + - maybe_scan_low_nm + - maybe_scan_high_nm + + CalorimetryRecord: + is_a: RecordBase + description: Calorimetry analysis record. + + FtnirRecord: + is_a: RecordBase + description: FT-NIR analysis record. + + RgbRecord: + is_a: RecordBase + description: RGB analysis record. + + PretreatmentRecord: + is_a: RecordBase + description: Pretreatment record. + slots: + - pretreatment_method + - eh_method_id + - reaction_block_id + - block_position + - temperature + - replicate_no + - analyst_id + + FermentationRecord: + is_a: RecordBase + description: Fermentation record. + slots: + - strain_id + - pretreatement_method_id + - eh_method_id + - replicate_no + - well_position + - temperature + - agitation_rpm + - vessel_id + - analyte_detection_equipment_id + - analyst_id + + GasificationRecord: + is_a: RecordBase + description: Gasification record. + slots: + - feedstock_mass + - bed_temperature + - gas_flow_rate + - analyst_id + + AutoclaveRecord: + is_a: RecordBase + description: Autoclave record. + slots: + - analyst_id + +slots: + technical_replicate_no: + range: integer + description: Technical replicate number. + + technical_replicate_total: + range: integer + description: Total technical replicates. + + raw_data_id: + range: integer + description: Reference to FileObjectMetadata. + + qc_pass: + range: boolean + description: Whether QC passed. + + maybe_wavelength_nm: + range: decimal + description: Wavelength in nm. + + maybe_intensity: + range: decimal + description: Intensity. + + maybe_energy_slope: + range: decimal + description: Energy slope. + + maybe_energy_offset: + range: decimal + description: Energy offset. + + maybe_scan_low_nm: + range: integer + description: Scan low nm. + + maybe_scan_high_nm: + range: integer + description: Scan high nm. + + pretreatment_method: + range: integer + description: Reference to Method (pretreatment). + + eh_method_id: + range: integer + description: Reference to Method (enzymatic hydrolysis). + + reaction_block_id: + range: integer + description: Reaction block ID. + + block_position: + range: string + description: Position in block. + + temperature: + range: decimal + description: Temperature. + + replicate_no: + range: integer + description: Replicate number. + + strain_id: + range: integer + description: Reference to Strain. + + pretreatement_method_id: + range: integer + description: Reference to Method (pretreatment). + + well_position: + range: string + description: Well position. + + agitation_rpm: + range: decimal + description: Agitation RPM. + + vessel_id: + range: integer + description: Reference to Equipment (vessel). + + analyte_detection_equipment_id: + range: integer + description: Reference to Equipment (detection). + + feedstock_mass: + range: decimal + description: Feedstock mass. + + bed_temperature: + range: decimal + description: Bed temperature. + + gas_flow_rate: + range: decimal + description: Gas flow rate. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml new file mode 100644 index 00000000..84eaa04c --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml @@ -0,0 +1,267 @@ +id: https://w3id.org/ca_biositing/core +name: core +title: Core Definitions +description: Base classes, lineage, and data source definitions. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + +classes: + BaseEntity: + mixin: true + description: Base entity included in all main entity tables. + slots: + - id + - created_at + - updated_at + - etl_run_id + - lineage_group_id + + LookupBase: + mixin: true + description: Base class for enum/ontology-like tables. + slots: + - id + - name + - description + - uri + + LineageGroup: + is_a: BaseEntity + description: Grouping for lineage information. + slots: + - note + + EntityLineage: + description: Lineage information for a specific entity. + slots: + - id + - lineage_group_id + - source_table + - source_row_id + - note + + EtlRun: + description: Information about an ETL run. + slots: + - id + - started_at + - completed_at + - pipeline_name + - status + - records_ingested + - note + slot_usage: + id: + identifier: true + range: string + + DataSource: + is_a: BaseEntity + description: Information about a data source. + slots: + - name + - description + - data_source_type_id + - full_title + - creator + - subject + - publisher + - contributor + - date + - type + - biocirv + - format + - language + - relation + - temporal_coverage + - location_coverage_id + - rights + - uri + + DataSourceType: + is_a: BaseEntity + description: Type of data source. + slots: + - source_type_id + + SourceType: + is_a: LookupBase + description: Lookup for source types (database, literature, etc.). + + LocationResolution: + is_a: LookupBase + description: Resolution of location coverage (nation, state, county, etc.). + + FileObjectMetadata: + is_a: BaseEntity + description: Metadata for file objects. + slots: + - data_source_id + - bucket_path + - file_format + - file_size + - checksum_md5 + - checksum_sha256 + +slots: + id: + identifier: true + range: integer + description: Unique identifier. + + created_at: + range: datetime + description: Timestamp when the record was created. + + updated_at: + range: datetime + description: Timestamp when the record was last updated. + + etl_run_id: + range: string + description: Identifier of the ETL run. + + lineage_group_id: + range: integer + description: Reference to the lineage group. + + name: + range: string + description: Name of the entity. + + description: + range: string + description: Description of the entity. + + uri: + range: uri + description: URI for the entity. + + note: + range: string + description: Additional notes. + + source_table: + range: string + description: Source table name. + + source_row_id: + range: string + description: Source row identifier. + + started_at: + range: datetime + description: Start time of the ETL run. + + completed_at: + range: datetime + description: Completion time of the ETL run. + + pipeline_name: + range: string + description: Name of the pipeline. + + status: + range: string + description: Status of the ETL run. + + records_ingested: + range: integer + description: Number of records ingested. + + data_source_type_id: + range: integer + description: Reference to data source type. + + full_title: + range: string + description: Full title of the data source. + + creator: + range: string + description: Creator of the data source. + + subject: + range: string + description: Subject of the data source. + + publisher: + range: string + description: Publisher of the data source. + + contributor: + range: string + description: Contributor to the data source. + + date: + range: datetime + description: Date associated with the data source. + + type: + range: string + description: Type of the data source. + + biocirv: + range: boolean + description: Whether the data source is internal to BioCirV. + + format: + range: string + description: Format of the data source. + + language: + range: string + description: Language of the data source. + + relation: + range: string + description: Relation of the data source. + + temporal_coverage: + range: string + description: Temporal coverage of the data source. + + location_coverage_id: + range: integer + description: Reference to location resolution. + + rights: + range: string + description: Rights associated with the data source. + + source_type_id: + range: integer + description: Reference to source type. + + data_source_id: + range: integer + description: Reference to data source. + + bucket_path: + range: string + description: Path to the file in the bucket. + + file_format: + range: string + description: Format of the file. + + file_size: + range: integer + description: Size of the file. + + checksum_md5: + range: string + description: MD5 checksum of the file. + + checksum_sha256: + range: string + description: SHA256 checksum of the file. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml new file mode 100644 index 00000000..7bb40074 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -0,0 +1,157 @@ +id: https://w3id.org/ca_biositing/data_sources_metadata +name: data_sources_metadata +title: Data Sources and Metadata +description: Data sources, types, and file metadata. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + DataSource: + is_a: BaseEntity + description: Source of data. + slots: + - name + - description + - data_source_type_id + - full_title + - creator + - subject + - publisher + - contributor + - date + - type + - biocirv + - format + - language + - relation + - temporal_coverage + - location_coverage_id + - rights + - uri + + DataSourceType: + is_a: LookupBase + description: Type of data source. + slots: + - source_type_id + + SourceType: + is_a: LookupBase + description: General source type. + + FileObjectMetadata: + is_a: BaseEntity + description: Metadata for file objects. + slots: + - data_source_id + - bucket_path + - file_format + - file_size + - checksum_md5 + - checksum_sha256 + + LocationResolution: + is_a: LookupBase + description: Resolution of location data. + +slots: + data_source_type_id: + range: integer + description: Reference to DataSourceType. + + source_type_id: + range: integer + description: Reference to SourceType. + + full_title: + range: string + description: Full title of the data source. + + creator: + range: string + description: Creator of the data source. + + subject: + range: string + description: Subject of the data source. + + publisher: + range: string + description: Publisher of the data source. + + contributor: + range: string + description: Contributor to the data source. + + date: + range: datetime + description: Date of the data source. + + type: + range: string + description: Type of the data source. + + biocirv: + range: boolean + description: Whether the data source is internal (BioCirV). + + format: + range: string + description: Format of the data source. + + language: + range: string + description: Language of the data source. + + relation: + range: string + description: Relation of the data source. + + temporal_coverage: + range: string + description: Temporal coverage of the data source. + + location_coverage_id: + range: integer + description: Reference to LocationResolution. + + rights: + range: string + description: Rights of the data source. + + uri: + range: string + description: URI of the resource. + + data_source_id: + range: integer + description: Reference to DataSource. + + bucket_path: + range: string + description: Path to the file in the bucket. + + file_format: + range: string + description: Format of the file. + + file_size: + range: integer + description: Size of the file in bytes. + + checksum_md5: + range: string + description: MD5 checksum of the file. + + checksum_sha256: + range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml new file mode 100644 index 00000000..4896706d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml @@ -0,0 +1,123 @@ +id: https://w3id.org/ca_biositing/experiment_equipment +name: experiment_equipment +title: Experiments and Equipment +description: Experimental data and equipment. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - places + - methods_parameters_units + - sample_preparation + - general_analysis + +classes: + Experiment: + is_a: BaseEntity + description: Experiment definition. + slots: + - analyst_id + - exper_start_date + - exper_duration + - exper_duration_unit_id + - exper_location_id + - description + + Equipment: + is_a: LookupBase + description: Equipment used in experiments. + slots: + - equipment_location_id + + ExperimentMethod: + description: Link between Experiment and Method. + slots: + - id + - experiment_id + - method_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentEquipment: + description: Link between Experiment and Equipment. + slots: + - id + - experiment_id + - equipment_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentAnalysis: + description: Link between Experiment and AnalysisType. + slots: + - id + - experiment_id + - analysis_type_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentPreparedSample: + description: Link between Experiment and PreparedSample. + slots: + - id + - experiment_id + - prepared_sample_id + slot_usage: + id: + identifier: true + range: integer + +slots: + analyst_id: + range: integer + description: Reference to Contact (analyst). + + exper_start_date: + range: date + description: Start date of the experiment. + + exper_duration: + range: decimal + description: Duration of the experiment. + + exper_duration_unit_id: + range: integer + description: Reference to Unit. + + exper_location_id: + range: integer + description: Reference to LocationAddress. + + equipment_location_id: + range: integer + description: Reference to LocationAddress. + + experiment_id: + range: integer + description: Reference to Experiment. + + equipment_id: + range: integer + description: Reference to Equipment. + + analysis_type_id: + range: integer + description: Reference to AnalysisType. + + prepared_sample_id: + range: integer + description: Reference to PreparedSample. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml new file mode 100644 index 00000000..56bf5322 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml @@ -0,0 +1,138 @@ +id: https://w3id.org/ca_biositing/experiments +name: experiments +title: Experiment Definitions +description: Experiments, equipment, and analysis. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - geography + - people + - methods + - sampling + - analysis + +classes: + Experiment: + is_a: BaseEntity + description: Experiment definition. + slots: + - analyst_id + - exper_start_date + - exper_duration + - exper_duration_unit_id + - exper_location_id + - description + + Equipment: + is_a: LookupBase + description: Equipment used in experiments. + slots: + - equipment_location_id + + ExperimentEquipment: + description: Link between experiment and equipment. + slots: + - id + - experiment_id + - equipment_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentAnalysis: + description: Link between experiment and analysis type. + slots: + - id + - experiment_id + - analysis_type_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentPreparedSample: + description: Link between experiment and prepared sample. + slots: + - id + - experiment_id + - prepared_sample_id + slot_usage: + id: + identifier: true + range: integer + + ExperimentMethod: + description: Link between experiment and method. + slots: + - id + - experiment_id + - method_id + slot_usage: + id: + identifier: true + range: integer + + Strain: + is_a: LookupBase + description: Strain of organism. + slots: + - parent_strain_id + +slots: + analyst_id: + range: integer + description: Reference to Contact (analyst). + + exper_start_date: + range: date + description: Start date of experiment. + + exper_duration: + range: decimal + description: Duration of experiment. + + exper_duration_unit_id: + range: integer + description: Reference to Unit. + + exper_location_id: + range: integer + description: Reference to LocationAddress. + + equipment_location_id: + range: integer + description: Reference to LocationAddress. + + experiment_id: + range: integer + description: Reference to Experiment. + + equipment_id: + range: integer + description: Reference to Equipment. + + analysis_type_id: + range: integer + description: Reference to AnalysisType. + + prepared_sample_id: + range: integer + description: Reference to PreparedSample. + + method_id: + range: integer + description: Reference to Method. + + parent_strain_id: + range: integer + description: Reference to Strain (parent). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml new file mode 100644 index 00000000..519632c0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml @@ -0,0 +1,425 @@ +id: https://w3id.org/ca_biositing/external_data +name: external_data +title: External Data +description: External datasets (USDA, LandIQ, etc.). +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - general_analysis + - places + - resource_information + - methods_parameters_units + - data_sources_metadata + +classes: + UsdaDomain: + is_a: LookupBase + description: USDA domain. + + UsdaStatisticCategory: + is_a: LookupBase + description: USDA statistic category. + + UsdaSurveyProgram: + is_a: LookupBase + description: USDA survey program. + + UsdaCommodity: + is_a: LookupBase + description: USDA commodity. + slots: + - usda_source + - usda_code + - parent_commodity_id + + UsdaTermMap: + is_a: BaseEntity + description: Mapping of raw terms to USDA commodities. + slots: + - source_system + - source_context + - raw_term + - usda_commodity_id + - is_verified + - note + + ResourceUsdaCommodityMap: + is_a: BaseEntity + description: Mapping between resources/crops and USDA commodities. + slots: + - resource_id + - primary_crop_id + - usda_commodity_id + - match_tier + - note + + UsdaCensusRecord: + is_a: BaseEntity + description: USDA census record. + slots: + - dataset_id + - geoid + - commodity_code + - year + - source_reference + - note + + UsdaSurveyRecord: + is_a: BaseEntity + description: USDA survey record. + slots: + - dataset_id + - geoid + - commodity_code + - year + - survey_program_id + - survey_period + - reference_month + - seasonal_flag + - note + + UsdaMarketReport: + is_a: BaseEntity + description: USDA market report. + slots: + - slug_id + - slug_name + - report_series_title + - frequency + - office_name + - office_city_id + - office_state_fips + - source_id + + UsdaMarketRecord: + is_a: BaseEntity + description: USDA market record. + slots: + - report_id + - dataset_id + - report_begin_date + - report_end_date + - report_date + - commodity_id + - market_type_id + - market_type_catagory + - grp + - market_catagory_id + - class_ + - grade + - variety + - protein_pct + - application + - pkg + - sale_type + - price_unit_id + - freight + - trans_mode + + LandiqRecord: + is_a: BaseEntity + description: LandIQ record. + slots: + - dataset_id + - polygon_id + - main_crop + - secondary_crop + - tertiary_crop + - quaternary_crop + - confidence + - irrigated + - acres + - version + - note + + BillionTon2023Record: + is_a: BaseEntity + description: Billion Ton 2023 record. + slots: + - subclass_id + - resource_id + - geoid + - county_square_miles + - model_name + - scenario_name + - price_offered_usd + - production + - production_unit_id + - btu_ton + - production_energy_content + - energy_content_unit_id + - product_density_dtpersqmi + - land_source + + Polygon: + description: Geospatial polygon. + slots: + - id + - geoid + - geom + slot_usage: + id: + identifier: true + range: integer + +slots: + usda_source: + range: string + description: Source of the USDA definition (NASS, AMS). + + usda_code: + range: string + description: Official USDA code. + + parent_commodity_id: + range: integer + description: Reference to parent UsdaCommodity. + + source_system: + range: string + description: Source system (NASS, AMS). + + source_context: + range: string + description: Context of the source (Group, Slug ID). + + raw_term: + range: string + description: Raw term from the source. + + usda_commodity_id: + range: integer + description: Reference to UsdaCommodity. + + is_verified: + range: boolean + description: Whether the mapping is verified. + + match_tier: + range: string + description: Tier of the match. + + commodity_code: + range: integer + description: Reference to UsdaCommodity. + + year: + range: integer + description: Year of the record. + + source_reference: + range: string + description: Reference to the source. + + survey_program_id: + range: integer + description: Reference to UsdaSurveyProgram. + + survey_period: + range: string + description: Period of the survey. + + reference_month: + range: string + description: Reference month. + + seasonal_flag: + range: boolean + description: Whether the record is seasonal. + + slug_id: + range: integer + description: Slug ID. + + slug_name: + range: string + description: Slug name. + + report_series_title: + range: string + description: Title of the report series. + + frequency: + range: string + description: Frequency of the report. + + office_name: + range: string + description: Name of the office. + + office_city_id: + range: integer + description: Reference to LocationAddress. + + office_state_fips: + range: string + description: FIPS code of the office state. + + report_id: + range: integer + description: Reference to UsdaMarketReport. + + report_begin_date: + range: datetime + description: Begin date of the report. + + report_end_date: + range: datetime + description: End date of the report. + + report_date: + range: datetime + description: Date of the report. + + commodity_id: + range: integer + description: Reference to UsdaCommodity. + + market_type_id: + range: integer + description: ID of the market type. + + market_type_catagory: + range: string + description: Category of the market type. + + grp: + range: string + description: Group. + + market_catagory_id: + range: integer + description: ID of the market category. + + class_: + range: string + description: Class. + + grade: + range: string + description: Grade. + + variety: + range: string + description: Variety. + + protein_pct: + range: decimal + description: Protein percentage. + + application: + range: string + description: Application. + + pkg: + range: string + description: Package. + + sale_type: + range: string + description: Sale type. + + price_unit_id: + range: integer + description: Reference to Unit. + + freight: + range: string + description: Freight. + + trans_mode: + range: string + description: Transportation mode. + + polygon_id: + range: integer + description: Reference to Polygon. + + main_crop: + range: integer + description: Reference to PrimaryCrop. + + secondary_crop: + range: integer + description: Reference to PrimaryCrop. + + tertiary_crop: + range: integer + description: Reference to PrimaryCrop. + + quaternary_crop: + range: integer + description: Reference to PrimaryCrop. + + confidence: + range: integer + description: Confidence level. + + irrigated: + range: boolean + description: Whether the land is irrigated. + + acres: + range: float + description: Number of acres. + + subclass_id: + range: integer + description: Reference to ResourceSubclass. + + county_square_miles: + range: float + description: Square miles of the county. + + model_name: + range: string + description: Name of the model. + + scenario_name: + range: string + description: Name of the scenario. + + price_offered_usd: + range: decimal + description: Price offered in USD. + + production: + range: integer + description: Production amount. + + production_unit_id: + range: integer + description: Reference to Unit. + + btu_ton: + range: integer + description: BTU per ton. + + production_energy_content: + range: integer + description: Energy content of production. + + energy_content_unit_id: + range: integer + description: Reference to Unit. + + product_density_dtpersqmi: + range: decimal + description: Product density in dry tons per square mile. + + land_source: + range: string + description: Source of land data. + + geom: + range: string + description: Geometry (WKT or similar). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml new file mode 100644 index 00000000..9eaedfd7 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml @@ -0,0 +1,200 @@ +id: https://w3id.org/ca_biositing/field_sampling +name: field_sampling +title: Field Sampling +description: Field sampling and preparation. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - places + - people + - resource_information + - methods_parameters_units + +classes: + FieldSample: + is_a: BaseEntity + description: Sample collected from the field. + slots: + - name + - resource_id + - provider_id + - collector_id + - sample_collection_source + - amount_collected + - amount_collected_unit_id + - sampling_location_id + - field_storage_method_id + - field_storage_duration_value + - field_storage_duration_unit_id + - field_storage_location_id + - collection_timestamp + - collection_method_id + - harvest_method_id + - harvest_date + - field_sample_storage_location_id + - note + + FieldStorageMethod: + is_a: LookupBase + description: Method of field storage. + + CollectionMethod: + is_a: LookupBase + description: Method of collection. + + HarvestMethod: + is_a: LookupBase + description: Method of harvest. + + ProcessingMethod: + is_a: LookupBase + description: Method of processing. + + PhysicalCharacteristic: + is_a: BaseEntity + description: Physical characteristics of a sample. + slots: + - field_sample_id + - particle_length + - particle_width + - particle_height + - particle_unit_id + + SoilType: + is_a: LookupBase + description: Type of soil. + + AgTreatment: + is_a: LookupBase + description: Agricultural treatment. + + FieldSampleCondition: + is_a: BaseEntity + description: Condition of the field sample. + slots: + - field_sample_id + - ag_treatment_id + - last_application_date + - treatment_amount_per_acre + - processing_method_id + + LocationSoilType: + is_a: BaseEntity + description: Soil type at a location. + slots: + - location_id + - soil_type_id + +slots: + provider_id: + range: integer + description: Reference to Provider. + + collector_id: + range: integer + description: Reference to Contact (collector). + + sample_collection_source: + range: string + description: Source of sample collection. + + amount_collected: + range: decimal + description: Amount collected. + + amount_collected_unit_id: + range: integer + description: Reference to Unit. + + sampling_location_id: + range: integer + description: Reference to LocationAddress. + + field_storage_method_id: + range: integer + description: Reference to FieldStorageMethod. + + field_storage_duration_value: + range: decimal + description: Duration of field storage. + + field_storage_duration_unit_id: + range: integer + description: Reference to Unit. + + field_storage_location_id: + range: integer + description: Reference to LocationAddress. + + collection_timestamp: + range: datetime + description: Timestamp of collection. + + collection_method_id: + range: integer + description: Reference to CollectionMethod. + + harvest_method_id: + range: integer + description: Reference to HarvestMethod. + + harvest_date: + range: date + description: Date of harvest. + + field_sample_storage_location_id: + range: integer + description: Reference to LocationAddress. + + field_sample_id: + range: integer + description: Reference to FieldSample. + + particle_length: + range: decimal + description: Length of particle. + + particle_width: + range: decimal + description: Width of particle. + + particle_height: + range: decimal + description: Height of particle. + + particle_unit_id: + range: integer + description: Reference to Unit. + + ag_treatment_id: + range: integer + description: Reference to AgTreatment. + + last_application_date: + range: date + description: Date of last application. + + treatment_amount_per_acre: + range: float + description: Amount of treatment per acre. + + processing_method_id: + range: integer + description: Reference to ProcessingMethod. + + location_id: + range: integer + description: Reference to LocationAddress. + + soil_type_id: + range: integer + description: Reference to SoilType. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml new file mode 100644 index 00000000..cc8a195a --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml @@ -0,0 +1,93 @@ +id: https://w3id.org/ca_biositing/general_analysis +name: general_analysis +title: General Analysis +description: General analysis definitions. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - data_sources_metadata + - methods_parameters_units + +classes: + AnalysisType: + is_a: LookupBase + description: Type of analysis. + + Dataset: + is_a: BaseEntity + description: Dataset definition. + slots: + - name + - record_type + - source_id + - start_date + - end_date + - description + + DimensionType: + is_a: LookupBase + description: Type of dimension. + + Observation: + is_a: BaseEntity + description: Observation data. + slots: + - dataset_id + - record_type + - record_id + - parameter_id + - value + - unit_id + - dimension_type_id + - dimension_value + - dimension_unit_id + - note + +slots: + record_type: + range: string + description: Type of record. + + start_date: + range: date + description: Start date of the dataset. + + end_date: + range: date + description: End date of the dataset. + + dataset_id: + range: integer + description: Reference to Dataset. + + record_id: + range: integer + description: ID of the record. + + value: + range: decimal + description: Value of the observation. + + unit_id: + range: integer + description: Reference to Unit. + + dimension_type_id: + range: integer + description: Reference to DimensionType. + + dimension_value: + range: decimal + description: Value of the dimension. + + dimension_unit_id: + range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml new file mode 100644 index 00000000..32a8a880 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml @@ -0,0 +1,120 @@ +id: https://w3id.org/ca_biositing/geography +name: geography +title: Geography Definitions +description: Geospatial entities and locations. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + Geography: + description: Geographic region definition (e.g. county, state). + slots: + - geoid + - state_name + - state_fips + - county_name + - county_fips + - region_name + - agg_level_desc + slot_usage: + geoid: + identifier: true + + LocationAddress: + is_a: BaseEntity + description: Specific physical location. + slots: + - geography_id + - address_line1 + - address_line2 + - city + - zip + - lat + - lon + - is_anonymous + + Polygon: + description: Geospatial polygon definition. + slots: + - id + - geoid + - geom + slot_usage: + id: + identifier: true + range: integer + +slots: + geoid: + range: string + description: Geographic identifier. + + state_name: + range: string + description: Name of the state. + + state_fips: + range: string + description: FIPS code of the state. + + county_name: + range: string + description: Name of the county. + + county_fips: + range: string + description: FIPS code of the county. + + region_name: + range: string + description: Name of the region. + + agg_level_desc: + range: string + description: Description of the aggregation level. + + geography_id: + range: string + description: Reference to Geography geoid. + + address_line1: + range: string + description: Address line 1. + + address_line2: + range: string + description: Address line 2. + + city: + range: string + description: City name. + + zip: + range: string + description: ZIP code. + + lat: + range: float + description: Latitude. + + lon: + range: float + description: Longitude. + + is_anonymous: + range: boolean + description: Whether the location is anonymous. + + geom: + range: string # TODO: Define geometry type properly, maybe using a custom type or string for WKT + description: Geometry of the polygon. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure.yaml new file mode 100644 index 00000000..6ce9edf9 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure.yaml @@ -0,0 +1,1069 @@ +id: https://w3id.org/ca_biositing/infrastructure +name: infrastructure +title: Infrastructure +description: Infrastructure and facility data. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - general_analysis + - places + - resource_information + +classes: + FacilityRecord: + is_a: BaseEntity + description: Facility record. + slots: + - dataset_id + - facility_name + - location_id + - capacity_mw + - resource_id + - operator + - start_year + - note + + InfrastructureBiodieselPlants: + description: Biodiesel plants infrastructure. + slots: + - biodiesel_plant_id + - company + - bbi_index + - city + - state + - capacity_mmg_per_y + - feedstock + - status + - address + - coordinates + - latitude + - longitude + - source + slot_usage: + biodiesel_plant_id: + identifier: true + range: integer + + InfrastructureBiosolidsFacilities: + description: Biosolids facilities infrastructure. + slots: + - biosolid_facility_id + - report_submitted_date + - latitude + - longitude + - facility + - authority + - plant_type + - aqmd + - facility_address + - facility_city + - state + - facility_zip + - facility_county + - mailing_street_1 + - mailing_city + - mailing_state + - mailing_zip + - biosolids_number + - biosolids_contact + - biosolids_contact_phone + - biosolids_contact_email + - adwf + - potw_biosolids_generated + - twtds_biosolids_treated + - class_b_land_app + - class_b_applier + - class_a_compost + - class_a_heat_dried + - class_a_other + - class_a_other_applier + - twtds_transfer_to_second_preparer + - twtds_second_preparer_name + - adc_or_final_c + - landfill + - landfill_name + - surface_disposal + - deepwell_injection + - stored + - longterm_treatment + - other + - name_of_other + - incineration + slot_usage: + biosolid_facility_id: + identifier: true + range: integer + + InfrastructureCafoManureLocations: + description: CAFO manure locations infrastructure. + slots: + - cafo_manure_id + - latitude + - longitude + - owner_name + - facility_name + - address + - town + - state + - zip + - animal + - animal_feed_operation_type + - animal_units + - animal_count + - manure_total_solids + - source + - date_accessed + slot_usage: + cafo_manure_id: + identifier: true + range: integer + + InfrastructureEthanolBiorefineries: + description: Ethanol biorefineries infrastructure. + slots: + - ethanol_biorefinery_id + - name + - city + - state + - address + - type + - capacity_mgy + - production_mgy + - constr_exp + slot_usage: + ethanol_biorefinery_id: + identifier: true + range: integer + + InfrastructureLandfills: + description: Landfills infrastructure. + slots: + - project_id + - project_int_id + - ghgrp_id + - landfill_id + - landfill_name + - state + - physical_address + - city + - county + - zip_code + - latitude + - longitude + - ownership_type + - landfill_owner_orgs + - landfill_opened_year + - landfill_closure_year + - landfill_status + - waste_in_place + - waste_in_place_year + - lfg_system_in_place + - lfg_collected + - lfg_flared + - project_status + - project_name + - project_start_date + - project_shutdown_date + - project_type_category + - lfg_energy_project_type + - rng_delivery_method + - actual_mw_generation + - rated_mw_capacity + - lfg_flow_to_project + - direct_emission_reductions + - avoided_emission_reductions + slot_usage: + project_id: + identifier: true + range: string + + InfrastructureLivestockAnaerobicDigesters: + description: Livestock anaerobic digesters infrastructure. + slots: + - digester_id + - project_name + - project_type + - city + - state + - digester_type + - profile + - year_operational + - animal_type_class + - animal_types + - pop_feeding_digester + - total_pop_feeding_digester + - cattle + - dairy + - poultry + - swine + - codigestion + - biogas_generation_estimate + - electricity_generated + - biogas_end_uses + - methane_emission_reductions + - latitude + - longitude + slot_usage: + digester_id: + identifier: true + range: integer + + InfrastructureSafAndRenewableDieselPlants: + description: SAF and renewable diesel plants infrastructure. + slots: + - ibcc_index + - company + - city + - state + - country + - capacity + - feedstock + - products + - status + - address + - coordinates + - latitude + - longitude + slot_usage: + ibcc_index: + identifier: true + range: integer + + InfrastructureWastewaterTreatmentPlants: + description: Wastewater treatment plants infrastructure. + slots: + - plant_id + - name + - state + - codigestion + - flow_design_adjusted + - flow_average + - biosolids + - excess_flow + - biogas_utilized + - flaring + - excess_mass_loading_rate + - excess_mass_loading_rate_wet + - methane_production + - energy_content + - electric_kw + - thermal_mmbtu_d + - electric_kwh + - thermal_annual_mmbtu_y + - anaerobic_digestion_facility + - county + - dayload_bdt + - dayload + - equivalent_generation + - facility_type + - feedstock + - type + - city + - latitude + - longitude + - zipcode + slot_usage: + plant_id: + identifier: true + range: integer + + InfrastructureCombustionPlants: + description: Combustion plants infrastructure. + slots: + - combustion_fid + - objectid + - status + - city + - name + - county + - equivalent_generation + - np_mw + - cf + - yearload + - fuel + - notes + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + combustion_fid: + identifier: true + range: integer + + InfrastructureDistrictEnergySystems: + description: District energy systems infrastructure. + slots: + - des_fid + - cbg_id + - name + - system + - object_id + - city + - state + - primary_fuel + - secondary_fuel + - usetype + - cap_st + - cap_hw + - cap_cw + - chpcg_cap + - excess_c + - excess_h + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + des_fid: + identifier: true + range: integer + + InfrastructureFoodProcessingFacilities: + description: Food processing facilities infrastructure. + slots: + - processing_facility_id + - address + - county + - city + - company + - join_count + - master_type + - state + - subtype + - target_fid + - processing_type + - zip + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + processing_facility_id: + identifier: true + range: integer + + InfrastructureMswToEnergyAnaerobicDigesters: + description: MSW to energy anaerobic digesters infrastructure. + slots: + - wte_id + - city + - county + - equivalent_generation + - feedstock + - dayload + - dayload_bdt + - facility_type + - status + - notes + - source + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + wte_id: + identifier: true + range: integer + +slots: + facility_name: + range: string + description: Name of the facility. + + capacity_mw: + range: decimal + description: Capacity in MW. + + operator: + range: string + description: Operator of the facility. + + start_year: + range: integer + description: Start year of the facility. + + biodiesel_plant_id: + range: integer + description: ID of the biodiesel plant. + + company: + range: string + description: Company name. + + bbi_index: + range: integer + description: BBI index. + + city: + range: string + description: City. + + state: + range: string + description: State. + + capacity_mmg_per_y: + range: integer + description: Capacity in MMG per year. + + feedstock: + range: string + description: Feedstock. + + status: + range: string + description: Status. + + address: + range: string + description: Address. + + coordinates: + range: string + description: Coordinates. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. + + source: + range: string + description: Source. + + biosolid_facility_id: + range: integer + description: ID of the biosolids facility. + + report_submitted_date: + range: date + description: Date report submitted. + + facility: + range: string + description: Facility name. + + authority: + range: string + description: Authority. + + plant_type: + range: string + description: Plant type. + + aqmd: + range: string + description: AQMD. + + facility_address: + range: string + description: Facility address. + + facility_city: + range: string + description: Facility city. + + facility_zip: + range: string + description: Facility zip. + + facility_county: + range: string + description: Facility county. + + mailing_street_1: + range: string + description: Mailing street 1. + + mailing_city: + range: string + description: Mailing city. + + mailing_state: + range: string + description: Mailing state. + + mailing_zip: + range: string + description: Mailing zip. + + biosolids_number: + range: string + description: Biosolids number. + + biosolids_contact: + range: string + description: Biosolids contact. + + biosolids_contact_phone: + range: string + description: Biosolids contact phone. + + biosolids_contact_email: + range: string + description: Biosolids contact email. + + adwf: + range: decimal + description: ADWF. + + potw_biosolids_generated: + range: integer + description: POTW biosolids generated. + + twtds_biosolids_treated: + range: integer + description: TWTDS biosolids treated. + + class_b_land_app: + range: integer + description: Class B land application. + + class_b_applier: + range: string + description: Class B applier. + + class_a_compost: + range: integer + description: Class A compost. + + class_a_heat_dried: + range: integer + description: Class A heat dried. + + class_a_other: + range: integer + description: Class A other. + + class_a_other_applier: + range: string + description: Class A other applier. + + twtds_transfer_to_second_preparer: + range: integer + description: TWTDS transfer to second preparer. + + twtds_second_preparer_name: + range: string + description: TWTDS second preparer name. + + adc_or_final_c: + range: integer + description: ADC or final cover. + + landfill: + range: integer + description: Landfill. + + landfill_name: + range: string + description: Landfill name. + + surface_disposal: + range: integer + description: Surface disposal. + + deepwell_injection: + range: string + description: Deepwell injection. + + stored: + range: integer + description: Stored. + + longterm_treatment: + range: integer + description: Longterm treatment. + + other: + range: integer + description: Other. + + name_of_other: + range: string + description: Name of other. + + incineration: + range: integer + description: Incineration. + + cafo_manure_id: + range: integer + description: ID of the CAFO manure location. + + owner_name: + range: string + description: Owner name. + + town: + range: string + description: Town. + + zip: + range: string + description: Zip code. + + animal: + range: string + description: Animal. + + animal_feed_operation_type: + range: string + description: Animal feed operation type. + + animal_units: + range: integer + description: Animal units. + + animal_count: + range: integer + description: Animal count. + + manure_total_solids: + range: decimal + description: Manure total solids. + + date_accessed: + range: date + description: Date accessed. + + ethanol_biorefinery_id: + range: integer + description: ID of the ethanol biorefinery. + + type: + range: string + description: Type. + + capacity_mgy: + range: integer + description: Capacity in MGY. + + production_mgy: + range: integer + description: Production in MGY. + + constr_exp: + range: integer + description: Construction/expansion. + + project_id: + range: string + description: Project ID. + + project_int_id: + range: integer + description: Project integer ID. + + ghgrp_id: + range: string + description: GHGRP ID. + + landfill_id: + range: integer + description: Landfill ID. + + physical_address: + range: string + description: Physical address. + + county: + range: string + description: County. + + zip_code: + range: string + description: Zip code. + + ownership_type: + range: string + description: Ownership type. + + landfill_owner_orgs: + range: string + description: Landfill owner organizations. + + landfill_opened_year: + range: date + description: Landfill opened year. + + landfill_closure_year: + range: date + description: Landfill closure year. + + landfill_status: + range: string + description: Landfill status. + + waste_in_place: + range: integer + description: Waste in place. + + waste_in_place_year: + range: date + description: Waste in place year. + + lfg_system_in_place: + range: boolean + description: LFG system in place. + + lfg_collected: + range: decimal + description: LFG collected. + + lfg_flared: + range: decimal + description: LFG flared. + + project_status: + range: string + description: Project status. + + project_name: + range: string + description: Project name. + + project_start_date: + range: date + description: Project start date. + + project_shutdown_date: + range: date + description: Project shutdown date. + + project_type_category: + range: string + description: Project type category. + + lfg_energy_project_type: + range: string + description: LFG energy project type. + + rng_delivery_method: + range: string + description: RNG delivery method. + + actual_mw_generation: + range: decimal + description: Actual MW generation. + + rated_mw_capacity: + range: decimal + description: Rated MW capacity. + + lfg_flow_to_project: + range: decimal + description: LFG flow to project. + + direct_emission_reductions: + range: decimal + description: Direct emission reductions. + + avoided_emission_reductions: + range: decimal + description: Avoided emission reductions. + + digester_id: + range: integer + description: ID of the digester. + + project_type: + range: string + description: Project type. + + digester_type: + range: string + description: Digester type. + + profile: + range: string + description: Profile. + + year_operational: + range: date + description: Year operational. + + animal_type_class: + range: string + description: Animal type class. + + animal_types: + range: string + description: Animal types. + + pop_feeding_digester: + range: string + description: Population feeding digester. + + total_pop_feeding_digester: + range: integer + description: Total population feeding digester. + + cattle: + range: integer + description: Cattle. + + dairy: + range: integer + description: Dairy. + + poultry: + range: integer + description: Poultry. + + swine: + range: integer + description: Swine. + + codigestion: + range: string + description: Codigestion. + + biogas_generation_estimate: + range: integer + description: Biogas generation estimate. + + electricity_generated: + range: integer + description: Electricity generated. + + biogas_end_uses: + range: string + description: Biogas end uses. + + methane_emission_reductions: + range: integer + description: Methane emission reductions. + + ibcc_index: + range: integer + description: IBCC index. + + country: + range: string + description: Country. + + capacity: + range: string + description: Capacity. + + products: + range: string + description: Products. + + plant_id: + range: integer + description: ID of the plant. + + flow_design_adjusted: + range: decimal + description: Flow design adjusted. + + flow_average: + range: decimal + description: Flow average. + + biosolids: + range: decimal + description: Biosolids. + + excess_flow: + range: decimal + description: Excess flow. + + biogas_utilized: + range: boolean + description: Biogas utilized. + + flaring: + range: boolean + description: Flaring. + + excess_mass_loading_rate: + range: decimal + description: Excess mass loading rate. + + excess_mass_loading_rate_wet: + range: decimal + description: Excess mass loading rate wet. + + methane_production: + range: decimal + description: Methane production. + + energy_content: + range: decimal + description: Energy content. + + electric_kw: + range: decimal + description: Electric KW. + + thermal_mmbtu_d: + range: decimal + description: Thermal MMBTU/d. + + electric_kwh: + range: decimal + description: Electric KWh. + + thermal_annual_mmbtu_y: + range: decimal + description: Thermal annual MMBTU/y. + + anaerobic_digestion_facility: + range: string + description: Anaerobic digestion facility. + + dayload_bdt: + range: decimal + description: Dayload BDT. + + dayload: + range: decimal + description: Dayload. + + equivalent_generation: + range: decimal + description: Equivalent generation. + + facility_type: + range: string + description: Facility type. + + zipcode: + range: string + description: Zipcode. + + combustion_fid: + range: integer + description: Combustion FID. + + objectid: + range: integer + description: Object ID. + + np_mw: + range: decimal + description: NP MW. + + cf: + range: decimal + description: CF. + + yearload: + range: integer + description: Yearload. + + fuel: + range: string + description: Fuel. + + notes: + range: string + description: Notes. + + wkt_geom: + range: string + description: WKT geometry. + + geom: + range: string + description: Geometry. + + des_fid: + range: integer + description: DES FID. + + cbg_id: + range: integer + description: CBG ID. + + system: + range: string + description: System. + + object_id: + range: integer + description: Object ID. + + primary_fuel: + range: string + description: Primary fuel. + + secondary_fuel: + range: string + description: Secondary fuel. + + usetype: + range: string + description: Use type. + + cap_st: + range: decimal + description: Cap ST. + + cap_hw: + range: decimal + description: Cap HW. + + cap_cw: + range: decimal + description: Cap CW. + + chpcg_cap: + range: decimal + description: CHPCG Cap. + + excess_c: + range: decimal + description: Excess C. + + excess_h: + range: decimal + description: Excess H. + + processing_facility_id: + range: integer + description: Processing facility ID. + + join_count: + range: integer + description: Join count. + + master_type: + range: string + description: Master type. + + subtype: + range: string + description: Subtype. + + target_fid: + range: integer + description: Target FID. + + processing_type: + range: string + description: Processing type. + + wte_id: + range: integer + description: WTE ID. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml new file mode 100644 index 00000000..b0014c90 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml @@ -0,0 +1,84 @@ +id: https://w3id.org/ca_biositing/lineage +name: lineage +title: Lineage Definitions +description: Data lineage and ETL tracking. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + LineageGroup: + is_a: BaseEntity + description: Grouping of lineage entities. + slots: + - name + - description + + EntityLineage: + description: Lineage relationship between entities. + slots: + - id + - parent_entity_id + - child_entity_id + - lineage_group_id + - relationship_type + slot_usage: + id: + identifier: true + range: integer + + EtlRun: + is_a: BaseEntity + description: ETL run information. + slots: + - run_id + - start_time + - end_time + - status + - log_uri + +slots: + parent_entity_id: + range: integer + description: ID of the parent entity. + + child_entity_id: + range: integer + description: ID of the child entity. + + lineage_group_id: + range: integer + description: Reference to LineageGroup. + + relationship_type: + range: string + description: Type of relationship. + + run_id: + range: string + description: Unique identifier for the ETL run. + + start_time: + range: datetime + description: Start time of the run. + + end_time: + range: datetime + description: End time of the run. + + status: + range: string + description: Status of the run. + + log_uri: + range: string + description: URI to the run logs. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml new file mode 100644 index 00000000..d370f253 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml @@ -0,0 +1,120 @@ +id: https://w3id.org/ca_biositing/methods +name: methods +title: Methods and Parameters +description: Methods, parameters, and units. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + Unit: + is_a: LookupBase + description: Unit of measurement. + + Method: + is_a: BaseEntity + description: Analytical method. + slots: + - name + - method_abbrev_id + - method_category_id + - method_standard_id + - description + - detection_limits + - source_id + + MethodAbbrev: + is_a: LookupBase + description: Abbreviation for a method. + + MethodCategory: + is_a: LookupBase + description: Category of a method. + + MethodStandard: + is_a: LookupBase + description: Standard associated with a method. + + Parameter: + is_a: BaseEntity + description: Parameter measured. + slots: + - name + - standard_unit_id + - calculated + - description + + ParameterCategory: + is_a: LookupBase + description: Category of a parameter. + + ParameterCategoryParameter: + description: Link between parameter and category. + slots: + - id + - parameter_id + - parameter_category_id + slot_usage: + id: + identifier: true + range: integer + + ParameterUnit: + description: Link between parameter and alternate units. + slots: + - id + - parameter_id + - alternate_unit_id + slot_usage: + id: + identifier: true + range: integer + +slots: + method_abbrev_id: + range: integer + description: Reference to MethodAbbrev. + + method_category_id: + range: integer + description: Reference to MethodCategory. + + method_standard_id: + range: integer + description: Reference to MethodStandard. + + detection_limits: + range: string + description: Detection limits of the method. + + source_id: + range: integer + description: Reference to DataSource. + + standard_unit_id: + range: integer + description: Reference to Unit (standard). + + calculated: + range: boolean + description: Whether the parameter is calculated. + + parameter_id: + range: integer + description: Reference to Parameter. + + parameter_category_id: + range: integer + description: Reference to ParameterCategory. + + alternate_unit_id: + range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml new file mode 100644 index 00000000..1f4b0c5d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml @@ -0,0 +1,122 @@ +id: https://w3id.org/ca_biositing/methods_parameters_units +name: methods_parameters_units +title: Methods, Parameters, and Units +description: Analytical methods, parameters, and units of measurement. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - data_sources_metadata + +classes: + Unit: + is_a: LookupBase + description: Unit of measurement. + + Method: + is_a: BaseEntity + description: Analytical method. + slots: + - name + - method_abbrev_id + - method_category_id + - method_standard_id + - description + - detection_limits + - source_id + + MethodAbbrev: + is_a: LookupBase + description: Abbreviation for method. + + MethodCategory: + is_a: LookupBase + description: Category of method. + + MethodStandard: + is_a: LookupBase + description: Standard associated with the method. + + Parameter: + is_a: BaseEntity + description: Parameter being measured. + slots: + - name + - standard_unit_id + - calculated + - description + + ParameterCategory: + is_a: LookupBase + description: Category of parameter. + + ParameterCategoryParameter: + description: Link between Parameter and ParameterCategory. + slots: + - id + - parameter_id + - parameter_category_id + slot_usage: + id: + identifier: true + range: integer + + ParameterUnit: + description: Link between Parameter and Unit (alternate units). + slots: + - id + - parameter_id + - alternate_unit_id + slot_usage: + id: + identifier: true + range: integer + +slots: + method_abbrev_id: + range: integer + description: Reference to MethodAbbrev. + + method_category_id: + range: integer + description: Reference to MethodCategory. + + method_standard_id: + range: integer + description: Reference to MethodStandard. + + detection_limits: + range: string + description: Detection limits of the method. + + source_id: + range: integer + description: Reference to DataSource. + + standard_unit_id: + range: integer + description: Reference to Unit. + + calculated: + range: boolean + description: Whether the parameter is calculated. + + parameter_id: + range: integer + description: Reference to Parameter. + + parameter_category_id: + range: integer + description: Reference to ParameterCategory. + + alternate_unit_id: + range: integer + description: Reference to Unit. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml new file mode 100644 index 00000000..818bce18 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml @@ -0,0 +1,65 @@ +id: https://w3id.org/ca_biositing/people +name: people +title: People Definitions +description: Contact and provider information. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + +classes: + Contact: + description: Contact information for a person. + slots: + - id + - first_name + - last_name + - email + - affiliation + slot_usage: + id: + identifier: true + range: integer + + Provider: + description: Provider information. + slots: + - id + - codename + slot_usage: + id: + identifier: true + range: integer + +slots: + id: + identifier: true + range: integer + description: Unique identifier. + + first_name: + range: string + description: First name. + + last_name: + range: string + description: Last name. + + email: + range: string + description: Email address. + + affiliation: + range: string + description: Affiliation. + + codename: + range: string + description: Codename for the provider. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml new file mode 100644 index 00000000..7cd2c18b --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml @@ -0,0 +1,73 @@ +id: https://w3id.org/ca_biositing/places +name: places +title: Places Definitions +description: Geographic locations and addresses. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + Geography: + is_a: BaseEntity + description: Geographic location. + slots: + - geoid + - name + - type + - geometry + slot_usage: + geoid: + identifier: true + + LocationAddress: + is_a: BaseEntity + description: Physical address. + slots: + - street_address + - city + - state + - zip_code + - country + - geoid + +slots: + geoid: + range: string + description: Unique identifier for geography. + + type: + range: string + description: Type of geography (e.g. county, state). + + geometry: + range: string + description: WKT geometry. + + street_address: + range: string + description: Street address. + + city: + range: string + description: City. + + state: + range: string + description: State. + + zip_code: + range: string + description: ZIP code. + + country: + range: string + description: Country. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml new file mode 100644 index 00000000..28d31e47 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml @@ -0,0 +1,178 @@ +id: https://w3id.org/ca_biositing/resource_information +name: resource_information +title: Resource Information +description: Biomass resources and their classifications. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - places + +classes: + Resource: + is_a: BaseEntity + description: Biomass resource definition. + slots: + - name + - primary_crop_id + - resource_class_id + - resource_subclass_id + - note + + ResourceClass: + is_a: LookupBase + description: Classification of resources. + + ResourceSubclass: + is_a: LookupBase + description: Sub-classification of resources. + + PrimaryCrop: + is_a: LookupBase + description: Primary crop definition. + slots: + - note + + ResourceAvailability: + is_a: BaseEntity + description: Availability of a resource in a location. + slots: + - resource_id + - geoid + - from_month + - to_month + - year_round + - note + + ResourceCounterfactual: + is_a: BaseEntity + description: Counterfactual uses of a resource. + slots: + - geoid + - resource_id + - counterfactual_description + - animal_bedding_percent + - animal_bedding_source_id + - animal_feed_percent + - animal_feed_source_id + - bioelectricty_percent + - bioelectricty_source_id + - burn_percent + - burn_source_id + - compost_percent + - compost_source_id + - landfill_percent + - landfill_source_id + - counterfactual_date + - note + + ResourceMorphology: + description: Morphology of a resource. + slots: + - id + - resource_id + - morphology_uri + slot_usage: + id: + identifier: true + range: integer + +slots: + primary_crop_id: + range: integer + description: Reference to PrimaryCrop. + + resource_class_id: + range: integer + description: Reference to ResourceClass. + + resource_subclass_id: + range: integer + description: Reference to ResourceSubclass. + + resource_id: + range: integer + description: Reference to Resource. + + geoid: + range: string + description: Reference to Geography. + + from_month: + range: integer + description: Start month of availability. + + to_month: + range: integer + description: End month of availability. + + year_round: + range: boolean + description: Whether available year-round. + + counterfactual_description: + range: string + description: Description of counterfactual scenario. + + animal_bedding_percent: + range: decimal + description: Percentage used for animal bedding. + + animal_bedding_source_id: + range: integer + description: Source for animal bedding data. + + animal_feed_percent: + range: decimal + description: Percentage used for animal feed. + + animal_feed_source_id: + range: integer + description: Source for animal feed data. + + bioelectricty_percent: + range: decimal + description: Percentage used for bioelectricity. + + bioelectricty_source_id: + range: integer + description: Source for bioelectricity data. + + burn_percent: + range: decimal + description: Percentage burned. + + burn_source_id: + range: integer + description: Source for burn data. + + compost_percent: + range: decimal + description: Percentage composted. + + compost_source_id: + range: integer + description: Source for compost data. + + landfill_percent: + range: decimal + description: Percentage landfilled. + + landfill_source_id: + range: integer + description: Source for landfill data. + + counterfactual_date: + range: date + description: Date of counterfactual data. + + morphology_uri: + range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml new file mode 100644 index 00000000..f3d26ede --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml @@ -0,0 +1,178 @@ +id: https://w3id.org/ca_biositing/resources +name: resources +title: Resource Definitions +description: Biomass resources and their classifications. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - geography + +classes: + Resource: + is_a: BaseEntity + description: Biomass resource definition. + slots: + - name + - primary_crop_id + - resource_class_id + - resource_subclass_id + - note + + ResourceClass: + is_a: LookupBase + description: Classification of resources. + + ResourceSubclass: + is_a: LookupBase + description: Sub-classification of resources. + + PrimaryCrop: + is_a: LookupBase + description: Primary crop definition. + slots: + - note + + ResourceAvailability: + is_a: BaseEntity + description: Availability of a resource in a location. + slots: + - resource_id + - geoid + - from_month + - to_month + - year_round + - note + + ResourceCounterfactual: + is_a: BaseEntity + description: Counterfactual uses of a resource. + slots: + - geoid + - resource_id + - counterfactual_description + - animal_bedding_percent + - animal_bedding_source_id + - animal_feed_percent + - animal_feed_source_id + - bioelectricty_percent + - bioelectricty_source_id + - burn_percent + - burn_source_id + - compost_percent + - compost_source_id + - landfill_percent + - landfill_source_id + - counterfactual_date + - note + + ResourceMorphology: + description: Morphology of a resource. + slots: + - id + - resource_id + - morphology_uri + slot_usage: + id: + identifier: true + range: integer + +slots: + primary_crop_id: + range: integer + description: Reference to PrimaryCrop. + + resource_class_id: + range: integer + description: Reference to ResourceClass. + + resource_subclass_id: + range: integer + description: Reference to ResourceSubclass. + + resource_id: + range: integer + description: Reference to Resource. + + geoid: + range: string + description: Reference to Geography. + + from_month: + range: integer + description: Start month of availability. + + to_month: + range: integer + description: End month of availability. + + year_round: + range: boolean + description: Whether available year-round. + + counterfactual_description: + range: string + description: Description of counterfactual scenario. + + animal_bedding_percent: + range: decimal + description: Percentage used for animal bedding. + + animal_bedding_source_id: + range: integer + description: Source for animal bedding data. + + animal_feed_percent: + range: decimal + description: Percentage used for animal feed. + + animal_feed_source_id: + range: integer + description: Source for animal feed data. + + bioelectricty_percent: + range: decimal + description: Percentage used for bioelectricity. + + bioelectricty_source_id: + range: integer + description: Source for bioelectricity data. + + burn_percent: + range: decimal + description: Percentage burned. + + burn_source_id: + range: integer + description: Source for burn data. + + compost_percent: + range: decimal + description: Percentage composted. + + compost_source_id: + range: integer + description: Source for compost data. + + landfill_percent: + range: decimal + description: Percentage landfilled. + + landfill_source_id: + range: integer + description: Source for landfill data. + + counterfactual_date: + range: date + description: Date of counterfactual data. + + morphology_uri: + range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation.yaml new file mode 100644 index 00000000..758bb6c8 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation.yaml @@ -0,0 +1,70 @@ +id: https://w3id.org/ca_biositing/sample_preparation +name: sample_preparation +title: Sample Preparation +description: Sample preparation methods and records. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - field_sampling + - people + +classes: + PreparationMethod: + is_a: BaseEntity + description: Method of sample preparation. + slots: + - name + - description + - prep_method_abbrev_id + - prep_temp_c + - uri + - drying_step + + PreparationMethodAbbreviation: + is_a: LookupBase + description: Abbreviation for preparation method. + + PreparedSample: + is_a: BaseEntity + description: Sample that has been prepared. + slots: + - name + - field_sample_id + - prep_method_id + - prep_date + - preparer_id + - note + +slots: + prep_method_abbrev_id: + range: integer + description: Reference to PreparationMethodAbbreviation. + + prep_temp_c: + range: decimal + description: Preparation temperature in Celsius. + + drying_step: + range: boolean + description: Whether drying step was involved. + + prep_method_id: + range: integer + description: Reference to PreparationMethod. + + prep_date: + range: date + description: Date of preparation. + + preparer_id: + range: integer + description: Reference to Contact (preparer). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml new file mode 100644 index 00000000..9b449f57 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml @@ -0,0 +1,250 @@ +id: https://w3id.org/ca_biositing/sampling +name: sampling +title: Sampling Definitions +description: Field sampling and preparation. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - geography + - people + - resources + - methods + +classes: + FieldSample: + is_a: BaseEntity + description: Sample collected from the field. + slots: + - name + - resource_id + - provider_id + - collector_id + - sample_collection_source + - amount_collected + - amount_collected_unit_id + - sampling_location_id + - field_storage_method_id + - field_storage_duration_value + - field_storage_duration_unit_id + - field_storage_location_id + - collection_timestamp + - collection_method_id + - harvest_method_id + - harvest_date + - field_sample_storage_location_id + - note + + FieldStorageMethod: + is_a: LookupBase + description: Method of field storage. + + CollectionMethod: + is_a: LookupBase + description: Method of collection. + + HarvestMethod: + is_a: LookupBase + description: Method of harvest. + + ProcessingMethod: + is_a: LookupBase + description: Method of processing. + + PhysicalCharacteristic: + is_a: BaseEntity + description: Physical characteristics of a sample. + slots: + - field_sample_id + - particle_length + - particle_width + - particle_height + - particle_unit_id + + SoilType: + is_a: LookupBase + description: Type of soil. + + AgTreatment: + is_a: LookupBase + description: Agricultural treatment. + + FieldSampleCondition: + is_a: BaseEntity + description: Condition of the field sample. + slots: + - field_sample_id + - ag_treatment_id + - last_application_date + - treatment_amount_per_acre + - processing_method_id + + LocationSoilType: + is_a: BaseEntity + description: Soil type at a location. + slots: + - location_id + - soil_type_id + + PreparationMethod: + is_a: BaseEntity + description: Method of sample preparation. + slots: + - name + - description + - prep_method_abbrev_id + - prep_temp_c + - uri + - drying_step + + PreparationMethodAbbreviation: + is_a: LookupBase + description: Abbreviation for preparation method. + + PreparedSample: + is_a: BaseEntity + description: Sample prepared for analysis. + slots: + - name + - field_sample_id + - prep_method_id + - prep_date + - preparer_id + - note + +slots: + provider_id: + range: integer + description: Reference to Provider. + + collector_id: + range: integer + description: Reference to Contact (collector). + + sample_collection_source: + range: string + description: Source of sample collection. + + amount_collected: + range: decimal + description: Amount collected. + + amount_collected_unit_id: + range: integer + description: Reference to Unit. + + sampling_location_id: + range: integer + description: Reference to LocationAddress. + + field_storage_method_id: + range: integer + description: Reference to FieldStorageMethod. + + field_storage_duration_value: + range: decimal + description: Duration of field storage. + + field_storage_duration_unit_id: + range: integer + description: Reference to Unit. + + field_storage_location_id: + range: integer + description: Reference to LocationAddress. + + collection_timestamp: + range: datetime + description: Timestamp of collection. + + collection_method_id: + range: integer + description: Reference to CollectionMethod. + + harvest_method_id: + range: integer + description: Reference to HarvestMethod. + + harvest_date: + range: date + description: Date of harvest. + + field_sample_storage_location_id: + range: integer + description: Reference to LocationAddress. + + field_sample_id: + range: integer + description: Reference to FieldSample. + + particle_length: + range: decimal + description: Length of particle. + + particle_width: + range: decimal + description: Width of particle. + + particle_height: + range: decimal + description: Height of particle. + + particle_unit_id: + range: integer + description: Reference to Unit. + + ag_treatment_id: + range: integer + description: Reference to AgTreatment. + + last_application_date: + range: date + description: Date of last application. + + treatment_amount_per_acre: + range: float + description: Amount of treatment per acre. + + processing_method_id: + range: integer + description: Reference to ProcessingMethod. + + location_id: + range: integer + description: Reference to LocationAddress. + + soil_type_id: + range: integer + description: Reference to SoilType. + + prep_method_abbrev_id: + range: integer + description: Reference to PreparationMethodAbbreviation. + + prep_temp_c: + range: decimal + description: Preparation temperature in Celsius. + + drying_step: + range: boolean + description: Whether drying step was included. + + prep_method_id: + range: integer + description: Reference to PreparationMethod. + + prep_date: + range: date + description: Date of preparation. + + preparer_id: + range: integer + description: Reference to Contact (preparer). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/initial_linkML_conversion/dbdiagram_dump.md b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/initial_linkML_conversion/dbdiagram_dump.md new file mode 100644 index 00000000..4583cf2c --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/initial_linkML_conversion/dbdiagram_dump.md @@ -0,0 +1,981 @@ +/////////////////////////////////////////////////////////// // BASE ENTITY +(included in all main entity tables) // id int [pk, increment] // created_at +datetime [default: `current_timestamp`] // updated_at datetime [default: +`current_timestamp`] // etl_run_id string // lineage_group_id int [ref: > +lineage_group.id] /////////////////////////////////////////////////////////// + +// LookupBase for enum/ontology-like tables // id int [pk, increment] // name +string [not null, unique] // description string // uri string +/////////////////////////////////////////////////////////// + +//===================TABLE GROUPS================== TableGroup "Resource +Information" [color: #1E69FD] { resource resource_class resource_subclass +primary_crop resource_availability resource_counterfactual resource_morphology } + +TableGroup "Field Sampling" [color: #d35400] { field_sample field_storage_method +collection_method harvest_method physical_characteristic soil_type ag_treatment +field_sample_condition processing_method location_soil_type } + +TableGroup "Places" { geography location_address } + +TableGroup "People" { provider contact } + +TableGroup "Lineage" { lineage_group entity_lineage etl_run } + +TableGroup "Data Sources & Metadata" [color: #990D0D]{ data_source +data_source_type source_type file_object_metadata location_resolution } + +TableGroup "Sample Preparation" [color:#F7AC5E] { preparation_method +preparation_method_abbreviation prepared_sample } + +TableGroup "Methods, Parameters, Units" [color: #F0B7B7]{ unit method_abbrev +method_category method_standard parameter_category method parameter +parameter_unit + +} + +TableGroup "Experiment, Equipment" [color: #CDFC9F]{ experiment +experiment_method equipment experiment_analysis experiment_equipment +experiment_prepared_sample } + +TableGroup "General Analysis" [color: #A15CF5]{ analysis_type observation +dataset dimension_type } + +TableGroup "Aim2 Records" [color: #cc0000]{ fermentation_record +gasification_record pretreatment_record autoclave_record strain } + +TableGroup "Aim1 Records" [color: #ffc84f] { proximate_record +compositional_record ultimate_record icp_record calorimetry_record xrf_record +xrd_record rgb_record ftnir_record } + +TableGroup "External Data" [color:#20b2aa] { usda_census_record //usda_commodity +//usda_commodity_to_primary_crop usda_domain usda_statistic_category +usda_survey_program usda_survey_record usda_market_record +billion_ton_2023_record landiq_record polygon //I think this is used to +essentially get all polygons in a county? + +} + +TableGroup "Infrastructure" [color:#6495ed]{ facility_record +infrastructure_biodiesel_plants infrastructure_biosolids_facilities +infrastructure_cafo_manure_locations infrastructure_ethanol_biorefineries +infrastructure_landfills infrastructure_livestock_anaerobic_digesters +infrastructure_saf_and_renewable_diesel_plants +infrastructure_wastewater_treatment_plants infrastructure_combustion_plants +infrastructure_district_energy_systems infrastructure_food_processing_facilities +infrastructure_msw_to_energy_anaerobic_digesters } + +/////////////////////////////////////////////////////////// // LINEAGE TABLES +/////////////////////////////////////////////////////////// + +Table lineage_group { id int [pk, increment] etl_run_id string [ref:> +etl_run.id] note text } + +Table entity_lineage { id int [pk, increment] lineage_group_id int [not null, +ref: > lineage_group.id] source_table string [not null] // sheet or raw table +source_row_id string [not null] // row index or key note text } + +Table etl_run { id string [pk] // UUID started_at datetime completed_at datetime +pipeline_name string status string // success/failure/partial records_ingested +int note text } + +/////////////////////////////////////////////////////////// // RESOURCE +/////////////////////////////////////////////////////////// + +Table resource { // BaseEntity id int [pk, increment] created_at datetime +[default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] + +// Domain fields name string [not null, unique] primary_crop_id int [not null, +ref: > primary_crop.id] resource_class_id int [not null, ref: > +resource_class.id] resource_subclass_id int [ref: > resource_subclass.id] note +text } + +Table resource_class { // LookupBase id int [pk, increment] name string [not +null, unique] description string uri string } + +Table resource_subclass { // LookupBase id int [pk, increment] name string [not +null, unique] description string uri string } + +/////////////////////////////////////////////////////////// // PRIMARY CROP +/////////////////////////////////////////////////////////// + +Table primary_crop { // LookupBase (+ ontology) id int [pk, increment] name +string [not null, unique] description string uri string note text } + +/////////////////////////////////////////////////////////// // RESOURCE +AVAILABILITY /////////////////////////////////////////////////////////// + +Table resource_availability { // BaseEntity id int [pk, increment] created_at +datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] + +// Domain fields resource_id int [not null, ref: > resource.id] geoid string +[not null, ref: > geography.geoid] + +from_month int to_month int year_round boolean note text } + +/////////////////////////////////////////////////////////// // RESOURCE +COUNTERFACTUAL /////////////////////////////////////////////////////////// + +Table resource_counterfactual { // BaseEntity id int [pk, increment] created_at +datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] // Domain fields geoid string [not null, ref: > +geography.geoid] //location resource_id int [not null, ref: > resource.id] +counterfactual_description text //animal is too broad. Want just livestock and +poultry animal_bedding_percent decimal animal_bedding_source_id int [ref:> +data_source.id] animal_feed_percent decimal animal_feed_source_id int [ref:> +data_source.id] bioelectricty_percent decimal bioelectricty_source_id int [ref:> +data_source.id] burn_percent decimal burn_source_id int [ref:> data_source.id] +compost_percent decimal compost_source_id int [ref:> data_source.id] +landfill_percent decimal landfill_source_id int [ref:> data_source.id] +counterfactual_date date //contained in source. Set a base year as a disclaimer +//scenario identifier note text } + +/////////////////////////////////////////////////////////// // RESOURCE +MORPHOLOGY (many-to-many) +/////////////////////////////////////////////////////////// + +//'Check morphology ontology with Andrea' Table resource_morphology { id int +[pk, increment] resource_id int [not null, ref: > resource.id] morphology_uri +string [not null] // ontology URI for plant part (stem, shell, leaf…) } + +/////////////////////////////////////////////////////////// // GEOGRAPHY / +PLACES /////////////////////////////////////////////////////////// + +Table geography { geoid string [pk] state_name string state_fips string +county_name string county_fips string region_name string agg_level_desc string } + +Table location_address { id int [pk, increment] geography_id string [ref: > +geography.geoid] address_line1 string address_line2 string city string zip +string lat float lon float is_anonymous boolean } + +/////////////////////////////////////////////////////////// // NOTES +/////////////////////////////////////////////////////////// + +///////////////////////////////////////////////////////// // FIELD SAMPLES TABLE +GROUP //////////////////////////////////////////////////////// + +Table field_sample [headercolor: #d35400] { //Base entity id int [pk, increment] +created_at datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] //Domain Specific name string [not null, note: "e.g., +Ene-WaHu018"] //Should link perfectly to Gsheet sample name resource_id integer +[not null, ref: > resource.id] provider_id integer [ref: > provider.id] // needs +to be anon //add this! collector_id integer [ref: > contact.id] +sample_collection_source text //this is kind of free for all in the sample +metadata gsheet amount_collected decimal //consider making not null +amount_collected_unit_id integer [ref:> unit.id] //consider making not null +//source_codename_id integer [note: "Anonymized source identifier"] //not sure +what to do with this? Should we keep? sampling_location_id integer [not null, +ref: > location_address.id] // needs to be anon. May be null if from external +sources //I think we can do this via permissions in the database itself... +field_storage_method_id integer [ref: > field_storage_method.id] +field_storage_duration_value decimal field_storage_duration_unit_id integer +[ref:> unit.id] field_storage_location_id integer [ref:> location_address.id] // +nullable; may be same as sampling_location_id collection_timestamp timestamp +collection_method_id integer [ref: > collection_method.id] harvest_method_id +integer [ref: > harvest_method.id] harvest_date date //soil_type_id integer +[ref:> soil_type.id] //I am not sure I like this here. Maybe morve to +field_sample_condition? field_sample_storage_location_id integer [ref:> +location_address.id] //Used to describe where the sample is now note text + +indexes { resource_id //will we use this often enough to index? +//source_codename_id } } + +Table field_storage_method [headercolor: #d35400]{ // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +description string uri string } + +Table collection_method [headercolor: #d35400]{ // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +description string uri string } + +Table harvest_method [headercolor: #d35400]{ // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +description string uri string } + +Table processing_method [headercolor: #d35400]{ // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +description string uri string } + +//consider moving this to the analysis table group Table physical_characteristic +[headercolor: #d35400]{ //Base entity id int [pk, increment] created_at datetime +[default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] // field_sample_id integer [not null, ref: > field_sample.id] +particle_length decimal particle_width decimal particle_height decimal +particle_unit_id integer [ref:> unit.id] //Could add index in here } + +Table soil_type [headercolor: #d35400] { // LookupBase for enum/ontology-like +tables id int [pk, increment] name string [not null, unique] description string +uri string //soil_location integer [ref: > geography.id] //not sure if this +should be in a different "Base" table } + +Table ag_treatment [headercolor: #d35400] { // LookupBase for enum/ontology-like +tables id int [pk, increment] name string [not null, unique] description string +uri string } + +Table field_sample_condition [headercolor: #d35400] { //Would like to find a +better name for this table, or maybe break it apart //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] // field_sample_id int [not null, ref:> +field_sample.id] ag_treatment_id int [not null, ref:> ag_treatment.id] +last_application_date date [note: "if applicable"] treatment_amount_per_acre +float processing_method_id int [ref:> processing_method.id] } + +Table location_soil_type [headercolor: #d35400] { //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] //Domain specific location_id int [not null, ref:> +location_address.id] soil_type_id int [not null, ref:> soil_type.id] } + +///////////////////////////////////////////////////////// ///////// UNITS +//////////////// //////////////////////////////////////////////////////// + +Table unit { id int [pk, increment] name string [not null, unique] // e.g., +"cm", "kg", "m3" description string //can be longform like centimeter, +kilograms, cubic meters uri url } + +//////////////////////////////////////////////////////// ///////SAMPLE +PREPARATION///////////// +//////////////////////////////////////////////////////// + +Table preparation_method [headercolor: #F7AC5E] { //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] // name string [note: "As Is, Knife Mill (2mm), Oven +Dry"] description text prep_method_abbrev_id integer [ref:- +preparation_method_abbreviation.id] prep_temp_c decimal //I feel like this +should just be in the method right? uri string //ideally a protocols.io linked +DOI drying_step boolean //I think this should also just be in the method +//method_ref_id integer //[ref: > references.reference_id] } + +Table preparation_method_abbreviation [headercolor: #F7AC5E] { // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +description string uri string } + +Table prepared_sample [headercolor: #f7ac5e] { //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] // name string // this should correspond with +prepro_material_name in Gsheets. field_sample_id integer [not null, ref:- +field_sample.id] prep_method_id integer [not null, ref:- preparation_method.id] +//amount_before_drying decimal //amount_after_drying decimal prep_date date +//storage_location_id integer [ref: > location_address.id] //We may want this to +be location with a room. Need to ask James how specific the storage location is +for the samples cus in th Gsheets it is only the building //amount_remaining +decimal //amount_remaining_unit_id integer [ref:> unit.id] //amount_as_of_date +date preparer_id integer //[ref: > analysts_contact.analyst_id] note text + +indexes { field_sample_id prep_method_id } + +} + +//////////////////////////////////////////////////////// ///////DATA SOURCES AND +METADATA///////////// //////////////////////////////////////////////////////// + +Table data_source [headercolor: #990D0D] { //Base entity id int [pk, increment] +created_at datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] // name string [not null] //a short english identifier for the +source, such as the in-text citation (e.g. "Smith 2019" "BT23" "ForageOne") +description text //purpose of the data maybe. Unabbreviated names +data_source_type_id int [not null, ref:- data_source_type.id] // Foreign key +referenceing source_types full_title string [not null] creator string subject +string publisher string contributor string date datetime type string [not null] +biocirv boolean // e.g. "External data" = FALSE, "Internal data" = TRUE format +string language string relation string temporal_coverage daterange //The spatial +or temporal topic of the resource. location_coverage int [ref:> +location_resolution.id] rights string uri string [not null] } + +Table data_source_type [headercolor: #990D0D] { //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] // source_type_id int [ref: > source_type.id] } + +Table location_resolution [headercolor: #990D0D] { //nation, state, county, +region, etc // LookupBase for enum/ontology-like tables id int [pk, increment] +name string [not null, unique] //database, literature, internal, etc description +string uri string } + +Table source_type [headercolor: #990D0D]{ // LookupBase for enum/ontology-like +tables id int [pk, increment] name string [not null, unique] //database, +literature, industry report, government report, etc description string uri +string } + +Table file_object_metadata [headercolor: #990D0D] { //Base entity id int [pk, +increment] created_at datetime [default: `current_timestamp`] updated_at +datetime [default: `current_timestamp`] etl_run_id string lineage_group_id int +[ref: > lineage_group.id] // data_source_id int [ref: > data_source.id] +bucket_path string file_format string file_size int checksum_md5 string +checksum_sha256 string } + +//THIS IS FOR LATER WHEN WE DO ANALYSIS RESULTS //analysis_result_file_object { +// analysis_result_id int [ref: > analysis_result.id] // file_object_id int +[ref: > file_object.id] // primary key (analysis_result_id, file_object_id) //} + +///////////////////////// ////// METHODS, PARAMETERS, UNITS +///////////////////////// + +Table method [headercolor: #F0B7B7] { //Base entity id int [pk, increment] +created_at datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] //Domain fields name string [unique] method_abbrev_id int +[ref: > method_abbrev.id] // Foreign key referencing method_abbrevs +method_category_id int [ref: > method_category.id] // Foreign key referencing +method_categories method_standard_id int [ref: > method_standard.id] // Foreign +key referencing method_standards description text detection_limits text //maybe +make this substantial in the future source_id int [ref: > data_source.id] +//protocols.io + +indexes { name } } + +Table method_abbrev [headercolor: #F0B7B7] { // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +// e.g. ICP, Ult description string uri string } + +Table method_category [headercolor: #F0B7B7] { //still need to better define +what this would be... // LookupBase for enum/ontology-like tables id int [pk, +increment] name string [not null, unique] //"ICP method, CompAna method, dry, +wet" description string uri string } + +Table method_standard [headercolor: #F0B7B7] { // LookupBase for +enum/ontology-like tables id int [pk, increment] name string [not null, unique] +// Standard associated with the method (e.g., AOAC 997.02, TAPPI T203) +description string uri string } + +Table parameter [headercolor:#F0B7B7] { //Base entity id int [pk, increment] +created_at datetime [default: `current_timestamp`] updated_at datetime [default: +`current_timestamp`] etl_run_id string lineage_group_id int [ref: > +lineage_group.id] // name string [not null, unique] //parameter_category_id +integer [ref: > parameter_catagory.id] //"Fermentation, Minerals, Elements, +Compositional Analysis, etc" standard_unit_id integer [ref : > unit.id] +//Expected unit of a result. Is this the right way to do this? Should we use a +different //table to facilitate the identification and coercing of mismathed +units across internal and external datasets? //alternate_units text [note: "JSON +array of alternative units"] //I think I have eled this in the parameter_units +bridge table calculated boolean [note:"if not calculated then it is measured +directly. E.g glucose vs glucan"] description text //typical_range_min decimal +//typical_range_max decimal } + +Table parameter_catagory_parameter [headercolor: #F0B7B7] { id int [pk, +increment] parameter_id int [not null, ref: > parameter.id] +parameter_catagory_id int [not null, ref: > parameter_category.id] } + +Table parameter_category [headercolor: #F0B7B7] { //need to better define // +LookupBase for enum/ontology-like tables id int [pk, increment] name string [not +null, unique] //[note: "Fermentation, Minerals, Elements, Compositional +Analysis, etc"] description string uri string } + +Table parameter_unit [headercolor: #F0B7B7] { id integer [pk] parameter_id +integer [ref: > parameter.id] //contains the standard unit alternate_unit_id +integer [not null, ref:> unit.id] } + +Ref: "experiment_prepared_sample"."id" < +"experiment_prepared_sample"."prepared_sample_id" + +///////////////////////// ////// Experiments, Equipment +///////////////////////// + +Table experiment { id int [pk, increment] // Primary key created_at datetime +[default: `current_timestamp`] // When this row was created updated_at datetime +[default: `current_timestamp`] // Last updated timestamp + +// ETL tracking / provenance etl_run_id string [note: "ETL process that +generated this experiment row"] lineage_group_id int [ref: > lineage_group.id, +note: "Links to original source data (sheet, row, file, etc.)"] + +// Domain-specific fields analyst_id int [note: "Person responsible for +experiment"] exper_start_date date [note: "Date the experiment started"] +exper_duration decimal [note: "Duration of experiment"] exper_duration_unit_id +int [ref: > unit.id, note: "Unit for exper_duration, e.g., days, hours"] +exper_location_id int [ref: > location_address.id, note: "Where the experiment +was performed"] description text [note: "Optional notes or description of the +experiment"] } + +Table equipment [headercolor: #CDFC9F]{ // LookupBase for enum/ontology-like +tables id int [pk, increment] name string [not null, unique] // description +string uri string // equipment_location_id integer [ref: > location_address.id] +//from room can access building, affiliation, address, etc } + +Table experiment_equipment [headercolor: #CDFC9F]{ id int [pk] experiment_id int +[not null, ref: > experiment.id] equipment_id int [not null, ref: > +equipment.id] } + +Table experiment_analysis [headercolor: #CDFC9F] { id int [pk, increment] +experiment_id int [ref:> experiment.id] analysis_type_id int [ref:> +analysis_type.id] } + +Table experiment_prepared_sample [headercolor: #CDFC9F] { id int [pk, increment] +experiment_id int [ref:> experiment.id] prepared_sample_id int [ref:> +prepared_sample.id] } + +Table experiment_method [headercolor: #CDFC9F] { id int [pk] experiment_id int +[ref: > experiment.id] method_id int [ref: > method.id] + +indexes { method_id experiment_id } } //====================================== +// DATASET TABLE //====================================== + +//A dataset is defined by a publisher and the time //period over which it took +observations which are grouped //but non-redundant. //so that methodology and +observation space is the same.? + +//Ex: LandIQ is a record_type but there are multiple years of //LandIQ data so +record_type is insufficient to differentiate //a polygon from 2020 and 2022. + +//Ex. Phyllis2 is a publisher, but it releases data in sections //based on +analysis type so we will import "Phyllis 2 Proximate //analysis" "Phyllis 2 +Ultimate Analysis" as datasets. //What is the problem though just have Phyllis2 +as a dataset that //is an aggregation of those datasets? + +//Ex: BioCirV is a publisher that takes data across a timeframe. //Should we +differentiate Aim1 and Aim2? I vote no. + +Table dataset { id int [pk, increment] name string // Human-readable dataset +name record_type string [note: "Determines which child record table rows belong +to this dataset"] // e.g. "ultimate_record", "compositional_record" +//experiment_id int [ref: > experiment.id, note: "Nullable; only applies for +lab-produced datasets"] source_id int [ref:> data_source.id] start_date date +end_date date description text } + +//=========================================================== // OBSERVATION +TABLE (parameter/value pairs) +//=========================================================== + +Table observation { id int [pk, increment] dataset_id int [ref: > dataset.id] + +// Polymorphic link to child record table record_type string [note: "ENUM of +child record tables"] record_id int [note: "Points to ID in table defined by +record_type"] + +parameter_id int [ref: > parameter.id] value decimal unit_id int [ref: > +unit.id] + +// Optional dimensions (e.g., timepoint for timeseries data, wavelength, +replicate time) dimension_type_id int [ref: > dimension_type.id] dimension_value +decimal dimension_unit_id int [ref: > unit.id] + +//observation_source_id int [ref: > data_source.id] note text + +indexes { (dataset_id, record_id, parameter_id) } } + +//=========================================================== // CHILD RECORD +TABLES – ANALYTICAL DATA +//=========================================================== + +//A record is the surrounding information needed to understand an observation. +//Record tables give context for the parameter + value + unit //from the +observation table. They explain which data groupings (samples, experiments, +//and datasets) that these observations belong to. + +//A technical replicate is defined by a sample and a given experiment +//(analyst, on a day, at a time, on a machine) + +//A sample replicate is defined by a sample and an analytical method + +////////////////////////////////////////////////// ////// INTERNAL RECORD BASE +CLASS///////////////// ////////////////////////////////////////////////// + +//id int [pk, increment] //dataset_id int [ref: > dataset.id] //experiment_id +int [ref: > experiment.id] //resource_id int [ref:> resource.id] //sample_id int +[ref: > prepared_sample.id] //technical_replicate_no int //which replicate this +record represents //technical_replicate_total int //total number of replicates +for a sample //method_id int [ref: > method.id] //we suspect this will be +captured in the experiment_id //raw_data_id int [ref:> file_object_metadata.id] +//qc_pass boolean //note text + +////////////////////////////////////////////////// + +Table proximate_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref: > prepared_sample.id] technical_replicate_no +int //which replicate this record represents technical_replicate_total int +//total number of replicates for a sample method_id int [ref: > method.id] //we +suspect this will be captured in the experiment_id //equipment_id int [ref: > +equipment.id] //we suspect this will be captured in the experiment_id +//analyst_id int [ref: > contact.id] //we suspect this will be captured in the +experiment_id raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean +note text } + +Table ultimate_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref: > prepared_sample.id] technical_replicate_no +int //which replicate this record represents technical_replicate_total int +//total number of replicates for a sample method_id int [ref: > method.id] +//equipment_id int [ref: > equipment.id] //analyst_id int [ref: > contact.id] +raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note text } + +Table compositional_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref: > prepared_sample.id] technical_replicate_no +int //which replicate this record represents technical_replicate_total int +//total number of replicates for a sample method_id int [ref: > method.id] +//equipment_id int [ref: > equipment.id] //analyst_id int [ref: > contact.id] +raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note text } + +Table icp_record { id int [pk, increment] dataset_id int [ref: > dataset.id] +experiment_id int [ref: > experiment.id] resource_id int [ref:> resource.id] +sample_id int [ref: > prepared_sample.id] technical_replicate_no int //which +replicate this record represents technical_replicate_total int //total number of +replicates for a sample method_id int [ref: > method.id] //equipment_id int +[ref: > equipment.id] //analyst_id int [ref: > contact.id] raw_data_id int +[ref:> file_object_metadata.id] qc_pass boolean note text } + +Table xrf_record { id int [pk, increment] dataset_id int [ref: > dataset.id] +experiment_id int [ref: > experiment.id] resource_id int [ref:> resource.id] +sample_id int [ref: > prepared_sample.id] technical_replicate_no int //which +replicate this record represents technical_replicate_total int //total number of +replicates for a sample method_id int [ref: > method.id] maybe_wavelength_nm +decimal ////might be in the method maybe_intensity decimal //might be in the +method maybe_energy_slope decimal //might be in the method maybe_energy_offset +decimal //might be in the method //equipment_id int [ref: > equipment.id] +//analyst_id int [ref: > contact.id] raw_data_id int [ref:> +file_object_metadata.id] qc_pass boolean note text } + +Table xrd_record { id int [pk, increment] dataset_id int [ref: > dataset.id] +experiment_id int [ref: > experiment.id] resource_id int [ref:> resource.id] +sample_id int [ref: > prepared_sample.id] technical_replicate_no int //which +replicate this record represents technical_replicate_total int //total number of +replicates for a sample maybe_scan_low_nm int ////might be in the method +maybe_scan_high_nm int ////might be in the method method_id int [ref: > +method.id] //equipment_id int [ref: > equipment.id] //analyst_id int [ref: > +contact.id] raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note +text } + +Table calorimetry_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref: > prepared_sample.id] technical_replicate_no +int //which replicate this record represents technical_replicate_total int +//total number of replicates for a sample method_id int [ref: > method.id] +//equipment_id int [ref: > equipment.id] //analyst_id int [ref: > contact.id] +raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note text } + +Table ftnir_record { id int [pk, increment] dataset_id int [ref: > dataset.id] +experiment_id int [ref: > experiment.id] resource_id int [ref:> resource.id] +sample_id int [ref: > prepared_sample.id] technical_replicate_no int //which +replicate this record represents technical_replicate_total int //total number of +replicates for a sample method_id int [ref: > method.id] //equipment_id int +[ref: > equipment.id] //analyst_id int [ref: > contact.id] raw_data_id int +[ref:> file_object_metadata.id] qc_pass boolean note text } + +Table rgb_record { id int [pk, increment] dataset_id int [ref: > dataset.id] +experiment_id int [ref: > experiment.id] resource_id int [ref:> resource.id] +sample_id int [ref: > prepared_sample.id] technical_replicate_no int //which +replicate this record represents technical_replicate_total int //total number of +replicates for a sample method_id int [ref: > method.id] //equipment_id int +[ref: > equipment.id] //analyst_id int [ref: > contact.id] raw_data_id int +[ref:> file_object_metadata.id] qc_pass boolean note text } + +///////////////////////////////////// ////// AIM2 EXPERIMENTAL DATA +///////////////////////////////////// + +Table pretreatment_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref: > prepared_sample.id] pretreatment_method int +[ref:> method.id] eh_method_id int [ref:> method.id] reaction_block_id int +block_position varchar temperature decimal replicate_no int analyst_id int +[ref:> contact.id] qc_pass boolean note text } + +Table fermentation_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref: > +resource.id] //this is denormalized, but maybe necessary for external data +sample_id int [ref: > prepared_sample.id] strain_id int [ref:> strain.id] +pretreatement_method_id int [ref:> method.id] //decon method in gsheet +eh_method_id int [ref:> method.id] //enzymatic hydrolysis method replicate_no +int well_position varchar temperature decimal //ph decimal //Is this at the +beginning? End? agitation_rpm decimal vessel_id int [ref:> equipment.id] +analyte_detection_equipment_id int [ref:> equipment.id] analyst_id int [ref: > +contact.id] raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note +text } + +Table gasification_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] experiment_id int [ref: > experiment.id] resource_id int [ref: > +resource.id] //this is denormalized, but maybe necessary for external data +sample_id int [ref:> prepared_sample.id] feedstock_mass decimal bed_temperature +decimal gas_flow_rate decimal technical_replicate_no int analyst_id int [ref: > +contact.id] raw_data_id int [ref:> file_object_metadata.id] qc_pass boolean note +text } + +Table autoclave_record { id int [pk, increment] dataset_id int [ref:> +dataset.id] experiment_id int [ref:> experiment.id] resource_id int [ref:> +resource.id] sample_id int [ref:> prepared_sample.id] technical_replicate_no int +analyst_id int [ref: > contact.id] raw_data_id int [ref:> +file_object_metadata.id] qc_pass boolean note text } + +//=========================================================== // CHILD RECORD +TABLES – USDA DATA //=========================================================== + +//I want to create a base "usda_record" class that will be used for both +usda_census and usda_survey //records. I would also like to explore the class +also being applicable to usda_market type records, //although these are much +more different. + +Table usda_census_record [headercolor: #ffc72f] { id int [pk, increment] +dataset_id int [ref: > dataset.id] geoid int [ref:> geography.geoid] +commodity_code int [ref: > usda_commodity.id] year int source_reference string +// this may be the same as any other source attribute note text } + +Table usda_survey_record [headercolor: #ffc72f] { id int [pk, increment] +dataset_id int [ref: > dataset.id] geoid int [ref:> geography.geoid] +commodity_code int [ref: > usda_commodity.id] year int survey_program_id int +[ref: > usda_survey_program.id] survey_period string reference_month string +seasonal_flag boolean note text } + +//=========================================================== // CHILD RECORD +TABLE – USDA MARKET NEWS +//=========================================================== + +Table usda_market_report [headercolor: #ffc72f]{ id int [pk, increment] + +// IDENTIFIERS slug_id int [not null, note: "The constant MARS ID, e.g., 3667. +Defines the 'Series'."] slug_name string report_series_title string //e.g. +"Feedstuffs Report" + +// FREQUENCY & ORIGIN frequency string // e.g., "Monthly", "Weekly" office_name +varchar office_city_id int [ref:> location_address.id] office_state_fips varchar +[ref:> geography.geoid] source int [ref : - data_source.id] //might be +unnecessary since data can be looked up by slug_id and data in this table + +// Note: Splitting this table is NORMALIZATION. // It prevents repeating +'Monthly Feedstuffs Report' 10,000 times. } + +Table usda_market_record [headercolor: #ffc72f] { id int [pk, increment] +report_id int [not null, ref: > usda_market_report.id] dataset_id int [ref:> +dataset.id] //office_name varchar //office_city_id int [ref:> +location_address.id] //office_state_fips varchar [ref:> geography.geoid] +report_begin_date datetime //This report refers to the report_end_date datetime +report_date datetime //not sure how this differs from the other dates, but it is +earlier... //published_date datetime commodity_id int [not null, ref: > +usda_commodity.id] //primary_crop_id int [not null, ref:> primary_crop.id] +//assumes we can control what USDA market data we input and import only data for +primary crops in our database. otherwise the "not null" designation may present +issue market_type_id int //[ref:> market_type.id] market_type_catagory varchar +//this could be normalized, but it is all just "summary" in the example data +//slug_id int //slug_name string //report_title string grp string +market_catagory_id int // [ref;> market_catagory.id] class string grade string +variety string protein_pct decimal application string pkg string // sale_type +string //"FOB" (Free on Board - buyer pays shipping) or "Delivered" (seller pays +shipping) price_unit_id int [ref:> unit.id] //price_min decimal //these all go +into the parameter unit observation table //price_max decimal //price_min_change +decimal //price_min_direction varchar //price_max_change decimal +//price_max_direction decimal //avg_price decimal //avg_price_year_ago decimal +freight string trans_mode string } + +//=========================================================== // CHILD RECORD +TABLE – LAND IQ //=========================================================== + +//I think I may want to create a base "polygon" or "geometry" record type //for +geospatial records. Please log this and flag for discussion later. + +Table landiq_record [headercolor: #808080] { id int [pk, increment] dataset_id +int [ref: > dataset.id] polygon_id int [ref: > polygon.id] main_crop int [ref: > +primary_crop.id] secondary_crop int [ref: > primary_crop.id] tertiary_crop int +[ref: > primary_crop.id] quaternary_crop int [ref: > primary_crop.id] confidence +int irrigated boolean acres float version string note text } + +//=========================================================== // CHILD RECORD +TABLE – FACILITY/INFRASTRUCTURE DATA +//=========================================================== + +Table facility_record { id int [pk, increment] dataset_id int [ref: > +dataset.id] facility_name string location_id int [ref: > location_address.id] +capacity_mw decimal resource_id int [ref:> resource.id] //could have multiple +resources per facility. For example almond shells and hulls. operator string +start_year int note text } + +//INFRASTRUCTURE RECORD SET PLACEHOLDER. + +//These records are for now to be simply modeled as + +//==================== TABLE GROUP ========================= +//==================== INFRASTRUCTURE INDUSTRIAL DATASETS +========================= + +Table infrastructure_biodiesel_plants [headercolor: #008B8B] { // two joined +datasets biodiesel_plant_id integer [pk] company varchar bbi_index integer // +blank for some companies city varchar state char(2) [note: "convert to state +abbreviation"] // some rows have whole names written out; reduce to +abbreviations capacity_mmg_per_y integer // should it be integer? feedstock +varchar [note: "multiselect"] // blank for some companies status varchar [note: +"select ; options listed are either 'operational' or 'idle'"] // blank for some +companies address varchar // blank for some companies coordinates varchar [note: +"currently string, convert to geometric point"] // blank for some companies +latitude decimal longitude decimal source text [note: "change to url later"] } + +Table infrastructure_biosolids_facilities [headercolor: #008B8B] { // lots of +mixed all-caps and proper formatting biosolid_facility_id integer [pk] +report_submitted_date date // one row says "06-Kan-24" - correct typo and +convert to date latitude decimal longitude decimal facility varchar authority +varchar plant_type varchar [note: "multiselect"] aqmd varchar // some blank +entries. could also make multiselect if we had a unified format? e.g. "feather +river" and "feather river aqmd" is the same facility_address varchar // some +blank facility_city varchar // some blank state varchar(2) facility_zip varchar +// some blank facility_county varchar // some blank (make multiselect?) +mailing_street_1 varchar // some blank mailing_city varchar // some blank (make +multiselect?) mailing_state varchar(2) // some blank? mailing_zip varchar +biosolids_number varchar // add custom check alter - should be CALX###### +biosolids_contact varchar biosolids_contact_phone varchar // convert to single +custom format biosolids_contact_email varchar // convert to single custom format +adwf decimal potw_biosolids_generated integer twtds_biosolids_treated integer // +very blank class_b_land_app integer // very blank class_b_applier varchar // +very blank class_a_compost integer // very blank class_a_heat_dried integer // +very blank class_a_other integer // very blank class_a_other_applier varchar // +very blank twtds_transfer_to_second_preparer int // very blank +twtds_second_preparer_name varchar [note: "sometimes multiple preparers are +reported along with respective amt of biosolids transferred"] adc_or_final_c +integer // very blank landfill integer landfill_name varchar // very blank +surface_disposal integer // VERY blank deepwell_injection varchar //I don't even +know what is this stored integer // has some random varchar content in there +longterm_treatment integer // very blank other integer // very blank +name_of_other varchar incineration integer Note: "probably could change to a +long format? a lot of blank fields and random columns near the bottom" } + +Table infrastructure_cafo_manure_locations [headercolor: #008B8B] { +cafo_manure_id integer [pk] latitude decimal longitude decimal owner_name +varchar // very blank facility_name varchar address varchar town varchar state +varchar(2) zip varchar(5) animal varchar [note: "select"] +animal_feed_operation_type varchar [note:"select"] animal_units integer // +partially blank animal_count integer // partially blank; also some of them end +with 333, 667, or 000? are these calculations? manure_total_solids decimal +[note: "million gallons a year"] source text [note: "change to url later"] +date_accessed date } + +Table infrastructure_ethanol_biorefineries [headercolor: #008B8B] { +ethanol_biorefinery_id integer [pk] name varchar city varchar state varchar(2) +address varchar type varchar [note: "multiselect"] capacity_mgy integer +production_mgy integer constr_exp integer // don't know what this is } + +Table infrastructure_landfills [headercolor: #008B8B] { project_int_id integer +project_id varchar [pk] ghgrp_id varchar landfill_id integer landfill_name +varchar state varchar(2) physical_address text city varchar county varchar +zip_code varchar latitude decimal longitude decimal ownership_type varchar +[note: "select, either Public or Private"] landfill_owner_orgs varchar +landfill_opened_year date [note: "year only; should it be int or date?"] +landfill_closure_year date [note: "year only; should it be int or date?"] +landfill_status varchar [note: "select"] waste_in_place integer [note: "in +tons"] waste_in_place_year date [note: "assuming year collected?"] +lfg_system_in_place boolean [note: "currently yes/no"] lfg_collected decimal +[note: "in mmscfd"] lfg_flared decimal [note: "in mmscfd"] project_status +varchar [note: "select"] project_name varchar [note: "select?"] +project_start_date date project_shutdown_date date // very empty +project_type_category varchar [note: "select"] lfg_energy_project_type varchar +[note: "select"] rng_delivery_method varchar actual_mw_generation decimal +rated_mw_capacity decimal lfg_flow_to_project decimal [note: "mmscfd"] +direct_emission_reductions decimal [note: "MMTCO2e/yr for current year"] +avoided_emission_reductions decimal [note: "MMTCO2e/yr for current year"] } + +Table infrastructure_livestock_anaerobic_digesters [headercolor: #008B8B] { +digester_id integer [pk] project_name varchar project_type varchar [note: +"select or multiselect"] city varchar state varchar(2) digester_type varchar +[note: "select or multiselect"] profile text [note: "url"] year_operational date +[note: "year only"] animal_type_class varchar [note: "select"] animal_types +varchar [note: "multiselect"] pop_feeding_digester varchar [note: "either single +integer or multiple integers separated by a semicolon"] // is this even +necessary? total_pop_feeding_digester integer cattle integer dairy integer +poultry integer swine integer codigestion varchar [note: "multiselect"] +biogas_generation_estimate integer [note: "cu/ft per day"] electricity_generated +integer [note: "kWh/yr"] biogas_end_uses varchar [note: "multiselect"] +methane_emission_reductions integer [note: "metric tons CO2e/yr"] latitude +decimal longitude decimal } + +Table infrastructure_saf_and_renewable_diesel_plants [headercolor: #008B8B] { +ibcc_index integer [pk] company varchar city varchar state varchar(2) country +varchar capacity varchar [note: "mmg per yr; mostly integers with some strings +in the format '#/#' where # is a number"] feedstock varchar [note: +"multiselect"] products varchar [note: "multiselect"] status varchar [note: +"multiselect"] address text coordinates text latitude decimal longitude decimal +} + +Table infrastructure_wastewater_treatment_plants [headercolor: #008B8B] { +plant_id integer [pk] name varchar state varchar(2) codigestion boolean [note: +"currently 0/1"] flow_design_adjusted decimal [note: "MGD"] flow_average decimal +[note: "MGD"] biosolids decimal [note: "BDT/yr"] excess_flow decimal [note: +"MGD"] biogas_utilized boolean [note: "currently 0/1"] flaring boolean [note: +"currently 0/1"] excess_mass_loading_rate decimal [note: "BDT/d"] +excess_mass_loading_rate_wet decimal [note: "tons per day?"] methane_production +decimal [note: "cubic ft/d"] energy_content decimal [note: "BTU/d"] electric_kw +decimal thermal_mmbtu_d decimal electric_kwh decimal thermal_annual_mmbtu_y +decimal anaerobic_digestion_facility varchar // partially blank county varchar +// partially blank dayload_bdt decimal // for ca only dayload decimal // what's +the difference between this and the prev one? for ca only equivalent_generation +decimal // for ca only facility_type varchar [note: "select"] // for ca only +feedstock varchar [note: "select"] // for ca only type varchar [note: "select"] +// for ca only city varchar latitude decimal longitude decimal zipcode varchar } + +Table infrastructure_combustion_plants [headercolor: #008B8B] { combustion_fid +integer [pk] objectid integer // several object ids are 0 status varchar [note: +"select: active, retired, unknown"] // has a random 0 in there. does that mean +unknown city varchar name varchar county varchar equivalent_generation decimal +np_mw decimal // what does this mean? look up cf decimal // what does this mean? +yearload integer [note: "in bdt"] fuel varchar [note: "select WDS, MSW, AB"] +notes varchar [note: "optional field, blanks replaced by zeroes"] type varchar +[note: "all COMB_pts; is it necessary"] wkt_geom text geom point latitude +decimal longitude decimal } + +Table infrastructure_district_energy_systems [headercolor: #008B8B] { des_fid +integer [pk] cbg_id integer name varchar system varchar // partially blank +object_id integer city varchar state varchar(2) primary_fuel varchar [note: +"selection of NG, E/Electric"] secondary_fuel varchar [note: "selection"] // +partially blank usetype varchar [note: "selection btwn College, +Downtown/Utility, Healthcare, Airport, Gov, Military"] cap_st decimal // what +does this mean? cap_hw decimal // what does this mean? cap_cw decimal // what +does this mean? chpcg_cap decimal // what does this mean? excess_c decimal +[note: 'all zeroes'] excess_h decimal [note: 'all zeroes'] type varchar [note: +'all DES_CBG'] wkt_geom text geom point latitude decimal longitude decimal } + +Table infrastructure_food_processing_facilities [headercolor: #008B8B] { +processing_facility_id integer [pk] address varchar county varchar city varchar +company varchar join_count integer // unsure if this is necessary. could omit? +master_type varchar [note: 'select; this is the main crop'] state varchar(2) +subtype varchar [note: 'select; this is also crop/product type'] target_fid +integer // lots of zeroes processing_type varchar [note: 'select'] zip varchar +type varchar [note: 'all PROC'] // unsure if this is needed wkt_geom text geom +point latitude decimal longitude decimal } + +Table infrastructure_msw_to_energy_anaerobic_digesters [headercolor: #008B8B] { +wte_id integer [pk] city varchar county varchar equivalent_generation decimal // +note: number stored as text feedstock varchar [note: 'multiselect'] dayload +decimal // note: number stored as text dayload_bdt decimal // note: number +stored as text facility_type varchar [note: 'select'] status varchar [note: +'select'] notes text source text type varchar [note: 'all W2E_pts'] // unsure if +needed wkt_geom text geom point latitude decimal longitude decimal } + +//=========================================================== // CHILD RECORD +TABLE – BT23 //=========================================================== + +Table billion_ton_2023_record [headercolor: #EB801B] { id int [pk, increment] +subclass_id int [ref:> resource_subclass.id] resource_id int [ref:> resource.id] +geoid varchar [ref:> geography.geoid] county_square_miles float model_name +varchar //enumerated list with POLYSIS, NASS, etc. scenario_name varchar +//Enumerated list of near-term, mature-market, etc price_offered_usd decimal +production int production_unit_id int [ref:> unit.id] btu_ton int +production_energy_content int energy_content_unit_id int [ref:> unit.id] +product_density_dtpersqmi decimal land_source varchar } + +/////////////////////////////////////////////////////////////// +/////////////////////////////////////////////////////////////// Table +usda_domain [headercolor: #ffc72f] { //domain still needs linkage! id int [pk, +increment] name string [not null, unique] description string uri string } + +// Table usda_commodity [headercolor: #ffc72f] { // id int [pk, increment] // +name string [not null, unique] // description string // uri string // } + +// Table usda_commodity_to_primary_crop [headercolor: #ffc72f] { // +usda_commodity_id int [ref: > usda_commodity.id] // primary_crop_id int [ref: > +primary_crop.id] // } + +Table usda_statistic_category [headercolor: #ffc72f] { id int [pk, increment] +name string [not null, unique] description string uri string } + +Table usda_survey_program [headercolor: #ffc72f] { id int [pk, increment] name +string [not null, unique] description string uri string } + +Table dimension_type [headercolor: #A15CF5] { id int [pk, increment] name string +[not null, unique, note: "E.g., TIMEPOINT, WAVELENGTH, DEPTH"] description text +uri string } + +Table analysis_type [headercolor: #A15CF5] { //we may want to be careful +difference between analysis and methods // LookupBase for enum/ontology-like +tables id int [pk, increment] name string [not null, unique, note: "X-Ray +Fluorescence analysis, Proximate analysis, Chemical Composition, Fermentation +Profile, etc"] // description string uri string // } + +Table polygon [headercolor: #808080] { id int [pk] geoid string [ref: > +geography.geoid] geom geometry } + +Table strain { // LookupBase for enum/ontology-like tables id int [pk, +increment] name string [not null, unique, note: "X-Ray Fluorescence analysis, +Proximate analysis, Chemical Composition, Fermentation Profile, etc"] // +parent_strain_id int [ref:> strain.id, note: "recursive"] description string uri +string // + +} + +# // ========================================== // USDA HIERARCHY & MAPPING // + +TableGroup "Resource Ontology Mapping" [color: #5D6D7E] { usda_commodity +resource_usda_commodity_map // usda_term_map // <--- The Dictionary (Raw Text -> +Clean USDA Node) + +} + +Table usda_commodity { // LookupBase id int [pk, increment] name string [not +null] // e.g., "Almonds", "Tree Nuts", "Rice, Long Grain" usda_source string // +"usda_source" = Who OWNS this official definition? // - "NASS": It is a census +crop (e.g., Almonds). // - "AMS": It is a market term not tracked by NASS (e.g., +Almond Hulls). usda_code string [note: "The official code used by USDA API"] + +// The Cleanup Mechanism (Self-Referencing Hierarchy) parent_commodity_id int +[ref: > usda_commodity.id, note: "If this is 'Almonds Hulls', parent might be +'Almonds'. There might be another row where commodity code is 'Almonds', and its +parent would be 'Tree Nuts'. 'Tree Nuts' would have NULL listed for parent."] +//Gemini has promised that the USDA NASS API already has structured commodity +relations so it should be a programmable task. + +description string uri string + +Note: ''' + +# ETL INGESTION RULE + +1. **Ingest NASS First:** The NASS API is the primary source of truth. + Programmatically populate this table using NASS "Group" -> "Commodity" -> + "Class" hierarchy. +2. **Ingest AMS Second:** The AMS API (Market Data) is messy. - When Python + encounters a term in AMS (e.g., "Almond Hulls"), it must check this table. - + If the term exists (from NASS), link to it. - If the term is NEW, create a + new node here with usda_source = "AMS". - **Manual Step:** A human must + periodically review new "AMS" nodes and link them to their NASS parent (e.g., + Link "Almond Hulls" -> "Almonds"). ''' } + +Table usda_term_map { id int [pk, increment] + +// THE INPUT (The Messy Reality) source_system string [note: " 'NASS' or 'AMS' +"] // "source_system" = Where did we FIND this specific messy text string. // We +need this so if we re-run the ingestion script, we know which rules apply (NASS +data is prioritized, AMS data is referenced and then added if not already +captured) source_context string [note: "For AMS: The Slug ID (e.g. 3667). For +NASS: The Group."] // "source_context" = The container where we found it. // - +For NASS: The Group Name (e.g., "Tree Nuts"). // - For AMS: The Slug ID (e.g., +"3668" = "Monthly National Grain and Oilseed Processor Feedstuff Report"). +raw_term string [not null, note: "The exact string from the API, e.g., 'Hulls', +'Hull/Shell Mix'"] + +// THE OUTPUT (The Decision) usda_commodity_id int [ref: > usda_commodity.id] +//We review this manually. + +// METADATA is_verified boolean [default: false] //Note whether we've confirmed +mapping note text } + +Table resource_usda_commodity_map { id int [pk, increment] + +// 1. THE INTERNAL TARGET (Who is asking?) // We allow linking to EITHER a +specific resource OR a general crop resource_id int [ref: > resource.id, null] +// Specific: "Almond Hulls" primary_crop_id int [ref: > primary_crop.id, null] +// General: "Almonds" + +// 2. THE EXTERNAL SOURCE (Who has the data?) usda_commodity_id int [ref: > +usda_commodity.id, not null] + +// 3. THE LOGIC (How good is the match?) match_tier string [not null, note: +"ENUM: 'DIRECT_MATCH', 'CROP_FALLBACK', 'AGGREGATE_PARENT'"] + +// Metadata created_at datetime [default: `current_timestamp`] note text [note: +"Explanation of why this link was made"] + +// LOGIC: A row must have EITHER a resource_id OR a primary_crop_id, but not +both null. } + +///////////////////////////////////////////////////////////// //////////// +PEOPLE ////////////// +//////////////////////////////////////////////////////////// + +Table contact { id int [pk] first_name varchar last_name varchar email varchar +[unique] affiliation varchar //maybe link to an enumerated list } + +Table provider { id int [pk] codename string } diff --git a/src/ca_biositing/datamodels/pyproject.toml b/src/ca_biositing/datamodels/pyproject.toml index 9d9a5d1c..6b4f49ee 100644 --- a/src/ca_biositing/datamodels/pyproject.toml +++ b/src/ca_biositing/datamodels/pyproject.toml @@ -27,6 +27,8 @@ dependencies = [ "psycopg2-binary>=2.9.6,<3", "pydantic>=2.0.0", "pydantic-settings>=2.0.0", + "linkml>=1.8.0", + "sqlalchemy>=2.0.0", ] [project.urls] diff --git a/src/pipeline/README.md b/src/pipeline/README.md deleted file mode 100644 index f2db60b9..00000000 --- a/src/pipeline/README.md +++ /dev/null @@ -1,168 +0,0 @@ -# ETL Pipeline Project - -This project implements a modular ETL (Extract, Transform, Load) pipeline that -extracts data from Google Sheets (or other sources), transforms it using Python, -and loads it into a PostgreSQL database. The entire environment is containerized -with Docker. - ---- - -## Core Workflows - -This project has three key development workflows. For detailed, step-by-step -instructions, please refer to the dedicated workflow guides. A high-level -overview is provided here to give conceptual understanding before you begin. - -### 1. Docker Environment Management - -- **Purpose:** Managing the lifecycle of your development containers (app and - database). -- **Details:** For starting, stopping, and rebuilding your environment. -- **[See the full guide: DOCKER_WORKFLOW.md](../../docs/pipeline/DOCKER_WORKFLOW.md)** - -### 2. Database Schema Migrations (Alembic) - -- **Purpose:** Making and applying changes to the database schema (e.g., adding - tables or columns). -- **Details:** How to automatically generate and apply migration scripts based - on your SQLModel changes. -- **[See the full guide: ALEMBIC_WORKFLOW.md](../../docs/pipeline/ALEMBIC_WORKFLOW.md)** - -### 3. ETL Pipeline Development (Prefect) - -- **Purpose:** Running the ETL pipeline and adding new data pipelines using - Prefect's "flow of flows" pattern. -- **Details:** The `run_prefect_flow.py` script acts as a master orchestrator - that runs all individual pipeline flows defined in the `src/flows/` directory. - To add a new pipeline, you must create a new flow file and add it to the - master flow. -- **[See the full guide: ETL_WORKFLOW.md](../../docs/pipeline/ETL_WORKFLOW.md)** - -### 4. Creating New Database Models - -- **Purpose:** Adding a new table to the database schema. -- **Details:** Use the `model_template.py` to define your new table, then follow - the Alembic workflow to generate and apply the migration. -- **[See the model template: src/models/templates/model_template.py](./src/models/templates/model_template.py)** -- **[See the migration guide: ALEMBIC_WORKFLOW.md](../../docs/pipeline/ALEMBIC_WORKFLOW.md)** - ---- - -## Local Development Environment (Pixi) - -This project uses **Pixi** to manage dependencies and run tasks for local -development. This environment is used for both running the application locally -and for code quality tools like `pre-commit`. The Docker container also uses -Pixi to install dependencies. - -**1. Install Pixi:** - -- Follow the official instructions to - [install Pixi](https://pixi.sh/latest/installation/) on your system. - -**2. Install Local Dependencies:** - -- Once Pixi is installed, navigate to the `ca-biositing` root directory and run: - - ```bash - pixi install - ``` - - This will install the required local tools (like `pre-commit`) into a managed - environment. - - If you have issues with the install on Windows, you may need to command: - - ``` - pixi workspace platform add win-64 - ``` - - Once pixi is installed, run the following command to set up pre-commit checks - on every commit: - - ```bash - pixi run pre-commit-install - ``` - -**3. Activate the Local Environment:** - -- To activate this environment in your shell, run: - - ```bash - pixi shell - ``` - - This command is the equivalent of a traditional `source venv/bin/activate`. - You will see a prefix in your shell prompt indicating that the environment is - active. You can now run commands like `pre-commit` directly. - ---- - -## Getting Started - -Follow these steps to set up and run the project for the first time. - -**1. Google Cloud Setup:** - -- To allow the application to access Google Sheets, you must first create a - service account and generate a `credentials.json` file. -- **[Follow the full guide here: GCP_SETUP.md](../../docs/pipeline/GCP_SETUP.md)** - -**2. Environment Setup:** - -- Create a `.env` file in the project root directory by copying the - `.env.example` file. -- The database connection settings (e.g., `POSTGRES_USER`) are used to connect - to the PostgreSQL container. The default values in `.env.example` are - sufficient for local development. You do not need to change them unless you - have a custom setup. - -**3. Build the Docker Image:** - -- From the project root directory, build the Docker image. - - ```bash - docker-compose build - ``` - -**4. Start the Services:** - -- Start the application and database containers in detached mode. - - ```bash - docker-compose up -d - ``` - -**5. Apply Database Migrations:** - -- The first time you start the project, you need to apply the database - migrations to create the tables. This command applies existing migrations; you - only need to consult the Alembic workflow guide when creating _new_ - migrations. - - ```bash - docker-compose exec app pixi run alembic upgrade head - ``` - -The environment is now fully set up and running. - ---- - -## Project Structure - -This `pipeline` directory is a self-contained ETL project located within the -larger `ca-biositing` repository. Here is a brief overview of its key -directories: - -``` -pipeline/ -├── alembic/ # Database migration scripts -├── etl/ -│ ├── extract/ # ETL Task: Modules for extracting data -│ ├── transform/ # ETL Task: Modules for transforming data -│ ├── load/ # ETL Task: Modules for loading data -│ └── templates/ # Templates for new ETL modules -├── flows/ # Prefect Flows: Individual pipeline definitions -├── models/ # SQLModel class definitions (database tables) -└── utils/ # Shared utility functions -``` From de92cb017f7d74c00a5e19ef040f3be84ec8dfe8 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Mon, 8 Dec 2025 09:22:39 -0700 Subject: [PATCH 51/81] AI hallucinations are messing up yaml files. Attempting to fix. --- .../datamodels/linkml/modules/analysis.yaml | 12 + .../linkml/modules/analysis_records.yaml | 4 + .../datamodels/linkml/modules/core.yaml | 166 -- .../linkml/modules/data_sources_metadata.yaml | 144 +- .../datamodels/linkml/modules/lineage.yaml | 73 +- .../datamodels/linkml/modules/places.yaml | 78 +- .../schemas/generated/aim2_records.py | 0 .../schemas/generated/analysis_records.py | 1919 +++++++++++++++++ .../schemas/generated/census_survey.py | 132 -- .../schemas/generated/field_sampling.py | 0 .../datamodels/schemas/generated/geography.py | 29 - src/ca_biositing/datamodels/generate_sqla.py | 49 + .../pipeline/utils/database_interaction.ipynb | 177 +- 13 files changed, 2254 insertions(+), 529 deletions(-) create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py create mode 100644 src/ca_biositing/datamodels/generate_sqla.py diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml index 987f0d1d..456b876d 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml @@ -91,3 +91,15 @@ slots: dimension_unit_id: range: integer description: Reference to Unit (dimension). + + source_id: + range: integer + description: Reference to Source. + + start_date: + range: datetime + description: Start date of the dataset. + + end_date: + range: datetime + description: End date of the dataset. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml index 35cc271d..4ec92ee7 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml @@ -227,3 +227,7 @@ slots: gas_flow_rate: range: decimal description: Gas flow rate. + + sample_id: + range: integer + description: Reference to Sample. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml index 84eaa04c..234b9b4f 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml @@ -34,84 +34,6 @@ classes: - description - uri - LineageGroup: - is_a: BaseEntity - description: Grouping for lineage information. - slots: - - note - - EntityLineage: - description: Lineage information for a specific entity. - slots: - - id - - lineage_group_id - - source_table - - source_row_id - - note - - EtlRun: - description: Information about an ETL run. - slots: - - id - - started_at - - completed_at - - pipeline_name - - status - - records_ingested - - note - slot_usage: - id: - identifier: true - range: string - - DataSource: - is_a: BaseEntity - description: Information about a data source. - slots: - - name - - description - - data_source_type_id - - full_title - - creator - - subject - - publisher - - contributor - - date - - type - - biocirv - - format - - language - - relation - - temporal_coverage - - location_coverage_id - - rights - - uri - - DataSourceType: - is_a: BaseEntity - description: Type of data source. - slots: - - source_type_id - - SourceType: - is_a: LookupBase - description: Lookup for source types (database, literature, etc.). - - LocationResolution: - is_a: LookupBase - description: Resolution of location coverage (nation, state, county, etc.). - - FileObjectMetadata: - is_a: BaseEntity - description: Metadata for file objects. - slots: - - data_source_id - - bucket_path - - file_format - - file_size - - checksum_md5 - - checksum_sha256 - slots: id: identifier: true @@ -177,91 +99,3 @@ slots: records_ingested: range: integer description: Number of records ingested. - - data_source_type_id: - range: integer - description: Reference to data source type. - - full_title: - range: string - description: Full title of the data source. - - creator: - range: string - description: Creator of the data source. - - subject: - range: string - description: Subject of the data source. - - publisher: - range: string - description: Publisher of the data source. - - contributor: - range: string - description: Contributor to the data source. - - date: - range: datetime - description: Date associated with the data source. - - type: - range: string - description: Type of the data source. - - biocirv: - range: boolean - description: Whether the data source is internal to BioCirV. - - format: - range: string - description: Format of the data source. - - language: - range: string - description: Language of the data source. - - relation: - range: string - description: Relation of the data source. - - temporal_coverage: - range: string - description: Temporal coverage of the data source. - - location_coverage_id: - range: integer - description: Reference to location resolution. - - rights: - range: string - description: Rights associated with the data source. - - source_type_id: - range: integer - description: Reference to source type. - - data_source_id: - range: integer - description: Reference to data source. - - bucket_path: - range: string - description: Path to the file in the bucket. - - file_format: - range: string - description: Format of the file. - - file_size: - range: integer - description: Size of the file. - - checksum_md5: - range: string - description: MD5 checksum of the file. - - checksum_sha256: - range: string - description: SHA256 checksum of the file. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index 7bb40074..fab12584 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -14,6 +14,7 @@ default_range: string imports: - linkml:types - core + - field_sampling classes: DataSource: @@ -22,136 +23,49 @@ classes: slots: - name - description - - data_source_type_id - - full_title - - creator - - subject - - publisher - - contributor - - date - - type - - biocirv - - format - - language - - relation - - temporal_coverage - - location_coverage_id - - rights - uri + - publication_date + - version + - publisher + - author + - license + - note - DataSourceType: - is_a: LookupBase - description: Type of data source. - slots: - - source_type_id - - SourceType: - is_a: LookupBase - description: General source type. - - FileObjectMetadata: + MetadataSample: is_a: BaseEntity - description: Metadata for file objects. + description: Metadata for a field sample. slots: - - data_source_id - - bucket_path - - file_format - - file_size - - checksum_md5 - - checksum_sha256 - - LocationResolution: - is_a: LookupBase - description: Resolution of location data. + - field_sample_id + - metadata_key + - metadata_value + - metadata_type + - note slots: - data_source_type_id: - range: integer - description: Reference to DataSourceType. - - source_type_id: - range: integer - description: Reference to SourceType. - - full_title: - range: string - description: Full title of the data source. - - creator: - range: string - description: Creator of the data source. - - subject: - range: string - description: Subject of the data source. - - publisher: - range: string - description: Publisher of the data source. - - contributor: - range: string - description: Contributor to the data source. - - date: - range: datetime - description: Date of the data source. - - type: - range: string - description: Type of the data source. - - biocirv: - range: boolean - description: Whether the data source is internal (BioCirV). - - format: - range: string - description: Format of the data source. - - language: - range: string - description: Language of the data source. - - relation: - range: string - description: Relation of the data source. - - temporal_coverage: - range: string - description: Temporal coverage of the data source. - - location_coverage_id: - range: integer - description: Reference to LocationResolution. + publication_date: + range: date + description: Date of publication. - rights: + version: range: string - description: Rights of the data source. + description: Version of the data source. - uri: + author: range: string - description: URI of the resource. + description: Author of the data source. - data_source_id: - range: integer - description: Reference to DataSource. - - bucket_path: + license: range: string - description: Path to the file in the bucket. + description: License of the data source. - file_format: + metadata_key: range: string - description: Format of the file. - - file_size: - range: integer - description: Size of the file in bytes. + description: Key for the metadata. - checksum_md5: + metadata_value: range: string - description: MD5 checksum of the file. + description: Value for the metadata. - checksum_sha256: + metadata_type: range: string + description: Type of the metadata value (e.g. string, int, float). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml index b0014c90..6d0fd301 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml @@ -17,68 +17,39 @@ imports: classes: LineageGroup: - is_a: BaseEntity - description: Grouping of lineage entities. + description: Grouping for lineage information. slots: - - name - - description + - id + - etl_run_id + - note + slot_usage: + id: + identifier: true + range: integer EntityLineage: - description: Lineage relationship between entities. + description: Lineage information for a specific entity. slots: - id - - parent_entity_id - - child_entity_id - lineage_group_id - - relationship_type + - source_table + - source_row_id + - note slot_usage: id: identifier: true range: integer EtlRun: - is_a: BaseEntity - description: ETL run information. + description: Information about an ETL run. slots: - - run_id - - start_time - - end_time + - id + - started_at + - completed_at + - pipeline_name - status - - log_uri - -slots: - parent_entity_id: - range: integer - description: ID of the parent entity. - - child_entity_id: - range: integer - description: ID of the child entity. - - lineage_group_id: - range: integer - description: Reference to LineageGroup. - - relationship_type: - range: string - description: Type of relationship. - - run_id: - range: string - description: Unique identifier for the ETL run. - - start_time: - range: datetime - description: Start time of the run. - - end_time: - range: datetime - description: End time of the run. - - status: - range: string - description: Status of the run. - - log_uri: - range: string - description: URI to the run logs. + - records_ingested + - note + slot_usage: + id: + identifier: true diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml index 7cd2c18b..5a6342d3 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml @@ -17,13 +17,15 @@ imports: classes: Geography: - is_a: BaseEntity description: Geographic location. slots: - geoid - - name - - type - - geometry + - state_name + - state_fips + - county_name + - county_fips + - region_name + - agg_level_desc slot_usage: geoid: identifier: true @@ -32,42 +34,72 @@ classes: is_a: BaseEntity description: Physical address. slots: - - street_address + - geography_id + - address_line1 + - address_line2 - city - - state - - zip_code - - country - - geoid + - zip + - lat + - lon + - is_anonymous slots: geoid: range: string description: Unique identifier for geography. - type: + state_name: range: string - description: Type of geography (e.g. county, state). + description: State name. - geometry: + state_fips: range: string - description: WKT geometry. + description: State FIPS code. - street_address: + county_name: range: string - description: Street address. + description: County name. - city: + county_fips: range: string - description: City. + description: County FIPS code. - state: + region_name: range: string - description: State. + description: Region name. - zip_code: + agg_level_desc: range: string - description: ZIP code. + description: Aggregation level description. - country: + geography_id: range: string - description: Country. + description: Reference to Geography. + + address_line1: + range: string + description: Address line 1. + + address_line2: + range: string + description: Address line 2. + + city: + range: string + description: City. + + zip: + range: string + description: ZIP code. + + lat: + range: float + description: Latitude. + + lon: + range: float + description: Longitude. + + is_anonymous: + range: boolean + description: Whether the location is anonymous. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py new file mode 100644 index 00000000..e69de29b diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py new file mode 100644 index 00000000..c7ac9023 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py @@ -0,0 +1,1919 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class RecordBase(Base): + """ + + """ + __tablename__ = 'RecordBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"RecordBase(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class EntityLineage(Base): + """ + Lineage information for a specific entity. + """ + __tablename__ = 'EntityLineage' + + id = Column(Integer(), primary_key=True, nullable=False ) + lineage_group_id = Column(Integer()) + source_table = Column(Text()) + source_row_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" + + + + + + +class EtlRun(Base): + """ + Information about an ETL run. + """ + __tablename__ = 'EtlRun' + + id = Column(Text(), primary_key=True, nullable=False ) + started_at = Column(DateTime()) + completed_at = Column(DateTime()) + pipeline_name = Column(Text()) + status = Column(Text()) + records_ingested = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" + + + + + + +class Dataset(Base): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(DateTime()) + end_date = Column(DateTime()) + description = Column(Text()) + + + def __repr__(self): + return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" + + + + + + +class Observation(Base): + """ + Observation data. + """ + __tablename__ = 'Observation' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon definition. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between experiment and equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between experiment and analysis type. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between experiment and prepared sample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between experiment and method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ProximateRecord(RecordBase): + """ + Proximate analysis record. + """ + __tablename__ = 'ProximateRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"ProximateRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UltimateRecord(RecordBase): + """ + Ultimate analysis record. + """ + __tablename__ = 'UltimateRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"UltimateRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CompositionalRecord(RecordBase): + """ + Compositional analysis record. + """ + __tablename__ = 'CompositionalRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"CompositionalRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class IcpRecord(RecordBase): + """ + ICP analysis record. + """ + __tablename__ = 'IcpRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"IcpRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrfRecord(RecordBase): + """ + XRF analysis record. + """ + __tablename__ = 'XrfRecord' + + maybe_wavelength_nm = Column(Numeric()) + maybe_intensity = Column(Numeric()) + maybe_energy_slope = Column(Numeric()) + maybe_energy_offset = Column(Numeric()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrdRecord(RecordBase): + """ + XRD analysis record. + """ + __tablename__ = 'XrdRecord' + + maybe_scan_low_nm = Column(Integer()) + maybe_scan_high_nm = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CalorimetryRecord(RecordBase): + """ + Calorimetry analysis record. + """ + __tablename__ = 'CalorimetryRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"CalorimetryRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FtnirRecord(RecordBase): + """ + FT-NIR analysis record. + """ + __tablename__ = 'FtnirRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"FtnirRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class RgbRecord(RecordBase): + """ + RGB analysis record. + """ + __tablename__ = 'RgbRecord' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"RgbRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PretreatmentRecord(RecordBase): + """ + Pretreatment record. + """ + __tablename__ = 'PretreatmentRecord' + + pretreatment_method = Column(Integer()) + eh_method_id = Column(Integer()) + reaction_block_id = Column(Integer()) + block_position = Column(Text()) + temperature = Column(Numeric()) + replicate_no = Column(Integer()) + analyst_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"PretreatmentRecord(pretreatment_method={self.pretreatment_method},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FermentationRecord(RecordBase): + """ + Fermentation record. + """ + __tablename__ = 'FermentationRecord' + + strain_id = Column(Integer()) + pretreatement_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + replicate_no = Column(Integer()) + well_position = Column(Text()) + temperature = Column(Numeric()) + agitation_rpm = Column(Numeric()) + vessel_id = Column(Integer()) + analyte_detection_equipment_id = Column(Integer()) + analyst_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"FermentationRecord(strain_id={self.strain_id},pretreatement_method_id={self.pretreatement_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class GasificationRecord(RecordBase): + """ + Gasification record. + """ + __tablename__ = 'GasificationRecord' + + feedstock_mass = Column(Numeric()) + bed_temperature = Column(Numeric()) + gas_flow_rate = Column(Numeric()) + analyst_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AutoclaveRecord(RecordBase): + """ + Autoclave record. + """ + __tablename__ = 'AutoclaveRecord' + + analyst_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + + + def __repr__(self): + return f"AutoclaveRecord(analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LineageGroup(BaseEntity): + """ + Grouping for lineage information. + """ + __tablename__ = 'LineageGroup' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LineageGroup(note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Information about a data source. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) + publisher = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) + uri = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},uri={self.uri},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Lookup for source types (database, literature, etc.). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of location coverage (nation, state, county, etc.). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for file objects. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension (e.g. timepoint, wavelength). + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample prepared for analysis. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Strain(LookupBase): + """ + Strain of organism. + """ + __tablename__ = 'Strain' + + parent_strain_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py deleted file mode 100644 index 158c32a4..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/census_survey.py +++ /dev/null @@ -1,132 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class USDARecord(Base): - """ - Base class for USDA agricultural data records. - """ - __tablename__ = 'USDARecord' - - id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) - year = Column(Integer(), nullable=False ) - crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) - variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) - unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) - value = Column(Float()) - bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) - class_desc = Column(Text()) - domain_desc = Column(Text()) - source = Column(Text()) - notes = Column(Text()) - geography_id = Column(Integer(), ForeignKey('Geography.id')) - geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) - - - def __repr__(self): - return f"USDARecord(id={self.id},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" - - - - - - -class Geography(Base): - """ - Reference table for U.S. geographic identifiers. - """ - __tablename__ = 'Geography' - - id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - geoid = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(id={self.id},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},geoid={self.geoid},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class CensusRecord(USDARecord): - """ - A USDA Census of Agriculture record (every 5 years). - """ - __tablename__ = 'CensusRecord' - - id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) - year = Column(Integer(), nullable=False ) - crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) - variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) - unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) - value = Column(Float()) - bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) - class_desc = Column(Text()) - domain_desc = Column(Text()) - source = Column(Text()) - notes = Column(Text()) - geography_id = Column(Integer(), ForeignKey('Geography.id')) - geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) - - - def __repr__(self): - return f"CensusRecord(id={self.id},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SurveyRecord(USDARecord): - """ - A USDA Survey record (annual, seasonal, or periodic). - """ - __tablename__ = 'SurveyRecord' - - id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) - period_desc = Column(Text()) - freq_desc = Column(Text()) - program_desc = Column(Text()) - year = Column(Integer(), nullable=False ) - crop = Column(Enum('Almond', 'Pistachio', 'Tomato', 'Olive', name='CropEnum')) - variable = Column(Enum('ACREAGE_TOTAL', 'ACREAGE_BEARING', 'ACREAGE_NONBEARING', 'YIELD', 'PRODUCTION', 'OPERATIONS', name='VariableEnum')) - unit = Column(Enum('ACRES', 'TONS', 'TONS_PER_ACRE', 'OPERATIONS', name='UnitEnum')) - value = Column(Float()) - bearing_status = Column(Enum('BEARING', 'NONBEARING', 'NA', name='BearingStatusEnum')) - class_desc = Column(Text()) - domain_desc = Column(Text()) - source = Column(Text()) - notes = Column(Text()) - geography_id = Column(Integer(), ForeignKey('Geography.id')) - geography = relationship("Geography", uselist=False, foreign_keys=[geography_id]) - - - def __repr__(self): - return f"SurveyRecord(id={self.id},period_desc={self.period_desc},freq_desc={self.freq_desc},program_desc={self.program_desc},year={self.year},crop={self.crop},variable={self.variable},unit={self.unit},value={self.value},bearing_status={self.bearing_status},class_desc={self.class_desc},domain_desc={self.domain_desc},source={self.source},notes={self.notes},geography_id={self.geography_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py new file mode 100644 index 00000000..e69de29b diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py deleted file mode 100644 index dcc8a564..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py +++ /dev/null @@ -1,29 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class Geography(Base): - """ - Reference table for U.S. geographic identifiers. - """ - __tablename__ = 'Geography' - - id = Column(Integer(), primary_key=True, autoincrement=True , nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - geoid = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(id={self.id},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},geoid={self.geoid},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" diff --git a/src/ca_biositing/datamodels/generate_sqla.py b/src/ca_biositing/datamodels/generate_sqla.py new file mode 100644 index 00000000..54fe4a59 --- /dev/null +++ b/src/ca_biositing/datamodels/generate_sqla.py @@ -0,0 +1,49 @@ +import os +import subprocess +from pathlib import Path + +def generate_sqla(): + """ + Generates SQLAlchemy models from LinkML schema modules. + """ + base_dir = Path(__file__).parent + linkml_dir = base_dir / "ca_biositing/datamodels/linkml" + modules_dir = linkml_dir / "modules" + output_dir = base_dir / "ca_biositing/datamodels/schemas/generated" + + # Ensure output directory exists + output_dir.mkdir(parents=True, exist_ok=True) + + # Generate for modules + for yaml_file in modules_dir.glob("*.yaml"): + module_name = yaml_file.stem + output_file = output_dir / f"{module_name}.py" + print(f"Generating {output_file} from {yaml_file}...") + + cmd = [ + "python", "-m", "linkml.generators.sqlalchemygen", + "--no-mergeimports", + str(yaml_file) + ] + + with open(output_file, "w") as f: + subprocess.run(cmd, stdout=f, check=True) + + # Generate for main schema + main_yaml = linkml_dir / "ca_biositing.yaml" + main_output = output_dir / "ca_biositing.py" + print(f"Generating {main_output} from {main_yaml}...") + + cmd = [ + "python", "-m", "linkml.generators.sqlalchemygen", + "--no-mergeimports", + str(main_yaml) + ] + + with open(main_output, "w") as f: + subprocess.run(cmd, stdout=f, check=True) + + print("Generation complete.") + +if __name__ == "__main__": + generate_sqla() diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb index 41d5e443..671f288a 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb @@ -23,9 +23,17 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Libraries and models imported successfully.\n" + ] + } + ], "source": [ "import pandas as pd\n", "from sqlmodel import create_engine, Session, select\n", @@ -53,9 +61,17 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Database engine created. Ready to connect to: postgresql+psycopg2://biocirv_user:@localhost:5432/biocirv_db\n" + ] + } + ], "source": [ "DATABASE_URL = \"postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db\"\n", "\n", @@ -77,9 +93,19 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "- Loaded 0 records from 'field_samples'.\n", + "- Loaded 0 records from 'geographic_locations'.\n", + "- Loaded 18 records from 'primary_product'.\n" + ] + } + ], "source": [ "field_samples_df = None\n", "locations_df = None\n", @@ -111,9 +137,118 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "analysis_type_id", + "rawType": "int64", + "type": "integer" + }, + { + "name": "analysis_name", + "rawType": "object", + "type": "string" + } + ], + "ref": "29cf402a-5519-4cf9-9c5d-27d39dd02736", + "rows": [ + [ + "1", + "Proximate analysis" + ], + [ + "2", + "ICP-OES" + ], + [ + "3", + "Chemical composition" + ], + [ + "4", + "XRF analysis" + ], + [ + "5", + "Ultimate analysis" + ] + ], + "shape": { + "columns": 1, + "rows": 5 + } + }, + "text/html": [ + "
\n", + "\n", + "\n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + " \n", + "
analysis_name
analysis_type_id
1Proximate analysis
2ICP-OES
3Chemical composition
4XRF analysis
5Ultimate analysis
\n", + "
" + ], + "text/plain": [ + " analysis_name\n", + "analysis_type_id \n", + "1 Proximate analysis\n", + "2 ICP-OES\n", + "3 Chemical composition\n", + "4 XRF analysis\n", + "5 Ultimate analysis" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "df2 = pd.read_sql(\"SELECT * FROM analysis_types\", engine)\n", "df2 = df2.set_index(\"analysis_type_id\")\n", @@ -134,9 +269,17 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Skipping join because 'field_samples' table is empty.\n" + ] + } + ], "source": [ "merged_df = None\n", "\n", @@ -169,9 +312,17 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "No data to display.\n" + ] + } + ], "source": [ "if merged_df is not None:\n", " display(merged_df.head())\n", @@ -196,7 +347,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.14.0" + "version": "3.13.9" } }, "nbformat": 4, From 269d11dcd5e6ed64bbec8d4e6e19d5012c4578fa Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Mon, 8 Dec 2025 10:50:11 -0700 Subject: [PATCH 52/81] generated sqla from linkml.STILL NEEDS A CHECK. Next up alembic. --- .../linkml/modules/aim1_records.yaml | 4 + .../linkml/modules/aim2_records.yaml | 24 +- .../linkml/modules/data_sources_metadata.yaml | 61 +- .../linkml/modules/experiment_equipment.yaml | 4 + .../schemas/generated/aim1_records.py | 1707 ++++++++++++ .../schemas/generated/aim2_records.py | 1565 +++++++++++ .../datamodels/schemas/generated/analysis.py | 375 +++ .../schemas/generated/analysis_records.py | 224 -- .../schemas/generated/ca_biositing.py | 2403 +++++++++++++++++ .../datamodels/schemas/generated/core.py | 46 + .../generated/data_sources_metadata.py | 1000 +++++++ .../schemas/generated/experiment_equipment.py | 1341 +++++++++ .../schemas/generated/experiments.py | 1224 +++++++++ .../schemas/generated/external_data.py | 1527 +++++++++++ .../schemas/generated/field_sampling.py | 1000 +++++++ .../schemas/generated/general_analysis.py | 1118 ++++++++ .../datamodels/schemas/generated/geography.py | 125 + .../schemas/generated/infrastructure.py | 1595 +++++++++++ .../datamodels/schemas/generated/lineage.py | 109 + .../datamodels/schemas/generated/methods.py | 275 ++ .../generated/methods_parameters_units.py | 1000 +++++++ .../datamodels/schemas/generated/people.py | 44 + .../datamodels/schemas/generated/places.py | 106 + .../schemas/generated/resource_information.py | 307 +++ .../datamodels/schemas/generated/resources.py | 326 +++ .../schemas/generated/sample_preparation.py | 1089 ++++++++ .../datamodels/schemas/generated/sampling.py | 964 +++++++ 27 files changed, 19323 insertions(+), 240 deletions(-) create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml index 179c4898..fc2ae1ff 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml @@ -121,3 +121,7 @@ slots: maybe_scan_high_nm: range: integer description: High scan range in nm. + + sample_id: + range: integer + description: Reference to PreparedSample. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml index 416589b7..8eabaa1f 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml @@ -35,6 +35,8 @@ classes: - raw_data_id - qc_pass - note + - technical_replicate_total + - technical_replicate_no PretreatmentRecord: is_a: Aim2RecordBase @@ -68,13 +70,11 @@ classes: - feedstock_mass - bed_temperature - gas_flow_rate - - technical_replicate_no AutoclaveRecord: is_a: Aim2RecordBase description: Autoclave record. - slots: - - technical_replicate_no + slots: [] Strain: is_a: LookupBase @@ -141,3 +141,21 @@ slots: parent_strain_id: range: integer + + sample_id: + range: integer + + raw_data_id: + range: integer + description: Reference to FileObjectMetadata. + + qc_pass: + range: boolean + description: Whether the record passed QC. + + technical_replicate_no: + range: integer + description: Replicate number. + + technical_replicate_total: + range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index fab12584..cc20fe83 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -31,15 +31,30 @@ classes: - license - note - MetadataSample: + FileObjectMetadata: is_a: BaseEntity - description: Metadata for a field sample. + description: Metadata for a file object. slots: - - field_sample_id - - metadata_key - - metadata_value - - metadata_type - - note + - data_source_id + - bucket_path + - file_format + - file_size + - checksum_md5 + - checksum_sha256 + + DataSourceType: + is_a: BaseEntity + description: Type of data source. + slots: + - source_type_id + + LocationResolution: + is_a: LookupBase + description: Resolution of the location (e.g. nation, state, county). + + SourceType: + is_a: LookupBase + description: Type of source (e.g. database, literature). slots: publication_date: @@ -50,6 +65,10 @@ slots: range: string description: Version of the data source. + publisher: + range: string + description: Publisher of the data source. + author: range: string description: Author of the data source. @@ -58,14 +77,30 @@ slots: range: string description: License of the data source. - metadata_key: + data_source_id: + range: integer + description: Reference to DataSource. + + bucket_path: + range: string + description: Path to the file in the bucket. + + file_format: range: string - description: Key for the metadata. + description: Format of the file. + + file_size: + range: integer + description: Size of the file in bytes. - metadata_value: + checksum_md5: range: string - description: Value for the metadata. + description: MD5 checksum of the file. - metadata_type: + checksum_sha256: range: string - description: Type of the metadata value (e.g. string, int, float). + description: SHA256 checksum of the file. + + source_type_id: + range: integer + description: Reference to SourceType. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml index 4896706d..bc76394b 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml @@ -121,3 +121,7 @@ slots: prepared_sample_id: range: integer description: Reference to PreparedSample. + + method_id: + range: integer + description: Reference to Method. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py new file mode 100644 index 00000000..9893aae0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py @@ -0,0 +1,1707 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between Experiment and Method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between Experiment and Equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between Experiment and AnalysisType. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between Experiment and PreparedSample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class Aim1RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'Aim1RecordBase' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProximateRecord(Aim1RecordBase): + """ + Proximate analysis record. + """ + __tablename__ = 'ProximateRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UltimateRecord(Aim1RecordBase): + """ + Ultimate analysis record. + """ + __tablename__ = 'UltimateRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CompositionalRecord(Aim1RecordBase): + """ + Compositional analysis record. + """ + __tablename__ = 'CompositionalRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class IcpRecord(Aim1RecordBase): + """ + ICP analysis record. + """ + __tablename__ = 'IcpRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrfRecord(Aim1RecordBase): + """ + XRF analysis record. + """ + __tablename__ = 'XrfRecord' + + maybe_wavelength_nm = Column(Numeric()) + maybe_intensity = Column(Numeric()) + maybe_energy_slope = Column(Numeric()) + maybe_energy_offset = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrdRecord(Aim1RecordBase): + """ + XRD analysis record. + """ + __tablename__ = 'XrdRecord' + + maybe_scan_low_nm = Column(Integer()) + maybe_scan_high_nm = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CalorimetryRecord(Aim1RecordBase): + """ + Calorimetry analysis record. + """ + __tablename__ = 'CalorimetryRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FtnirRecord(Aim1RecordBase): + """ + FT-NIR analysis record. + """ + __tablename__ = 'FtnirRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class RgbRecord(Aim1RecordBase): + """ + RGB analysis record. + """ + __tablename__ = 'RgbRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py index e69de29b..e212029e 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py @@ -0,0 +1,1565 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between Experiment and Method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between Experiment and Equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between Experiment and AnalysisType. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between Experiment and PreparedSample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class Aim2RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'Aim2RecordBase' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Strain(LookupBase): + """ + Strain used in fermentation. + """ + __tablename__ = 'Strain' + + parent_strain_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PretreatmentRecord(Aim2RecordBase): + """ + Pretreatment record. + """ + __tablename__ = 'PretreatmentRecord' + + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + reaction_block_id = Column(Integer()) + block_position = Column(Text()) + temperature = Column(Numeric()) + replicate_no = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FermentationRecord(Aim2RecordBase): + """ + Fermentation record. + """ + __tablename__ = 'FermentationRecord' + + strain_id = Column(Integer()) + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + replicate_no = Column(Integer()) + well_position = Column(Text()) + temperature = Column(Numeric()) + agitation_rpm = Column(Numeric()) + vessel_id = Column(Integer()) + analyte_detection_equipment_id = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class GasificationRecord(Aim2RecordBase): + """ + Gasification record. + """ + __tablename__ = 'GasificationRecord' + + feedstock_mass = Column(Numeric()) + bed_temperature = Column(Numeric()) + gas_flow_rate = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AutoclaveRecord(Aim2RecordBase): + """ + Autoclave record. + """ + __tablename__ = 'AutoclaveRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py new file mode 100644 index 00000000..31e8b6fb --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py @@ -0,0 +1,375 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Dataset(Base): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(DateTime()) + end_date = Column(DateTime()) + description = Column(Text()) + + + def __repr__(self): + return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" + + + + + + +class Observation(Base): + """ + Observation data. + """ + __tablename__ = 'Observation' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class DimensionType(LookupBase): + """ + Type of dimension (e.g. timepoint, wavelength). + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py index c7ac9023..44a65db4 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py @@ -77,50 +77,6 @@ def __repr__(self): -class EntityLineage(Base): - """ - Lineage information for a specific entity. - """ - __tablename__ = 'EntityLineage' - - id = Column(Integer(), primary_key=True, nullable=False ) - lineage_group_id = Column(Integer()) - source_table = Column(Text()) - source_row_id = Column(Text()) - note = Column(Text()) - - - def __repr__(self): - return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" - - - - - - -class EtlRun(Base): - """ - Information about an ETL run. - """ - __tablename__ = 'EtlRun' - - id = Column(Text(), primary_key=True, nullable=False ) - started_at = Column(DateTime()) - completed_at = Column(DateTime()) - pipeline_name = Column(Text()) - status = Column(Text()) - records_ingested = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" - - - - - - class Dataset(Base): """ Dataset definition. @@ -829,186 +785,6 @@ def __repr__(self): -class LineageGroup(BaseEntity): - """ - Grouping for lineage information. - """ - __tablename__ = 'LineageGroup' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LineageGroup(note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Information about a data source. - """ - __tablename__ = 'DataSource' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - uri = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},uri={self.uri},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source. - """ - __tablename__ = 'DataSourceType' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Lookup for source types (database, literature, etc.). - """ - __tablename__ = 'SourceType' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of location coverage (nation, state, county, etc.). - """ - __tablename__ = 'LocationResolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for file objects. - """ - __tablename__ = 'FileObjectMetadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - class DimensionType(LookupBase): """ Type of dimension (e.g. timepoint, wavelength). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py new file mode 100644 index 00000000..bbbb9a74 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py @@ -0,0 +1,2403 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class LineageGroup(Base): + """ + Grouping for lineage information. + """ + __tablename__ = 'LineageGroup' + + id = Column(Integer(), primary_key=True, nullable=False ) + etl_run_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"LineageGroup(id={self.id},etl_run_id={self.etl_run_id},note={self.note},)" + + + + + + +class EntityLineage(Base): + """ + Lineage information for a specific entity. + """ + __tablename__ = 'EntityLineage' + + id = Column(Integer(), primary_key=True, nullable=False ) + lineage_group_id = Column(Integer()) + source_table = Column(Text()) + source_row_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" + + + + + + +class EtlRun(Base): + """ + Information about an ETL run. + """ + __tablename__ = 'EtlRun' + + id = Column(Integer(), primary_key=True, nullable=False ) + started_at = Column(DateTime()) + completed_at = Column(DateTime()) + pipeline_name = Column(Text()) + status = Column(Text()) + records_ingested = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between Experiment and Method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between Experiment and Equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between Experiment and AnalysisType. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between Experiment and PreparedSample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Aim1RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'Aim1RecordBase' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Aim2RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'Aim2RecordBase' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Strain(LookupBase): + """ + Strain used in fermentation. + """ + __tablename__ = 'Strain' + + parent_strain_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaDomain(LookupBase): + """ + USDA domain. + """ + __tablename__ = 'UsdaDomain' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaDomain(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaStatisticCategory(LookupBase): + """ + USDA statistic category. + """ + __tablename__ = 'UsdaStatisticCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaStatisticCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyProgram(LookupBase): + """ + USDA survey program. + """ + __tablename__ = 'UsdaSurveyProgram' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaSurveyProgram(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCommodity(LookupBase): + """ + USDA commodity. + """ + __tablename__ = 'UsdaCommodity' + + usda_source = Column(Text()) + usda_code = Column(Text()) + parent_commodity_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaTermMap(BaseEntity): + """ + Mapping of raw terms to USDA commodities. + """ + __tablename__ = 'UsdaTermMap' + + source_system = Column(Text()) + source_context = Column(Text()) + raw_term = Column(Text()) + usda_commodity_id = Column(Integer()) + is_verified = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceUsdaCommodityMap(BaseEntity): + """ + Mapping between resources/crops and USDA commodities. + """ + __tablename__ = 'ResourceUsdaCommodityMap' + + resource_id = Column(Integer()) + primary_crop_id = Column(Integer()) + usda_commodity_id = Column(Integer()) + match_tier = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCensusRecord(BaseEntity): + """ + USDA census record. + """ + __tablename__ = 'UsdaCensusRecord' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + source_reference = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyRecord(BaseEntity): + """ + USDA survey record. + """ + __tablename__ = 'UsdaSurveyRecord' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + survey_program_id = Column(Integer()) + survey_period = Column(Text()) + reference_month = Column(Text()) + seasonal_flag = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketReport(BaseEntity): + """ + USDA market report. + """ + __tablename__ = 'UsdaMarketReport' + + slug_id = Column(Integer()) + slug_name = Column(Text()) + report_series_title = Column(Text()) + frequency = Column(Text()) + office_name = Column(Text()) + office_city_id = Column(Integer()) + office_state_fips = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketReport(slug_id={self.slug_id},slug_name={self.slug_name},report_series_title={self.report_series_title},frequency={self.frequency},office_name={self.office_name},office_city_id={self.office_city_id},office_state_fips={self.office_state_fips},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketRecord(BaseEntity): + """ + USDA market record. + """ + __tablename__ = 'UsdaMarketRecord' + + report_id = Column(Integer()) + dataset_id = Column(Integer()) + report_begin_date = Column(DateTime()) + report_end_date = Column(DateTime()) + report_date = Column(DateTime()) + commodity_id = Column(Integer()) + market_type_id = Column(Integer()) + market_type_catagory = Column(Text()) + grp = Column(Text()) + market_catagory_id = Column(Integer()) + class_ = Column(Text()) + grade = Column(Text()) + variety = Column(Text()) + protein_pct = Column(Numeric()) + application = Column(Text()) + pkg = Column(Text()) + sale_type = Column(Text()) + price_unit_id = Column(Integer()) + freight = Column(Text()) + trans_mode = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_catagory={self.market_type_catagory},grp={self.grp},market_catagory_id={self.market_catagory_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LandiqRecord(BaseEntity): + """ + LandIQ record. + """ + __tablename__ = 'LandiqRecord' + + dataset_id = Column(Integer()) + polygon_id = Column(Integer()) + main_crop = Column(Integer()) + secondary_crop = Column(Integer()) + tertiary_crop = Column(Integer()) + quaternary_crop = Column(Integer()) + confidence = Column(Integer()) + irrigated = Column(Boolean()) + acres = Column(Float()) + version = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class BillionTon2023Record(BaseEntity): + """ + Billion Ton 2023 record. + """ + __tablename__ = 'BillionTon2023Record' + + subclass_id = Column(Integer()) + resource_id = Column(Integer()) + geoid = Column(Text()) + county_square_miles = Column(Float()) + model_name = Column(Text()) + scenario_name = Column(Text()) + price_offered_usd = Column(Numeric()) + production = Column(Integer()) + production_unit_id = Column(Integer()) + btu_ton = Column(Integer()) + production_energy_content = Column(Integer()) + energy_content_unit_id = Column(Integer()) + product_density_dtpersqmi = Column(Numeric()) + land_source = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BillionTon2023Record(subclass_id={self.subclass_id},resource_id={self.resource_id},geoid={self.geoid},county_square_miles={self.county_square_miles},model_name={self.model_name},scenario_name={self.scenario_name},price_offered_usd={self.price_offered_usd},production={self.production},production_unit_id={self.production_unit_id},btu_ton={self.btu_ton},production_energy_content={self.production_energy_content},energy_content_unit_id={self.energy_content_unit_id},product_density_dtpersqmi={self.product_density_dtpersqmi},land_source={self.land_source},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProximateRecord(Aim1RecordBase): + """ + Proximate analysis record. + """ + __tablename__ = 'ProximateRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UltimateRecord(Aim1RecordBase): + """ + Ultimate analysis record. + """ + __tablename__ = 'UltimateRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CompositionalRecord(Aim1RecordBase): + """ + Compositional analysis record. + """ + __tablename__ = 'CompositionalRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class IcpRecord(Aim1RecordBase): + """ + ICP analysis record. + """ + __tablename__ = 'IcpRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrfRecord(Aim1RecordBase): + """ + XRF analysis record. + """ + __tablename__ = 'XrfRecord' + + maybe_wavelength_nm = Column(Numeric()) + maybe_intensity = Column(Numeric()) + maybe_energy_slope = Column(Numeric()) + maybe_energy_offset = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrdRecord(Aim1RecordBase): + """ + XRD analysis record. + """ + __tablename__ = 'XrdRecord' + + maybe_scan_low_nm = Column(Integer()) + maybe_scan_high_nm = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CalorimetryRecord(Aim1RecordBase): + """ + Calorimetry analysis record. + """ + __tablename__ = 'CalorimetryRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FtnirRecord(Aim1RecordBase): + """ + FT-NIR analysis record. + """ + __tablename__ = 'FtnirRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class RgbRecord(Aim1RecordBase): + """ + RGB analysis record. + """ + __tablename__ = 'RgbRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PretreatmentRecord(Aim2RecordBase): + """ + Pretreatment record. + """ + __tablename__ = 'PretreatmentRecord' + + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + reaction_block_id = Column(Integer()) + block_position = Column(Text()) + temperature = Column(Numeric()) + replicate_no = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FermentationRecord(Aim2RecordBase): + """ + Fermentation record. + """ + __tablename__ = 'FermentationRecord' + + strain_id = Column(Integer()) + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + replicate_no = Column(Integer()) + well_position = Column(Text()) + temperature = Column(Numeric()) + agitation_rpm = Column(Numeric()) + vessel_id = Column(Integer()) + analyte_detection_equipment_id = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class GasificationRecord(Aim2RecordBase): + """ + Gasification record. + """ + __tablename__ = 'GasificationRecord' + + feedstock_mass = Column(Numeric()) + bed_temperature = Column(Numeric()) + gas_flow_rate = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AutoclaveRecord(Aim2RecordBase): + """ + Autoclave record. + """ + __tablename__ = 'AutoclaveRecord' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py new file mode 100644 index 00000000..1f2a5b30 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py @@ -0,0 +1,46 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py new file mode 100644 index 00000000..e8ad5281 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py @@ -0,0 +1,1000 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py new file mode 100644 index 00000000..542f4cd0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py @@ -0,0 +1,1341 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ExperimentMethod(Base): + """ + Link between Experiment and Method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between Experiment and Equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between Experiment and AnalysisType. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between Experiment and PreparedSample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py new file mode 100644 index 00000000..c34d8d9a --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py @@ -0,0 +1,1224 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ExperimentEquipment(Base): + """ + Link between experiment and equipment. + """ + __tablename__ = 'ExperimentEquipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between experiment and analysis type. + """ + __tablename__ = 'ExperimentAnalysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between experiment and prepared sample. + """ + __tablename__ = 'ExperimentPreparedSample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between experiment and method. + """ + __tablename__ = 'ExperimentMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon definition. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Dataset(Base): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(DateTime()) + end_date = Column(DateTime()) + description = Column(Text()) + + + def __repr__(self): + return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" + + + + + + +class Observation(Base): + """ + Observation data. + """ + __tablename__ = 'Observation' + + id = Column(Integer(), primary_key=True, nullable=False ) + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" + + + + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'Experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'Equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Strain(LookupBase): + """ + Strain of organism. + """ + __tablename__ = 'Strain' + + parent_strain_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample prepared for analysis. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension (e.g. timepoint, wavelength). + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py new file mode 100644 index 00000000..16cf80f9 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py @@ -0,0 +1,1527 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Polygon(Base): + """ + Geospatial polygon. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class UsdaDomain(LookupBase): + """ + USDA domain. + """ + __tablename__ = 'UsdaDomain' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaDomain(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaStatisticCategory(LookupBase): + """ + USDA statistic category. + """ + __tablename__ = 'UsdaStatisticCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaStatisticCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyProgram(LookupBase): + """ + USDA survey program. + """ + __tablename__ = 'UsdaSurveyProgram' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaSurveyProgram(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCommodity(LookupBase): + """ + USDA commodity. + """ + __tablename__ = 'UsdaCommodity' + + usda_source = Column(Text()) + usda_code = Column(Text()) + parent_commodity_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaTermMap(BaseEntity): + """ + Mapping of raw terms to USDA commodities. + """ + __tablename__ = 'UsdaTermMap' + + source_system = Column(Text()) + source_context = Column(Text()) + raw_term = Column(Text()) + usda_commodity_id = Column(Integer()) + is_verified = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceUsdaCommodityMap(BaseEntity): + """ + Mapping between resources/crops and USDA commodities. + """ + __tablename__ = 'ResourceUsdaCommodityMap' + + resource_id = Column(Integer()) + primary_crop_id = Column(Integer()) + usda_commodity_id = Column(Integer()) + match_tier = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCensusRecord(BaseEntity): + """ + USDA census record. + """ + __tablename__ = 'UsdaCensusRecord' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + source_reference = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyRecord(BaseEntity): + """ + USDA survey record. + """ + __tablename__ = 'UsdaSurveyRecord' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + survey_program_id = Column(Integer()) + survey_period = Column(Text()) + reference_month = Column(Text()) + seasonal_flag = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketReport(BaseEntity): + """ + USDA market report. + """ + __tablename__ = 'UsdaMarketReport' + + slug_id = Column(Integer()) + slug_name = Column(Text()) + report_series_title = Column(Text()) + frequency = Column(Text()) + office_name = Column(Text()) + office_city_id = Column(Integer()) + office_state_fips = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketReport(slug_id={self.slug_id},slug_name={self.slug_name},report_series_title={self.report_series_title},frequency={self.frequency},office_name={self.office_name},office_city_id={self.office_city_id},office_state_fips={self.office_state_fips},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketRecord(BaseEntity): + """ + USDA market record. + """ + __tablename__ = 'UsdaMarketRecord' + + report_id = Column(Integer()) + dataset_id = Column(Integer()) + report_begin_date = Column(DateTime()) + report_end_date = Column(DateTime()) + report_date = Column(DateTime()) + commodity_id = Column(Integer()) + market_type_id = Column(Integer()) + market_type_catagory = Column(Text()) + grp = Column(Text()) + market_catagory_id = Column(Integer()) + class_ = Column(Text()) + grade = Column(Text()) + variety = Column(Text()) + protein_pct = Column(Numeric()) + application = Column(Text()) + pkg = Column(Text()) + sale_type = Column(Text()) + price_unit_id = Column(Integer()) + freight = Column(Text()) + trans_mode = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_catagory={self.market_type_catagory},grp={self.grp},market_catagory_id={self.market_catagory_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LandiqRecord(BaseEntity): + """ + LandIQ record. + """ + __tablename__ = 'LandiqRecord' + + dataset_id = Column(Integer()) + polygon_id = Column(Integer()) + main_crop = Column(Integer()) + secondary_crop = Column(Integer()) + tertiary_crop = Column(Integer()) + quaternary_crop = Column(Integer()) + confidence = Column(Integer()) + irrigated = Column(Boolean()) + acres = Column(Float()) + version = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class BillionTon2023Record(BaseEntity): + """ + Billion Ton 2023 record. + """ + __tablename__ = 'BillionTon2023Record' + + subclass_id = Column(Integer()) + resource_id = Column(Integer()) + geoid = Column(Text()) + county_square_miles = Column(Float()) + model_name = Column(Text()) + scenario_name = Column(Text()) + price_offered_usd = Column(Numeric()) + production = Column(Integer()) + production_unit_id = Column(Integer()) + btu_ton = Column(Integer()) + production_energy_content = Column(Integer()) + energy_content_unit_id = Column(Integer()) + product_density_dtpersqmi = Column(Numeric()) + land_source = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BillionTon2023Record(subclass_id={self.subclass_id},resource_id={self.resource_id},geoid={self.geoid},county_square_miles={self.county_square_miles},model_name={self.model_name},scenario_name={self.scenario_name},price_offered_usd={self.price_offered_usd},production={self.production},production_unit_id={self.production_unit_id},btu_ton={self.btu_ton},production_energy_content={self.production_energy_content},energy_content_unit_id={self.energy_content_unit_id},product_density_dtpersqmi={self.product_density_dtpersqmi},land_source={self.land_source},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py index e69de29b..f941eeae 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py @@ -0,0 +1,1000 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py new file mode 100644 index 00000000..bffb89f8 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py @@ -0,0 +1,1118 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py new file mode 100644 index 00000000..acb4d3c4 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py @@ -0,0 +1,125 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon definition. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py new file mode 100644 index 00000000..76adbad5 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py @@ -0,0 +1,1595 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class InfrastructureBiodieselPlants(Base): + """ + Biodiesel plants infrastructure. + """ + __tablename__ = 'InfrastructureBiodieselPlants' + + biodiesel_plant_id = Column(Integer(), primary_key=True, nullable=False ) + company = Column(Text()) + bbi_index = Column(Integer()) + city = Column(Text()) + state = Column(Text()) + capacity_mmg_per_y = Column(Integer()) + feedstock = Column(Text()) + status = Column(Text()) + address = Column(Text()) + coordinates = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + source = Column(Text()) + + + def __repr__(self): + return f"InfrastructureBiodieselPlants(biodiesel_plant_id={self.biodiesel_plant_id},company={self.company},bbi_index={self.bbi_index},city={self.city},state={self.state},capacity_mmg_per_y={self.capacity_mmg_per_y},feedstock={self.feedstock},status={self.status},address={self.address},coordinates={self.coordinates},latitude={self.latitude},longitude={self.longitude},source={self.source},)" + + + + + + +class InfrastructureBiosolidsFacilities(Base): + """ + Biosolids facilities infrastructure. + """ + __tablename__ = 'InfrastructureBiosolidsFacilities' + + biosolid_facility_id = Column(Integer(), primary_key=True, nullable=False ) + report_submitted_date = Column(Date()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + facility = Column(Text()) + authority = Column(Text()) + plant_type = Column(Text()) + aqmd = Column(Text()) + facility_address = Column(Text()) + facility_city = Column(Text()) + state = Column(Text()) + facility_zip = Column(Text()) + facility_county = Column(Text()) + mailing_street_1 = Column(Text()) + mailing_city = Column(Text()) + mailing_state = Column(Text()) + mailing_zip = Column(Text()) + biosolids_number = Column(Text()) + biosolids_contact = Column(Text()) + biosolids_contact_phone = Column(Text()) + biosolids_contact_email = Column(Text()) + adwf = Column(Numeric()) + potw_biosolids_generated = Column(Integer()) + twtds_biosolids_treated = Column(Integer()) + class_b_land_app = Column(Integer()) + class_b_applier = Column(Text()) + class_a_compost = Column(Integer()) + class_a_heat_dried = Column(Integer()) + class_a_other = Column(Integer()) + class_a_other_applier = Column(Text()) + twtds_transfer_to_second_preparer = Column(Integer()) + twtds_second_preparer_name = Column(Text()) + adc_or_final_c = Column(Integer()) + landfill = Column(Integer()) + landfill_name = Column(Text()) + surface_disposal = Column(Integer()) + deepwell_injection = Column(Text()) + stored = Column(Integer()) + longterm_treatment = Column(Integer()) + other = Column(Integer()) + name_of_other = Column(Text()) + incineration = Column(Integer()) + + + def __repr__(self): + return f"InfrastructureBiosolidsFacilities(biosolid_facility_id={self.biosolid_facility_id},report_submitted_date={self.report_submitted_date},latitude={self.latitude},longitude={self.longitude},facility={self.facility},authority={self.authority},plant_type={self.plant_type},aqmd={self.aqmd},facility_address={self.facility_address},facility_city={self.facility_city},state={self.state},facility_zip={self.facility_zip},facility_county={self.facility_county},mailing_street_1={self.mailing_street_1},mailing_city={self.mailing_city},mailing_state={self.mailing_state},mailing_zip={self.mailing_zip},biosolids_number={self.biosolids_number},biosolids_contact={self.biosolids_contact},biosolids_contact_phone={self.biosolids_contact_phone},biosolids_contact_email={self.biosolids_contact_email},adwf={self.adwf},potw_biosolids_generated={self.potw_biosolids_generated},twtds_biosolids_treated={self.twtds_biosolids_treated},class_b_land_app={self.class_b_land_app},class_b_applier={self.class_b_applier},class_a_compost={self.class_a_compost},class_a_heat_dried={self.class_a_heat_dried},class_a_other={self.class_a_other},class_a_other_applier={self.class_a_other_applier},twtds_transfer_to_second_preparer={self.twtds_transfer_to_second_preparer},twtds_second_preparer_name={self.twtds_second_preparer_name},adc_or_final_c={self.adc_or_final_c},landfill={self.landfill},landfill_name={self.landfill_name},surface_disposal={self.surface_disposal},deepwell_injection={self.deepwell_injection},stored={self.stored},longterm_treatment={self.longterm_treatment},other={self.other},name_of_other={self.name_of_other},incineration={self.incineration},)" + + + + + + +class InfrastructureCafoManureLocations(Base): + """ + CAFO manure locations infrastructure. + """ + __tablename__ = 'InfrastructureCafoManureLocations' + + cafo_manure_id = Column(Integer(), primary_key=True, nullable=False ) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + owner_name = Column(Text()) + facility_name = Column(Text()) + address = Column(Text()) + town = Column(Text()) + state = Column(Text()) + zip = Column(Text()) + animal = Column(Text()) + animal_feed_operation_type = Column(Text()) + animal_units = Column(Integer()) + animal_count = Column(Integer()) + manure_total_solids = Column(Numeric()) + source = Column(Text()) + date_accessed = Column(Date()) + + + def __repr__(self): + return f"InfrastructureCafoManureLocations(cafo_manure_id={self.cafo_manure_id},latitude={self.latitude},longitude={self.longitude},owner_name={self.owner_name},facility_name={self.facility_name},address={self.address},town={self.town},state={self.state},zip={self.zip},animal={self.animal},animal_feed_operation_type={self.animal_feed_operation_type},animal_units={self.animal_units},animal_count={self.animal_count},manure_total_solids={self.manure_total_solids},source={self.source},date_accessed={self.date_accessed},)" + + + + + + +class InfrastructureEthanolBiorefineries(Base): + """ + Ethanol biorefineries infrastructure. + """ + __tablename__ = 'InfrastructureEthanolBiorefineries' + + ethanol_biorefinery_id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + city = Column(Text()) + state = Column(Text()) + address = Column(Text()) + type = Column(Text()) + capacity_mgy = Column(Integer()) + production_mgy = Column(Integer()) + constr_exp = Column(Integer()) + + + def __repr__(self): + return f"InfrastructureEthanolBiorefineries(ethanol_biorefinery_id={self.ethanol_biorefinery_id},name={self.name},city={self.city},state={self.state},address={self.address},type={self.type},capacity_mgy={self.capacity_mgy},production_mgy={self.production_mgy},constr_exp={self.constr_exp},)" + + + + + + +class InfrastructureLandfills(Base): + """ + Landfills infrastructure. + """ + __tablename__ = 'InfrastructureLandfills' + + project_id = Column(Text(), primary_key=True, nullable=False ) + project_int_id = Column(Integer()) + ghgrp_id = Column(Text()) + landfill_id = Column(Integer()) + landfill_name = Column(Text()) + state = Column(Text()) + physical_address = Column(Text()) + city = Column(Text()) + county = Column(Text()) + zip_code = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + ownership_type = Column(Text()) + landfill_owner_orgs = Column(Text()) + landfill_opened_year = Column(Date()) + landfill_closure_year = Column(Date()) + landfill_status = Column(Text()) + waste_in_place = Column(Integer()) + waste_in_place_year = Column(Date()) + lfg_system_in_place = Column(Boolean()) + lfg_collected = Column(Numeric()) + lfg_flared = Column(Numeric()) + project_status = Column(Text()) + project_name = Column(Text()) + project_start_date = Column(Date()) + project_shutdown_date = Column(Date()) + project_type_category = Column(Text()) + lfg_energy_project_type = Column(Text()) + rng_delivery_method = Column(Text()) + actual_mw_generation = Column(Numeric()) + rated_mw_capacity = Column(Numeric()) + lfg_flow_to_project = Column(Numeric()) + direct_emission_reductions = Column(Numeric()) + avoided_emission_reductions = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureLandfills(project_id={self.project_id},project_int_id={self.project_int_id},ghgrp_id={self.ghgrp_id},landfill_id={self.landfill_id},landfill_name={self.landfill_name},state={self.state},physical_address={self.physical_address},city={self.city},county={self.county},zip_code={self.zip_code},latitude={self.latitude},longitude={self.longitude},ownership_type={self.ownership_type},landfill_owner_orgs={self.landfill_owner_orgs},landfill_opened_year={self.landfill_opened_year},landfill_closure_year={self.landfill_closure_year},landfill_status={self.landfill_status},waste_in_place={self.waste_in_place},waste_in_place_year={self.waste_in_place_year},lfg_system_in_place={self.lfg_system_in_place},lfg_collected={self.lfg_collected},lfg_flared={self.lfg_flared},project_status={self.project_status},project_name={self.project_name},project_start_date={self.project_start_date},project_shutdown_date={self.project_shutdown_date},project_type_category={self.project_type_category},lfg_energy_project_type={self.lfg_energy_project_type},rng_delivery_method={self.rng_delivery_method},actual_mw_generation={self.actual_mw_generation},rated_mw_capacity={self.rated_mw_capacity},lfg_flow_to_project={self.lfg_flow_to_project},direct_emission_reductions={self.direct_emission_reductions},avoided_emission_reductions={self.avoided_emission_reductions},)" + + + + + + +class InfrastructureLivestockAnaerobicDigesters(Base): + """ + Livestock anaerobic digesters infrastructure. + """ + __tablename__ = 'InfrastructureLivestockAnaerobicDigesters' + + digester_id = Column(Integer(), primary_key=True, nullable=False ) + project_name = Column(Text()) + project_type = Column(Text()) + city = Column(Text()) + state = Column(Text()) + digester_type = Column(Text()) + profile = Column(Text()) + year_operational = Column(Date()) + animal_type_class = Column(Text()) + animal_types = Column(Text()) + pop_feeding_digester = Column(Text()) + total_pop_feeding_digester = Column(Integer()) + cattle = Column(Integer()) + dairy = Column(Integer()) + poultry = Column(Integer()) + swine = Column(Integer()) + codigestion = Column(Text()) + biogas_generation_estimate = Column(Integer()) + electricity_generated = Column(Integer()) + biogas_end_uses = Column(Text()) + methane_emission_reductions = Column(Integer()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureLivestockAnaerobicDigesters(digester_id={self.digester_id},project_name={self.project_name},project_type={self.project_type},city={self.city},state={self.state},digester_type={self.digester_type},profile={self.profile},year_operational={self.year_operational},animal_type_class={self.animal_type_class},animal_types={self.animal_types},pop_feeding_digester={self.pop_feeding_digester},total_pop_feeding_digester={self.total_pop_feeding_digester},cattle={self.cattle},dairy={self.dairy},poultry={self.poultry},swine={self.swine},codigestion={self.codigestion},biogas_generation_estimate={self.biogas_generation_estimate},electricity_generated={self.electricity_generated},biogas_end_uses={self.biogas_end_uses},methane_emission_reductions={self.methane_emission_reductions},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureSafAndRenewableDieselPlants(Base): + """ + SAF and renewable diesel plants infrastructure. + """ + __tablename__ = 'InfrastructureSafAndRenewableDieselPlants' + + ibcc_index = Column(Integer(), primary_key=True, nullable=False ) + company = Column(Text()) + city = Column(Text()) + state = Column(Text()) + country = Column(Text()) + capacity = Column(Text()) + feedstock = Column(Text()) + products = Column(Text()) + status = Column(Text()) + address = Column(Text()) + coordinates = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureSafAndRenewableDieselPlants(ibcc_index={self.ibcc_index},company={self.company},city={self.city},state={self.state},country={self.country},capacity={self.capacity},feedstock={self.feedstock},products={self.products},status={self.status},address={self.address},coordinates={self.coordinates},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureWastewaterTreatmentPlants(Base): + """ + Wastewater treatment plants infrastructure. + """ + __tablename__ = 'InfrastructureWastewaterTreatmentPlants' + + plant_id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + state = Column(Text()) + codigestion = Column(Text()) + flow_design_adjusted = Column(Numeric()) + flow_average = Column(Numeric()) + biosolids = Column(Numeric()) + excess_flow = Column(Numeric()) + biogas_utilized = Column(Boolean()) + flaring = Column(Boolean()) + excess_mass_loading_rate = Column(Numeric()) + excess_mass_loading_rate_wet = Column(Numeric()) + methane_production = Column(Numeric()) + energy_content = Column(Numeric()) + electric_kw = Column(Numeric()) + thermal_mmbtu_d = Column(Numeric()) + electric_kwh = Column(Numeric()) + thermal_annual_mmbtu_y = Column(Numeric()) + anaerobic_digestion_facility = Column(Text()) + county = Column(Text()) + dayload_bdt = Column(Numeric()) + dayload = Column(Numeric()) + equivalent_generation = Column(Numeric()) + facility_type = Column(Text()) + feedstock = Column(Text()) + type = Column(Text()) + city = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + zipcode = Column(Text()) + + + def __repr__(self): + return f"InfrastructureWastewaterTreatmentPlants(plant_id={self.plant_id},name={self.name},state={self.state},codigestion={self.codigestion},flow_design_adjusted={self.flow_design_adjusted},flow_average={self.flow_average},biosolids={self.biosolids},excess_flow={self.excess_flow},biogas_utilized={self.biogas_utilized},flaring={self.flaring},excess_mass_loading_rate={self.excess_mass_loading_rate},excess_mass_loading_rate_wet={self.excess_mass_loading_rate_wet},methane_production={self.methane_production},energy_content={self.energy_content},electric_kw={self.electric_kw},thermal_mmbtu_d={self.thermal_mmbtu_d},electric_kwh={self.electric_kwh},thermal_annual_mmbtu_y={self.thermal_annual_mmbtu_y},anaerobic_digestion_facility={self.anaerobic_digestion_facility},county={self.county},dayload_bdt={self.dayload_bdt},dayload={self.dayload},equivalent_generation={self.equivalent_generation},facility_type={self.facility_type},feedstock={self.feedstock},type={self.type},city={self.city},latitude={self.latitude},longitude={self.longitude},zipcode={self.zipcode},)" + + + + + + +class InfrastructureCombustionPlants(Base): + """ + Combustion plants infrastructure. + """ + __tablename__ = 'InfrastructureCombustionPlants' + + combustion_fid = Column(Integer(), primary_key=True, nullable=False ) + objectid = Column(Integer()) + status = Column(Text()) + city = Column(Text()) + name = Column(Text()) + county = Column(Text()) + equivalent_generation = Column(Numeric()) + np_mw = Column(Numeric()) + cf = Column(Numeric()) + yearload = Column(Integer()) + fuel = Column(Text()) + notes = Column(Text()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureCombustionPlants(combustion_fid={self.combustion_fid},objectid={self.objectid},status={self.status},city={self.city},name={self.name},county={self.county},equivalent_generation={self.equivalent_generation},np_mw={self.np_mw},cf={self.cf},yearload={self.yearload},fuel={self.fuel},notes={self.notes},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureDistrictEnergySystems(Base): + """ + District energy systems infrastructure. + """ + __tablename__ = 'InfrastructureDistrictEnergySystems' + + des_fid = Column(Integer(), primary_key=True, nullable=False ) + cbg_id = Column(Integer()) + name = Column(Text()) + system = Column(Text()) + object_id = Column(Integer()) + city = Column(Text()) + state = Column(Text()) + primary_fuel = Column(Text()) + secondary_fuel = Column(Text()) + usetype = Column(Text()) + cap_st = Column(Numeric()) + cap_hw = Column(Numeric()) + cap_cw = Column(Numeric()) + chpcg_cap = Column(Numeric()) + excess_c = Column(Numeric()) + excess_h = Column(Numeric()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureDistrictEnergySystems(des_fid={self.des_fid},cbg_id={self.cbg_id},name={self.name},system={self.system},object_id={self.object_id},city={self.city},state={self.state},primary_fuel={self.primary_fuel},secondary_fuel={self.secondary_fuel},usetype={self.usetype},cap_st={self.cap_st},cap_hw={self.cap_hw},cap_cw={self.cap_cw},chpcg_cap={self.chpcg_cap},excess_c={self.excess_c},excess_h={self.excess_h},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureFoodProcessingFacilities(Base): + """ + Food processing facilities infrastructure. + """ + __tablename__ = 'InfrastructureFoodProcessingFacilities' + + processing_facility_id = Column(Integer(), primary_key=True, nullable=False ) + address = Column(Text()) + county = Column(Text()) + city = Column(Text()) + company = Column(Text()) + join_count = Column(Integer()) + master_type = Column(Text()) + state = Column(Text()) + subtype = Column(Text()) + target_fid = Column(Integer()) + processing_type = Column(Text()) + zip = Column(Text()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureFoodProcessingFacilities(processing_facility_id={self.processing_facility_id},address={self.address},county={self.county},city={self.city},company={self.company},join_count={self.join_count},master_type={self.master_type},state={self.state},subtype={self.subtype},target_fid={self.target_fid},processing_type={self.processing_type},zip={self.zip},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureMswToEnergyAnaerobicDigesters(Base): + """ + MSW to energy anaerobic digesters infrastructure. + """ + __tablename__ = 'InfrastructureMswToEnergyAnaerobicDigesters' + + wte_id = Column(Integer(), primary_key=True, nullable=False ) + city = Column(Text()) + county = Column(Text()) + equivalent_generation = Column(Numeric()) + feedstock = Column(Text()) + dayload = Column(Numeric()) + dayload_bdt = Column(Numeric()) + facility_type = Column(Text()) + status = Column(Text()) + notes = Column(Text()) + source = Column(Text()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureMswToEnergyAnaerobicDigesters(wte_id={self.wte_id},city={self.city},county={self.county},equivalent_generation={self.equivalent_generation},feedstock={self.feedstock},dayload={self.dayload},dayload_bdt={self.dayload_bdt},facility_type={self.facility_type},status={self.status},notes={self.notes},source={self.source},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class FacilityRecord(BaseEntity): + """ + Facility record. + """ + __tablename__ = 'FacilityRecord' + + dataset_id = Column(Integer()) + facility_name = Column(Text()) + location_id = Column(Integer()) + capacity_mw = Column(Numeric()) + resource_id = Column(Integer()) + operator = Column(Text()) + start_year = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FacilityRecord(dataset_id={self.dataset_id},facility_name={self.facility_name},location_id={self.location_id},capacity_mw={self.capacity_mw},resource_id={self.resource_id},operator={self.operator},start_year={self.start_year},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'AnalysisType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'Dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'DimensionType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'Observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py new file mode 100644 index 00000000..56bbfa6d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py @@ -0,0 +1,109 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class LineageGroup(Base): + """ + Grouping for lineage information. + """ + __tablename__ = 'LineageGroup' + + id = Column(Integer(), primary_key=True, nullable=False ) + etl_run_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"LineageGroup(id={self.id},etl_run_id={self.etl_run_id},note={self.note},)" + + + + + + +class EntityLineage(Base): + """ + Lineage information for a specific entity. + """ + __tablename__ = 'EntityLineage' + + id = Column(Integer(), primary_key=True, nullable=False ) + lineage_group_id = Column(Integer()) + source_table = Column(Text()) + source_row_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" + + + + + + +class EtlRun(Base): + """ + Information about an ETL run. + """ + __tablename__ = 'EtlRun' + + id = Column(Integer(), primary_key=True, nullable=False ) + started_at = Column(DateTime()) + completed_at = Column(DateTime()) + pipeline_name = Column(Text()) + status = Column(Text()) + records_ingested = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py new file mode 100644 index 00000000..7aceee05 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py @@ -0,0 +1,275 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py new file mode 100644 index 00000000..3b0c7511 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py @@ -0,0 +1,1000 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py new file mode 100644 index 00000000..c5825f29 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py @@ -0,0 +1,44 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py new file mode 100644 index 00000000..f721c286 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py @@ -0,0 +1,106 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py new file mode 100644 index 00000000..9350f964 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py @@ -0,0 +1,307 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py new file mode 100644 index 00000000..cb16a4a0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py @@ -0,0 +1,326 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon definition. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py new file mode 100644 index 00000000..9f3eb1e5 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py @@ -0,0 +1,1089 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'DataSource' + + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + publication_date = Column(Date()) + version = Column(Text()) + publisher = Column(Text()) + author = Column(Text()) + license = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'FileObjectMetadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source. + """ + __tablename__ = 'DataSourceType' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'LocationResolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'SourceType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py new file mode 100644 index 00000000..d37b7688 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py @@ -0,0 +1,964 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'BaseEntity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'LookupBase' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'Geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon definition. + """ + __tablename__ = 'Polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Contact(Base): + """ + Contact information for a person. + """ + __tablename__ = 'Contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" + + + + + + +class Provider(Base): + """ + Provider information. + """ + __tablename__ = 'Provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'ResourceMorphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'ParameterCategoryParameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'ParameterUnit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'FieldSample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'FieldStorageMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'CollectionMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'HarvestMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'ProcessingMethod' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'PhysicalCharacteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'SoilType' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'AgTreatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'FieldSampleCondition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'LocationSoilType' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'PreparationMethod' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'PreparationMethodAbbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample prepared for analysis. + """ + __tablename__ = 'PreparedSample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'LocationAddress' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'Resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'ResourceClass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'ResourceSubclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'PrimaryCrop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'ResourceAvailability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'ResourceCounterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'Unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'Method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'MethodAbbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'MethodCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'MethodStandard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'Parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'ParameterCategory' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } From e81650d1694412cc37b5745be2c169d4d7083019 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Mon, 8 Dec 2025 13:02:38 -0700 Subject: [PATCH 53/81] feat: generated sqlA now is being read by Alembic and schema was successfully migrated --- alembic/env.py | 26 +- .../301006b4795f_initial_migration.py | 32 - .../e22149be0d9c_initial_migration.py | 1111 +++++++++++++++++ 3 files changed, 1125 insertions(+), 44 deletions(-) delete mode 100644 alembic/versions/301006b4795f_initial_migration.py create mode 100644 alembic/versions/e22149be0d9c_initial_migration.py diff --git a/alembic/env.py b/alembic/env.py index cd3a09ea..068e73bb 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -13,17 +13,18 @@ load_dotenv(dotenv_path=PROJECT_ROOT / ".env") # Looks for .env in the project root by default # --- Import your models so Alembic knows about them --- -from ca_biositing.datamodels.biomass import * -from ca_biositing.datamodels.data_and_references import * -from ca_biositing.datamodels.experiments_analysis import * -from ca_biositing.datamodels.external_datasets import * -from ca_biositing.datamodels.geographic_locations import * -from ca_biositing.datamodels.metadata_samples import * -from ca_biositing.datamodels.organizations import * -from ca_biositing.datamodels.people_contacts import * -from ca_biositing.datamodels.sample_preprocessing import * -from ca_biositing.datamodels.specific_aalysis_results import * -from ca_biositing.datamodels.user import * +# from ca_biositing.datamodels.biomass import * +# from ca_biositing.datamodels.data_and_references import * +# from ca_biositing.datamodels.experiments_analysis import * +# from ca_biositing.datamodels.external_datasets import * +# from ca_biositing.datamodels.geographic_locations import * +# from ca_biositing.datamodels.metadata_samples import * +# from ca_biositing.datamodels.organizations import * +# from ca_biositing.datamodels.people_contacts import * +# from ca_biositing.datamodels.sample_preprocessing import * +# from ca_biositing.datamodels.specific_aalysis_results import * +# from ca_biositing.datamodels.user import * +from ca_biositing.datamodels.schemas.generated.ca_biositing import * from sqlmodel import SQLModel import importlib.util from pathlib import Path @@ -51,7 +52,8 @@ # See: https://alembic.sqlalchemy.org/en/latest/autogenerate.html#affecting-the-autogenerate-process # Start with the default SQLModel metadata -target_metadata = SQLModel.metadata +# target_metadata = SQLModel.metadata +target_metadata = Base.metadata # Manually merge metadata from generated modules # for table in census_metadata.tables.values(): diff --git a/alembic/versions/301006b4795f_initial_migration.py b/alembic/versions/301006b4795f_initial_migration.py deleted file mode 100644 index 8e4f7afd..00000000 --- a/alembic/versions/301006b4795f_initial_migration.py +++ /dev/null @@ -1,32 +0,0 @@ -"""Initial migration - -Revision ID: 301006b4795f -Revises: e15bda744fef -Create Date: 2025-11-12 20:54:01.573577 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '301006b4795f' -down_revision: Union[str, Sequence[str], None] = 'e15bda744fef' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### diff --git a/alembic/versions/e22149be0d9c_initial_migration.py b/alembic/versions/e22149be0d9c_initial_migration.py new file mode 100644 index 00000000..574739e6 --- /dev/null +++ b/alembic/versions/e22149be0d9c_initial_migration.py @@ -0,0 +1,1111 @@ +"""Initial migration + +Revision ID: e22149be0d9c +Revises: +Create Date: 2025-12-08 18:01:48.554213 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'e22149be0d9c' +down_revision: Union[str, Sequence[str], None] = None +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('AgTreatment', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Aim1RecordBase', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Aim2RecordBase', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('AnalysisType', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('AutoclaveRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('BaseEntity', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('BillionTon2023Record', + sa.Column('subclass_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('county_square_miles', sa.Float(), nullable=True), + sa.Column('model_name', sa.Text(), nullable=True), + sa.Column('scenario_name', sa.Text(), nullable=True), + sa.Column('price_offered_usd', sa.Numeric(), nullable=True), + sa.Column('production', sa.Integer(), nullable=True), + sa.Column('production_unit_id', sa.Integer(), nullable=True), + sa.Column('btu_ton', sa.Integer(), nullable=True), + sa.Column('production_energy_content', sa.Integer(), nullable=True), + sa.Column('energy_content_unit_id', sa.Integer(), nullable=True), + sa.Column('product_density_dtpersqmi', sa.Numeric(), nullable=True), + sa.Column('land_source', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('CalorimetryRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('CollectionMethod', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('CompositionalRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Contact', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('first_name', sa.Text(), nullable=True), + sa.Column('last_name', sa.Text(), nullable=True), + sa.Column('email', sa.Text(), nullable=True), + sa.Column('affiliation', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('DataSource', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.Column('publication_date', sa.Date(), nullable=True), + sa.Column('version', sa.Text(), nullable=True), + sa.Column('publisher', sa.Text(), nullable=True), + sa.Column('author', sa.Text(), nullable=True), + sa.Column('license', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('DataSourceType', + sa.Column('source_type_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Dataset', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('record_type', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('start_date', sa.Date(), nullable=True), + sa.Column('end_date', sa.Date(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('DimensionType', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('EntityLineage', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.Column('source_table', sa.Text(), nullable=True), + sa.Column('source_row_id', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Equipment', + sa.Column('equipment_location_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('EtlRun', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('started_at', sa.DateTime(), nullable=True), + sa.Column('completed_at', sa.DateTime(), nullable=True), + sa.Column('pipeline_name', sa.Text(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('records_ingested', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Experiment', + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('exper_start_date', sa.Date(), nullable=True), + sa.Column('exper_duration', sa.Numeric(), nullable=True), + sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('exper_location_id', sa.Integer(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ExperimentAnalysis', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ExperimentEquipment', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('equipment_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ExperimentMethod', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ExperimentPreparedSample', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('prepared_sample_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FermentationRecord', + sa.Column('strain_id', sa.Integer(), nullable=True), + sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), + sa.Column('eh_method_id', sa.Integer(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('well_position', sa.Text(), nullable=True), + sa.Column('temperature', sa.Numeric(), nullable=True), + sa.Column('agitation_rpm', sa.Numeric(), nullable=True), + sa.Column('vessel_id', sa.Integer(), nullable=True), + sa.Column('analyte_detection_equipment_id', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FieldSample', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('provider_id', sa.Integer(), nullable=True), + sa.Column('collector_id', sa.Integer(), nullable=True), + sa.Column('sample_collection_source', sa.Text(), nullable=True), + sa.Column('amount_collected', sa.Numeric(), nullable=True), + sa.Column('amount_collected_unit_id', sa.Integer(), nullable=True), + sa.Column('sampling_location_id', sa.Integer(), nullable=True), + sa.Column('field_storage_method_id', sa.Integer(), nullable=True), + sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), + sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('field_storage_location_id', sa.Integer(), nullable=True), + sa.Column('collection_timestamp', sa.DateTime(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_date', sa.Date(), nullable=True), + sa.Column('field_sample_storage_location_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FieldSampleCondition', + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('ag_treatment_id', sa.Integer(), nullable=True), + sa.Column('last_application_date', sa.Date(), nullable=True), + sa.Column('treatment_amount_per_acre', sa.Float(), nullable=True), + sa.Column('processing_method_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FieldStorageMethod', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FileObjectMetadata', + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('bucket_path', sa.Text(), nullable=True), + sa.Column('file_format', sa.Text(), nullable=True), + sa.Column('file_size', sa.Integer(), nullable=True), + sa.Column('checksum_md5', sa.Text(), nullable=True), + sa.Column('checksum_sha256', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('FtnirRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('GasificationRecord', + sa.Column('feedstock_mass', sa.Numeric(), nullable=True), + sa.Column('bed_temperature', sa.Numeric(), nullable=True), + sa.Column('gas_flow_rate', sa.Numeric(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Geography', + sa.Column('geoid', sa.Text(), nullable=False), + sa.Column('state_name', sa.Text(), nullable=True), + sa.Column('state_fips', sa.Text(), nullable=True), + sa.Column('county_name', sa.Text(), nullable=True), + sa.Column('county_fips', sa.Text(), nullable=True), + sa.Column('region_name', sa.Text(), nullable=True), + sa.Column('agg_level_desc', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('geoid') + ) + op.create_table('HarvestMethod', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('IcpRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LandiqRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('polygon_id', sa.Integer(), nullable=True), + sa.Column('main_crop', sa.Integer(), nullable=True), + sa.Column('secondary_crop', sa.Integer(), nullable=True), + sa.Column('tertiary_crop', sa.Integer(), nullable=True), + sa.Column('quaternary_crop', sa.Integer(), nullable=True), + sa.Column('confidence', sa.Integer(), nullable=True), + sa.Column('irrigated', sa.Boolean(), nullable=True), + sa.Column('acres', sa.Float(), nullable=True), + sa.Column('version', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LineageGroup', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LocationAddress', + sa.Column('geography_id', sa.Text(), nullable=True), + sa.Column('address_line1', sa.Text(), nullable=True), + sa.Column('address_line2', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('zip', sa.Text(), nullable=True), + sa.Column('lat', sa.Float(), nullable=True), + sa.Column('lon', sa.Float(), nullable=True), + sa.Column('is_anonymous', sa.Boolean(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LocationResolution', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LocationSoilType', + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('soil_type_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('LookupBase', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Method', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('method_category_id', sa.Integer(), nullable=True), + sa.Column('method_standard_id', sa.Integer(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('detection_limits', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('MethodAbbrev', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('MethodCategory', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('MethodStandard', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Observation', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('record_type', sa.Text(), nullable=True), + sa.Column('record_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('dimension_type_id', sa.Integer(), nullable=True), + sa.Column('dimension_value', sa.Numeric(), nullable=True), + sa.Column('dimension_unit_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Parameter', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('standard_unit_id', sa.Integer(), nullable=True), + sa.Column('calculated', sa.Boolean(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ParameterCategory', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ParameterCategoryParameter', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_category_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ParameterUnit', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('alternate_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PhysicalCharacteristic', + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('particle_length', sa.Numeric(), nullable=True), + sa.Column('particle_width', sa.Numeric(), nullable=True), + sa.Column('particle_height', sa.Numeric(), nullable=True), + sa.Column('particle_unit_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Polygon', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PreparationMethod', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('prep_method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('prep_temp_c', sa.Numeric(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.Column('drying_step', sa.Boolean(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PreparationMethodAbbreviation', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PreparedSample', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('prep_method_id', sa.Integer(), nullable=True), + sa.Column('prep_date', sa.Date(), nullable=True), + sa.Column('preparer_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PretreatmentRecord', + sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), + sa.Column('eh_method_id', sa.Integer(), nullable=True), + sa.Column('reaction_block_id', sa.Integer(), nullable=True), + sa.Column('block_position', sa.Text(), nullable=True), + sa.Column('temperature', sa.Numeric(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('PrimaryCrop', + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ProcessingMethod', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Provider', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('codename', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ProximateRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Resource', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('primary_crop_id', sa.Integer(), nullable=True), + sa.Column('resource_class_id', sa.Integer(), nullable=True), + sa.Column('resource_subclass_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceAvailability', + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('from_month', sa.Integer(), nullable=True), + sa.Column('to_month', sa.Integer(), nullable=True), + sa.Column('year_round', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceClass', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceCounterfactual', + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('counterfactual_description', sa.Text(), nullable=True), + sa.Column('animal_bedding_percent', sa.Numeric(), nullable=True), + sa.Column('animal_bedding_source_id', sa.Integer(), nullable=True), + sa.Column('animal_feed_percent', sa.Numeric(), nullable=True), + sa.Column('animal_feed_source_id', sa.Integer(), nullable=True), + sa.Column('bioelectricty_percent', sa.Numeric(), nullable=True), + sa.Column('bioelectricty_source_id', sa.Integer(), nullable=True), + sa.Column('burn_percent', sa.Numeric(), nullable=True), + sa.Column('burn_source_id', sa.Integer(), nullable=True), + sa.Column('compost_percent', sa.Numeric(), nullable=True), + sa.Column('compost_source_id', sa.Integer(), nullable=True), + sa.Column('landfill_percent', sa.Numeric(), nullable=True), + sa.Column('landfill_source_id', sa.Integer(), nullable=True), + sa.Column('counterfactual_date', sa.Date(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceMorphology', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('morphology_uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceSubclass', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ResourceUsdaCommodityMap', + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('primary_crop_id', sa.Integer(), nullable=True), + sa.Column('usda_commodity_id', sa.Integer(), nullable=True), + sa.Column('match_tier', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('RgbRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('SoilType', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('SourceType', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Strain', + sa.Column('parent_strain_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UltimateRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('Unit', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaCensusRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('commodity_code', sa.Integer(), nullable=True), + sa.Column('year', sa.Integer(), nullable=True), + sa.Column('source_reference', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaCommodity', + sa.Column('usda_source', sa.Text(), nullable=True), + sa.Column('usda_code', sa.Text(), nullable=True), + sa.Column('parent_commodity_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaDomain', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaMarketRecord', + sa.Column('report_id', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('report_begin_date', sa.DateTime(), nullable=True), + sa.Column('report_end_date', sa.DateTime(), nullable=True), + sa.Column('report_date', sa.DateTime(), nullable=True), + sa.Column('commodity_id', sa.Integer(), nullable=True), + sa.Column('market_type_id', sa.Integer(), nullable=True), + sa.Column('market_type_catagory', sa.Text(), nullable=True), + sa.Column('grp', sa.Text(), nullable=True), + sa.Column('market_catagory_id', sa.Integer(), nullable=True), + sa.Column('class_', sa.Text(), nullable=True), + sa.Column('grade', sa.Text(), nullable=True), + sa.Column('variety', sa.Text(), nullable=True), + sa.Column('protein_pct', sa.Numeric(), nullable=True), + sa.Column('application', sa.Text(), nullable=True), + sa.Column('pkg', sa.Text(), nullable=True), + sa.Column('sale_type', sa.Text(), nullable=True), + sa.Column('price_unit_id', sa.Integer(), nullable=True), + sa.Column('freight', sa.Text(), nullable=True), + sa.Column('trans_mode', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaMarketReport', + sa.Column('slug_id', sa.Integer(), nullable=True), + sa.Column('slug_name', sa.Text(), nullable=True), + sa.Column('report_series_title', sa.Text(), nullable=True), + sa.Column('frequency', sa.Text(), nullable=True), + sa.Column('office_name', sa.Text(), nullable=True), + sa.Column('office_city_id', sa.Integer(), nullable=True), + sa.Column('office_state_fips', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaStatisticCategory', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaSurveyProgram', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaSurveyRecord', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('commodity_code', sa.Integer(), nullable=True), + sa.Column('year', sa.Integer(), nullable=True), + sa.Column('survey_program_id', sa.Integer(), nullable=True), + sa.Column('survey_period', sa.Text(), nullable=True), + sa.Column('reference_month', sa.Text(), nullable=True), + sa.Column('seasonal_flag', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('UsdaTermMap', + sa.Column('source_system', sa.Text(), nullable=True), + sa.Column('source_context', sa.Text(), nullable=True), + sa.Column('raw_term', sa.Text(), nullable=True), + sa.Column('usda_commodity_id', sa.Integer(), nullable=True), + sa.Column('is_verified', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('XrdRecord', + sa.Column('maybe_scan_low_nm', sa.Integer(), nullable=True), + sa.Column('maybe_scan_high_nm', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('XrfRecord', + sa.Column('maybe_wavelength_nm', sa.Numeric(), nullable=True), + sa.Column('maybe_intensity', sa.Numeric(), nullable=True), + sa.Column('maybe_energy_slope', sa.Numeric(), nullable=True), + sa.Column('maybe_energy_offset', sa.Numeric(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('XrfRecord') + op.drop_table('XrdRecord') + op.drop_table('UsdaTermMap') + op.drop_table('UsdaSurveyRecord') + op.drop_table('UsdaSurveyProgram') + op.drop_table('UsdaStatisticCategory') + op.drop_table('UsdaMarketReport') + op.drop_table('UsdaMarketRecord') + op.drop_table('UsdaDomain') + op.drop_table('UsdaCommodity') + op.drop_table('UsdaCensusRecord') + op.drop_table('Unit') + op.drop_table('UltimateRecord') + op.drop_table('Strain') + op.drop_table('SourceType') + op.drop_table('SoilType') + op.drop_table('RgbRecord') + op.drop_table('ResourceUsdaCommodityMap') + op.drop_table('ResourceSubclass') + op.drop_table('ResourceMorphology') + op.drop_table('ResourceCounterfactual') + op.drop_table('ResourceClass') + op.drop_table('ResourceAvailability') + op.drop_table('Resource') + op.drop_table('ProximateRecord') + op.drop_table('Provider') + op.drop_table('ProcessingMethod') + op.drop_table('PrimaryCrop') + op.drop_table('PretreatmentRecord') + op.drop_table('PreparedSample') + op.drop_table('PreparationMethodAbbreviation') + op.drop_table('PreparationMethod') + op.drop_table('Polygon') + op.drop_table('PhysicalCharacteristic') + op.drop_table('ParameterUnit') + op.drop_table('ParameterCategoryParameter') + op.drop_table('ParameterCategory') + op.drop_table('Parameter') + op.drop_table('Observation') + op.drop_table('MethodStandard') + op.drop_table('MethodCategory') + op.drop_table('MethodAbbrev') + op.drop_table('Method') + op.drop_table('LookupBase') + op.drop_table('LocationSoilType') + op.drop_table('LocationResolution') + op.drop_table('LocationAddress') + op.drop_table('LineageGroup') + op.drop_table('LandiqRecord') + op.drop_table('IcpRecord') + op.drop_table('HarvestMethod') + op.drop_table('Geography') + op.drop_table('GasificationRecord') + op.drop_table('FtnirRecord') + op.drop_table('FileObjectMetadata') + op.drop_table('FieldStorageMethod') + op.drop_table('FieldSampleCondition') + op.drop_table('FieldSample') + op.drop_table('FermentationRecord') + op.drop_table('ExperimentPreparedSample') + op.drop_table('ExperimentMethod') + op.drop_table('ExperimentEquipment') + op.drop_table('ExperimentAnalysis') + op.drop_table('Experiment') + op.drop_table('EtlRun') + op.drop_table('Equipment') + op.drop_table('EntityLineage') + op.drop_table('DimensionType') + op.drop_table('Dataset') + op.drop_table('DataSourceType') + op.drop_table('DataSource') + op.drop_table('Contact') + op.drop_table('CompositionalRecord') + op.drop_table('CollectionMethod') + op.drop_table('CalorimetryRecord') + op.drop_table('BillionTon2023Record') + op.drop_table('BaseEntity') + op.drop_table('AutoclaveRecord') + op.drop_table('AnalysisType') + op.drop_table('Aim2RecordBase') + op.drop_table('Aim1RecordBase') + op.drop_table('AgTreatment') + # ### end Alembic commands ### From 2e0b778e216b68f45aef2baf003ba88a2eeee651 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Mon, 8 Dec 2025 15:45:01 -0700 Subject: [PATCH 54/81] feat: sqla to alembic complete. new pixi task. docs updated. --- README.md | 14 +- ...2618fe6b09b_rename_tables_to_snake_case.py | 2192 +++++++++++++++++ ...8c837616b_adding_a_test_to_landiqrecord.py | 32 + pixi.toml | 2 + src/ca_biositing/datamodels/README.md | 175 +- .../linkml/modules/external_data.yaml | 5 + .../schemas/generated/aim1_records.py | 120 +- .../schemas/generated/aim2_records.py | 112 +- .../datamodels/schemas/generated/analysis.py | 30 +- .../schemas/generated/analysis_records.py | 122 +- .../schemas/generated/ca_biositing.py | 167 +- .../datamodels/schemas/generated/core.py | 4 +- .../generated/data_sources_metadata.py | 74 +- .../schemas/generated/experiment_equipment.py | 100 +- .../schemas/generated/experiments.py | 94 +- .../schemas/generated/external_data.py | 111 +- .../schemas/generated/field_sampling.py | 74 +- .../schemas/generated/general_analysis.py | 82 +- .../datamodels/schemas/generated/geography.py | 10 +- .../schemas/generated/infrastructure.py | 108 +- .../datamodels/schemas/generated/lineage.py | 10 +- .../datamodels/schemas/generated/methods.py | 22 +- .../generated/methods_parameters_units.py | 74 +- .../datamodels/schemas/generated/people.py | 4 +- .../datamodels/schemas/generated/places.py | 8 +- .../schemas/generated/resource_information.py | 22 +- .../datamodels/schemas/generated/resources.py | 24 +- .../schemas/generated/sample_preparation.py | 80 +- .../datamodels/schemas/generated/sampling.py | 72 +- .../datamodels/{ => utils}/generate_sqla.py | 39 +- .../utils/orchestrate_schema_update.py | 58 + 31 files changed, 3205 insertions(+), 836 deletions(-) create mode 100644 alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py create mode 100644 alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py rename src/ca_biositing/datamodels/{ => utils}/generate_sqla.py (54%) create mode 100644 src/ca_biositing/datamodels/utils/orchestrate_schema_update.py diff --git a/README.md b/README.md index 114d504c..3eacc3b9 100644 --- a/README.md +++ b/README.md @@ -10,8 +10,8 @@ data access. This project uses a **PEP 420 namespace package** structure with three main components: -- **`ca_biositing.datamodels`**: Shared SQLModel database models and database - configuration +- **`ca_biositing.datamodels`**: Shared LinkML/SQLModel database models and + database configuration - **`ca_biositing.pipeline`**: ETL pipelines orchestrated with Prefect, deployed via Docker - **`ca_biositing.webservice`**: FastAPI REST API for data access @@ -152,6 +152,7 @@ Key tasks: - **Development**: `test`, `test-cov`, `pre-commit`, `pre-commit-all` - **Applications**: `start-webservice`, `qgis` - **Database**: `access-db`, `check-db-health` +- **Datamodels**: `update-schema`, `migrate` ## Architecture @@ -181,6 +182,15 @@ Pipeline architecture: ### Database Models +We use a **LinkML-first approach** for defining our data schema. The workflow +is: + +1. **LinkML Schema**: The schema is defined in YAML files (source of truth). +2. **SQLAlchemy Generation**: Python classes are automatically generated from + LinkML. +3. **Alembic Migrations**: Database migrations are generated from the Python + classes. + SQLModel-based models provide: - Type-safe database operations diff --git a/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py b/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py new file mode 100644 index 00000000..22464c6b --- /dev/null +++ b/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py @@ -0,0 +1,2192 @@ +"""rename_tables_to_snake_case + +Revision ID: 42618fe6b09b +Revises: e22149be0d9c +Create Date: 2025-12-08 21:37:30.253589 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa +from sqlalchemy.dialects import postgresql + +# revision identifiers, used by Alembic. +revision: str = '42618fe6b09b' +down_revision: Union[str, Sequence[str], None] = 'e22149be0d9c' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('ag_treatment', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('aim1_record_base', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('aim2_record_base', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('analysis_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('autoclave_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('base_entity', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('billion_ton2023_record', + sa.Column('subclass_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('county_square_miles', sa.Float(), nullable=True), + sa.Column('model_name', sa.Text(), nullable=True), + sa.Column('scenario_name', sa.Text(), nullable=True), + sa.Column('price_offered_usd', sa.Numeric(), nullable=True), + sa.Column('production', sa.Integer(), nullable=True), + sa.Column('production_unit_id', sa.Integer(), nullable=True), + sa.Column('btu_ton', sa.Integer(), nullable=True), + sa.Column('production_energy_content', sa.Integer(), nullable=True), + sa.Column('energy_content_unit_id', sa.Integer(), nullable=True), + sa.Column('product_density_dtpersqmi', sa.Numeric(), nullable=True), + sa.Column('land_source', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('calorimetry_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('collection_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('compositional_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('contact', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('first_name', sa.Text(), nullable=True), + sa.Column('last_name', sa.Text(), nullable=True), + sa.Column('email', sa.Text(), nullable=True), + sa.Column('affiliation', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('data_source', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.Column('publication_date', sa.Date(), nullable=True), + sa.Column('version', sa.Text(), nullable=True), + sa.Column('publisher', sa.Text(), nullable=True), + sa.Column('author', sa.Text(), nullable=True), + sa.Column('license', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('data_source_type', + sa.Column('source_type_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('dataset', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('record_type', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('start_date', sa.Date(), nullable=True), + sa.Column('end_date', sa.Date(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('dimension_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('entity_lineage', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.Column('source_table', sa.Text(), nullable=True), + sa.Column('source_row_id', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('equipment', + sa.Column('equipment_location_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('etl_run', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('started_at', sa.DateTime(), nullable=True), + sa.Column('completed_at', sa.DateTime(), nullable=True), + sa.Column('pipeline_name', sa.Text(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('records_ingested', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment', + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('exper_start_date', sa.Date(), nullable=True), + sa.Column('exper_duration', sa.Numeric(), nullable=True), + sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('exper_location_id', sa.Integer(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_analysis', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_equipment', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('equipment_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_prepared_sample', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('prepared_sample_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('fermentation_record', + sa.Column('strain_id', sa.Integer(), nullable=True), + sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), + sa.Column('eh_method_id', sa.Integer(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('well_position', sa.Text(), nullable=True), + sa.Column('temperature', sa.Numeric(), nullable=True), + sa.Column('agitation_rpm', sa.Numeric(), nullable=True), + sa.Column('vessel_id', sa.Integer(), nullable=True), + sa.Column('analyte_detection_equipment_id', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('field_sample', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('provider_id', sa.Integer(), nullable=True), + sa.Column('collector_id', sa.Integer(), nullable=True), + sa.Column('sample_collection_source', sa.Text(), nullable=True), + sa.Column('amount_collected', sa.Numeric(), nullable=True), + sa.Column('amount_collected_unit_id', sa.Integer(), nullable=True), + sa.Column('sampling_location_id', sa.Integer(), nullable=True), + sa.Column('field_storage_method_id', sa.Integer(), nullable=True), + sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), + sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('field_storage_location_id', sa.Integer(), nullable=True), + sa.Column('collection_timestamp', sa.DateTime(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_date', sa.Date(), nullable=True), + sa.Column('field_sample_storage_location_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('field_sample_condition', + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('ag_treatment_id', sa.Integer(), nullable=True), + sa.Column('last_application_date', sa.Date(), nullable=True), + sa.Column('treatment_amount_per_acre', sa.Float(), nullable=True), + sa.Column('processing_method_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('field_storage_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('file_object_metadata', + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('bucket_path', sa.Text(), nullable=True), + sa.Column('file_format', sa.Text(), nullable=True), + sa.Column('file_size', sa.Integer(), nullable=True), + sa.Column('checksum_md5', sa.Text(), nullable=True), + sa.Column('checksum_sha256', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ftnir_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('gasification_record', + sa.Column('feedstock_mass', sa.Numeric(), nullable=True), + sa.Column('bed_temperature', sa.Numeric(), nullable=True), + sa.Column('gas_flow_rate', sa.Numeric(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('geography', + sa.Column('geoid', sa.Text(), nullable=False), + sa.Column('state_name', sa.Text(), nullable=True), + sa.Column('state_fips', sa.Text(), nullable=True), + sa.Column('county_name', sa.Text(), nullable=True), + sa.Column('county_fips', sa.Text(), nullable=True), + sa.Column('region_name', sa.Text(), nullable=True), + sa.Column('agg_level_desc', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('geoid') + ) + op.create_table('harvest_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('icp_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('landiq_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('polygon_id', sa.Integer(), nullable=True), + sa.Column('main_crop', sa.Integer(), nullable=True), + sa.Column('secondary_crop', sa.Integer(), nullable=True), + sa.Column('tertiary_crop', sa.Integer(), nullable=True), + sa.Column('quaternary_crop', sa.Integer(), nullable=True), + sa.Column('confidence', sa.Integer(), nullable=True), + sa.Column('irrigated', sa.Boolean(), nullable=True), + sa.Column('acres', sa.Float(), nullable=True), + sa.Column('version', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('lineage_group', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('location_address', + sa.Column('geography_id', sa.Text(), nullable=True), + sa.Column('address_line1', sa.Text(), nullable=True), + sa.Column('address_line2', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('zip', sa.Text(), nullable=True), + sa.Column('lat', sa.Float(), nullable=True), + sa.Column('lon', sa.Float(), nullable=True), + sa.Column('is_anonymous', sa.Boolean(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('location_resolution', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('location_soil_type', + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('soil_type_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('lookup_base', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('method_category_id', sa.Integer(), nullable=True), + sa.Column('method_standard_id', sa.Integer(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('detection_limits', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method_abbrev', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method_category', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method_standard', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('observation', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('record_type', sa.Text(), nullable=True), + sa.Column('record_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('dimension_type_id', sa.Integer(), nullable=True), + sa.Column('dimension_value', sa.Numeric(), nullable=True), + sa.Column('dimension_unit_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('standard_unit_id', sa.Integer(), nullable=True), + sa.Column('calculated', sa.Boolean(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter_category', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter_category_parameter', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_category_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter_unit', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('alternate_unit_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('physical_characteristic', + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('particle_length', sa.Numeric(), nullable=True), + sa.Column('particle_width', sa.Numeric(), nullable=True), + sa.Column('particle_height', sa.Numeric(), nullable=True), + sa.Column('particle_unit_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('polygon', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('preparation_method', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('prep_method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('prep_temp_c', sa.Numeric(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.Column('drying_step', sa.Boolean(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('preparation_method_abbreviation', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('prepared_sample', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('prep_method_id', sa.Integer(), nullable=True), + sa.Column('prep_date', sa.Date(), nullable=True), + sa.Column('preparer_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('pretreatment_record', + sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), + sa.Column('eh_method_id', sa.Integer(), nullable=True), + sa.Column('reaction_block_id', sa.Integer(), nullable=True), + sa.Column('block_position', sa.Text(), nullable=True), + sa.Column('temperature', sa.Numeric(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('primary_crop', + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('processing_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('provider', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('codename', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('proximate_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('primary_crop_id', sa.Integer(), nullable=True), + sa.Column('resource_class_id', sa.Integer(), nullable=True), + sa.Column('resource_subclass_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_availability', + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('from_month', sa.Integer(), nullable=True), + sa.Column('to_month', sa.Integer(), nullable=True), + sa.Column('year_round', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_class', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_counterfactual', + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('counterfactual_description', sa.Text(), nullable=True), + sa.Column('animal_bedding_percent', sa.Numeric(), nullable=True), + sa.Column('animal_bedding_source_id', sa.Integer(), nullable=True), + sa.Column('animal_feed_percent', sa.Numeric(), nullable=True), + sa.Column('animal_feed_source_id', sa.Integer(), nullable=True), + sa.Column('bioelectricty_percent', sa.Numeric(), nullable=True), + sa.Column('bioelectricty_source_id', sa.Integer(), nullable=True), + sa.Column('burn_percent', sa.Numeric(), nullable=True), + sa.Column('burn_source_id', sa.Integer(), nullable=True), + sa.Column('compost_percent', sa.Numeric(), nullable=True), + sa.Column('compost_source_id', sa.Integer(), nullable=True), + sa.Column('landfill_percent', sa.Numeric(), nullable=True), + sa.Column('landfill_source_id', sa.Integer(), nullable=True), + sa.Column('counterfactual_date', sa.Date(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_morphology', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('morphology_uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_subclass', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_usda_commodity_map', + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('primary_crop_id', sa.Integer(), nullable=True), + sa.Column('usda_commodity_id', sa.Integer(), nullable=True), + sa.Column('match_tier', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('rgb_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('soil_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('source_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('strain', + sa.Column('parent_strain_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ultimate_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('unit', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_census_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('commodity_code', sa.Integer(), nullable=True), + sa.Column('year', sa.Integer(), nullable=True), + sa.Column('source_reference', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_commodity', + sa.Column('usda_source', sa.Text(), nullable=True), + sa.Column('usda_code', sa.Text(), nullable=True), + sa.Column('parent_commodity_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_domain', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_market_record', + sa.Column('report_id', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('report_begin_date', sa.DateTime(), nullable=True), + sa.Column('report_end_date', sa.DateTime(), nullable=True), + sa.Column('report_date', sa.DateTime(), nullable=True), + sa.Column('commodity_id', sa.Integer(), nullable=True), + sa.Column('market_type_id', sa.Integer(), nullable=True), + sa.Column('market_type_catagory', sa.Text(), nullable=True), + sa.Column('grp', sa.Text(), nullable=True), + sa.Column('market_catagory_id', sa.Integer(), nullable=True), + sa.Column('class_', sa.Text(), nullable=True), + sa.Column('grade', sa.Text(), nullable=True), + sa.Column('variety', sa.Text(), nullable=True), + sa.Column('protein_pct', sa.Numeric(), nullable=True), + sa.Column('application', sa.Text(), nullable=True), + sa.Column('pkg', sa.Text(), nullable=True), + sa.Column('sale_type', sa.Text(), nullable=True), + sa.Column('price_unit_id', sa.Integer(), nullable=True), + sa.Column('freight', sa.Text(), nullable=True), + sa.Column('trans_mode', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_market_report', + sa.Column('slug_id', sa.Integer(), nullable=True), + sa.Column('slug_name', sa.Text(), nullable=True), + sa.Column('report_series_title', sa.Text(), nullable=True), + sa.Column('frequency', sa.Text(), nullable=True), + sa.Column('office_name', sa.Text(), nullable=True), + sa.Column('office_city_id', sa.Integer(), nullable=True), + sa.Column('office_state_fips', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_statistic_category', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_survey_program', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_survey_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('commodity_code', sa.Integer(), nullable=True), + sa.Column('year', sa.Integer(), nullable=True), + sa.Column('survey_program_id', sa.Integer(), nullable=True), + sa.Column('survey_period', sa.Text(), nullable=True), + sa.Column('reference_month', sa.Text(), nullable=True), + sa.Column('seasonal_flag', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_term_map', + sa.Column('source_system', sa.Text(), nullable=True), + sa.Column('source_context', sa.Text(), nullable=True), + sa.Column('raw_term', sa.Text(), nullable=True), + sa.Column('usda_commodity_id', sa.Integer(), nullable=True), + sa.Column('is_verified', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('xrd_record', + sa.Column('maybe_scan_low_nm', sa.Integer(), nullable=True), + sa.Column('maybe_scan_high_nm', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('xrf_record', + sa.Column('maybe_wavelength_nm', sa.Numeric(), nullable=True), + sa.Column('maybe_intensity', sa.Numeric(), nullable=True), + sa.Column('maybe_energy_slope', sa.Numeric(), nullable=True), + sa.Column('maybe_energy_offset', sa.Numeric(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.drop_table('UsdaMarketRecord') + op.drop_table('ResourceAvailability') + op.drop_table('PreparedSample') + op.drop_table('UsdaStatisticCategory') + op.drop_table('PrimaryCrop') + op.drop_table('BaseEntity') + op.drop_table('ResourceCounterfactual') + op.drop_table('UltimateRecord') + op.drop_table('SourceType') + op.drop_table('Contact') + op.drop_table('DataSourceType') + op.drop_table('ParameterUnit') + op.drop_table('Parameter') + op.drop_table('UsdaTermMap') + op.drop_table('Experiment') + op.drop_table('ParameterCategory') + op.drop_table('ExperimentEquipment') + op.drop_table('Aim1RecordBase') + op.drop_table('Geography') + op.drop_table('Method') + op.drop_table('LineageGroup') + op.drop_table('RgbRecord') + op.drop_table('MethodStandard') + op.drop_table('PretreatmentRecord') + op.drop_table('ResourceSubclass') + op.drop_table('UsdaMarketReport') + op.drop_table('Polygon') + op.drop_table('LocationResolution') + op.drop_table('ResourceMorphology') + op.drop_table('AutoclaveRecord') + op.drop_table('DimensionType') + op.drop_table('CompositionalRecord') + op.drop_table('PhysicalCharacteristic') + op.drop_table('Aim2RecordBase') + op.drop_table('UsdaCensusRecord') + op.drop_table('ResourceUsdaCommodityMap') + op.drop_table('AnalysisType') + op.drop_table('ParameterCategoryParameter') + op.drop_table('ExperimentAnalysis') + op.drop_table('UsdaDomain') + op.drop_table('HarvestMethod') + op.drop_table('LookupBase') + op.drop_table('FtnirRecord') + op.drop_table('Resource') + op.drop_table('Equipment') + op.drop_table('DataSource') + op.drop_table('ResourceClass') + op.drop_table('LocationAddress') + op.drop_table('UsdaSurveyRecord') + op.drop_table('FermentationRecord') + op.drop_table('XrdRecord') + op.drop_table('AgTreatment') + op.drop_table('ExperimentMethod') + op.drop_table('Dataset') + op.drop_table('LocationSoilType') + op.drop_table('FieldSampleCondition') + op.drop_table('XrfRecord') + op.drop_table('MethodAbbrev') + op.drop_table('Provider') + op.drop_table('LandiqRecord') + op.drop_table('EntityLineage') + op.drop_table('Unit') + op.drop_table('CalorimetryRecord') + op.drop_table('ExperimentPreparedSample') + op.drop_table('CollectionMethod') + op.drop_table('IcpRecord') + op.drop_table('PreparationMethodAbbreviation') + op.drop_table('BillionTon2023Record') + op.drop_table('ProcessingMethod') + op.drop_table('EtlRun') + op.drop_table('FileObjectMetadata') + op.drop_table('MethodCategory') + op.drop_table('GasificationRecord') + op.drop_table('UsdaCommodity') + op.drop_table('PreparationMethod') + op.drop_table('Observation') + op.drop_table('SoilType') + op.drop_table('FieldSample') + op.drop_table('FieldStorageMethod') + op.drop_table('Strain') + op.drop_table('ProximateRecord') + op.drop_table('UsdaSurveyProgram') + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('UsdaSurveyProgram', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaSurveyProgram_pkey')) + ) + op.create_table('ProximateRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ProximateRecord_pkey')) + ) + op.create_table('Strain', + sa.Column('parent_strain_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Strain_pkey')) + ) + op.create_table('FieldStorageMethod', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FieldStorageMethod_pkey')) + ) + op.create_table('FieldSample', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('provider_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('collector_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_collection_source', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('amount_collected', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('amount_collected_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sampling_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('field_storage_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('field_storage_duration_value', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('field_storage_duration_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('field_storage_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('collection_timestamp', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('collection_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('harvest_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('harvest_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('field_sample_storage_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FieldSample_pkey')) + ) + op.create_table('SoilType', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('SoilType_pkey')) + ) + op.create_table('Observation', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('record_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('record_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('value', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dimension_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dimension_value', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('dimension_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Observation_pkey')) + ) + op.create_table('PreparationMethod', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('prep_method_abbrev_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prep_temp_c', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('drying_step', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PreparationMethod_pkey')) + ) + op.create_table('UsdaCommodity', + sa.Column('usda_source', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('usda_code', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('parent_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaCommodity_pkey')) + ) + op.create_table('GasificationRecord', + sa.Column('feedstock_mass', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('bed_temperature', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('gas_flow_rate', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('GasificationRecord_pkey')) + ) + op.create_table('MethodCategory', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('MethodCategory_pkey')) + ) + op.create_table('FileObjectMetadata', + sa.Column('data_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('bucket_path', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('file_format', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('file_size', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('checksum_md5', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('checksum_sha256', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FileObjectMetadata_pkey')) + ) + op.create_table('EtlRun', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('started_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('completed_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('pipeline_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('records_ingested', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('EtlRun_pkey')) + ) + op.create_table('ProcessingMethod', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ProcessingMethod_pkey')) + ) + op.create_table('BillionTon2023Record', + sa.Column('subclass_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county_square_miles', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('model_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('scenario_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('price_offered_usd', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('production', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('production_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('btu_ton', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('production_energy_content', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('energy_content_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('product_density_dtpersqmi', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('land_source', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('BillionTon2023Record_pkey')) + ) + op.create_table('PreparationMethodAbbreviation', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PreparationMethodAbbreviation_pkey')) + ) + op.create_table('IcpRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('IcpRecord_pkey')) + ) + op.create_table('CollectionMethod', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('CollectionMethod_pkey')) + ) + op.create_table('ExperimentPreparedSample', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prepared_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ExperimentPreparedSample_pkey')) + ) + op.create_table('CalorimetryRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('CalorimetryRecord_pkey')) + ) + op.create_table('Unit', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Unit_pkey')) + ) + op.create_table('EntityLineage', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('source_table', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_row_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('EntityLineage_pkey')) + ) + op.create_table('LandiqRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('polygon_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('main_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('secondary_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('tertiary_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('quaternary_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('confidence', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('irrigated', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('acres', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('version', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LandiqRecord_pkey')) + ) + op.create_table('Provider', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('codename', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Provider_pkey')) + ) + op.create_table('MethodAbbrev', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('MethodAbbrev_pkey')) + ) + op.create_table('XrfRecord', + sa.Column('maybe_wavelength_nm', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('maybe_intensity', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('maybe_energy_slope', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('maybe_energy_offset', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('XrfRecord_pkey')) + ) + op.create_table('FieldSampleCondition', + sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('ag_treatment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('last_application_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('treatment_amount_per_acre', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('processing_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FieldSampleCondition_pkey')) + ) + op.create_table('LocationSoilType', + sa.Column('location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('soil_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LocationSoilType_pkey')) + ) + op.create_table('Dataset', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('record_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('start_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('end_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Dataset_pkey')) + ) + op.create_table('ExperimentMethod', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ExperimentMethod_pkey')) + ) + op.create_table('AgTreatment', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('AgTreatment_pkey')) + ) + op.create_table('XrdRecord', + sa.Column('maybe_scan_low_nm', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('maybe_scan_high_nm', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('XrdRecord_pkey')) + ) + op.create_table('FermentationRecord', + sa.Column('strain_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('pretreatment_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('eh_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('well_position', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('temperature', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('agitation_rpm', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('vessel_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyte_detection_equipment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FermentationRecord_pkey')) + ) + op.create_table('UsdaSurveyRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('commodity_code', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('year', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('survey_program_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('survey_period', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('reference_month', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('seasonal_flag', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaSurveyRecord_pkey')) + ) + op.create_table('LocationAddress', + sa.Column('geography_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('address_line1', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('address_line2', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('zip', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lat', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('lon', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('is_anonymous', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LocationAddress_pkey')) + ) + op.create_table('ResourceClass', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceClass_pkey')) + ) + op.create_table('DataSource', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('publication_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('version', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('publisher', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('author', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('license', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('DataSource_pkey')) + ) + op.create_table('Equipment', + sa.Column('equipment_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Equipment_pkey')) + ) + op.create_table('Resource', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('primary_crop_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_class_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_subclass_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Resource_pkey')) + ) + op.create_table('FtnirRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('FtnirRecord_pkey')) + ) + op.create_table('LookupBase', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LookupBase_pkey')) + ) + op.create_table('HarvestMethod', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('HarvestMethod_pkey')) + ) + op.create_table('UsdaDomain', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaDomain_pkey')) + ) + op.create_table('ExperimentAnalysis', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analysis_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ExperimentAnalysis_pkey')) + ) + op.create_table('ParameterCategoryParameter', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('parameter_category_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ParameterCategoryParameter_pkey')) + ) + op.create_table('AnalysisType', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('AnalysisType_pkey')) + ) + op.create_table('ResourceUsdaCommodityMap', + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('primary_crop_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('usda_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('match_tier', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceUsdaCommodityMap_pkey')) + ) + op.create_table('UsdaCensusRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('commodity_code', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('year', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('source_reference', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaCensusRecord_pkey')) + ) + op.create_table('Aim2RecordBase', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Aim2RecordBase_pkey')) + ) + op.create_table('PhysicalCharacteristic', + sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('particle_length', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('particle_width', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('particle_height', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('particle_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PhysicalCharacteristic_pkey')) + ) + op.create_table('CompositionalRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('CompositionalRecord_pkey')) + ) + op.create_table('DimensionType', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('DimensionType_pkey')) + ) + op.create_table('AutoclaveRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('AutoclaveRecord_pkey')) + ) + op.create_table('ResourceMorphology', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('morphology_uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceMorphology_pkey')) + ) + op.create_table('LocationResolution', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LocationResolution_pkey')) + ) + op.create_table('Polygon', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('geom', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Polygon_pkey')) + ) + op.create_table('UsdaMarketReport', + sa.Column('slug_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('slug_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('report_series_title', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('frequency', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('office_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('office_city_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('office_state_fips', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaMarketReport_pkey')) + ) + op.create_table('ResourceSubclass', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceSubclass_pkey')) + ) + op.create_table('PretreatmentRecord', + sa.Column('pretreatment_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('eh_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('reaction_block_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('block_position', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('temperature', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PretreatmentRecord_pkey')) + ) + op.create_table('MethodStandard', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('MethodStandard_pkey')) + ) + op.create_table('RgbRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('RgbRecord_pkey')) + ) + op.create_table('LineageGroup', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('LineageGroup_pkey')) + ) + op.create_table('Method', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('method_abbrev_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_category_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_standard_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('detection_limits', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Method_pkey')) + ) + op.create_table('Geography', + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=False), + sa.Column('state_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state_fips', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county_fips', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('region_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('agg_level_desc', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('geoid', name=op.f('Geography_pkey')) + ) + op.create_table('Aim1RecordBase', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Aim1RecordBase_pkey')) + ) + op.create_table('ExperimentEquipment', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('equipment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ExperimentEquipment_pkey')) + ) + op.create_table('ParameterCategory', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ParameterCategory_pkey')) + ) + op.create_table('Experiment', + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('exper_start_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('exper_duration', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('exper_duration_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('exper_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Experiment_pkey')) + ) + op.create_table('UsdaTermMap', + sa.Column('source_system', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_context', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('raw_term', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('usda_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('is_verified', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaTermMap_pkey')) + ) + op.create_table('Parameter', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('standard_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calculated', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Parameter_pkey')) + ) + op.create_table('ParameterUnit', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('alternate_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ParameterUnit_pkey')) + ) + op.create_table('DataSourceType', + sa.Column('source_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('DataSourceType_pkey')) + ) + op.create_table('Contact', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('first_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('last_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('email', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('affiliation', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('Contact_pkey')) + ) + op.create_table('SourceType', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('SourceType_pkey')) + ) + op.create_table('UltimateRecord', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UltimateRecord_pkey')) + ) + op.create_table('ResourceCounterfactual', + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('counterfactual_description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('animal_bedding_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('animal_bedding_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('animal_feed_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('animal_feed_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('bioelectricty_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('bioelectricty_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('burn_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('burn_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('compost_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('compost_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('landfill_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('landfill_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('counterfactual_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceCounterfactual_pkey')) + ) + op.create_table('BaseEntity', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('BaseEntity_pkey')) + ) + op.create_table('PrimaryCrop', + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PrimaryCrop_pkey')) + ) + op.create_table('UsdaStatisticCategory', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaStatisticCategory_pkey')) + ) + op.create_table('PreparedSample', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prep_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prep_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('preparer_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('PreparedSample_pkey')) + ) + op.create_table('ResourceAvailability', + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('from_month', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('to_month', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('year_round', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ResourceAvailability_pkey')) + ) + op.create_table('UsdaMarketRecord', + sa.Column('report_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('report_begin_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('report_end_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('report_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('market_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('market_type_catagory', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('grp', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('market_catagory_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('class_', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('grade', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('variety', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('protein_pct', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('application', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('pkg', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('sale_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('price_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('freight', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('trans_mode', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('UsdaMarketRecord_pkey')) + ) + op.drop_table('xrf_record') + op.drop_table('xrd_record') + op.drop_table('usda_term_map') + op.drop_table('usda_survey_record') + op.drop_table('usda_survey_program') + op.drop_table('usda_statistic_category') + op.drop_table('usda_market_report') + op.drop_table('usda_market_record') + op.drop_table('usda_domain') + op.drop_table('usda_commodity') + op.drop_table('usda_census_record') + op.drop_table('unit') + op.drop_table('ultimate_record') + op.drop_table('strain') + op.drop_table('source_type') + op.drop_table('soil_type') + op.drop_table('rgb_record') + op.drop_table('resource_usda_commodity_map') + op.drop_table('resource_subclass') + op.drop_table('resource_morphology') + op.drop_table('resource_counterfactual') + op.drop_table('resource_class') + op.drop_table('resource_availability') + op.drop_table('resource') + op.drop_table('proximate_record') + op.drop_table('provider') + op.drop_table('processing_method') + op.drop_table('primary_crop') + op.drop_table('pretreatment_record') + op.drop_table('prepared_sample') + op.drop_table('preparation_method_abbreviation') + op.drop_table('preparation_method') + op.drop_table('polygon') + op.drop_table('physical_characteristic') + op.drop_table('parameter_unit') + op.drop_table('parameter_category_parameter') + op.drop_table('parameter_category') + op.drop_table('parameter') + op.drop_table('observation') + op.drop_table('method_standard') + op.drop_table('method_category') + op.drop_table('method_abbrev') + op.drop_table('method') + op.drop_table('lookup_base') + op.drop_table('location_soil_type') + op.drop_table('location_resolution') + op.drop_table('location_address') + op.drop_table('lineage_group') + op.drop_table('landiq_record') + op.drop_table('icp_record') + op.drop_table('harvest_method') + op.drop_table('geography') + op.drop_table('gasification_record') + op.drop_table('ftnir_record') + op.drop_table('file_object_metadata') + op.drop_table('field_storage_method') + op.drop_table('field_sample_condition') + op.drop_table('field_sample') + op.drop_table('fermentation_record') + op.drop_table('experiment_prepared_sample') + op.drop_table('experiment_method') + op.drop_table('experiment_equipment') + op.drop_table('experiment_analysis') + op.drop_table('experiment') + op.drop_table('etl_run') + op.drop_table('equipment') + op.drop_table('entity_lineage') + op.drop_table('dimension_type') + op.drop_table('dataset') + op.drop_table('data_source_type') + op.drop_table('data_source') + op.drop_table('contact') + op.drop_table('compositional_record') + op.drop_table('collection_method') + op.drop_table('calorimetry_record') + op.drop_table('billion_ton2023_record') + op.drop_table('base_entity') + op.drop_table('autoclave_record') + op.drop_table('analysis_type') + op.drop_table('aim2_record_base') + op.drop_table('aim1_record_base') + op.drop_table('ag_treatment') + # ### end Alembic commands ### diff --git a/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py b/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py new file mode 100644 index 00000000..c1db3ff6 --- /dev/null +++ b/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py @@ -0,0 +1,32 @@ +"""adding a test to landiqrecord + +Revision ID: b838c837616b +Revises: 42618fe6b09b +Create Date: 2025-12-08 22:33:34.608783 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'b838c837616b' +down_revision: Union[str, Sequence[str], None] = '42618fe6b09b' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('landiq_record', sa.Column('test', sa.Text(), nullable=True)) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column('landiq_record', 'test') + # ### end Alembic commands ### diff --git a/pixi.toml b/pixi.toml index bd7e5fdd..4f48ca56 100644 --- a/pixi.toml +++ b/pixi.toml @@ -183,6 +183,8 @@ migrate = { cmd = [ "start-services", ] } +update-schema = { cmd = "python src/ca_biositing/datamodels/utils/orchestrate_schema_update.py", description = "Orchestrate schema update: generate models, rebuild services, and create migration." } + [tasks.qgis] depends-on = [{ task = "run-qgis", environment = "gis" }] diff --git a/src/ca_biositing/datamodels/README.md b/src/ca_biositing/datamodels/README.md index a363db01..75239724 100644 --- a/src/ca_biositing/datamodels/README.md +++ b/src/ca_biositing/datamodels/README.md @@ -9,13 +9,42 @@ etc.). The `ca_biositing.datamodels` package provides: -- **Database Models**: SQLModel classes representing database tables for - biomass, geographic locations, experiments, samples, and more +- **LinkML Schema**: The single source of truth for the data model, defined in + YAML. +- **Generated Database Models**: SQLModel classes automatically generated from + the LinkML schema. - **Database Configuration**: Database connection and session management - utilities + utilities. - **Model Configuration**: Shared configuration for model behavior using - Pydantic Settings -- **Type Safety**: Full type annotations for all models and fields + Pydantic Settings. +- **Type Safety**: Full type annotations for all models and fields. + +## Schema Management Workflow + +We use **LinkML** as the source of truth for our data schema. The workflow for +making schema changes is: + +1. **Modify LinkML Schema**: Edit the YAML files in + `src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/`. +2. **Update Schema**: Run the orchestration command to generate Python models, + rebuild services, and create a migration. + ```bash + pixi run update-schema -m "Description of changes" + ``` + This command performs the following steps: + - Cleans the generated models directory. + - Generates new SQLAlchemy/SQLModel classes from the LinkML schema. + - Rebuilds the Docker services to include the new code. + - Starts the services. + - Generates an Alembic migration script. +3. **Apply Migration**: Apply the changes to the database. + ```bash + pixi run migrate + ``` + +The generated Python models are saved in +`src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/`. **Do +not edit these files directly.** Always modify the LinkML schema and regenerate. ## Structure @@ -24,20 +53,16 @@ src/ca_biositing/datamodels/ ├── ca_biositing/ │ └── datamodels/ │ ├── __init__.py # Package initialization and version -│ ├── biomass.py # Biomass-related models (FieldSample, Biomass, etc.) │ ├── config.py # Model configuration │ ├── database.py # Database connection setup -│ ├── data_and_references.py # Data and reference models -│ ├── experiments_analysis.py # Experiment analysis models -│ ├── external_datasets.py # External dataset models -│ ├── geographic_locations.py # Geographic location models -│ ├── metadata_samples.py # Sample metadata models -│ ├── organizations.py # Organization models -│ ├── people_contacts.py # People and contact models -│ ├── sample_preprocessing.py # Sample preprocessing models -│ ├── specific_aalysis_results.py # Analysis results models -│ ├── user.py # User models -│ └── templates/ # Model templates for new tables +│ ├── linkml/ # LinkML schema source files +│ │ ├── ca_biositing.yaml # Main schema entrypoint +│ │ └── modules/ # Modular schema definitions +│ ├── schemas/ +│ │ └── generated/ # Generated SQLModel classes (DO NOT EDIT) +│ └── utils/ # Schema management scripts +│ ├── generate_sqla.py # Script to generate models from LinkML +│ └── orchestrate_schema_update.py # Orchestration script ├── tests/ │ ├── __init__.py │ ├── conftest.py # Pytest fixtures and configuration @@ -76,32 +101,34 @@ pip install -e . ### Importing Models +Models are generated into separate modules based on the LinkML schema structure. +You should import them from `ca_biositing.datamodels.schemas.generated`. + ```python -from ca_biositing.datamodels.biomass import ( - Biomass, - FieldSample, - BiomassType, - PrimaryProduct +from ca_biositing.datamodels.schemas.generated.resource_information import ( + Resource, + ResourceClass, + PrimaryCrop ) -from ca_biositing.datamodels.geographic_locations import ( - GeographicLocation, - City, - State +from ca_biositing.datamodels.schemas.generated.field_sampling import FieldSample +from ca_biositing.datamodels.schemas.generated.places import ( + Geography, + LocationAddress ) # Create a model instance sample = FieldSample( - biomass_id=1, - sample_name="Sample-001", - amount_collected_kg=50.5 + name="Sample-001", + resource_id=1, + amount_collected=50.5 ) ``` ### Database Operations ```python -from sqlmodel import Session, create_engine -from ca_biositing.datamodels.biomass import Biomass +from sqlmodel import Session, create_engine, select +from ca_biositing.datamodels.schemas.generated.resource_information import Resource # Create engine and session engine = create_engine("postgresql://user:pass@localhost/dbname") @@ -109,11 +136,12 @@ engine = create_engine("postgresql://user:pass@localhost/dbname") # Use with SQLModel Session with Session(engine) as session: # Query models - biomass_items = session.query(Biomass).all() + statement = select(Resource) + resources = session.exec(statement).all() # Add new records - new_biomass = Biomass(biomass_name="Corn Stover") - session.add(new_biomass) + new_resource = Resource(name="Corn Stover") + session.add(new_resource) session.commit() ``` @@ -142,42 +170,49 @@ pixi run pytest src/ca_biositing/datamodels --cov=ca_biositing.datamodels --cov- See `tests/README.md` for detailed information about the test suite. -## Model Categories +## Model Categories (LinkML Modules) + +The schema is organized into modular YAML files in `linkml/modules/`. Each +module generates a corresponding Python file in `schemas/generated/`. -### Biomass Models (`biomass.py`) +### Core & Infrastructure -Core models for biomass entities, field samples, and related data: +- **`core.yaml`**: Base classes and shared types used across the schema. +- **`infrastructure.yaml`**: Infrastructure-related entities (e.g., + `InfrastructureType`, `Infrastructure`). +- **`places.yaml`**: Geographic location models (`GeographicLocation`, `City`, + `State`, `County`, `Region`, `FIPS`). +- **`people.yaml`**: People and contact information (`Person`, `ContactInfo`, + `Role`). +- **`data_sources_metadata.yaml`**: Metadata about data sources and references + (`DataSource`, `Reference`). -- `Biomass`: Core biomass entity -- `FieldSample`: Sample metadata collected in the field -- `BiomassType`: Lookup table for biomass types -- `PrimaryProduct`: Lookup table for primary products -- `BiomassAvailability`: Seasonal and quantitative availability -- `BiomassQuality`: Qualitative attributes -- `BiomassPrice`: Pricing information -- `HarvestMethod`, `CollectionMethod`, `FieldStorage`: Lookup tables +### Biomass & Sampling -### Geographic Models (`geographic_locations.py`) +- **`resource_information.yaml`**: Core biomass entities (`Biomass`, + `BiomassType`, `PrimaryProduct`, `BiomassAvailability`, `BiomassQuality`, + `BiomassPrice`). +- **`field_sampling.yaml`**: Field sampling data (`FieldSample`, + `HarvestMethod`, `CollectionMethod`, `FieldStorage`). +- **`sample_preparation.yaml`**: Sample preprocessing steps + (`SamplePreprocessing`, `PreprocessingMethod`). +- **`lineage.yaml`**: Tracking sample lineage (`SampleLineage`). -Models for location data (can be anonymized): +### Experiments & Analysis -- `GeographicLocation`: Main geographic location entity -- `StreetAddress`, `City`, `Zip`, `County`, `State`, `Region`: Location - components -- `FIPS`: FIPS codes -- `LocationResolution`: Resolution types (GPS, county, etc.) +- **`experiment_equipment.yaml`**: Experimental setup and equipment + (`Experiment`, `Equipment`). +- **`methods_parameters_units.yaml`**: Methods, parameters, and units (`Method`, + `Parameter`, `Unit`). +- **`general_analysis.yaml`**: General analysis results (`AnalysisResult`, + `AnalysisType`). +- **`aim1_records.yaml`**: Specific records for Aim 1 (`Aim1Record`). +- **`aim2_records.yaml`**: Specific records for Aim 2 (`Aim2Record`). -### Other Model Files +### External Data -- `data_and_references.py`: Data sources and references -- `experiments_analysis.py`: Experimental analysis data -- `external_datasets.py`: External dataset integration -- `metadata_samples.py`: Sample metadata -- `organizations.py`: Organization information -- `people_contacts.py`: People and contact information -- `sample_preprocessing.py`: Sample preprocessing steps -- `specific_aalysis_results.py`: Analysis results -- `user.py`: User management +- **`external_data.yaml`**: Integration with external datasets + (`ExternalDataset`). ## Dependencies @@ -201,16 +236,12 @@ pixi run pre-commit run --files src/ca_biositing/datamodels/**/* ### Adding New Models -1. Create or modify model files in `ca_biositing/datamodels/` -2. Follow the existing patterns (use SQLModel, Field definitions, type hints) -3. Add corresponding tests in `tests/` -4. Generate Alembic migrations if needed (see main project documentation) -5. Run tests and pre-commit checks - -### Model Templates - -Template files are available in `ca_biositing/datamodels/templates/` to help -create new models following the project conventions. +1. **Modify LinkML**: Add the new class to the appropriate YAML file in + `linkml/modules/`. +2. **Update Schema**: Run `pixi run update-schema -m "Add new model"`. +3. **Verify**: Check the generated file in `schemas/generated/` to ensure it + looks correct. +4. **Apply**: Run `pixi run migrate` to update the database. ## Package Information diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml index 519632c0..cfca5168 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml @@ -140,6 +140,7 @@ classes: - acres - version - note + - test BillionTon2023Record: is_a: BaseEntity @@ -423,3 +424,7 @@ slots: geom: range: string description: Geometry (WKT or similar). + + test: + range: string + description: A test slot. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py index 9893aae0..6a5fd758 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -96,7 +96,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -115,7 +115,7 @@ class ExperimentMethod(Base): """ Link between Experiment and Method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -134,7 +134,7 @@ class ExperimentEquipment(Base): """ Link between Experiment and Equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -153,7 +153,7 @@ class ExperimentAnalysis(Base): """ Link between Experiment and AnalysisType. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -172,7 +172,7 @@ class ExperimentPreparedSample(Base): """ Link between Experiment and PreparedSample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -191,7 +191,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -210,7 +210,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -231,7 +231,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -249,7 +249,7 @@ class Aim1RecordBase(BaseEntity): """ """ - __tablename__ = 'Aim1RecordBase' + __tablename__ = 'aim1_record_base' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -285,7 +285,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -310,7 +310,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -342,7 +342,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -367,7 +367,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) @@ -403,7 +403,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -437,7 +437,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -462,7 +462,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -495,7 +495,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -520,7 +520,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -545,7 +545,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -570,7 +570,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -600,7 +600,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -625,7 +625,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -657,7 +657,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -682,7 +682,7 @@ class PreparedSample(BaseEntity): """ Sample that has been prepared. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -714,7 +714,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -749,7 +749,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -781,7 +781,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -808,7 +808,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -833,7 +833,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -858,7 +858,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -890,7 +890,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -916,7 +916,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -947,7 +947,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -972,7 +972,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -997,7 +997,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1023,7 +1023,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -1055,7 +1055,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -1098,7 +1098,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -1142,7 +1142,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1167,7 +1167,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1192,7 +1192,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1217,7 +1217,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1242,7 +1242,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1273,7 +1273,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1298,7 +1298,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1323,7 +1323,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1354,7 +1354,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -1382,7 +1382,7 @@ class ProximateRecord(Aim1RecordBase): """ Proximate analysis record. """ - __tablename__ = 'ProximateRecord' + __tablename__ = 'proximate_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1418,7 +1418,7 @@ class UltimateRecord(Aim1RecordBase): """ Ultimate analysis record. """ - __tablename__ = 'UltimateRecord' + __tablename__ = 'ultimate_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1454,7 +1454,7 @@ class CompositionalRecord(Aim1RecordBase): """ Compositional analysis record. """ - __tablename__ = 'CompositionalRecord' + __tablename__ = 'compositional_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1490,7 +1490,7 @@ class IcpRecord(Aim1RecordBase): """ ICP analysis record. """ - __tablename__ = 'IcpRecord' + __tablename__ = 'icp_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1526,7 +1526,7 @@ class XrfRecord(Aim1RecordBase): """ XRF analysis record. """ - __tablename__ = 'XrfRecord' + __tablename__ = 'xrf_record' maybe_wavelength_nm = Column(Numeric()) maybe_intensity = Column(Numeric()) @@ -1566,7 +1566,7 @@ class XrdRecord(Aim1RecordBase): """ XRD analysis record. """ - __tablename__ = 'XrdRecord' + __tablename__ = 'xrd_record' maybe_scan_low_nm = Column(Integer()) maybe_scan_high_nm = Column(Integer()) @@ -1604,7 +1604,7 @@ class CalorimetryRecord(Aim1RecordBase): """ Calorimetry analysis record. """ - __tablename__ = 'CalorimetryRecord' + __tablename__ = 'calorimetry_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1640,7 +1640,7 @@ class FtnirRecord(Aim1RecordBase): """ FT-NIR analysis record. """ - __tablename__ = 'FtnirRecord' + __tablename__ = 'ftnir_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1676,7 +1676,7 @@ class RgbRecord(Aim1RecordBase): """ RGB analysis record. """ - __tablename__ = 'RgbRecord' + __tablename__ = 'rgb_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py index e212029e..b282c9da 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -96,7 +96,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -115,7 +115,7 @@ class ExperimentMethod(Base): """ Link between Experiment and Method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -134,7 +134,7 @@ class ExperimentEquipment(Base): """ Link between Experiment and Equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -153,7 +153,7 @@ class ExperimentAnalysis(Base): """ Link between Experiment and AnalysisType. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -172,7 +172,7 @@ class ExperimentPreparedSample(Base): """ Link between Experiment and PreparedSample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -191,7 +191,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -210,7 +210,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -231,7 +231,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -249,7 +249,7 @@ class Aim2RecordBase(BaseEntity): """ """ - __tablename__ = 'Aim2RecordBase' + __tablename__ = 'aim2_record_base' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -285,7 +285,7 @@ class Strain(LookupBase): """ Strain used in fermentation. """ - __tablename__ = 'Strain' + __tablename__ = 'strain' parent_strain_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -311,7 +311,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -336,7 +336,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -368,7 +368,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -393,7 +393,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) @@ -429,7 +429,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -463,7 +463,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -488,7 +488,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -521,7 +521,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -546,7 +546,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -571,7 +571,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -596,7 +596,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -626,7 +626,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -651,7 +651,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -683,7 +683,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -708,7 +708,7 @@ class PreparedSample(BaseEntity): """ Sample that has been prepared. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -740,7 +740,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -775,7 +775,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -807,7 +807,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -834,7 +834,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -859,7 +859,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -884,7 +884,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -916,7 +916,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -942,7 +942,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -973,7 +973,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -998,7 +998,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1023,7 +1023,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1049,7 +1049,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -1081,7 +1081,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -1124,7 +1124,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -1168,7 +1168,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1193,7 +1193,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1218,7 +1218,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1243,7 +1243,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1268,7 +1268,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1299,7 +1299,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1324,7 +1324,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1349,7 +1349,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1380,7 +1380,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -1408,7 +1408,7 @@ class PretreatmentRecord(Aim2RecordBase): """ Pretreatment record. """ - __tablename__ = 'PretreatmentRecord' + __tablename__ = 'pretreatment_record' pretreatment_method_id = Column(Integer()) eh_method_id = Column(Integer()) @@ -1450,7 +1450,7 @@ class FermentationRecord(Aim2RecordBase): """ Fermentation record. """ - __tablename__ = 'FermentationRecord' + __tablename__ = 'fermentation_record' strain_id = Column(Integer()) pretreatment_method_id = Column(Integer()) @@ -1495,7 +1495,7 @@ class GasificationRecord(Aim2RecordBase): """ Gasification record. """ - __tablename__ = 'GasificationRecord' + __tablename__ = 'gasification_record' feedstock_mass = Column(Numeric()) bed_temperature = Column(Numeric()) @@ -1534,7 +1534,7 @@ class AutoclaveRecord(Aim2RecordBase): """ Autoclave record. """ - __tablename__ = 'AutoclaveRecord' + __tablename__ = 'autoclave_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py index 31e8b6fb..f860432f 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py @@ -13,7 +13,7 @@ class Dataset(Base): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -36,7 +36,7 @@ class Observation(Base): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -63,7 +63,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -84,7 +84,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -104,7 +104,7 @@ class ParameterCategoryParameter(Base): """ Link between parameter and category. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -123,7 +123,7 @@ class ParameterUnit(Base): """ Link between parameter and alternate units. """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -142,7 +142,7 @@ class DimensionType(LookupBase): """ Type of dimension (e.g. timepoint, wavelength). """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -167,7 +167,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -192,7 +192,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -217,7 +217,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -250,7 +250,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for a method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -275,7 +275,7 @@ class MethodCategory(LookupBase): """ Category of a method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -300,7 +300,7 @@ class MethodStandard(LookupBase): """ Standard associated with a method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -325,7 +325,7 @@ class Parameter(BaseEntity): """ Parameter measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -355,7 +355,7 @@ class ParameterCategory(LookupBase): """ Category of a parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py index 44a65db4..b8968702 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py @@ -13,7 +13,7 @@ class RecordBase(Base): """ """ - __tablename__ = 'RecordBase' + __tablename__ = 'record_base' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -40,7 +40,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -61,7 +61,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -81,7 +81,7 @@ class Dataset(Base): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -104,7 +104,7 @@ class Observation(Base): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -131,7 +131,7 @@ class Geography(Base): """ Geographic region definition (e.g. county, state). """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -154,7 +154,7 @@ class Polygon(Base): """ Geospatial polygon definition. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -173,7 +173,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -194,7 +194,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -212,7 +212,7 @@ class ParameterCategoryParameter(Base): """ Link between parameter and category. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -231,7 +231,7 @@ class ParameterUnit(Base): """ Link between parameter and alternate units. """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -250,7 +250,7 @@ class ExperimentEquipment(Base): """ Link between experiment and equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -269,7 +269,7 @@ class ExperimentAnalysis(Base): """ Link between experiment and analysis type. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -288,7 +288,7 @@ class ExperimentPreparedSample(Base): """ Link between experiment and prepared sample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -307,7 +307,7 @@ class ExperimentMethod(Base): """ Link between experiment and method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -326,7 +326,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -345,7 +345,7 @@ class ProximateRecord(RecordBase): """ Proximate analysis record. """ - __tablename__ = 'ProximateRecord' + __tablename__ = 'proximate_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -377,7 +377,7 @@ class UltimateRecord(RecordBase): """ Ultimate analysis record. """ - __tablename__ = 'UltimateRecord' + __tablename__ = 'ultimate_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -409,7 +409,7 @@ class CompositionalRecord(RecordBase): """ Compositional analysis record. """ - __tablename__ = 'CompositionalRecord' + __tablename__ = 'compositional_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -441,7 +441,7 @@ class IcpRecord(RecordBase): """ ICP analysis record. """ - __tablename__ = 'IcpRecord' + __tablename__ = 'icp_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -473,7 +473,7 @@ class XrfRecord(RecordBase): """ XRF analysis record. """ - __tablename__ = 'XrfRecord' + __tablename__ = 'xrf_record' maybe_wavelength_nm = Column(Numeric()) maybe_intensity = Column(Numeric()) @@ -509,7 +509,7 @@ class XrdRecord(RecordBase): """ XRD analysis record. """ - __tablename__ = 'XrdRecord' + __tablename__ = 'xrd_record' maybe_scan_low_nm = Column(Integer()) maybe_scan_high_nm = Column(Integer()) @@ -543,7 +543,7 @@ class CalorimetryRecord(RecordBase): """ Calorimetry analysis record. """ - __tablename__ = 'CalorimetryRecord' + __tablename__ = 'calorimetry_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -575,7 +575,7 @@ class FtnirRecord(RecordBase): """ FT-NIR analysis record. """ - __tablename__ = 'FtnirRecord' + __tablename__ = 'ftnir_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -607,7 +607,7 @@ class RgbRecord(RecordBase): """ RGB analysis record. """ - __tablename__ = 'RgbRecord' + __tablename__ = 'rgb_record' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -639,7 +639,7 @@ class PretreatmentRecord(RecordBase): """ Pretreatment record. """ - __tablename__ = 'PretreatmentRecord' + __tablename__ = 'pretreatment_record' pretreatment_method = Column(Integer()) eh_method_id = Column(Integer()) @@ -678,7 +678,7 @@ class FermentationRecord(RecordBase): """ Fermentation record. """ - __tablename__ = 'FermentationRecord' + __tablename__ = 'fermentation_record' strain_id = Column(Integer()) pretreatement_method_id = Column(Integer()) @@ -720,7 +720,7 @@ class GasificationRecord(RecordBase): """ Gasification record. """ - __tablename__ = 'GasificationRecord' + __tablename__ = 'gasification_record' feedstock_mass = Column(Numeric()) bed_temperature = Column(Numeric()) @@ -756,7 +756,7 @@ class AutoclaveRecord(RecordBase): """ Autoclave record. """ - __tablename__ = 'AutoclaveRecord' + __tablename__ = 'autoclave_record' analyst_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -789,7 +789,7 @@ class DimensionType(LookupBase): """ Type of dimension (e.g. timepoint, wavelength). """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -814,7 +814,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -839,7 +839,7 @@ class LocationAddress(BaseEntity): """ Specific physical location. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -873,7 +873,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -898,7 +898,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -931,7 +931,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for a method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -956,7 +956,7 @@ class MethodCategory(LookupBase): """ Category of a method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -981,7 +981,7 @@ class MethodStandard(LookupBase): """ Standard associated with a method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1006,7 +1006,7 @@ class Parameter(BaseEntity): """ Parameter measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -1036,7 +1036,7 @@ class ParameterCategory(LookupBase): """ Category of a parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1061,7 +1061,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -1105,7 +1105,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1130,7 +1130,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1155,7 +1155,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1180,7 +1180,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1205,7 +1205,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1236,7 +1236,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1261,7 +1261,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1286,7 +1286,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1317,7 +1317,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -1345,7 +1345,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -1377,7 +1377,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1402,7 +1402,7 @@ class PreparedSample(BaseEntity): """ Sample prepared for analysis. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -1434,7 +1434,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -1466,7 +1466,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1492,7 +1492,7 @@ class Strain(LookupBase): """ Strain of organism. """ - __tablename__ = 'Strain' + __tablename__ = 'strain' parent_strain_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1518,7 +1518,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -1549,7 +1549,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1574,7 +1574,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1599,7 +1599,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1625,7 +1625,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -1657,7 +1657,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py index bbbb9a74..87fb054a 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -73,7 +73,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -96,7 +96,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -117,7 +117,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -135,7 +135,7 @@ class LineageGroup(Base): """ Grouping for lineage information. """ - __tablename__ = 'LineageGroup' + __tablename__ = 'lineage_group' id = Column(Integer(), primary_key=True, nullable=False ) etl_run_id = Column(Text()) @@ -154,7 +154,7 @@ class EntityLineage(Base): """ Lineage information for a specific entity. """ - __tablename__ = 'EntityLineage' + __tablename__ = 'entity_lineage' id = Column(Integer(), primary_key=True, nullable=False ) lineage_group_id = Column(Integer()) @@ -175,7 +175,7 @@ class EtlRun(Base): """ Information about an ETL run. """ - __tablename__ = 'EtlRun' + __tablename__ = 'etl_run' id = Column(Integer(), primary_key=True, nullable=False ) started_at = Column(DateTime()) @@ -198,7 +198,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -217,7 +217,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -236,7 +236,7 @@ class ExperimentMethod(Base): """ Link between Experiment and Method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -255,7 +255,7 @@ class ExperimentEquipment(Base): """ Link between Experiment and Equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -274,7 +274,7 @@ class ExperimentAnalysis(Base): """ Link between Experiment and AnalysisType. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -293,7 +293,7 @@ class ExperimentPreparedSample(Base): """ Link between Experiment and PreparedSample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -312,7 +312,7 @@ class Polygon(Base): """ Geospatial polygon. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -331,7 +331,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -362,7 +362,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -387,7 +387,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -412,7 +412,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -438,7 +438,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -470,7 +470,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -513,7 +513,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -557,7 +557,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -582,7 +582,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -607,7 +607,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -632,7 +632,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -657,7 +657,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -688,7 +688,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -713,7 +713,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -738,7 +738,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -769,7 +769,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -797,7 +797,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -831,7 +831,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -866,7 +866,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -898,7 +898,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -925,7 +925,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -950,7 +950,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -975,7 +975,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -1007,7 +1007,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1032,7 +1032,7 @@ class PreparedSample(BaseEntity): """ Sample that has been prepared. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -1064,7 +1064,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1089,7 +1089,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -1122,7 +1122,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1147,7 +1147,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1172,7 +1172,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1197,7 +1197,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -1227,7 +1227,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1252,7 +1252,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -1284,7 +1284,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1310,7 +1310,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1335,7 +1335,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -1367,7 +1367,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1392,7 +1392,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) @@ -1428,7 +1428,7 @@ class Aim1RecordBase(BaseEntity): """ """ - __tablename__ = 'Aim1RecordBase' + __tablename__ = 'aim1_record_base' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1464,7 +1464,7 @@ class Aim2RecordBase(BaseEntity): """ """ - __tablename__ = 'Aim2RecordBase' + __tablename__ = 'aim2_record_base' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1500,7 +1500,7 @@ class Strain(LookupBase): """ Strain used in fermentation. """ - __tablename__ = 'Strain' + __tablename__ = 'strain' parent_strain_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1526,7 +1526,7 @@ class UsdaDomain(LookupBase): """ USDA domain. """ - __tablename__ = 'UsdaDomain' + __tablename__ = 'usda_domain' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1551,7 +1551,7 @@ class UsdaStatisticCategory(LookupBase): """ USDA statistic category. """ - __tablename__ = 'UsdaStatisticCategory' + __tablename__ = 'usda_statistic_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1576,7 +1576,7 @@ class UsdaSurveyProgram(LookupBase): """ USDA survey program. """ - __tablename__ = 'UsdaSurveyProgram' + __tablename__ = 'usda_survey_program' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1601,7 +1601,7 @@ class UsdaCommodity(LookupBase): """ USDA commodity. """ - __tablename__ = 'UsdaCommodity' + __tablename__ = 'usda_commodity' usda_source = Column(Text()) usda_code = Column(Text()) @@ -1629,7 +1629,7 @@ class UsdaTermMap(BaseEntity): """ Mapping of raw terms to USDA commodities. """ - __tablename__ = 'UsdaTermMap' + __tablename__ = 'usda_term_map' source_system = Column(Text()) source_context = Column(Text()) @@ -1661,7 +1661,7 @@ class ResourceUsdaCommodityMap(BaseEntity): """ Mapping between resources/crops and USDA commodities. """ - __tablename__ = 'ResourceUsdaCommodityMap' + __tablename__ = 'resource_usda_commodity_map' resource_id = Column(Integer()) primary_crop_id = Column(Integer()) @@ -1692,7 +1692,7 @@ class UsdaCensusRecord(BaseEntity): """ USDA census record. """ - __tablename__ = 'UsdaCensusRecord' + __tablename__ = 'usda_census_record' dataset_id = Column(Integer()) geoid = Column(Text()) @@ -1724,7 +1724,7 @@ class UsdaSurveyRecord(BaseEntity): """ USDA survey record. """ - __tablename__ = 'UsdaSurveyRecord' + __tablename__ = 'usda_survey_record' dataset_id = Column(Integer()) geoid = Column(Text()) @@ -1759,7 +1759,7 @@ class UsdaMarketReport(BaseEntity): """ USDA market report. """ - __tablename__ = 'UsdaMarketReport' + __tablename__ = 'usda_market_report' slug_id = Column(Integer()) slug_name = Column(Text()) @@ -1793,7 +1793,7 @@ class UsdaMarketRecord(BaseEntity): """ USDA market record. """ - __tablename__ = 'UsdaMarketRecord' + __tablename__ = 'usda_market_record' report_id = Column(Integer()) dataset_id = Column(Integer()) @@ -1839,7 +1839,7 @@ class LandiqRecord(BaseEntity): """ LandIQ record. """ - __tablename__ = 'LandiqRecord' + __tablename__ = 'landiq_record' dataset_id = Column(Integer()) polygon_id = Column(Integer()) @@ -1852,6 +1852,7 @@ class LandiqRecord(BaseEntity): acres = Column(Float()) version = Column(Text()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1860,7 +1861,7 @@ class LandiqRecord(BaseEntity): def __repr__(self): - return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1876,7 +1877,7 @@ class BillionTon2023Record(BaseEntity): """ Billion Ton 2023 record. """ - __tablename__ = 'BillionTon2023Record' + __tablename__ = 'billion_ton2023_record' subclass_id = Column(Integer()) resource_id = Column(Integer()) @@ -1916,7 +1917,7 @@ class ProximateRecord(Aim1RecordBase): """ Proximate analysis record. """ - __tablename__ = 'ProximateRecord' + __tablename__ = 'proximate_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1952,7 +1953,7 @@ class UltimateRecord(Aim1RecordBase): """ Ultimate analysis record. """ - __tablename__ = 'UltimateRecord' + __tablename__ = 'ultimate_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -1988,7 +1989,7 @@ class CompositionalRecord(Aim1RecordBase): """ Compositional analysis record. """ - __tablename__ = 'CompositionalRecord' + __tablename__ = 'compositional_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -2024,7 +2025,7 @@ class IcpRecord(Aim1RecordBase): """ ICP analysis record. """ - __tablename__ = 'IcpRecord' + __tablename__ = 'icp_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -2060,7 +2061,7 @@ class XrfRecord(Aim1RecordBase): """ XRF analysis record. """ - __tablename__ = 'XrfRecord' + __tablename__ = 'xrf_record' maybe_wavelength_nm = Column(Numeric()) maybe_intensity = Column(Numeric()) @@ -2100,7 +2101,7 @@ class XrdRecord(Aim1RecordBase): """ XRD analysis record. """ - __tablename__ = 'XrdRecord' + __tablename__ = 'xrd_record' maybe_scan_low_nm = Column(Integer()) maybe_scan_high_nm = Column(Integer()) @@ -2138,7 +2139,7 @@ class CalorimetryRecord(Aim1RecordBase): """ Calorimetry analysis record. """ - __tablename__ = 'CalorimetryRecord' + __tablename__ = 'calorimetry_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -2174,7 +2175,7 @@ class FtnirRecord(Aim1RecordBase): """ FT-NIR analysis record. """ - __tablename__ = 'FtnirRecord' + __tablename__ = 'ftnir_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -2210,7 +2211,7 @@ class RgbRecord(Aim1RecordBase): """ RGB analysis record. """ - __tablename__ = 'RgbRecord' + __tablename__ = 'rgb_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) @@ -2246,7 +2247,7 @@ class PretreatmentRecord(Aim2RecordBase): """ Pretreatment record. """ - __tablename__ = 'PretreatmentRecord' + __tablename__ = 'pretreatment_record' pretreatment_method_id = Column(Integer()) eh_method_id = Column(Integer()) @@ -2288,7 +2289,7 @@ class FermentationRecord(Aim2RecordBase): """ Fermentation record. """ - __tablename__ = 'FermentationRecord' + __tablename__ = 'fermentation_record' strain_id = Column(Integer()) pretreatment_method_id = Column(Integer()) @@ -2333,7 +2334,7 @@ class GasificationRecord(Aim2RecordBase): """ Gasification record. """ - __tablename__ = 'GasificationRecord' + __tablename__ = 'gasification_record' feedstock_mass = Column(Numeric()) bed_temperature = Column(Numeric()) @@ -2372,7 +2373,7 @@ class AutoclaveRecord(Aim2RecordBase): """ Autoclave record. """ - __tablename__ = 'AutoclaveRecord' + __tablename__ = 'autoclave_record' dataset_id = Column(Integer()) experiment_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py index 1f2a5b30..20ba55a2 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py index e8ad5281..48fe18d7 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -98,7 +98,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -116,7 +116,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -135,7 +135,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -154,7 +154,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -173,7 +173,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -208,7 +208,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -240,7 +240,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -267,7 +267,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -292,7 +292,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -317,7 +317,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -351,7 +351,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -382,7 +382,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -407,7 +407,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -432,7 +432,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -458,7 +458,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -490,7 +490,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -533,7 +533,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -558,7 +558,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -591,7 +591,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -616,7 +616,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -641,7 +641,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -666,7 +666,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -696,7 +696,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -721,7 +721,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -765,7 +765,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -790,7 +790,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -815,7 +815,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -840,7 +840,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -865,7 +865,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -896,7 +896,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -921,7 +921,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -946,7 +946,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -977,7 +977,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py index 542f4cd0..3f2ab322 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py @@ -13,7 +13,7 @@ class ExperimentMethod(Base): """ Link between Experiment and Method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -32,7 +32,7 @@ class ExperimentEquipment(Base): """ Link between Experiment and Equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -51,7 +51,7 @@ class ExperimentAnalysis(Base): """ Link between Experiment and AnalysisType. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -70,7 +70,7 @@ class ExperimentPreparedSample(Base): """ Link between Experiment and PreparedSample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -89,7 +89,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -110,7 +110,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -130,7 +130,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -153,7 +153,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -172,7 +172,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -191,7 +191,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -212,7 +212,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -230,7 +230,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -249,7 +249,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -281,7 +281,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -307,7 +307,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -341,7 +341,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -366,7 +366,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -399,7 +399,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -424,7 +424,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -449,7 +449,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -474,7 +474,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -504,7 +504,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -529,7 +529,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -573,7 +573,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -598,7 +598,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -623,7 +623,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -648,7 +648,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -673,7 +673,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -704,7 +704,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -729,7 +729,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -754,7 +754,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -785,7 +785,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -813,7 +813,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -845,7 +845,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -870,7 +870,7 @@ class PreparedSample(BaseEntity): """ Sample that has been prepared. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -902,7 +902,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -937,7 +937,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -969,7 +969,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -996,7 +996,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1021,7 +1021,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1046,7 +1046,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -1077,7 +1077,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1102,7 +1102,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1127,7 +1127,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1153,7 +1153,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -1185,7 +1185,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -1228,7 +1228,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1253,7 +1253,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -1285,7 +1285,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1310,7 +1310,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py index c34d8d9a..4d5b8097 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py @@ -13,7 +13,7 @@ class ExperimentEquipment(Base): """ Link between experiment and equipment. """ - __tablename__ = 'ExperimentEquipment' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -32,7 +32,7 @@ class ExperimentAnalysis(Base): """ Link between experiment and analysis type. """ - __tablename__ = 'ExperimentAnalysis' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -51,7 +51,7 @@ class ExperimentPreparedSample(Base): """ Link between experiment and prepared sample. """ - __tablename__ = 'ExperimentPreparedSample' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -70,7 +70,7 @@ class ExperimentMethod(Base): """ Link between experiment and method. """ - __tablename__ = 'ExperimentMethod' + __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) experiment_id = Column(Integer()) @@ -89,7 +89,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -110,7 +110,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -130,7 +130,7 @@ class Geography(Base): """ Geographic region definition (e.g. county, state). """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -153,7 +153,7 @@ class Polygon(Base): """ Geospatial polygon definition. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -172,7 +172,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -193,7 +193,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -211,7 +211,7 @@ class ParameterCategoryParameter(Base): """ Link between parameter and category. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -230,7 +230,7 @@ class ParameterUnit(Base): """ Link between parameter and alternate units. """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -249,7 +249,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -268,7 +268,7 @@ class Dataset(Base): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -291,7 +291,7 @@ class Observation(Base): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' id = Column(Integer(), primary_key=True, nullable=False ) dataset_id = Column(Integer()) @@ -318,7 +318,7 @@ class Experiment(BaseEntity): """ Experiment definition. """ - __tablename__ = 'Experiment' + __tablename__ = 'experiment' analyst_id = Column(Integer()) exper_start_date = Column(Date()) @@ -350,7 +350,7 @@ class Equipment(LookupBase): """ Equipment used in experiments. """ - __tablename__ = 'Equipment' + __tablename__ = 'equipment' equipment_location_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -376,7 +376,7 @@ class Strain(LookupBase): """ Strain of organism. """ - __tablename__ = 'Strain' + __tablename__ = 'strain' parent_strain_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -402,7 +402,7 @@ class LocationAddress(BaseEntity): """ Specific physical location. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -436,7 +436,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -461,7 +461,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -494,7 +494,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for a method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -519,7 +519,7 @@ class MethodCategory(LookupBase): """ Category of a method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -544,7 +544,7 @@ class MethodStandard(LookupBase): """ Standard associated with a method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -569,7 +569,7 @@ class Parameter(BaseEntity): """ Parameter measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -599,7 +599,7 @@ class ParameterCategory(LookupBase): """ Category of a parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -624,7 +624,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -655,7 +655,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -680,7 +680,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -705,7 +705,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -731,7 +731,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -763,7 +763,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -806,7 +806,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -850,7 +850,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -875,7 +875,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -900,7 +900,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -925,7 +925,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -950,7 +950,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -981,7 +981,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1006,7 +1006,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1031,7 +1031,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1062,7 +1062,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -1090,7 +1090,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -1122,7 +1122,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1147,7 +1147,7 @@ class PreparedSample(BaseEntity): """ Sample prepared for analysis. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -1179,7 +1179,7 @@ class DimensionType(LookupBase): """ Type of dimension (e.g. timepoint, wavelength). """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1204,7 +1204,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py index 16cf80f9..c1e3bad5 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py @@ -13,7 +13,7 @@ class Polygon(Base): """ Geospatial polygon. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -32,7 +32,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -53,7 +53,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -73,7 +73,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -92,7 +92,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -111,7 +111,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -134,7 +134,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -153,7 +153,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -174,7 +174,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -192,7 +192,7 @@ class UsdaDomain(LookupBase): """ USDA domain. """ - __tablename__ = 'UsdaDomain' + __tablename__ = 'usda_domain' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -217,7 +217,7 @@ class UsdaStatisticCategory(LookupBase): """ USDA statistic category. """ - __tablename__ = 'UsdaStatisticCategory' + __tablename__ = 'usda_statistic_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -242,7 +242,7 @@ class UsdaSurveyProgram(LookupBase): """ USDA survey program. """ - __tablename__ = 'UsdaSurveyProgram' + __tablename__ = 'usda_survey_program' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -267,7 +267,7 @@ class UsdaCommodity(LookupBase): """ USDA commodity. """ - __tablename__ = 'UsdaCommodity' + __tablename__ = 'usda_commodity' usda_source = Column(Text()) usda_code = Column(Text()) @@ -295,7 +295,7 @@ class UsdaTermMap(BaseEntity): """ Mapping of raw terms to USDA commodities. """ - __tablename__ = 'UsdaTermMap' + __tablename__ = 'usda_term_map' source_system = Column(Text()) source_context = Column(Text()) @@ -327,7 +327,7 @@ class ResourceUsdaCommodityMap(BaseEntity): """ Mapping between resources/crops and USDA commodities. """ - __tablename__ = 'ResourceUsdaCommodityMap' + __tablename__ = 'resource_usda_commodity_map' resource_id = Column(Integer()) primary_crop_id = Column(Integer()) @@ -358,7 +358,7 @@ class UsdaCensusRecord(BaseEntity): """ USDA census record. """ - __tablename__ = 'UsdaCensusRecord' + __tablename__ = 'usda_census_record' dataset_id = Column(Integer()) geoid = Column(Text()) @@ -390,7 +390,7 @@ class UsdaSurveyRecord(BaseEntity): """ USDA survey record. """ - __tablename__ = 'UsdaSurveyRecord' + __tablename__ = 'usda_survey_record' dataset_id = Column(Integer()) geoid = Column(Text()) @@ -425,7 +425,7 @@ class UsdaMarketReport(BaseEntity): """ USDA market report. """ - __tablename__ = 'UsdaMarketReport' + __tablename__ = 'usda_market_report' slug_id = Column(Integer()) slug_name = Column(Text()) @@ -459,7 +459,7 @@ class UsdaMarketRecord(BaseEntity): """ USDA market record. """ - __tablename__ = 'UsdaMarketRecord' + __tablename__ = 'usda_market_record' report_id = Column(Integer()) dataset_id = Column(Integer()) @@ -505,7 +505,7 @@ class LandiqRecord(BaseEntity): """ LandIQ record. """ - __tablename__ = 'LandiqRecord' + __tablename__ = 'landiq_record' dataset_id = Column(Integer()) polygon_id = Column(Integer()) @@ -518,6 +518,7 @@ class LandiqRecord(BaseEntity): acres = Column(Float()) version = Column(Text()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -526,7 +527,7 @@ class LandiqRecord(BaseEntity): def __repr__(self): - return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -542,7 +543,7 @@ class BillionTon2023Record(BaseEntity): """ Billion Ton 2023 record. """ - __tablename__ = 'BillionTon2023Record' + __tablename__ = 'billion_ton2023_record' subclass_id = Column(Integer()) resource_id = Column(Integer()) @@ -582,7 +583,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -617,7 +618,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -649,7 +650,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -676,7 +677,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -701,7 +702,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -726,7 +727,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -751,7 +752,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -784,7 +785,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -809,7 +810,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -834,7 +835,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -859,7 +860,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -889,7 +890,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -914,7 +915,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -939,7 +940,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -971,7 +972,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -996,7 +997,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) @@ -1032,7 +1033,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -1066,7 +1067,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -1097,7 +1098,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1122,7 +1123,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1147,7 +1148,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1173,7 +1174,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -1205,7 +1206,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -1248,7 +1249,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -1292,7 +1293,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1317,7 +1318,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1342,7 +1343,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1367,7 +1368,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1392,7 +1393,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1423,7 +1424,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1448,7 +1449,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1473,7 +1474,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1504,7 +1505,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py index f941eeae..6fed28ad 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -98,7 +98,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -116,7 +116,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -135,7 +135,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -154,7 +154,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -173,7 +173,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -217,7 +217,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -242,7 +242,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -267,7 +267,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -292,7 +292,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -317,7 +317,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -348,7 +348,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -373,7 +373,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -398,7 +398,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -429,7 +429,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -457,7 +457,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -491,7 +491,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -522,7 +522,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -547,7 +547,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -572,7 +572,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -598,7 +598,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -630,7 +630,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -673,7 +673,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -708,7 +708,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -740,7 +740,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -767,7 +767,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -792,7 +792,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -817,7 +817,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -842,7 +842,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -875,7 +875,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -900,7 +900,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -925,7 +925,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -950,7 +950,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -980,7 +980,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py index bffb89f8..5b4bbd8c 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -98,7 +98,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -116,7 +116,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -135,7 +135,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -154,7 +154,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -173,7 +173,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -198,7 +198,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -230,7 +230,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -255,7 +255,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) @@ -291,7 +291,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -326,7 +326,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -358,7 +358,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -385,7 +385,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -410,7 +410,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -435,7 +435,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -469,7 +469,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -500,7 +500,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -525,7 +525,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -550,7 +550,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -576,7 +576,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -608,7 +608,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -651,7 +651,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -676,7 +676,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -709,7 +709,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -734,7 +734,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -759,7 +759,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -784,7 +784,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -814,7 +814,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -839,7 +839,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -883,7 +883,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -908,7 +908,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -933,7 +933,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -958,7 +958,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -983,7 +983,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1014,7 +1014,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1039,7 +1039,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1064,7 +1064,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1095,7 +1095,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py index acb4d3c4..2de38d94 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py @@ -13,7 +13,7 @@ class Geography(Base): """ Geographic region definition (e.g. county, state). """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -36,7 +36,7 @@ class Polygon(Base): """ Geospatial polygon definition. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -55,7 +55,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -76,7 +76,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -96,7 +96,7 @@ class LocationAddress(BaseEntity): """ Specific physical location. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py index 76adbad5..20dfafc8 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py @@ -13,7 +13,7 @@ class InfrastructureBiodieselPlants(Base): """ Biodiesel plants infrastructure. """ - __tablename__ = 'InfrastructureBiodieselPlants' + __tablename__ = 'infrastructure_biodiesel_plants' biodiesel_plant_id = Column(Integer(), primary_key=True, nullable=False ) company = Column(Text()) @@ -42,7 +42,7 @@ class InfrastructureBiosolidsFacilities(Base): """ Biosolids facilities infrastructure. """ - __tablename__ = 'InfrastructureBiosolidsFacilities' + __tablename__ = 'infrastructure_biosolids_facilities' biosolid_facility_id = Column(Integer(), primary_key=True, nullable=False ) report_submitted_date = Column(Date()) @@ -100,7 +100,7 @@ class InfrastructureCafoManureLocations(Base): """ CAFO manure locations infrastructure. """ - __tablename__ = 'InfrastructureCafoManureLocations' + __tablename__ = 'infrastructure_cafo_manure_locations' cafo_manure_id = Column(Integer(), primary_key=True, nullable=False ) latitude = Column(Numeric()) @@ -132,7 +132,7 @@ class InfrastructureEthanolBiorefineries(Base): """ Ethanol biorefineries infrastructure. """ - __tablename__ = 'InfrastructureEthanolBiorefineries' + __tablename__ = 'infrastructure_ethanol_biorefineries' ethanol_biorefinery_id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -157,7 +157,7 @@ class InfrastructureLandfills(Base): """ Landfills infrastructure. """ - __tablename__ = 'InfrastructureLandfills' + __tablename__ = 'infrastructure_landfills' project_id = Column(Text(), primary_key=True, nullable=False ) project_int_id = Column(Integer()) @@ -207,7 +207,7 @@ class InfrastructureLivestockAnaerobicDigesters(Base): """ Livestock anaerobic digesters infrastructure. """ - __tablename__ = 'InfrastructureLivestockAnaerobicDigesters' + __tablename__ = 'infrastructure_livestock_anaerobic_digesters' digester_id = Column(Integer(), primary_key=True, nullable=False ) project_name = Column(Text()) @@ -246,7 +246,7 @@ class InfrastructureSafAndRenewableDieselPlants(Base): """ SAF and renewable diesel plants infrastructure. """ - __tablename__ = 'InfrastructureSafAndRenewableDieselPlants' + __tablename__ = 'infrastructure_saf_and_renewable_diesel_plants' ibcc_index = Column(Integer(), primary_key=True, nullable=False ) company = Column(Text()) @@ -275,7 +275,7 @@ class InfrastructureWastewaterTreatmentPlants(Base): """ Wastewater treatment plants infrastructure. """ - __tablename__ = 'InfrastructureWastewaterTreatmentPlants' + __tablename__ = 'infrastructure_wastewater_treatment_plants' plant_id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -321,7 +321,7 @@ class InfrastructureCombustionPlants(Base): """ Combustion plants infrastructure. """ - __tablename__ = 'InfrastructureCombustionPlants' + __tablename__ = 'infrastructure_combustion_plants' combustion_fid = Column(Integer(), primary_key=True, nullable=False ) objectid = Column(Integer()) @@ -354,7 +354,7 @@ class InfrastructureDistrictEnergySystems(Base): """ District energy systems infrastructure. """ - __tablename__ = 'InfrastructureDistrictEnergySystems' + __tablename__ = 'infrastructure_district_energy_systems' des_fid = Column(Integer(), primary_key=True, nullable=False ) cbg_id = Column(Integer()) @@ -391,7 +391,7 @@ class InfrastructureFoodProcessingFacilities(Base): """ Food processing facilities infrastructure. """ - __tablename__ = 'InfrastructureFoodProcessingFacilities' + __tablename__ = 'infrastructure_food_processing_facilities' processing_facility_id = Column(Integer(), primary_key=True, nullable=False ) address = Column(Text()) @@ -424,7 +424,7 @@ class InfrastructureMswToEnergyAnaerobicDigesters(Base): """ MSW to energy anaerobic digesters infrastructure. """ - __tablename__ = 'InfrastructureMswToEnergyAnaerobicDigesters' + __tablename__ = 'infrastructure_msw_to_energy_anaerobic_digesters' wte_id = Column(Integer(), primary_key=True, nullable=False ) city = Column(Text()) @@ -456,7 +456,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -477,7 +477,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -497,7 +497,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -520,7 +520,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -541,7 +541,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -559,7 +559,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -578,7 +578,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -597,7 +597,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -616,7 +616,7 @@ class FacilityRecord(BaseEntity): """ Facility record. """ - __tablename__ = 'FacilityRecord' + __tablename__ = 'facility_record' dataset_id = Column(Integer()) facility_name = Column(Text()) @@ -650,7 +650,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -685,7 +685,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -717,7 +717,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -744,7 +744,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -769,7 +769,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -794,7 +794,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -828,7 +828,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -859,7 +859,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -884,7 +884,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -909,7 +909,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -935,7 +935,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -967,7 +967,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -1010,7 +1010,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1035,7 +1035,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -1068,7 +1068,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1093,7 +1093,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1118,7 +1118,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1143,7 +1143,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -1173,7 +1173,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1198,7 +1198,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -1242,7 +1242,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1267,7 +1267,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1292,7 +1292,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1317,7 +1317,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1342,7 +1342,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -1373,7 +1373,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1398,7 +1398,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1423,7 +1423,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -1454,7 +1454,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -1482,7 +1482,7 @@ class AnalysisType(LookupBase): """ Type of analysis. """ - __tablename__ = 'AnalysisType' + __tablename__ = 'analysis_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1507,7 +1507,7 @@ class Dataset(BaseEntity): """ Dataset definition. """ - __tablename__ = 'Dataset' + __tablename__ = 'dataset' name = Column(Text()) record_type = Column(Text()) @@ -1539,7 +1539,7 @@ class DimensionType(LookupBase): """ Type of dimension. """ - __tablename__ = 'DimensionType' + __tablename__ = 'dimension_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1564,7 +1564,7 @@ class Observation(BaseEntity): """ Observation data. """ - __tablename__ = 'Observation' + __tablename__ = 'observation' dataset_id = Column(Integer()) record_type = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py index 56bbfa6d..c1fb6e9a 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py @@ -13,7 +13,7 @@ class LineageGroup(Base): """ Grouping for lineage information. """ - __tablename__ = 'LineageGroup' + __tablename__ = 'lineage_group' id = Column(Integer(), primary_key=True, nullable=False ) etl_run_id = Column(Text()) @@ -32,7 +32,7 @@ class EntityLineage(Base): """ Lineage information for a specific entity. """ - __tablename__ = 'EntityLineage' + __tablename__ = 'entity_lineage' id = Column(Integer(), primary_key=True, nullable=False ) lineage_group_id = Column(Integer()) @@ -53,7 +53,7 @@ class EtlRun(Base): """ Information about an ETL run. """ - __tablename__ = 'EtlRun' + __tablename__ = 'etl_run' id = Column(Integer(), primary_key=True, nullable=False ) started_at = Column(DateTime()) @@ -76,7 +76,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -97,7 +97,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py index 7aceee05..5a5c33e9 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py @@ -13,7 +13,7 @@ class ParameterCategoryParameter(Base): """ Link between parameter and category. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -32,7 +32,7 @@ class ParameterUnit(Base): """ Link between parameter and alternate units. """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -51,7 +51,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -72,7 +72,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -92,7 +92,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -117,7 +117,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -150,7 +150,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for a method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -175,7 +175,7 @@ class MethodCategory(LookupBase): """ Category of a method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -200,7 +200,7 @@ class MethodStandard(LookupBase): """ Standard associated with a method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -225,7 +225,7 @@ class Parameter(BaseEntity): """ Parameter measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -255,7 +255,7 @@ class ParameterCategory(LookupBase): """ Category of a parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py index 3b0c7511..4e50f484 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py @@ -13,7 +13,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -32,7 +32,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -51,7 +51,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -72,7 +72,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -92,7 +92,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -115,7 +115,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -136,7 +136,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -154,7 +154,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -173,7 +173,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -198,7 +198,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -231,7 +231,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -256,7 +256,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -281,7 +281,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -306,7 +306,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -336,7 +336,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -361,7 +361,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -395,7 +395,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -426,7 +426,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -451,7 +451,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -476,7 +476,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -502,7 +502,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -534,7 +534,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -577,7 +577,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -621,7 +621,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -646,7 +646,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -671,7 +671,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -696,7 +696,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -721,7 +721,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -752,7 +752,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -777,7 +777,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -802,7 +802,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -833,7 +833,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -861,7 +861,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -896,7 +896,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -928,7 +928,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -955,7 +955,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -980,7 +980,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py index c5825f29..7eacc534 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py @@ -13,7 +13,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -34,7 +34,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py index f721c286..4eccd8ac 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py @@ -13,7 +13,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -36,7 +36,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -57,7 +57,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -77,7 +77,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py index 9350f964..b1d3d70e 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py @@ -13,7 +13,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -32,7 +32,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -53,7 +53,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -73,7 +73,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -96,7 +96,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -127,7 +127,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -152,7 +152,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -177,7 +177,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -203,7 +203,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -235,7 +235,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -278,7 +278,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py index cb16a4a0..bec06909 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py @@ -13,7 +13,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -32,7 +32,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -53,7 +53,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -73,7 +73,7 @@ class Geography(Base): """ Geographic region definition (e.g. county, state). """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -96,7 +96,7 @@ class Polygon(Base): """ Geospatial polygon definition. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -115,7 +115,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -146,7 +146,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -171,7 +171,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -196,7 +196,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -222,7 +222,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -254,7 +254,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -297,7 +297,7 @@ class LocationAddress(BaseEntity): """ Specific physical location. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py index 9f3eb1e5..a3da8a03 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic location. """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -98,7 +98,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -116,7 +116,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -135,7 +135,7 @@ class ParameterCategoryParameter(Base): """ Link between Parameter and ParameterCategory. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -154,7 +154,7 @@ class ParameterUnit(Base): """ Link between Parameter and Unit (alternate units). """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -173,7 +173,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -205,7 +205,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -230,7 +230,7 @@ class PreparedSample(BaseEntity): """ Sample that has been prepared. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -262,7 +262,7 @@ class LocationAddress(BaseEntity): """ Physical address. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -296,7 +296,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -327,7 +327,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -352,7 +352,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -377,7 +377,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -403,7 +403,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -435,7 +435,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -478,7 +478,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -522,7 +522,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -547,7 +547,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -572,7 +572,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -597,7 +597,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -622,7 +622,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -653,7 +653,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -678,7 +678,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -703,7 +703,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -734,7 +734,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -762,7 +762,7 @@ class DataSource(BaseEntity): """ Source of data. """ - __tablename__ = 'DataSource' + __tablename__ = 'data_source' name = Column(Text()) description = Column(Text()) @@ -797,7 +797,7 @@ class FileObjectMetadata(BaseEntity): """ Metadata for a file object. """ - __tablename__ = 'FileObjectMetadata' + __tablename__ = 'file_object_metadata' data_source_id = Column(Integer()) bucket_path = Column(Text()) @@ -829,7 +829,7 @@ class DataSourceType(BaseEntity): """ Type of data source. """ - __tablename__ = 'DataSourceType' + __tablename__ = 'data_source_type' source_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -856,7 +856,7 @@ class LocationResolution(LookupBase): """ Resolution of the location (e.g. nation, state, county). """ - __tablename__ = 'LocationResolution' + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -881,7 +881,7 @@ class SourceType(LookupBase): """ Type of source (e.g. database, literature). """ - __tablename__ = 'SourceType' + __tablename__ = 'source_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -906,7 +906,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -931,7 +931,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -964,7 +964,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -989,7 +989,7 @@ class MethodCategory(LookupBase): """ Category of method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1014,7 +1014,7 @@ class MethodStandard(LookupBase): """ Standard associated with the method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1039,7 +1039,7 @@ class Parameter(BaseEntity): """ Parameter being measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -1069,7 +1069,7 @@ class ParameterCategory(LookupBase): """ Category of parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py index d37b7688..63f68798 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py @@ -13,7 +13,7 @@ class BaseEntity(Base): """ Base entity included in all main entity tables. """ - __tablename__ = 'BaseEntity' + __tablename__ = 'base_entity' id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -34,7 +34,7 @@ class LookupBase(Base): """ Base class for enum/ontology-like tables. """ - __tablename__ = 'LookupBase' + __tablename__ = 'lookup_base' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -54,7 +54,7 @@ class Geography(Base): """ Geographic region definition (e.g. county, state). """ - __tablename__ = 'Geography' + __tablename__ = 'geography' geoid = Column(Text(), primary_key=True, nullable=False ) state_name = Column(Text()) @@ -77,7 +77,7 @@ class Polygon(Base): """ Geospatial polygon definition. """ - __tablename__ = 'Polygon' + __tablename__ = 'polygon' id = Column(Integer(), primary_key=True, nullable=False ) geoid = Column(Text()) @@ -96,7 +96,7 @@ class Contact(Base): """ Contact information for a person. """ - __tablename__ = 'Contact' + __tablename__ = 'contact' id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) @@ -117,7 +117,7 @@ class Provider(Base): """ Provider information. """ - __tablename__ = 'Provider' + __tablename__ = 'provider' id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) @@ -135,7 +135,7 @@ class ResourceMorphology(Base): """ Morphology of a resource. """ - __tablename__ = 'ResourceMorphology' + __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) resource_id = Column(Integer()) @@ -154,7 +154,7 @@ class ParameterCategoryParameter(Base): """ Link between parameter and category. """ - __tablename__ = 'ParameterCategoryParameter' + __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -173,7 +173,7 @@ class ParameterUnit(Base): """ Link between parameter and alternate units. """ - __tablename__ = 'ParameterUnit' + __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) parameter_id = Column(Integer()) @@ -192,7 +192,7 @@ class FieldSample(BaseEntity): """ Sample collected from the field. """ - __tablename__ = 'FieldSample' + __tablename__ = 'field_sample' name = Column(Text()) resource_id = Column(Integer()) @@ -236,7 +236,7 @@ class FieldStorageMethod(LookupBase): """ Method of field storage. """ - __tablename__ = 'FieldStorageMethod' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -261,7 +261,7 @@ class CollectionMethod(LookupBase): """ Method of collection. """ - __tablename__ = 'CollectionMethod' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -286,7 +286,7 @@ class HarvestMethod(LookupBase): """ Method of harvest. """ - __tablename__ = 'HarvestMethod' + __tablename__ = 'harvest_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -311,7 +311,7 @@ class ProcessingMethod(LookupBase): """ Method of processing. """ - __tablename__ = 'ProcessingMethod' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -336,7 +336,7 @@ class PhysicalCharacteristic(BaseEntity): """ Physical characteristics of a sample. """ - __tablename__ = 'PhysicalCharacteristic' + __tablename__ = 'physical_characteristic' field_sample_id = Column(Integer()) particle_length = Column(Numeric()) @@ -367,7 +367,7 @@ class SoilType(LookupBase): """ Type of soil. """ - __tablename__ = 'SoilType' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -392,7 +392,7 @@ class AgTreatment(LookupBase): """ Agricultural treatment. """ - __tablename__ = 'AgTreatment' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -417,7 +417,7 @@ class FieldSampleCondition(BaseEntity): """ Condition of the field sample. """ - __tablename__ = 'FieldSampleCondition' + __tablename__ = 'field_sample_condition' field_sample_id = Column(Integer()) ag_treatment_id = Column(Integer()) @@ -448,7 +448,7 @@ class LocationSoilType(BaseEntity): """ Soil type at a location. """ - __tablename__ = 'LocationSoilType' + __tablename__ = 'location_soil_type' location_id = Column(Integer()) soil_type_id = Column(Integer()) @@ -476,7 +476,7 @@ class PreparationMethod(BaseEntity): """ Method of sample preparation. """ - __tablename__ = 'PreparationMethod' + __tablename__ = 'preparation_method' name = Column(Text()) description = Column(Text()) @@ -508,7 +508,7 @@ class PreparationMethodAbbreviation(LookupBase): """ Abbreviation for preparation method. """ - __tablename__ = 'PreparationMethodAbbreviation' + __tablename__ = 'preparation_method_abbreviation' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -533,7 +533,7 @@ class PreparedSample(BaseEntity): """ Sample prepared for analysis. """ - __tablename__ = 'PreparedSample' + __tablename__ = 'prepared_sample' name = Column(Text()) field_sample_id = Column(Integer()) @@ -565,7 +565,7 @@ class LocationAddress(BaseEntity): """ Specific physical location. """ - __tablename__ = 'LocationAddress' + __tablename__ = 'location_address' geography_id = Column(Text()) address_line1 = Column(Text()) @@ -599,7 +599,7 @@ class Resource(BaseEntity): """ Biomass resource definition. """ - __tablename__ = 'Resource' + __tablename__ = 'resource' name = Column(Text()) primary_crop_id = Column(Integer()) @@ -630,7 +630,7 @@ class ResourceClass(LookupBase): """ Classification of resources. """ - __tablename__ = 'ResourceClass' + __tablename__ = 'resource_class' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -655,7 +655,7 @@ class ResourceSubclass(LookupBase): """ Sub-classification of resources. """ - __tablename__ = 'ResourceSubclass' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -680,7 +680,7 @@ class PrimaryCrop(LookupBase): """ Primary crop definition. """ - __tablename__ = 'PrimaryCrop' + __tablename__ = 'primary_crop' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -706,7 +706,7 @@ class ResourceAvailability(BaseEntity): """ Availability of a resource in a location. """ - __tablename__ = 'ResourceAvailability' + __tablename__ = 'resource_availability' resource_id = Column(Integer()) geoid = Column(Text()) @@ -738,7 +738,7 @@ class ResourceCounterfactual(BaseEntity): """ Counterfactual uses of a resource. """ - __tablename__ = 'ResourceCounterfactual' + __tablename__ = 'resource_counterfactual' geoid = Column(Text()) resource_id = Column(Integer()) @@ -781,7 +781,7 @@ class Unit(LookupBase): """ Unit of measurement. """ - __tablename__ = 'Unit' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -806,7 +806,7 @@ class Method(BaseEntity): """ Analytical method. """ - __tablename__ = 'Method' + __tablename__ = 'method' name = Column(Text()) method_abbrev_id = Column(Integer()) @@ -839,7 +839,7 @@ class MethodAbbrev(LookupBase): """ Abbreviation for a method. """ - __tablename__ = 'MethodAbbrev' + __tablename__ = 'method_abbrev' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -864,7 +864,7 @@ class MethodCategory(LookupBase): """ Category of a method. """ - __tablename__ = 'MethodCategory' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -889,7 +889,7 @@ class MethodStandard(LookupBase): """ Standard associated with a method. """ - __tablename__ = 'MethodStandard' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -914,7 +914,7 @@ class Parameter(BaseEntity): """ Parameter measured. """ - __tablename__ = 'Parameter' + __tablename__ = 'parameter' name = Column(Text()) standard_unit_id = Column(Integer()) @@ -944,7 +944,7 @@ class ParameterCategory(LookupBase): """ Category of a parameter. """ - __tablename__ = 'ParameterCategory' + __tablename__ = 'parameter_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) diff --git a/src/ca_biositing/datamodels/generate_sqla.py b/src/ca_biositing/datamodels/utils/generate_sqla.py similarity index 54% rename from src/ca_biositing/datamodels/generate_sqla.py rename to src/ca_biositing/datamodels/utils/generate_sqla.py index 54fe4a59..50c0825f 100644 --- a/src/ca_biositing/datamodels/generate_sqla.py +++ b/src/ca_biositing/datamodels/utils/generate_sqla.py @@ -1,12 +1,39 @@ import os +import re import subprocess from pathlib import Path +def to_snake_case(name): + """Converts PascalCase to snake_case.""" + s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name) + return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower() + +def post_process_file(file_path): + """ + Post-processes the generated file to convert table names to snake_case. + """ + with open(file_path, 'r') as f: + content = f.read() + + # Regex to find __tablename__ assignments + # Matches: __tablename__ = 'SomeName' + pattern = r"__tablename__ = '([A-Za-z0-9]+)'" + + def replace_tablename(match): + original_name = match.group(1) + snake_name = to_snake_case(original_name) + return f"__tablename__ = '{snake_name}'" + + new_content = re.sub(pattern, replace_tablename, content) + + with open(file_path, 'w') as f: + f.write(new_content) + def generate_sqla(): """ Generates SQLAlchemy models from LinkML schema modules. """ - base_dir = Path(__file__).parent + base_dir = Path(__file__).parent.parent linkml_dir = base_dir / "ca_biositing/datamodels/linkml" modules_dir = linkml_dir / "modules" output_dir = base_dir / "ca_biositing/datamodels/schemas/generated" @@ -14,6 +41,12 @@ def generate_sqla(): # Ensure output directory exists output_dir.mkdir(parents=True, exist_ok=True) + # Clean output directory + print(f"Cleaning output directory: {output_dir}") + for file in output_dir.glob("*.py"): + if file.name != "__init__.py": + file.unlink() + # Generate for modules for yaml_file in modules_dir.glob("*.yaml"): module_name = yaml_file.stem @@ -29,6 +62,8 @@ def generate_sqla(): with open(output_file, "w") as f: subprocess.run(cmd, stdout=f, check=True) + post_process_file(output_file) + # Generate for main schema main_yaml = linkml_dir / "ca_biositing.yaml" main_output = output_dir / "ca_biositing.py" @@ -43,6 +78,8 @@ def generate_sqla(): with open(main_output, "w") as f: subprocess.run(cmd, stdout=f, check=True) + post_process_file(main_output) + print("Generation complete.") if __name__ == "__main__": diff --git a/src/ca_biositing/datamodels/utils/orchestrate_schema_update.py b/src/ca_biositing/datamodels/utils/orchestrate_schema_update.py new file mode 100644 index 00000000..07281d32 --- /dev/null +++ b/src/ca_biositing/datamodels/utils/orchestrate_schema_update.py @@ -0,0 +1,58 @@ +import subprocess +import sys +import argparse +import shlex +from pathlib import Path + +def run_command(command, cwd=None): + print(f"Running: {command}") + try: + # If command is a string, use shell=True. If list, use shell=False. + shell = isinstance(command, str) + subprocess.run(command, shell=shell, check=True, cwd=cwd) + except subprocess.CalledProcessError as e: + print(f"Error running command: {command}") + sys.exit(e.returncode) + +def main(): + parser = argparse.ArgumentParser(description="Orchestrate schema update workflow.") + parser.add_argument("-m", "--message", required=True, help="Migration message") + args = parser.parse_args() + + # 1. Generate SQLAlchemy models + print("--- Generating SQLAlchemy models ---") + script_path = Path(__file__).parent / "generate_sqla.py" + run_command(f"python {script_path}") + + # 2. Rebuild services + print("--- Rebuilding services ---") + # We assume we are in the project root or pixi handles the path + run_command("pixi run rebuild-services") + + # 3. Start services + print("--- Starting services ---") + run_command("pixi run start-services") + + # 4. Generate migration + print(f"--- Generating migration: {args.message} ---") + + # Construct the bash command to run inside the container + # usage of shlex.quote ensures the message is safely quoted for the inner bash shell + safe_message = shlex.quote(args.message) + inner_cmd = f"source /shell-hook.sh && alembic revision --autogenerate -m {safe_message}" + + # We invoke docker-compose directly via pixi to avoid potential argument parsing issues + # with pixi task aliases when handling complex nested quotes. + cmd = [ + "pixi", "run", "docker-compose", + "-f", "resources/docker/docker-compose.yml", + "exec", "prefect-worker", + "/bin/bash", "-c", inner_cmd + ] + run_command(cmd) + + print("--- Schema update orchestration complete! ---") + print("Don't forget to run 'pixi run migrate' to apply the changes.") + +if __name__ == "__main__": + main() From 89344298e55842c78c306d3d0aa8c3b53f9f9e21 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Tue, 9 Dec 2025 15:58:44 -0700 Subject: [PATCH 55/81] quick clean up before push to upstream --- ...n.py => 1e9784d75e62_initial_migration.py} | 335 +-- ...2618fe6b09b_rename_tables_to_snake_case.py | 2192 ----------------- ...8c837616b_adding_a_test_to_landiqrecord.py | 32 - .../ca_biositing/datamodels/biomass.py | 306 --- .../ca_biositing/datamodels/config.py | 37 - .../datamodels/data_and_references.py | 85 - .../ca_biositing/datamodels/database.py | 27 - .../datamodels/experiments_analysis.py | 296 --- .../datamodels/external_datasets.py | 295 --- .../datamodels/geographic_locations.py | 113 - .../datamodels/linkml/modules/resources.yaml | 2 - .../datamodels/metadata_samples.py | 79 - .../ca_biositing/datamodels/organizations.py | 46 - .../datamodels/people_contacts.py | 59 - .../datamodels/sample_preprocessing.py | 68 - .../datamodels/specific_aalysis_results.py | 199 -- .../ca_biositing/datamodels/user.py | 13 - 17 files changed, 168 insertions(+), 4016 deletions(-) rename alembic/versions/{e22149be0d9c_initial_migration.py => 1e9784d75e62_initial_migration.py} (88%) delete mode 100644 alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py delete mode 100644 alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/biomass.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/config.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/data_and_references.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/database.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/experiments_analysis.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/external_datasets.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/geographic_locations.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/metadata_samples.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/organizations.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/people_contacts.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/sample_preprocessing.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/specific_aalysis_results.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/user.py diff --git a/alembic/versions/e22149be0d9c_initial_migration.py b/alembic/versions/1e9784d75e62_initial_migration.py similarity index 88% rename from alembic/versions/e22149be0d9c_initial_migration.py rename to alembic/versions/1e9784d75e62_initial_migration.py index 574739e6..83745dc2 100644 --- a/alembic/versions/e22149be0d9c_initial_migration.py +++ b/alembic/versions/1e9784d75e62_initial_migration.py @@ -1,8 +1,8 @@ """Initial migration -Revision ID: e22149be0d9c +Revision ID: 1e9784d75e62 Revises: -Create Date: 2025-12-08 18:01:48.554213 +Create Date: 2025-12-08 22:50:05.973054 """ from typing import Sequence, Union @@ -12,7 +12,7 @@ # revision identifiers, used by Alembic. -revision: str = 'e22149be0d9c' +revision: str = '1e9784d75e62' down_revision: Union[str, Sequence[str], None] = None branch_labels: Union[str, Sequence[str], None] = None depends_on: Union[str, Sequence[str], None] = None @@ -21,14 +21,14 @@ def upgrade() -> None: """Upgrade schema.""" # ### commands auto generated by Alembic - please adjust! ### - op.create_table('AgTreatment', + op.create_table('ag_treatment', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Aim1RecordBase', + op.create_table('aim1_record_base', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -46,7 +46,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Aim2RecordBase', + op.create_table('aim2_record_base', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -64,14 +64,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('AnalysisType', + op.create_table('analysis_type', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('AutoclaveRecord', + op.create_table('autoclave_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -89,7 +89,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('BaseEntity', + op.create_table('base_entity', sa.Column('id', sa.Integer(), nullable=False), sa.Column('created_at', sa.DateTime(), nullable=True), sa.Column('updated_at', sa.DateTime(), nullable=True), @@ -97,7 +97,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('BillionTon2023Record', + op.create_table('billion_ton2023_record', sa.Column('subclass_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('geoid', sa.Text(), nullable=True), @@ -119,7 +119,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('CalorimetryRecord', + op.create_table('calorimetry_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -137,14 +137,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('CollectionMethod', + op.create_table('collection_method', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('CompositionalRecord', + op.create_table('compositional_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -162,7 +162,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Contact', + op.create_table('contact', sa.Column('id', sa.Integer(), nullable=False), sa.Column('first_name', sa.Text(), nullable=True), sa.Column('last_name', sa.Text(), nullable=True), @@ -170,7 +170,7 @@ def upgrade() -> None: sa.Column('affiliation', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('DataSource', + op.create_table('data_source', sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), @@ -187,7 +187,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('DataSourceType', + op.create_table('data_source_type', sa.Column('source_type_id', sa.Integer(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), sa.Column('created_at', sa.DateTime(), nullable=True), @@ -196,7 +196,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Dataset', + op.create_table('dataset', sa.Column('name', sa.Text(), nullable=True), sa.Column('record_type', sa.Text(), nullable=True), sa.Column('source_id', sa.Integer(), nullable=True), @@ -210,14 +210,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('DimensionType', + op.create_table('dimension_type', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('EntityLineage', + op.create_table('entity_lineage', sa.Column('id', sa.Integer(), nullable=False), sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.Column('source_table', sa.Text(), nullable=True), @@ -225,7 +225,7 @@ def upgrade() -> None: sa.Column('note', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Equipment', + op.create_table('equipment', sa.Column('equipment_location_id', sa.Integer(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), @@ -233,7 +233,7 @@ def upgrade() -> None: sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('EtlRun', + op.create_table('etl_run', sa.Column('id', sa.Integer(), nullable=False), sa.Column('started_at', sa.DateTime(), nullable=True), sa.Column('completed_at', sa.DateTime(), nullable=True), @@ -243,7 +243,7 @@ def upgrade() -> None: sa.Column('note', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Experiment', + op.create_table('experiment', sa.Column('analyst_id', sa.Integer(), nullable=True), sa.Column('exper_start_date', sa.Date(), nullable=True), sa.Column('exper_duration', sa.Numeric(), nullable=True), @@ -257,31 +257,31 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ExperimentAnalysis', + op.create_table('experiment_analysis', sa.Column('id', sa.Integer(), nullable=False), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('analysis_type_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ExperimentEquipment', + op.create_table('experiment_equipment', sa.Column('id', sa.Integer(), nullable=False), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('equipment_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ExperimentMethod', + op.create_table('experiment_method', sa.Column('id', sa.Integer(), nullable=False), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('method_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ExperimentPreparedSample', + op.create_table('experiment_prepared_sample', sa.Column('id', sa.Integer(), nullable=False), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('prepared_sample_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FermentationRecord', + op.create_table('fermentation_record', sa.Column('strain_id', sa.Integer(), nullable=True), sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), sa.Column('eh_method_id', sa.Integer(), nullable=True), @@ -308,7 +308,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FieldSample', + op.create_table('field_sample', sa.Column('name', sa.Text(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('provider_id', sa.Integer(), nullable=True), @@ -334,7 +334,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FieldSampleCondition', + op.create_table('field_sample_condition', sa.Column('field_sample_id', sa.Integer(), nullable=True), sa.Column('ag_treatment_id', sa.Integer(), nullable=True), sa.Column('last_application_date', sa.Date(), nullable=True), @@ -347,14 +347,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FieldStorageMethod', + op.create_table('field_storage_method', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FileObjectMetadata', + op.create_table('file_object_metadata', sa.Column('data_source_id', sa.Integer(), nullable=True), sa.Column('bucket_path', sa.Text(), nullable=True), sa.Column('file_format', sa.Text(), nullable=True), @@ -368,7 +368,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('FtnirRecord', + op.create_table('ftnir_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -386,7 +386,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('GasificationRecord', + op.create_table('gasification_record', sa.Column('feedstock_mass', sa.Numeric(), nullable=True), sa.Column('bed_temperature', sa.Numeric(), nullable=True), sa.Column('gas_flow_rate', sa.Numeric(), nullable=True), @@ -407,7 +407,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Geography', + op.create_table('geography', sa.Column('geoid', sa.Text(), nullable=False), sa.Column('state_name', sa.Text(), nullable=True), sa.Column('state_fips', sa.Text(), nullable=True), @@ -417,14 +417,14 @@ def upgrade() -> None: sa.Column('agg_level_desc', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('geoid') ) - op.create_table('HarvestMethod', + op.create_table('harvest_method', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('IcpRecord', + op.create_table('icp_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -442,7 +442,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LandiqRecord', + op.create_table('landiq_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('polygon_id', sa.Integer(), nullable=True), sa.Column('main_crop', sa.Integer(), nullable=True), @@ -454,6 +454,7 @@ def upgrade() -> None: sa.Column('acres', sa.Float(), nullable=True), sa.Column('version', sa.Text(), nullable=True), sa.Column('note', sa.Text(), nullable=True), + sa.Column('test', sa.Text(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), sa.Column('created_at', sa.DateTime(), nullable=True), sa.Column('updated_at', sa.DateTime(), nullable=True), @@ -461,13 +462,13 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LineageGroup', + op.create_table('lineage_group', sa.Column('id', sa.Integer(), nullable=False), sa.Column('etl_run_id', sa.Text(), nullable=True), sa.Column('note', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LocationAddress', + op.create_table('location_address', sa.Column('geography_id', sa.Text(), nullable=True), sa.Column('address_line1', sa.Text(), nullable=True), sa.Column('address_line2', sa.Text(), nullable=True), @@ -483,14 +484,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LocationResolution', + op.create_table('location_resolution', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LocationSoilType', + op.create_table('location_soil_type', sa.Column('location_id', sa.Integer(), nullable=True), sa.Column('soil_type_id', sa.Integer(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), @@ -500,14 +501,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('LookupBase', + op.create_table('lookup_base', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Method', + op.create_table('method', sa.Column('name', sa.Text(), nullable=True), sa.Column('method_abbrev_id', sa.Integer(), nullable=True), sa.Column('method_category_id', sa.Integer(), nullable=True), @@ -522,28 +523,28 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('MethodAbbrev', + op.create_table('method_abbrev', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('MethodCategory', + op.create_table('method_category', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('MethodStandard', + op.create_table('method_standard', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Observation', + op.create_table('observation', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('record_type', sa.Text(), nullable=True), sa.Column('record_id', sa.Integer(), nullable=True), @@ -561,7 +562,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Parameter', + op.create_table('parameter', sa.Column('name', sa.Text(), nullable=True), sa.Column('standard_unit_id', sa.Integer(), nullable=True), sa.Column('calculated', sa.Boolean(), nullable=True), @@ -573,26 +574,26 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ParameterCategory', + op.create_table('parameter_category', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ParameterCategoryParameter', + op.create_table('parameter_category_parameter', sa.Column('id', sa.Integer(), nullable=False), sa.Column('parameter_id', sa.Integer(), nullable=True), sa.Column('parameter_category_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ParameterUnit', + op.create_table('parameter_unit', sa.Column('id', sa.Integer(), nullable=False), sa.Column('parameter_id', sa.Integer(), nullable=True), sa.Column('alternate_unit_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PhysicalCharacteristic', + op.create_table('physical_characteristic', sa.Column('field_sample_id', sa.Integer(), nullable=True), sa.Column('particle_length', sa.Numeric(), nullable=True), sa.Column('particle_width', sa.Numeric(), nullable=True), @@ -605,13 +606,13 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Polygon', + op.create_table('polygon', sa.Column('id', sa.Integer(), nullable=False), sa.Column('geoid', sa.Text(), nullable=True), sa.Column('geom', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PreparationMethod', + op.create_table('preparation_method', sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('prep_method_abbrev_id', sa.Integer(), nullable=True), @@ -625,14 +626,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PreparationMethodAbbreviation', + op.create_table('preparation_method_abbreviation', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PreparedSample', + op.create_table('prepared_sample', sa.Column('name', sa.Text(), nullable=True), sa.Column('field_sample_id', sa.Integer(), nullable=True), sa.Column('prep_method_id', sa.Integer(), nullable=True), @@ -646,7 +647,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PretreatmentRecord', + op.create_table('pretreatment_record', sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), sa.Column('eh_method_id', sa.Integer(), nullable=True), sa.Column('reaction_block_id', sa.Integer(), nullable=True), @@ -670,7 +671,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('PrimaryCrop', + op.create_table('primary_crop', sa.Column('note', sa.Text(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), @@ -678,19 +679,19 @@ def upgrade() -> None: sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ProcessingMethod', + op.create_table('processing_method', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Provider', + op.create_table('provider', sa.Column('id', sa.Integer(), nullable=False), sa.Column('codename', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ProximateRecord', + op.create_table('proximate_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -708,7 +709,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Resource', + op.create_table('resource', sa.Column('name', sa.Text(), nullable=True), sa.Column('primary_crop_id', sa.Integer(), nullable=True), sa.Column('resource_class_id', sa.Integer(), nullable=True), @@ -721,7 +722,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceAvailability', + op.create_table('resource_availability', sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('geoid', sa.Text(), nullable=True), sa.Column('from_month', sa.Integer(), nullable=True), @@ -735,14 +736,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceClass', + op.create_table('resource_class', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceCounterfactual', + op.create_table('resource_counterfactual', sa.Column('geoid', sa.Text(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('counterfactual_description', sa.Text(), nullable=True), @@ -767,20 +768,20 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceMorphology', + op.create_table('resource_morphology', sa.Column('id', sa.Integer(), nullable=False), sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('morphology_uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceSubclass', + op.create_table('resource_subclass', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('ResourceUsdaCommodityMap', + op.create_table('resource_usda_commodity_map', sa.Column('resource_id', sa.Integer(), nullable=True), sa.Column('primary_crop_id', sa.Integer(), nullable=True), sa.Column('usda_commodity_id', sa.Integer(), nullable=True), @@ -793,7 +794,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('RgbRecord', + op.create_table('rgb_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -811,21 +812,21 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('SoilType', + op.create_table('soil_type', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('SourceType', + op.create_table('source_type', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Strain', + op.create_table('strain', sa.Column('parent_strain_id', sa.Integer(), nullable=True), sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), @@ -833,7 +834,7 @@ def upgrade() -> None: sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UltimateRecord', + op.create_table('ultimate_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('experiment_id', sa.Integer(), nullable=True), sa.Column('resource_id', sa.Integer(), nullable=True), @@ -851,14 +852,14 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('Unit', + op.create_table('unit', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaCensusRecord', + op.create_table('usda_census_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('geoid', sa.Text(), nullable=True), sa.Column('commodity_code', sa.Integer(), nullable=True), @@ -872,7 +873,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaCommodity', + op.create_table('usda_commodity', sa.Column('usda_source', sa.Text(), nullable=True), sa.Column('usda_code', sa.Text(), nullable=True), sa.Column('parent_commodity_id', sa.Integer(), nullable=True), @@ -882,14 +883,14 @@ def upgrade() -> None: sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaDomain', + op.create_table('usda_domain', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaMarketRecord', + op.create_table('usda_market_record', sa.Column('report_id', sa.Integer(), nullable=True), sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('report_begin_date', sa.DateTime(), nullable=True), @@ -917,7 +918,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaMarketReport', + op.create_table('usda_market_report', sa.Column('slug_id', sa.Integer(), nullable=True), sa.Column('slug_name', sa.Text(), nullable=True), sa.Column('report_series_title', sa.Text(), nullable=True), @@ -933,21 +934,21 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaStatisticCategory', + op.create_table('usda_statistic_category', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaSurveyProgram', + op.create_table('usda_survey_program', sa.Column('id', sa.Integer(), nullable=False), sa.Column('name', sa.Text(), nullable=True), sa.Column('description', sa.Text(), nullable=True), sa.Column('uri', sa.Text(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaSurveyRecord', + op.create_table('usda_survey_record', sa.Column('dataset_id', sa.Integer(), nullable=True), sa.Column('geoid', sa.Text(), nullable=True), sa.Column('commodity_code', sa.Integer(), nullable=True), @@ -964,7 +965,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('UsdaTermMap', + op.create_table('usda_term_map', sa.Column('source_system', sa.Text(), nullable=True), sa.Column('source_context', sa.Text(), nullable=True), sa.Column('raw_term', sa.Text(), nullable=True), @@ -978,7 +979,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('XrdRecord', + op.create_table('xrd_record', sa.Column('maybe_scan_low_nm', sa.Integer(), nullable=True), sa.Column('maybe_scan_high_nm', sa.Integer(), nullable=True), sa.Column('dataset_id', sa.Integer(), nullable=True), @@ -998,7 +999,7 @@ def upgrade() -> None: sa.Column('lineage_group_id', sa.Integer(), nullable=True), sa.PrimaryKeyConstraint('id') ) - op.create_table('XrfRecord', + op.create_table('xrf_record', sa.Column('maybe_wavelength_nm', sa.Numeric(), nullable=True), sa.Column('maybe_intensity', sa.Numeric(), nullable=True), sa.Column('maybe_energy_slope', sa.Numeric(), nullable=True), @@ -1026,86 +1027,86 @@ def upgrade() -> None: def downgrade() -> None: """Downgrade schema.""" # ### commands auto generated by Alembic - please adjust! ### - op.drop_table('XrfRecord') - op.drop_table('XrdRecord') - op.drop_table('UsdaTermMap') - op.drop_table('UsdaSurveyRecord') - op.drop_table('UsdaSurveyProgram') - op.drop_table('UsdaStatisticCategory') - op.drop_table('UsdaMarketReport') - op.drop_table('UsdaMarketRecord') - op.drop_table('UsdaDomain') - op.drop_table('UsdaCommodity') - op.drop_table('UsdaCensusRecord') - op.drop_table('Unit') - op.drop_table('UltimateRecord') - op.drop_table('Strain') - op.drop_table('SourceType') - op.drop_table('SoilType') - op.drop_table('RgbRecord') - op.drop_table('ResourceUsdaCommodityMap') - op.drop_table('ResourceSubclass') - op.drop_table('ResourceMorphology') - op.drop_table('ResourceCounterfactual') - op.drop_table('ResourceClass') - op.drop_table('ResourceAvailability') - op.drop_table('Resource') - op.drop_table('ProximateRecord') - op.drop_table('Provider') - op.drop_table('ProcessingMethod') - op.drop_table('PrimaryCrop') - op.drop_table('PretreatmentRecord') - op.drop_table('PreparedSample') - op.drop_table('PreparationMethodAbbreviation') - op.drop_table('PreparationMethod') - op.drop_table('Polygon') - op.drop_table('PhysicalCharacteristic') - op.drop_table('ParameterUnit') - op.drop_table('ParameterCategoryParameter') - op.drop_table('ParameterCategory') - op.drop_table('Parameter') - op.drop_table('Observation') - op.drop_table('MethodStandard') - op.drop_table('MethodCategory') - op.drop_table('MethodAbbrev') - op.drop_table('Method') - op.drop_table('LookupBase') - op.drop_table('LocationSoilType') - op.drop_table('LocationResolution') - op.drop_table('LocationAddress') - op.drop_table('LineageGroup') - op.drop_table('LandiqRecord') - op.drop_table('IcpRecord') - op.drop_table('HarvestMethod') - op.drop_table('Geography') - op.drop_table('GasificationRecord') - op.drop_table('FtnirRecord') - op.drop_table('FileObjectMetadata') - op.drop_table('FieldStorageMethod') - op.drop_table('FieldSampleCondition') - op.drop_table('FieldSample') - op.drop_table('FermentationRecord') - op.drop_table('ExperimentPreparedSample') - op.drop_table('ExperimentMethod') - op.drop_table('ExperimentEquipment') - op.drop_table('ExperimentAnalysis') - op.drop_table('Experiment') - op.drop_table('EtlRun') - op.drop_table('Equipment') - op.drop_table('EntityLineage') - op.drop_table('DimensionType') - op.drop_table('Dataset') - op.drop_table('DataSourceType') - op.drop_table('DataSource') - op.drop_table('Contact') - op.drop_table('CompositionalRecord') - op.drop_table('CollectionMethod') - op.drop_table('CalorimetryRecord') - op.drop_table('BillionTon2023Record') - op.drop_table('BaseEntity') - op.drop_table('AutoclaveRecord') - op.drop_table('AnalysisType') - op.drop_table('Aim2RecordBase') - op.drop_table('Aim1RecordBase') - op.drop_table('AgTreatment') + op.drop_table('xrf_record') + op.drop_table('xrd_record') + op.drop_table('usda_term_map') + op.drop_table('usda_survey_record') + op.drop_table('usda_survey_program') + op.drop_table('usda_statistic_category') + op.drop_table('usda_market_report') + op.drop_table('usda_market_record') + op.drop_table('usda_domain') + op.drop_table('usda_commodity') + op.drop_table('usda_census_record') + op.drop_table('unit') + op.drop_table('ultimate_record') + op.drop_table('strain') + op.drop_table('source_type') + op.drop_table('soil_type') + op.drop_table('rgb_record') + op.drop_table('resource_usda_commodity_map') + op.drop_table('resource_subclass') + op.drop_table('resource_morphology') + op.drop_table('resource_counterfactual') + op.drop_table('resource_class') + op.drop_table('resource_availability') + op.drop_table('resource') + op.drop_table('proximate_record') + op.drop_table('provider') + op.drop_table('processing_method') + op.drop_table('primary_crop') + op.drop_table('pretreatment_record') + op.drop_table('prepared_sample') + op.drop_table('preparation_method_abbreviation') + op.drop_table('preparation_method') + op.drop_table('polygon') + op.drop_table('physical_characteristic') + op.drop_table('parameter_unit') + op.drop_table('parameter_category_parameter') + op.drop_table('parameter_category') + op.drop_table('parameter') + op.drop_table('observation') + op.drop_table('method_standard') + op.drop_table('method_category') + op.drop_table('method_abbrev') + op.drop_table('method') + op.drop_table('lookup_base') + op.drop_table('location_soil_type') + op.drop_table('location_resolution') + op.drop_table('location_address') + op.drop_table('lineage_group') + op.drop_table('landiq_record') + op.drop_table('icp_record') + op.drop_table('harvest_method') + op.drop_table('geography') + op.drop_table('gasification_record') + op.drop_table('ftnir_record') + op.drop_table('file_object_metadata') + op.drop_table('field_storage_method') + op.drop_table('field_sample_condition') + op.drop_table('field_sample') + op.drop_table('fermentation_record') + op.drop_table('experiment_prepared_sample') + op.drop_table('experiment_method') + op.drop_table('experiment_equipment') + op.drop_table('experiment_analysis') + op.drop_table('experiment') + op.drop_table('etl_run') + op.drop_table('equipment') + op.drop_table('entity_lineage') + op.drop_table('dimension_type') + op.drop_table('dataset') + op.drop_table('data_source_type') + op.drop_table('data_source') + op.drop_table('contact') + op.drop_table('compositional_record') + op.drop_table('collection_method') + op.drop_table('calorimetry_record') + op.drop_table('billion_ton2023_record') + op.drop_table('base_entity') + op.drop_table('autoclave_record') + op.drop_table('analysis_type') + op.drop_table('aim2_record_base') + op.drop_table('aim1_record_base') + op.drop_table('ag_treatment') # ### end Alembic commands ### diff --git a/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py b/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py deleted file mode 100644 index 22464c6b..00000000 --- a/alembic/versions/42618fe6b09b_rename_tables_to_snake_case.py +++ /dev/null @@ -1,2192 +0,0 @@ -"""rename_tables_to_snake_case - -Revision ID: 42618fe6b09b -Revises: e22149be0d9c -Create Date: 2025-12-08 21:37:30.253589 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa -from sqlalchemy.dialects import postgresql - -# revision identifiers, used by Alembic. -revision: str = '42618fe6b09b' -down_revision: Union[str, Sequence[str], None] = 'e22149be0d9c' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.create_table('ag_treatment', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('aim1_record_base', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('aim2_record_base', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('analysis_type', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('autoclave_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('base_entity', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('billion_ton2023_record', - sa.Column('subclass_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('county_square_miles', sa.Float(), nullable=True), - sa.Column('model_name', sa.Text(), nullable=True), - sa.Column('scenario_name', sa.Text(), nullable=True), - sa.Column('price_offered_usd', sa.Numeric(), nullable=True), - sa.Column('production', sa.Integer(), nullable=True), - sa.Column('production_unit_id', sa.Integer(), nullable=True), - sa.Column('btu_ton', sa.Integer(), nullable=True), - sa.Column('production_energy_content', sa.Integer(), nullable=True), - sa.Column('energy_content_unit_id', sa.Integer(), nullable=True), - sa.Column('product_density_dtpersqmi', sa.Numeric(), nullable=True), - sa.Column('land_source', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('calorimetry_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('collection_method', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('compositional_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('contact', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('first_name', sa.Text(), nullable=True), - sa.Column('last_name', sa.Text(), nullable=True), - sa.Column('email', sa.Text(), nullable=True), - sa.Column('affiliation', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('data_source', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.Column('publication_date', sa.Date(), nullable=True), - sa.Column('version', sa.Text(), nullable=True), - sa.Column('publisher', sa.Text(), nullable=True), - sa.Column('author', sa.Text(), nullable=True), - sa.Column('license', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('data_source_type', - sa.Column('source_type_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('dataset', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('record_type', sa.Text(), nullable=True), - sa.Column('source_id', sa.Integer(), nullable=True), - sa.Column('start_date', sa.Date(), nullable=True), - sa.Column('end_date', sa.Date(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('dimension_type', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('entity_lineage', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.Column('source_table', sa.Text(), nullable=True), - sa.Column('source_row_id', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('equipment', - sa.Column('equipment_location_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('etl_run', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('started_at', sa.DateTime(), nullable=True), - sa.Column('completed_at', sa.DateTime(), nullable=True), - sa.Column('pipeline_name', sa.Text(), nullable=True), - sa.Column('status', sa.Text(), nullable=True), - sa.Column('records_ingested', sa.Integer(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('experiment', - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('exper_start_date', sa.Date(), nullable=True), - sa.Column('exper_duration', sa.Numeric(), nullable=True), - sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('exper_location_id', sa.Integer(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('experiment_analysis', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('analysis_type_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('experiment_equipment', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('equipment_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('experiment_method', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('experiment_prepared_sample', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('prepared_sample_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('fermentation_record', - sa.Column('strain_id', sa.Integer(), nullable=True), - sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), - sa.Column('eh_method_id', sa.Integer(), nullable=True), - sa.Column('replicate_no', sa.Integer(), nullable=True), - sa.Column('well_position', sa.Text(), nullable=True), - sa.Column('temperature', sa.Numeric(), nullable=True), - sa.Column('agitation_rpm', sa.Numeric(), nullable=True), - sa.Column('vessel_id', sa.Integer(), nullable=True), - sa.Column('analyte_detection_equipment_id', sa.Integer(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('field_sample', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('provider_id', sa.Integer(), nullable=True), - sa.Column('collector_id', sa.Integer(), nullable=True), - sa.Column('sample_collection_source', sa.Text(), nullable=True), - sa.Column('amount_collected', sa.Numeric(), nullable=True), - sa.Column('amount_collected_unit_id', sa.Integer(), nullable=True), - sa.Column('sampling_location_id', sa.Integer(), nullable=True), - sa.Column('field_storage_method_id', sa.Integer(), nullable=True), - sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), - sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), - sa.Column('field_storage_location_id', sa.Integer(), nullable=True), - sa.Column('collection_timestamp', sa.DateTime(), nullable=True), - sa.Column('collection_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_method_id', sa.Integer(), nullable=True), - sa.Column('harvest_date', sa.Date(), nullable=True), - sa.Column('field_sample_storage_location_id', sa.Integer(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('field_sample_condition', - sa.Column('field_sample_id', sa.Integer(), nullable=True), - sa.Column('ag_treatment_id', sa.Integer(), nullable=True), - sa.Column('last_application_date', sa.Date(), nullable=True), - sa.Column('treatment_amount_per_acre', sa.Float(), nullable=True), - sa.Column('processing_method_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('field_storage_method', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('file_object_metadata', - sa.Column('data_source_id', sa.Integer(), nullable=True), - sa.Column('bucket_path', sa.Text(), nullable=True), - sa.Column('file_format', sa.Text(), nullable=True), - sa.Column('file_size', sa.Integer(), nullable=True), - sa.Column('checksum_md5', sa.Text(), nullable=True), - sa.Column('checksum_sha256', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('ftnir_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('gasification_record', - sa.Column('feedstock_mass', sa.Numeric(), nullable=True), - sa.Column('bed_temperature', sa.Numeric(), nullable=True), - sa.Column('gas_flow_rate', sa.Numeric(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('geography', - sa.Column('geoid', sa.Text(), nullable=False), - sa.Column('state_name', sa.Text(), nullable=True), - sa.Column('state_fips', sa.Text(), nullable=True), - sa.Column('county_name', sa.Text(), nullable=True), - sa.Column('county_fips', sa.Text(), nullable=True), - sa.Column('region_name', sa.Text(), nullable=True), - sa.Column('agg_level_desc', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('geoid') - ) - op.create_table('harvest_method', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('icp_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('landiq_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('polygon_id', sa.Integer(), nullable=True), - sa.Column('main_crop', sa.Integer(), nullable=True), - sa.Column('secondary_crop', sa.Integer(), nullable=True), - sa.Column('tertiary_crop', sa.Integer(), nullable=True), - sa.Column('quaternary_crop', sa.Integer(), nullable=True), - sa.Column('confidence', sa.Integer(), nullable=True), - sa.Column('irrigated', sa.Boolean(), nullable=True), - sa.Column('acres', sa.Float(), nullable=True), - sa.Column('version', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('lineage_group', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('location_address', - sa.Column('geography_id', sa.Text(), nullable=True), - sa.Column('address_line1', sa.Text(), nullable=True), - sa.Column('address_line2', sa.Text(), nullable=True), - sa.Column('city', sa.Text(), nullable=True), - sa.Column('zip', sa.Text(), nullable=True), - sa.Column('lat', sa.Float(), nullable=True), - sa.Column('lon', sa.Float(), nullable=True), - sa.Column('is_anonymous', sa.Boolean(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('location_resolution', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('location_soil_type', - sa.Column('location_id', sa.Integer(), nullable=True), - sa.Column('soil_type_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('lookup_base', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('method', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('method_category_id', sa.Integer(), nullable=True), - sa.Column('method_standard_id', sa.Integer(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('detection_limits', sa.Text(), nullable=True), - sa.Column('source_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('method_abbrev', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('method_category', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('method_standard', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('observation', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('record_type', sa.Text(), nullable=True), - sa.Column('record_id', sa.Integer(), nullable=True), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('value', sa.Numeric(), nullable=True), - sa.Column('unit_id', sa.Integer(), nullable=True), - sa.Column('dimension_type_id', sa.Integer(), nullable=True), - sa.Column('dimension_value', sa.Numeric(), nullable=True), - sa.Column('dimension_unit_id', sa.Integer(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('parameter', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('standard_unit_id', sa.Integer(), nullable=True), - sa.Column('calculated', sa.Boolean(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('parameter_category', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('parameter_category_parameter', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('parameter_category_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('parameter_unit', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('parameter_id', sa.Integer(), nullable=True), - sa.Column('alternate_unit_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('physical_characteristic', - sa.Column('field_sample_id', sa.Integer(), nullable=True), - sa.Column('particle_length', sa.Numeric(), nullable=True), - sa.Column('particle_width', sa.Numeric(), nullable=True), - sa.Column('particle_height', sa.Numeric(), nullable=True), - sa.Column('particle_unit_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('polygon', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('geom', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('preparation_method', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('prep_method_abbrev_id', sa.Integer(), nullable=True), - sa.Column('prep_temp_c', sa.Numeric(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.Column('drying_step', sa.Boolean(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('preparation_method_abbreviation', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('prepared_sample', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('field_sample_id', sa.Integer(), nullable=True), - sa.Column('prep_method_id', sa.Integer(), nullable=True), - sa.Column('prep_date', sa.Date(), nullable=True), - sa.Column('preparer_id', sa.Integer(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('pretreatment_record', - sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), - sa.Column('eh_method_id', sa.Integer(), nullable=True), - sa.Column('reaction_block_id', sa.Integer(), nullable=True), - sa.Column('block_position', sa.Text(), nullable=True), - sa.Column('temperature', sa.Numeric(), nullable=True), - sa.Column('replicate_no', sa.Integer(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('analyst_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('primary_crop', - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('processing_method', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('provider', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('codename', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('proximate_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource', - sa.Column('name', sa.Text(), nullable=True), - sa.Column('primary_crop_id', sa.Integer(), nullable=True), - sa.Column('resource_class_id', sa.Integer(), nullable=True), - sa.Column('resource_subclass_id', sa.Integer(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_availability', - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('from_month', sa.Integer(), nullable=True), - sa.Column('to_month', sa.Integer(), nullable=True), - sa.Column('year_round', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_class', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_counterfactual', - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('counterfactual_description', sa.Text(), nullable=True), - sa.Column('animal_bedding_percent', sa.Numeric(), nullable=True), - sa.Column('animal_bedding_source_id', sa.Integer(), nullable=True), - sa.Column('animal_feed_percent', sa.Numeric(), nullable=True), - sa.Column('animal_feed_source_id', sa.Integer(), nullable=True), - sa.Column('bioelectricty_percent', sa.Numeric(), nullable=True), - sa.Column('bioelectricty_source_id', sa.Integer(), nullable=True), - sa.Column('burn_percent', sa.Numeric(), nullable=True), - sa.Column('burn_source_id', sa.Integer(), nullable=True), - sa.Column('compost_percent', sa.Numeric(), nullable=True), - sa.Column('compost_source_id', sa.Integer(), nullable=True), - sa.Column('landfill_percent', sa.Numeric(), nullable=True), - sa.Column('landfill_source_id', sa.Integer(), nullable=True), - sa.Column('counterfactual_date', sa.Date(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_morphology', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('morphology_uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_subclass', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('resource_usda_commodity_map', - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('primary_crop_id', sa.Integer(), nullable=True), - sa.Column('usda_commodity_id', sa.Integer(), nullable=True), - sa.Column('match_tier', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('rgb_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('soil_type', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('source_type', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('strain', - sa.Column('parent_strain_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('ultimate_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('unit', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_census_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('commodity_code', sa.Integer(), nullable=True), - sa.Column('year', sa.Integer(), nullable=True), - sa.Column('source_reference', sa.Text(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_commodity', - sa.Column('usda_source', sa.Text(), nullable=True), - sa.Column('usda_code', sa.Text(), nullable=True), - sa.Column('parent_commodity_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_domain', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_market_record', - sa.Column('report_id', sa.Integer(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('report_begin_date', sa.DateTime(), nullable=True), - sa.Column('report_end_date', sa.DateTime(), nullable=True), - sa.Column('report_date', sa.DateTime(), nullable=True), - sa.Column('commodity_id', sa.Integer(), nullable=True), - sa.Column('market_type_id', sa.Integer(), nullable=True), - sa.Column('market_type_catagory', sa.Text(), nullable=True), - sa.Column('grp', sa.Text(), nullable=True), - sa.Column('market_catagory_id', sa.Integer(), nullable=True), - sa.Column('class_', sa.Text(), nullable=True), - sa.Column('grade', sa.Text(), nullable=True), - sa.Column('variety', sa.Text(), nullable=True), - sa.Column('protein_pct', sa.Numeric(), nullable=True), - sa.Column('application', sa.Text(), nullable=True), - sa.Column('pkg', sa.Text(), nullable=True), - sa.Column('sale_type', sa.Text(), nullable=True), - sa.Column('price_unit_id', sa.Integer(), nullable=True), - sa.Column('freight', sa.Text(), nullable=True), - sa.Column('trans_mode', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_market_report', - sa.Column('slug_id', sa.Integer(), nullable=True), - sa.Column('slug_name', sa.Text(), nullable=True), - sa.Column('report_series_title', sa.Text(), nullable=True), - sa.Column('frequency', sa.Text(), nullable=True), - sa.Column('office_name', sa.Text(), nullable=True), - sa.Column('office_city_id', sa.Integer(), nullable=True), - sa.Column('office_state_fips', sa.Text(), nullable=True), - sa.Column('source_id', sa.Integer(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_statistic_category', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_survey_program', - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('name', sa.Text(), nullable=True), - sa.Column('description', sa.Text(), nullable=True), - sa.Column('uri', sa.Text(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_survey_record', - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('geoid', sa.Text(), nullable=True), - sa.Column('commodity_code', sa.Integer(), nullable=True), - sa.Column('year', sa.Integer(), nullable=True), - sa.Column('survey_program_id', sa.Integer(), nullable=True), - sa.Column('survey_period', sa.Text(), nullable=True), - sa.Column('reference_month', sa.Text(), nullable=True), - sa.Column('seasonal_flag', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('usda_term_map', - sa.Column('source_system', sa.Text(), nullable=True), - sa.Column('source_context', sa.Text(), nullable=True), - sa.Column('raw_term', sa.Text(), nullable=True), - sa.Column('usda_commodity_id', sa.Integer(), nullable=True), - sa.Column('is_verified', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('xrd_record', - sa.Column('maybe_scan_low_nm', sa.Integer(), nullable=True), - sa.Column('maybe_scan_high_nm', sa.Integer(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.create_table('xrf_record', - sa.Column('maybe_wavelength_nm', sa.Numeric(), nullable=True), - sa.Column('maybe_intensity', sa.Numeric(), nullable=True), - sa.Column('maybe_energy_slope', sa.Numeric(), nullable=True), - sa.Column('maybe_energy_offset', sa.Numeric(), nullable=True), - sa.Column('dataset_id', sa.Integer(), nullable=True), - sa.Column('experiment_id', sa.Integer(), nullable=True), - sa.Column('resource_id', sa.Integer(), nullable=True), - sa.Column('sample_id', sa.Integer(), nullable=True), - sa.Column('technical_replicate_no', sa.Integer(), nullable=True), - sa.Column('technical_replicate_total', sa.Integer(), nullable=True), - sa.Column('method_id', sa.Integer(), nullable=True), - sa.Column('raw_data_id', sa.Integer(), nullable=True), - sa.Column('qc_pass', sa.Boolean(), nullable=True), - sa.Column('note', sa.Text(), nullable=True), - sa.Column('id', sa.Integer(), nullable=False), - sa.Column('created_at', sa.DateTime(), nullable=True), - sa.Column('updated_at', sa.DateTime(), nullable=True), - sa.Column('etl_run_id', sa.Text(), nullable=True), - sa.Column('lineage_group_id', sa.Integer(), nullable=True), - sa.PrimaryKeyConstraint('id') - ) - op.drop_table('UsdaMarketRecord') - op.drop_table('ResourceAvailability') - op.drop_table('PreparedSample') - op.drop_table('UsdaStatisticCategory') - op.drop_table('PrimaryCrop') - op.drop_table('BaseEntity') - op.drop_table('ResourceCounterfactual') - op.drop_table('UltimateRecord') - op.drop_table('SourceType') - op.drop_table('Contact') - op.drop_table('DataSourceType') - op.drop_table('ParameterUnit') - op.drop_table('Parameter') - op.drop_table('UsdaTermMap') - op.drop_table('Experiment') - op.drop_table('ParameterCategory') - op.drop_table('ExperimentEquipment') - op.drop_table('Aim1RecordBase') - op.drop_table('Geography') - op.drop_table('Method') - op.drop_table('LineageGroup') - op.drop_table('RgbRecord') - op.drop_table('MethodStandard') - op.drop_table('PretreatmentRecord') - op.drop_table('ResourceSubclass') - op.drop_table('UsdaMarketReport') - op.drop_table('Polygon') - op.drop_table('LocationResolution') - op.drop_table('ResourceMorphology') - op.drop_table('AutoclaveRecord') - op.drop_table('DimensionType') - op.drop_table('CompositionalRecord') - op.drop_table('PhysicalCharacteristic') - op.drop_table('Aim2RecordBase') - op.drop_table('UsdaCensusRecord') - op.drop_table('ResourceUsdaCommodityMap') - op.drop_table('AnalysisType') - op.drop_table('ParameterCategoryParameter') - op.drop_table('ExperimentAnalysis') - op.drop_table('UsdaDomain') - op.drop_table('HarvestMethod') - op.drop_table('LookupBase') - op.drop_table('FtnirRecord') - op.drop_table('Resource') - op.drop_table('Equipment') - op.drop_table('DataSource') - op.drop_table('ResourceClass') - op.drop_table('LocationAddress') - op.drop_table('UsdaSurveyRecord') - op.drop_table('FermentationRecord') - op.drop_table('XrdRecord') - op.drop_table('AgTreatment') - op.drop_table('ExperimentMethod') - op.drop_table('Dataset') - op.drop_table('LocationSoilType') - op.drop_table('FieldSampleCondition') - op.drop_table('XrfRecord') - op.drop_table('MethodAbbrev') - op.drop_table('Provider') - op.drop_table('LandiqRecord') - op.drop_table('EntityLineage') - op.drop_table('Unit') - op.drop_table('CalorimetryRecord') - op.drop_table('ExperimentPreparedSample') - op.drop_table('CollectionMethod') - op.drop_table('IcpRecord') - op.drop_table('PreparationMethodAbbreviation') - op.drop_table('BillionTon2023Record') - op.drop_table('ProcessingMethod') - op.drop_table('EtlRun') - op.drop_table('FileObjectMetadata') - op.drop_table('MethodCategory') - op.drop_table('GasificationRecord') - op.drop_table('UsdaCommodity') - op.drop_table('PreparationMethod') - op.drop_table('Observation') - op.drop_table('SoilType') - op.drop_table('FieldSample') - op.drop_table('FieldStorageMethod') - op.drop_table('Strain') - op.drop_table('ProximateRecord') - op.drop_table('UsdaSurveyProgram') - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.create_table('UsdaSurveyProgram', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaSurveyProgram_pkey')) - ) - op.create_table('ProximateRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ProximateRecord_pkey')) - ) - op.create_table('Strain', - sa.Column('parent_strain_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Strain_pkey')) - ) - op.create_table('FieldStorageMethod', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FieldStorageMethod_pkey')) - ) - op.create_table('FieldSample', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('provider_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('collector_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_collection_source', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('amount_collected', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('amount_collected_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sampling_location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('field_storage_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('field_storage_duration_value', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('field_storage_duration_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('field_storage_location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('collection_timestamp', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('collection_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('harvest_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('harvest_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('field_sample_storage_location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FieldSample_pkey')) - ) - op.create_table('SoilType', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('SoilType_pkey')) - ) - op.create_table('Observation', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('record_type', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('record_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('value', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dimension_type_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dimension_value', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('dimension_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Observation_pkey')) - ) - op.create_table('PreparationMethod', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('prep_method_abbrev_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('prep_temp_c', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('drying_step', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PreparationMethod_pkey')) - ) - op.create_table('UsdaCommodity', - sa.Column('usda_source', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('usda_code', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('parent_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaCommodity_pkey')) - ) - op.create_table('GasificationRecord', - sa.Column('feedstock_mass', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('bed_temperature', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('gas_flow_rate', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('GasificationRecord_pkey')) - ) - op.create_table('MethodCategory', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('MethodCategory_pkey')) - ) - op.create_table('FileObjectMetadata', - sa.Column('data_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('bucket_path', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('file_format', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('file_size', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('checksum_md5', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('checksum_sha256', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FileObjectMetadata_pkey')) - ) - op.create_table('EtlRun', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('started_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('completed_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('pipeline_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('records_ingested', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('EtlRun_pkey')) - ) - op.create_table('ProcessingMethod', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ProcessingMethod_pkey')) - ) - op.create_table('BillionTon2023Record', - sa.Column('subclass_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('county_square_miles', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), - sa.Column('model_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('scenario_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('price_offered_usd', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('production', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('production_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('btu_ton', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('production_energy_content', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('energy_content_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('product_density_dtpersqmi', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('land_source', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('BillionTon2023Record_pkey')) - ) - op.create_table('PreparationMethodAbbreviation', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PreparationMethodAbbreviation_pkey')) - ) - op.create_table('IcpRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('IcpRecord_pkey')) - ) - op.create_table('CollectionMethod', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('CollectionMethod_pkey')) - ) - op.create_table('ExperimentPreparedSample', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('prepared_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ExperimentPreparedSample_pkey')) - ) - op.create_table('CalorimetryRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('CalorimetryRecord_pkey')) - ) - op.create_table('Unit', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Unit_pkey')) - ) - op.create_table('EntityLineage', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('source_table', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('source_row_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('EntityLineage_pkey')) - ) - op.create_table('LandiqRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('polygon_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('main_crop', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('secondary_crop', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('tertiary_crop', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('quaternary_crop', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('confidence', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('irrigated', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('acres', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), - sa.Column('version', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LandiqRecord_pkey')) - ) - op.create_table('Provider', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('codename', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Provider_pkey')) - ) - op.create_table('MethodAbbrev', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('MethodAbbrev_pkey')) - ) - op.create_table('XrfRecord', - sa.Column('maybe_wavelength_nm', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('maybe_intensity', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('maybe_energy_slope', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('maybe_energy_offset', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('XrfRecord_pkey')) - ) - op.create_table('FieldSampleCondition', - sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('ag_treatment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('last_application_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('treatment_amount_per_acre', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), - sa.Column('processing_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FieldSampleCondition_pkey')) - ) - op.create_table('LocationSoilType', - sa.Column('location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('soil_type_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LocationSoilType_pkey')) - ) - op.create_table('Dataset', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('record_type', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('start_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('end_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Dataset_pkey')) - ) - op.create_table('ExperimentMethod', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ExperimentMethod_pkey')) - ) - op.create_table('AgTreatment', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('AgTreatment_pkey')) - ) - op.create_table('XrdRecord', - sa.Column('maybe_scan_low_nm', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('maybe_scan_high_nm', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('XrdRecord_pkey')) - ) - op.create_table('FermentationRecord', - sa.Column('strain_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('pretreatment_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('eh_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('well_position', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('temperature', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('agitation_rpm', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('vessel_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyte_detection_equipment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FermentationRecord_pkey')) - ) - op.create_table('UsdaSurveyRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('commodity_code', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('year', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('survey_program_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('survey_period', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('reference_month', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('seasonal_flag', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaSurveyRecord_pkey')) - ) - op.create_table('LocationAddress', - sa.Column('geography_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('address_line1', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('address_line2', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('zip', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lat', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), - sa.Column('lon', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), - sa.Column('is_anonymous', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LocationAddress_pkey')) - ) - op.create_table('ResourceClass', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceClass_pkey')) - ) - op.create_table('DataSource', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('publication_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('version', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('publisher', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('author', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('license', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('DataSource_pkey')) - ) - op.create_table('Equipment', - sa.Column('equipment_location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Equipment_pkey')) - ) - op.create_table('Resource', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('primary_crop_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_class_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_subclass_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Resource_pkey')) - ) - op.create_table('FtnirRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('FtnirRecord_pkey')) - ) - op.create_table('LookupBase', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LookupBase_pkey')) - ) - op.create_table('HarvestMethod', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('HarvestMethod_pkey')) - ) - op.create_table('UsdaDomain', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaDomain_pkey')) - ) - op.create_table('ExperimentAnalysis', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analysis_type_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ExperimentAnalysis_pkey')) - ) - op.create_table('ParameterCategoryParameter', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('parameter_category_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ParameterCategoryParameter_pkey')) - ) - op.create_table('AnalysisType', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('AnalysisType_pkey')) - ) - op.create_table('ResourceUsdaCommodityMap', - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('primary_crop_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('usda_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('match_tier', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceUsdaCommodityMap_pkey')) - ) - op.create_table('UsdaCensusRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('commodity_code', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('year', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('source_reference', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaCensusRecord_pkey')) - ) - op.create_table('Aim2RecordBase', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Aim2RecordBase_pkey')) - ) - op.create_table('PhysicalCharacteristic', - sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('particle_length', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('particle_width', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('particle_height', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('particle_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PhysicalCharacteristic_pkey')) - ) - op.create_table('CompositionalRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('CompositionalRecord_pkey')) - ) - op.create_table('DimensionType', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('DimensionType_pkey')) - ) - op.create_table('AutoclaveRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('AutoclaveRecord_pkey')) - ) - op.create_table('ResourceMorphology', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('morphology_uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceMorphology_pkey')) - ) - op.create_table('LocationResolution', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LocationResolution_pkey')) - ) - op.create_table('Polygon', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('geom', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Polygon_pkey')) - ) - op.create_table('UsdaMarketReport', - sa.Column('slug_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('slug_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('report_series_title', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('frequency', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('office_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('office_city_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('office_state_fips', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaMarketReport_pkey')) - ) - op.create_table('ResourceSubclass', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceSubclass_pkey')) - ) - op.create_table('PretreatmentRecord', - sa.Column('pretreatment_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('eh_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('reaction_block_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('block_position', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('temperature', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PretreatmentRecord_pkey')) - ) - op.create_table('MethodStandard', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('MethodStandard_pkey')) - ) - op.create_table('RgbRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('RgbRecord_pkey')) - ) - op.create_table('LineageGroup', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('LineageGroup_pkey')) - ) - op.create_table('Method', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('method_abbrev_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_category_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_standard_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('detection_limits', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Method_pkey')) - ) - op.create_table('Geography', - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=False), - sa.Column('state_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('state_fips', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('county_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('county_fips', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('region_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('agg_level_desc', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('geoid', name=op.f('Geography_pkey')) - ) - op.create_table('Aim1RecordBase', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Aim1RecordBase_pkey')) - ) - op.create_table('ExperimentEquipment', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('equipment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ExperimentEquipment_pkey')) - ) - op.create_table('ParameterCategory', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ParameterCategory_pkey')) - ) - op.create_table('Experiment', - sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('exper_start_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('exper_duration', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('exper_duration_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('exper_location_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Experiment_pkey')) - ) - op.create_table('UsdaTermMap', - sa.Column('source_system', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('source_context', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('raw_term', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('usda_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('is_verified', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaTermMap_pkey')) - ) - op.create_table('Parameter', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('standard_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('calculated', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Parameter_pkey')) - ) - op.create_table('ParameterUnit', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('alternate_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ParameterUnit_pkey')) - ) - op.create_table('DataSourceType', - sa.Column('source_type_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('DataSourceType_pkey')) - ) - op.create_table('Contact', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('first_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('last_name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('email', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('affiliation', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('Contact_pkey')) - ) - op.create_table('SourceType', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('SourceType_pkey')) - ) - op.create_table('UltimateRecord', - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UltimateRecord_pkey')) - ) - op.create_table('ResourceCounterfactual', - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('counterfactual_description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('animal_bedding_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('animal_bedding_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('animal_feed_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('animal_feed_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('bioelectricty_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('bioelectricty_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('burn_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('burn_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('compost_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('compost_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('landfill_percent', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('landfill_source_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('counterfactual_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceCounterfactual_pkey')) - ) - op.create_table('BaseEntity', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('BaseEntity_pkey')) - ) - op.create_table('PrimaryCrop', - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PrimaryCrop_pkey')) - ) - op.create_table('UsdaStatisticCategory', - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaStatisticCategory_pkey')) - ) - op.create_table('PreparedSample', - sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('prep_method_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('prep_date', sa.DATE(), autoincrement=False, nullable=True), - sa.Column('preparer_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('PreparedSample_pkey')) - ) - op.create_table('ResourceAvailability', - sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('from_month', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('to_month', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('year_round', sa.BOOLEAN(), autoincrement=False, nullable=True), - sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('ResourceAvailability_pkey')) - ) - op.create_table('UsdaMarketRecord', - sa.Column('report_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('report_begin_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('report_end_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('report_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('market_type_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('market_type_catagory', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('grp', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('market_catagory_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('class_', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('grade', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('variety', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('protein_pct', sa.NUMERIC(), autoincrement=False, nullable=True), - sa.Column('application', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('pkg', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('sale_type', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('price_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.Column('freight', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('trans_mode', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), - sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), - sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), - sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), - sa.PrimaryKeyConstraint('id', name=op.f('UsdaMarketRecord_pkey')) - ) - op.drop_table('xrf_record') - op.drop_table('xrd_record') - op.drop_table('usda_term_map') - op.drop_table('usda_survey_record') - op.drop_table('usda_survey_program') - op.drop_table('usda_statistic_category') - op.drop_table('usda_market_report') - op.drop_table('usda_market_record') - op.drop_table('usda_domain') - op.drop_table('usda_commodity') - op.drop_table('usda_census_record') - op.drop_table('unit') - op.drop_table('ultimate_record') - op.drop_table('strain') - op.drop_table('source_type') - op.drop_table('soil_type') - op.drop_table('rgb_record') - op.drop_table('resource_usda_commodity_map') - op.drop_table('resource_subclass') - op.drop_table('resource_morphology') - op.drop_table('resource_counterfactual') - op.drop_table('resource_class') - op.drop_table('resource_availability') - op.drop_table('resource') - op.drop_table('proximate_record') - op.drop_table('provider') - op.drop_table('processing_method') - op.drop_table('primary_crop') - op.drop_table('pretreatment_record') - op.drop_table('prepared_sample') - op.drop_table('preparation_method_abbreviation') - op.drop_table('preparation_method') - op.drop_table('polygon') - op.drop_table('physical_characteristic') - op.drop_table('parameter_unit') - op.drop_table('parameter_category_parameter') - op.drop_table('parameter_category') - op.drop_table('parameter') - op.drop_table('observation') - op.drop_table('method_standard') - op.drop_table('method_category') - op.drop_table('method_abbrev') - op.drop_table('method') - op.drop_table('lookup_base') - op.drop_table('location_soil_type') - op.drop_table('location_resolution') - op.drop_table('location_address') - op.drop_table('lineage_group') - op.drop_table('landiq_record') - op.drop_table('icp_record') - op.drop_table('harvest_method') - op.drop_table('geography') - op.drop_table('gasification_record') - op.drop_table('ftnir_record') - op.drop_table('file_object_metadata') - op.drop_table('field_storage_method') - op.drop_table('field_sample_condition') - op.drop_table('field_sample') - op.drop_table('fermentation_record') - op.drop_table('experiment_prepared_sample') - op.drop_table('experiment_method') - op.drop_table('experiment_equipment') - op.drop_table('experiment_analysis') - op.drop_table('experiment') - op.drop_table('etl_run') - op.drop_table('equipment') - op.drop_table('entity_lineage') - op.drop_table('dimension_type') - op.drop_table('dataset') - op.drop_table('data_source_type') - op.drop_table('data_source') - op.drop_table('contact') - op.drop_table('compositional_record') - op.drop_table('collection_method') - op.drop_table('calorimetry_record') - op.drop_table('billion_ton2023_record') - op.drop_table('base_entity') - op.drop_table('autoclave_record') - op.drop_table('analysis_type') - op.drop_table('aim2_record_base') - op.drop_table('aim1_record_base') - op.drop_table('ag_treatment') - # ### end Alembic commands ### diff --git a/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py b/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py deleted file mode 100644 index c1db3ff6..00000000 --- a/alembic/versions/b838c837616b_adding_a_test_to_landiqrecord.py +++ /dev/null @@ -1,32 +0,0 @@ -"""adding a test to landiqrecord - -Revision ID: b838c837616b -Revises: 42618fe6b09b -Create Date: 2025-12-08 22:33:34.608783 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = 'b838c837616b' -down_revision: Union[str, Sequence[str], None] = '42618fe6b09b' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.add_column('landiq_record', sa.Column('test', sa.Text(), nullable=True)) - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.drop_column('landiq_record', 'test') - # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/biomass.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/biomass.py deleted file mode 100644 index 03d4bfb1..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/biomass.py +++ /dev/null @@ -1,306 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - - -# ------------------------------------------------------------ -# SQLModel classes generated from the DBdiagram schema -# ------------------------------------------------------------ - - - -# If you later want to add real FK constraints you can uncomment the import below -# from sqlalchemy import Column, Numeric, DateTime, func - - -# ---------------------------------------------------------------------- -# Table: field_samples -# ---------------------------------------------------------------------- -class FieldSample(SQLModel, table=True): - """Sample metadata collected in the field.""" - __tablename__ = "field_samples" - - sample_id: Optional[int] = Field( - default=None, - primary_key=True, - description="Unique identifier for each sample", - ) - biomass_id: int = Field( - default=None, - index=True, - description="Reference to biomass" - # foreign_key="biomass.biomass_id" - ) - sample_name: str = Field( - default=None, - description='e.g., "Ene‑WaHu018"', - ) - source_codename_id: Optional[int] = Field( - default=None, - index=True, - description="Anonymized source identifier", - ) - data_source_id: Optional[int] = Field( - default=None, - description="Reference to data source" - # foreign_key="data_sources.source_id" - ) - location_id: Optional[int] = Field( - default=None, - description="Reference to geographic location (may be null)" - # foreign_key="geographic_locations.location_id" - ) - field_storage_id: Optional[int] = Field( - default=None, - description="Reference to field storage" - # foreign_key="field_storage.field_storage_id" - ) - field_storage_duration_value: Optional[Decimal] = Field( - default=None, - description="Duration value for field storage", - ) - field_storage_duration_unit_id: Optional[int] = Field( - default=None, - description="Reference to unit of storage duration" - # foreign_key="units.unit_id" - ) - collection_timestamp: Optional[datetime] = Field(default=None) - collection_method_id: Optional[int] = Field( - default=None, - description="Reference to collection method" - # foreign_key="collection_methods.collection_method_id" - ) - harvest_method_id: Optional[int] = Field( - default=None, - description="Reference to harvest method" - # foreign_key="harvest_methods.harvest_method_id" - ) - harvest_date: Optional[date] = Field(default=None) - amount_collected_kg: Optional[Decimal] = Field(default=None) - provider_id: Optional[int] = Field( - default=None, - description="Reference to provider (anonymized)" - # foreign_key="providers.provider_id" - ) - collector_id: Optional[int] = Field( - default=None, - description="Reference to collector" - # foreign_key="collectors.collector_id" - ) - basic_sample_info_note: Optional[str] = Field(default=None) - created_at: datetime = Field( - default_factory=datetime.utcnow, - description="Timestamp when the record was created", - ) - - -# ---------------------------------------------------------------------- -# Table: biomass -# ---------------------------------------------------------------------- -class Biomass(SQLModel, table=True): - """Core biomass entity.""" - __tablename__ = "biomass" - - biomass_id: Optional[int] = Field(default=None, primary_key=True) - biomass_name: str = Field(default=None, index=True) - primary_product_id: Optional[int] = Field( - default=None, - description="Reference to primary product" - # foreign_key="primary_product.primary_product_id" - ) - taxonomy_id: Optional[int] = Field( - default=None, - description="Reference to taxonomy" - # foreign_key="taxonomy.taxonomy_id" - ) - biomass_type_id: Optional[int] = Field( - default=None, - index=True, - description="Reference to biomass type" - # foreign_key="biomass_type.biomass_type_id" - ) - biomass_notes: Optional[str] = Field(default=None) - - -# ---------------------------------------------------------------------- -# Table: biomass_test -# ---------------------------------------------------------------------- - -class BiomassTest(SQLModel, table=True): - """Testing Table""" - __tablename__ = "biomass_test" - - biomass_test_id: Optional[int] = Field(default=None, primary_key=True) - biomass_test_name: str = Field(default=None, index=True) - biomass_test_notes: Optional[str] = Field(default=None) - - - -# ---------------------------------------------------------------------- -# Table: biomass_type -# ---------------------------------------------------------------------- -class BiomassType(SQLModel, table=True): - """Lookup table for biomass type (e.g., crop by‑product, wood residue).""" - __tablename__ = "biomass_type" - - biomass_type_id: Optional[int] = Field(default=None, primary_key=True) - biomass_type: str = Field( - default=None, - unique=True, - description="Crop by‑product, Wood residue, etc.", - ) - - -# ---------------------------------------------------------------------- -# Table: primary_product -# ---------------------------------------------------------------------- -class PrimaryProduct(SQLModel, table=True): - """Lookup table for primary products derived from biomass.""" - __tablename__ = "primary_product" - - primary_product_id: Optional[int] = Field(default=None, primary_key=True) - primary_product_name: str = Field(default=None, unique=True) - - -# ---------------------------------------------------------------------- -# Table: biomass_availability -# ---------------------------------------------------------------------- -class BiomassAvailability(SQLModel, table=True): - """Seasonal and quantitative availability of a biomass.""" - __tablename__ = "biomass_availability" - - availability_id: Optional[int] = Field(default=None, primary_key=True) - biomass_id: int = Field( - default=None, - index=True, - description="Reference to biomass" - # foreign_key="biomass.biomass_id" - ) - location_id: Optional[int] = Field( - default=None, - description="Reference to geographic location" - # foreign_key="geographic_locations.location_id" - ) - primary_product_id: Optional[int] = Field( - default=None, - description="Reference to primary product" - # foreign_key="primary_product.primary_product_id" - ) - from_month: Optional[Decimal] = Field( - default=None, - description="Start month (e.g. 1 = Jan, 6.5 = mid‑June)", - ) - to_month: Optional[Decimal] = Field( - default=None, - description="End month (e.g. 12 = Dec)", - ) - kg_low: Optional[Decimal] = Field(default=None, description="Annual low estimate (kg)") - kg_avg: Optional[Decimal] = Field(default=None, description="Annual average estimate (kg)") - kg_high: Optional[Decimal] = Field(default=None, description="Annual high estimate (kg)") - bdt_low: Optional[Decimal] = Field(default=None, description="Bone‑dry tons low estimate") - bdt_avg: Optional[Decimal] = Field(default=None, description="Bone‑dry tons average") - bdt_high: Optional[Decimal] = Field(default=None, description="Bone‑dry tons high estimate") - data_source: Optional[int] = Field( - default=None, - description="Reference to data source" - # foreign_key="data_sources.source_id" - ) - availability_notes: Optional[str] = Field(default=None) - - -# ---------------------------------------------------------------------- -# Table: biomass_quality -# ---------------------------------------------------------------------- -class BiomassQuality(SQLModel, table=True): - """Qualitative attributes of a biomass.""" - __tablename__ = "biomass_quality" - - quality_id: Optional[int] = Field(default=None, primary_key=True) - biomass_id: int = Field( - default=None, - index=True, - description="Reference to biomass" - # foreign_key="biomass.biomass_id" - ) - expected_quality: Optional[str] = Field(default=None) - output_feedstocks: Optional[str] = Field( - default=None, - description="(Optional) Output feedstocks – may be moved to another table", - ) - convertibility: Optional[str] = Field(default=None) - disposal_challenges: Optional[str] = Field( - default=None, - description="Nondisposability issues", - ) - existing_markets: Optional[str] = Field( - default=None, - description="Substitutability information", - ) - substitute_materials: Optional[str] = Field(default=None) - regulatory_issues: Optional[str] = Field(default=None) - quality_data_sources: Optional[int] = Field( - default=None, - description="Reference to data source" - # foreign_key="data_sources.source_id" - ) - notes: Optional[str] = Field(default=None) - - -# ---------------------------------------------------------------------- -# Table: biomass_price -# ---------------------------------------------------------------------- -class BiomassPrice(SQLModel, table=True): - """Pricing information for a biomass.""" - __tablename__ = "biomass_price" - - price_id: Optional[int] = Field(default=None, primary_key=True) - biomass_id: int = Field( - default=None, - index=True, - description="Reference to biomass" - # foreign_key="biomass.biomass_id" - ) - price_per_kg_low: Optional[Decimal] = Field(default=None) - price_per_kg_avg: Optional[Decimal] = Field(default=None) - price_per_kg_high: Optional[Decimal] = Field(default=None) - price_data_sources: Optional[int] = Field( - default=None, - description="Reference to data source" - # foreign_key="data_sources.source_id" - ) - notes: Optional[str] = Field(default=None) - -# ---------------------------------------------------------------------- -# Table: harvest_methods -# ---------------------------------------------------------------------- -class HarvestMethod(SQLModel, table=True): - """Lookup table for harvest methods.""" - __tablename__ = "harvest_methods" - - harvest_method_id: Optional[int] = Field(default=None, primary_key=True) - harvest_method_name: str = Field(default=None, unique=True) - -# ---------------------------------------------------------------------- -# Table: collection_methods -# ---------------------------------------------------------------------- -class CollectionMethod(SQLModel, table=True): - """Lookup table for collection methods.""" - __tablename__ = "collection_methods" - - collection_method_id: Optional[int] = Field(default=None, primary_key=True) - collection_method_name: str = Field(default=None, unique=True) - -# ---------------------------------------------------------------------- -# Table: field_storage -# ---------------------------------------------------------------------- -class FieldStorage(SQLModel, table=True): - """Lookup table for field storage methods.""" - __tablename__ = "field_storage" - - field_storage_id: Optional[int] = Field(default=None, primary_key=True) - storage_method: str = Field(default=None, unique=True) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/config.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/config.py deleted file mode 100644 index 40f4f9da..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/config.py +++ /dev/null @@ -1,37 +0,0 @@ -"""Configuration for CA Biositing data models. - -This module provides configuration management for database models using Pydantic Settings. -""" - -from __future__ import annotations - -from typing import Optional - -from pydantic_settings import BaseSettings, SettingsConfigDict - - -class ModelConfig(BaseSettings): - """Configuration for database models. - - Attributes: - database_url: PostgreSQL database connection URL - echo_sql: Whether to echo SQL statements (for debugging) - pool_size: Database connection pool size - max_overflow: Maximum number of connections that can be created beyond pool_size - """ - - model_config = SettingsConfigDict( - env_file=".env", - env_file_encoding="utf-8", - case_sensitive=False, - extra="ignore", - ) - - database_url: str = "postgresql://user:password@localhost:5432/ca_biositing" - echo_sql: bool = False - pool_size: int = 5 - max_overflow: int = 10 - - -# Global configuration instance -config = ModelConfig() diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/data_and_references.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/data_and_references.py deleted file mode 100644 index 0634e482..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/data_and_references.py +++ /dev/null @@ -1,85 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - - -# ---------------------------------------------------------------------- -# Data source / reference tables -# ---------------------------------------------------------------------- - - -class DataSource(SQLModel, table=True): - """Source of data (internal / external).""" - __tablename__ = "data_sources" - - source_id: Optional[int] = Field(default=None, primary_key=True) - source_name_id: Optional[int] = Field(default=None, - description="Reference to source_names.source_name_id") - # foreign_key="source_names.source_name_id") - source_type_id: Optional[int] = Field(default=None, - description="Reference to source_types.source_type_id") - # foreign_key="source_types.source_type_id") - data_resolution_id: Optional[int] = Field(default=None, - description="Reference to location_resolutions.location_resolution_id") - # foreign_key="location_resolutions.location_resolution_id") - description: Optional[str] = Field(default=None) - url_id: Optional[int] = Field(default=None, - description="Reference to url.url_id") - # foreign_key="url.url_id") - import_timestamp: Optional[datetime] = Field(default=None) - - __table_args__ = (Index("idx_data_sources_source_name_id", "source_name_id"),) - - -class SourceName(SQLModel, table=True): - """Human‑readable name for a data source.""" - __tablename__ = "source_names" - - source_name_id: Optional[int] = Field(default=None, primary_key=True) - source_name: str = Field(..., unique=True, description="Not null") - - -class SourceType(SQLModel, table=True): - """Type of source (e.g., internal, external).""" - __tablename__ = "source_types" - - source_type_id: Optional[int] = Field(default=None, primary_key=True) - source_type: str = Field(..., unique=True, description="Not null") - - -class Reference(SQLModel, table=True): - """Bibliographic reference.""" - __tablename__ = "references" - - reference_id: Optional[int] = Field(default=None, primary_key=True) - reference_title: Optional[str] = Field(default=None) - reference_author: Optional[str] = Field(default=None) - reference_publication: Optional[str] = Field(default=None) - reference_date: Optional[date] = Field(default=None) - reference_doi_id: Optional[int] = Field(default=None, - description="Reference to DOI.doi_id") - # foreign_key="doi.doi_id") - url_id: Optional[int] = Field(default=None, - description="Reference to url.url_id") - # foreign_key="url.url_id") - - -class DOI(SQLModel, table=True): - """Digital Object Identifier.""" - __tablename__ = "doi" - - doi_id: Optional[int] = Field(default=None, primary_key=True) - doi: Optional[str] = Field(default=None) - - -class URL(SQLModel, table=True): - """Unique URL.""" - __tablename__ = "url" - - url_id: Optional[int] = Field(default=None, primary_key=True) - url: Optional[str] = Field(default=None, unique=True) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py deleted file mode 100644 index 77e970af..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py +++ /dev/null @@ -1,27 +0,0 @@ -"""Database connection and session management for CA Biositing data models.""" - -from __future__ import annotations - -from typing import Generator - -from sqlmodel import Session, create_engine - -from ca_biositing.datamodels.config import config - -# Create database engine -engine = create_engine( - config.database_url, - echo=config.echo_sql, - pool_size=config.pool_size, - max_overflow=config.max_overflow, -) - - -def get_session() -> Generator[Session, None, None]: - """Get a database session. - - Yields: - Session: SQLModel database session - """ - with Session(engine) as session: - yield session diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/experiments_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/experiments_analysis.py deleted file mode 100644 index ff68ecbb..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/experiments_analysis.py +++ /dev/null @@ -1,296 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# Experiments & analyses -# ---------------------------------------------------------------------- - - -class Experiment(SQLModel, table=True): - """Experiment definition.""" - __tablename__ = "experiments" - - experiment_id: Optional[int] = Field(default=None, primary_key=True) - exper_uuid: Optional[str] = Field(default=None, unique=True) - gsheet_exper_id: Optional[int] = Field(default=None, unique=True, - description="e.g., Ex05") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id",) - # foreign_key="analysis_types.analysis_type_id") - analysis_abbrev_id: Optional[int] = Field(default=None, - description="Reference to analysis_abbreviations.analysis_abbreviations_id",) - # foreign_key="analysis_abbreviations.analysis_abbreviations_id") - exper_start_date: Optional[date] = Field(default=None) - exper_duration: Optional[Decimal] = Field(default=None) - exper_duration_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id",) - # foreign_key="units.unit_id") - exper_location_id: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id",) - # foreign_key="geographic_locations.location_id") - exper_description: Optional[str] = Field(default=None) - - __table_args__ = (Index("idx_experiments_analysis_type_id", "analysis_type_id"),) - - -class ExperimentMethod(SQLModel, table=True): - """Link table for many‑to‑many relationship between experiments and methods.""" - __tablename__ = "experiment_methods" - - experiment_method_id: Optional[int] = Field(default=None, primary_key=True) - experiment_id: Optional[int] = Field(default=None, - description="Reference to experiments.experiment_id",) - # foreign_key="experiments.experiment_id") - method_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id",) - # foreign_key="methods.method_id") - - __table_args__ = ( - Index("idx_experiment_methods_method_id", "method_id"), - Index("idx_experiment_methods_experiment_id", "experiment_id"), - ) - - -class AnalysisType(SQLModel, table=True): - """Type of analysis (e.g., XRF, proximate).""" - __tablename__ = "analysis_types" - - analysis_type_id: Optional[int] = Field(default=None, primary_key=True) - analysis_name: Optional[str] = Field(default=None, unique=True, - description="X‑Ray Fluorescence analysis, Proximate analysis, Chemical Composition, Fermentation Profile, etc.") - - -class AnalysisAbbreviation(SQLModel, table=True): - """Abbreviation for an analysis type.""" - __tablename__ = "analysis_abbreviations" - - analysis_abbreviations_id: Optional[int] = Field(default=None, primary_key=True) - analysis_abbreviation: Optional[str] = Field(default=None, unique=True, - description="XRF, Prox, Comp, etc.") - - -class AnalysisResult(SQLModel, table=True): - """Result of a single analysis measurement.""" - __tablename__ = "analysis_results" - - result_id: Optional[int] = Field(default=None, primary_key=True) - anlaysis_sample: Optional[int] = Field(default=None, - description="Reference to preprocessed_samples.prepro_material_id",) - # foreign_key="preprocessed_samples.prepro_material_id") - experiment_id: Optional[int] = Field(default=None, - description="Reference to experiments.experiment_id",) - # foreign_key="experiments.experiment_id") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id",) - # foreign_key="analysis_types.analysis_type_id") - replicate_no: Optional[int] = Field(default=None) - analysis_timestamp: Optional[datetime] = Field(default=None) - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id",) - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id",) - # foreign_key="units.unit_id") - qc_result_id: Optional[int] = Field(default=None, - description="Reference to qc_results.qc_result_id",) - # foreign_key="qc_results.qc_result_id") - measurement_equipment_id: Optional[int] = Field(default=None, - description="Reference to equipment.equipment_id",) - # foreign_key="equipment.equipment_id") - raw_data_url_id: Optional[int] = Field(default=None, - description="Reference to url.url_id",) - # foreign_key="url.url_id") - analyst_id: Optional[int] = Field(default=None, - description="Reference to analyst_contact.analyst_id",) - # foreign_key="analyst_contact.analyst_id") - analysis_note: Optional[str] = Field(default=None) - - __table_args__ = ( - Index("idx_analysis_results_parameter_id", "parameter_id"), - Index("uq_analysis_results_experiment_parameter_replicate", - "experiment_id", "parameter_id", "replicate_no", unique=True), - ) - - -class QCResult(SQLModel, table=True): - """Quality‑control result (Pass/Fail).""" - __tablename__ = "qc_results" - - qc_result_id: Optional[int] = Field(default=None, primary_key=True) - qc_result: Optional[str] = Field(default=None, unique=True, - description="Pass/Fail") - - -class Unit(SQLModel, table=True): - """Unit of measurement.""" - __tablename__ = "units" - - unit_id: Optional[int] = Field(default=None, primary_key=True) - unit: Optional[str] = Field(default=None, unique=True, - description="% total weight, % dry weight, ppm, %") - - -class ParameterMethod(SQLModel, table=True): - """Bridge table linking parameters to the methods that generate them.""" - __tablename__ = "parameter_methods" - - param_method_id: Optional[int] = Field(default=None, primary_key=True) - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id",) - # foreign_key="parameters.parameter_id") - method_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id",) - # foreign_key="methods.method_id") - - -class Method(SQLModel, table=True): - """Analytical method definition.""" - __tablename__ = "methods" - - method_id: Optional[int] = Field(default=None, primary_key=True) - method_name: Optional[str] = Field(default=None, unique=True) - method_abbrev_id: Optional[int] = Field(default=None, - description="Reference to method_abbrevs.method_abbrev_id",) - # foreign_key="method_abbrevs.method_abbrev_id") - method_category_id: Optional[int] = Field(default=None, - description="Reference to method_categories.method_category_id",) - # foreign_key="method_categories.method_category_id") - method_standard_id: Optional[int] = Field(default=None, - description="Reference to method_standards.method_standard_id",) - # foreign_key="method_standards.method_standard_id") - description: Optional[str] = Field(default=None) - detection_limits: Optional[str] = Field(default=None) - procedure_reference_id: Optional[int] = Field(default=None, - description="Reference to references.reference_id",) - # foreign_key="references.reference_id") - method_url_id: Optional[int] = Field(default=None, - description="Reference to url.url_id",) - # foreign_key="url.url_id") - - __table_args__ = (Index("idx_methods_method_name", "method_name"),) - - -class MethodAbbreviation(SQLModel, table=True): - """Abbreviation for a method (e.g., NREL, ASTM).""" - __tablename__ = "method_abbrevs" - - method_abbrev_id: Optional[int] = Field(default=None, primary_key=True) - method_abbrev: str = Field(..., unique=True, - description="NREL, ASTM") - - -class MethodCategory(SQLModel, table=True): - """Category of a method (e.g., ICP, dry, wet).""" - __tablename__ = "method_categories" - - method_category_id: Optional[int] = Field(default=None, primary_key=True) - method_category: str = Field(..., unique=True, - description="ICP method, CompAna method, dry, wet") - - -class MethodStandard(SQLModel, table=True): - """Standard associated with a method (e.g., AOAC 997.02).""" - __tablename__ = "method_standards" - - method_standard_id: Optional[int] = Field(default=None, primary_key=True) - method_standard: str = Field(..., unique=True) - - -class Equipment(SQLModel, table=True): - """Laboratory or field equipment.""" - __tablename__ = "equipment" - - equipment_id: Optional[int] = Field(default=None, primary_key=True) - equipment_name: str = Field(..., unique=True, - description="Not null") - equipment_room_id: Optional[int] = Field(default=None, - description="Reference to rooms.room_id",) - # foreign_key="rooms.room_id") - description: Optional[str] = Field(default=None) - - -class MethodEquipment(SQLModel, table=True): - """Many‑to‑many link between methods and equipment.""" - __tablename__ = "method_equipment" - - method_equipment_id: Optional[int] = Field(default=None, primary_key=True) - method_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id",) - # foreign_key="methods.method_id") - equipment_id: Optional[int] = Field(default=None, - description="Reference to equipment.equipment_id",) - # foreign_key="equipment.equipment_id") - - __table_args__ = ( - Index("idx_method_equipment_method_id", "method_id"), - Index("idx_method_equipment_equipment_id", "equipment_id"), - ) - - -class Parameter(SQLModel, table=True): - """Parameter that can be measured or calculated.""" - __tablename__ = "parameters" - - parameter_id: Optional[int] = Field(default=None, primary_key=True) - parameter_name: Optional[str] = Field(default=None, unique=True) - parameter_category_id: Optional[int] = Field(default=None, - description="Reference to parameter_catagories.parameter_catagory_id",) - # foreign_key="parameter_catagories.parameter_catagory_id") - standard_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id",) - # foreign_key="units.unit_id") - calculated: Optional[bool] = Field(default=None, - description="If not calculated then it is measured directly. E.g. glucose vs glucan") - description: Optional[str] = Field(default=None) - typical_range_min: Optional[Decimal] = Field(default=None) - typical_range_max: Optional[Decimal] = Field(default=None) - - -class ParameterCategory(SQLModel, table=True): - """Category of a parameter (e.g., Fermentation, Minerals).""" - __tablename__ = "parameter_catagories" - - parameter_catagory_id: Optional[int] = Field(default=None, primary_key=True) - parameter_catagory: Optional[str] = Field(default=None, - description="Fermentation, Minerals, Elements, Compositional Analysis, etc") - - -class ParameterUnit(SQLModel, table=True): - """Bridge table linking parameters to alternative units.""" - __tablename__ = "parameter_units" - - parameter_unit_id: Optional[int] = Field(default=None, primary_key=True) - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id",) - # foreign_key="parameters.parameter_id") - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id",) - # foreign_key="units.unit_id") - - __table_args__ = ( - Index("idx_parameter_units_parameter_id", "parameter_id"), - Index("idx_parameter_units_unit_id", "unit_id"), - ) - - -class ImportLog(SQLModel, table=True): - """Log of data‑import operations.""" - __tablename__ = "import_log" - - import_id: Optional[int] = Field(default=None, primary_key=True) - import_timestamp: Optional[datetime] = Field(default=None) - destination: Optional[str] = Field(default=None) - source_file: Optional[str] = Field(default=None) - source_type: Optional[str] = Field(default=None, - description="CSV, Excel, PDF extraction") - records_imported: Optional[int] = Field(default=None) - import_status: Optional[str] = Field(default=None) - error_log: Optional[str] = Field(default=None) - import_user: Optional[str] = Field(default=None) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/external_datasets.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/external_datasets.py deleted file mode 100644 index ad33d397..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/external_datasets.py +++ /dev/null @@ -1,295 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# External / third‑party data tables -# ---------------------------------------------------------------------- - - -class ExternalDairyOne(SQLModel, table=True): - """External data from the Dairy‑One dataset.""" - __tablename__ = "external_dairy_one" - - dairy_one_id: Optional[int] = Field(default=None, primary_key=True) - data_source_id: Optional[int] = Field(default=None, - description="Reference to data_sources.source_id") - # foreign_key="data_sources.source_id") - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id") - # foreign_key="analysis_types.analysis_type_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - parameter_method_id: Optional[int] = Field(default=None, - description="Reference to parameter_methods.param_method_id") - # foreign_key="parameter_methods.param_method_id") - samples_count: Optional[int] = Field(default=None) - mean_value: Optional[Decimal] = Field(default=None) - std_dev: Optional[Decimal] = Field(default=None) - min_value: Optional[Decimal] = Field(default=None) - max_value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - methodology_reference_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id") - # foreign_key="methods.method_id") - accumulated_years_from: Optional[date] = Field(default=None) - accumulated_years_to: Optional[date] = Field(default=None) - import_date: Optional[date] = Field(default=None) - - __table_args__ = ( - Index("idx_external_dairy_one_biomass_id", "biomass_id"), - Index("idx_external_dairy_one_parameter_id", "parameter_id"), - ) - - -class ExternalINLBiofeedstockLibrary(SQLModel, table=True): - """INL Bio‑Feedstock Library external data.""" - __tablename__ = "external_inl_biofeedstock_library" - - bfl_id: Optional[int] = Field(default=None, primary_key=True) - data_source_id: Optional[int] = Field(default=None, - description="Reference to data_sources.source_id") - # foreign_key="data_sources.source_id") - sample_id: Optional[int] = Field(default=None, - description="Reference to field_samples.sample_id") - # foreign_key="field_samples.sample_id") - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id") - # foreign_key="analysis_types.analysis_type_id") - state_id: Optional[int] = Field(default=None, - description="Reference to states.state_id") - # foreign_key="states.state_id") - affiliations_id: Optional[int] = Field(default=None, - description="Reference to affiliations.affiliation_id") - # foreign_key="affiliations.affiliation_id") - harvest_method_id: Optional[int] = Field(default=None, - description="Reference to harvest_methods.harvest_method_id") - # foreign_key="harvest_methods.harvest_method_id") - collection_method_id: Optional[int] = Field(default=None, - description="Reference to collection_methods.collection_method_id") - # foreign_key="collection_methods.collection_method_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - parameter_method_id: Optional[int] = Field(default=None, - description="Reference to parameter_methods.param_method_id") - # foreign_key="parameter_methods.param_method_id") - mean_value: Optional[Decimal] = Field(default=None) - std_dev: Optional[Decimal] = Field(default=None) - min_value: Optional[Decimal] = Field(default=None) - max_value: Optional[Decimal] = Field(default=None) - sample_count: Optional[int] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - methodology_reference_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id") - # foreign_key="methods.method_id") - accumulated_years_from: Optional[date] = Field(default=None) - accumulated_years_to: Optional[date] = Field(default=None) - import_date: Optional[date] = Field(default=None) - - __table_args__ = ( - Index("idx_external_inl_biofeedstock_library_biomass_id", "biomass_id"), - ) - - -class ExternalPhyllis2(SQLModel, table=True): - """External literature data (Phyllis2).""" - __tablename__ = "external_phyllis2" - - phyllis_id: Optional[int] = Field(default=None, primary_key=True) - data_source_id: Optional[int] = Field(default=None, - description="Reference to data_sources.source_id") - # foreign_key="data_sources.source_id") - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id") - # foreign_key="analysis_types.analysis_type_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - parameter_method_id: Optional[int] = Field(default=None, - description="Reference to parameter_methods.param_method_id") - # foreign_key="parameter_methods.param_method_id") - mean_value: Optional[Decimal] = Field(default=None) - std_dev: Optional[Decimal] = Field(default=None) - max_value: Optional[Decimal] = Field(default=None) - sample_count: Optional[int] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - methodology_reference_id: Optional[int] = Field(default=None, - description="Reference to methods.method_id") - # foreign_key="methods.method_id") - import_date: Optional[date] = Field(default=None) - - __table_args__ = ( - Index("idx_external_phyllis2_biomass_id", "biomass_id"), - Index("idx_external_phyllis2_analysis_type_id", "analysis_type_id"), - ) - - -class ExternalEBMUD(SQLModel, table=True): - """External EBMUD dataset.""" - __tablename__ = "external_ebmud" - - ebmud_id: Optional[int] = Field(default=None, primary_key=True) - data_source_id: Optional[int] = Field(default=None, - description="Reference to data_sources.source_id") - # foreign_key="data_sources.source_id") - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - analysis_type_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id") - # foreign_key="analysis_types.analysis_type_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - parameter_method_id: Optional[int] = Field(default=None, - description="Reference to parameter_methods.param_method_id") - # foreign_key="parameter_methods.param_method_id") - mean_value: Optional[Decimal] = Field(default=None) - std_dev: Optional[Decimal] = Field(default=None) - min_value: Optional[Decimal] = Field(default=None) - max_value: Optional[Decimal] = Field(default=None) - sample_count: Optional[int] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - import_date: Optional[date] = Field(default=None) - - -class VectorizedRasterPolygon(SQLModel, table=True): - """Polygon derived from a raster (PostGIS geometry).""" - __tablename__ = "vectorized_raster_polygons" - - vectorized_ID: Optional[int] = Field(default=None, primary_key=True) - geometry: Optional[str] = Field(default=None, - description="Polygon geometry (PostGIS), use appropriate SRID") - raster_id: Optional[int] = Field(default=None, - description="Optional foreign key to raster_metadata.id") - # foreign_key="raster_metadata.id") - class_: Optional[str] = Field(default=None, - description="Classification label or category (e.g., land use type)", - alias="class") - value: Optional[float] = Field(default=None, - description="Raw pixel value this polygon was derived from") - mean_value: Optional[float] = Field(default=None, - description="Mean raster value within the polygon") - std_dev: Optional[float] = Field(default=None, - description="Standard deviation of raster values in the polygon") - area_m2: Optional[float] = Field(default=None, - description="Area of the polygon in square meters") - date_acquired: Optional[date] = Field(default=None, - description="Date the source raster was collected") - source: Optional[str] = Field(default=None, - description="Source of the raster (e.g., Sentinel‑2)") - notes: Optional[str] = Field(default=None, - description="Additional optional metadata or remarks") - - -class RasterMetadata(SQLModel, table=True): - """Metadata for raster layers.""" - __tablename__ = "raster_metadata" - - id: Optional[int] = Field(default=None, primary_key=True) - source: Optional[str] = Field(default=None, - description="Data source name or provider") - resolution: Optional[float] = Field(default=None, - description="Raster resolution in meters") - srid: Optional[int] = Field(default=None, - description="Spatial reference ID used in raster") - acquisition_date: Optional[date] = Field(default=None, - description="Date of raster acquisition") - notes: Optional[str] = Field(default=None, - description="Any additional metadata") - - -class ExternalATIP(SQLModel, table=True): - """ATIP external geospatial data.""" - __tablename__ = "external_atip" - - atip_ID: Optional[int] = Field(default=None, primary_key=True) - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - location_id: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id") - # foreign_key="geographic_locations.location_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - geometry_id: Optional[int] = Field(default=None) - geometry: Optional[str] = Field(default=None, - description="Geometry (PostGIS geom type)") - import_date: Optional[date] = Field(default=None) - - -class ExternalLandIQ(SQLModel, table=True): - """Land‑IQ external geospatial data.""" - __tablename__ = "external_land_id" - - land_id: Optional[int] = Field(default=None, primary_key=True) # renamed from land_id_id - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - location_id: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id") - # foreign_key="geographic_locations.location_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - geometry_id: Optional[int] = Field(default=None) - geometry: Optional[str] = Field(default=None, - description="Geometry (PostGIS geom type)") - import_date: Optional[date] = Field(default=None) - - -class ExternalUSDA(SQLModel, table=True): - """USDA external geospatial data.""" - __tablename__ = "external_usda" - - usda_id: Optional[int] = Field(default=None, primary_key=True) - biomass_id: Optional[int] = Field(default=None, - description="Reference to biomass.biomass_id") - # foreign_key="biomass.biomass_id") - location_id: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id") - # foreign_key="geographic_locations.location_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - geometry_id: Optional[int] = Field(default=None) - geometry: Optional[str] = Field(default=None, - description="Geometry (PostGIS geom type)") - import_date: Optional[date] = Field(default=None) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/geographic_locations.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/geographic_locations.py deleted file mode 100644 index 84e6e21e..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/geographic_locations.py +++ /dev/null @@ -1,113 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# Geographic / Location tables -# ---------------------------------------------------------------------- - - -class GeographicLocation(SQLModel, table=True): - """Geographic location (can be anonymised).""" - __tablename__ = "geographic_locations" - - location_id: Optional[int] = Field(default=None, primary_key=True) - street_address_id: Optional[int] = Field(default=None, - description="Reference to street_addresses.street_address_id") - # foreign_key="street_addresses.street_address_id") - city_id: Optional[int] = Field(default=None, - description="Reference to cities.city_id") - # foreign_key="cities.city_id") - zip_id: Optional[int] = Field(default=None, - description="Reference to zips.zip_id") - # foreign_key="zips.zip_id") - county_id: Optional[int] = Field(default=None, - description="Reference to counties.county_id") - # foreign_key="counties.county_id") - state_id: Optional[int] = Field(default=None, - description="Reference to states.state_id") - # foreign_key="states.state_id") - region_id: Optional[int] = Field(default=None, - description="Reference to regions.region_id") - # foreign_key="regions.region_id") - fips_id: Optional[int] = Field(default=None, - description="Reference to fips.fips_id") - # foreign_key="fips.fips_id") - latitude: Optional[Decimal] = Field(default=None, - description="Can be null or generalized") - longitude: Optional[Decimal] = Field(default=None, - description="Can be null or generalized") - location_resolution_id: Optional[int] = Field(default=None, - description="Reference to location_resolutions.location_resolution_id") - # foreign_key="location_resolutions.location_resolution_id") - is_anonymous: Optional[bool] = Field(default=None) - - -class StreetAddress(SQLModel, table=True): - """Street address (may be null for privacy).""" - __tablename__ = "street_addresses" - - street_address_id: Optional[int] = Field(default=None, primary_key=True) - street_address: str = Field(..., description="Not null") - - -class City(SQLModel, table=True): - """City lookup.""" - __tablename__ = "cities" - - city_id: Optional[int] = Field(default=None, primary_key=True) - city_name: str = Field(..., unique=True, description="Not null") - - -class Zip(SQLModel, table=True): - """ZIP code lookup.""" - __tablename__ = "zips" - - zip_id: Optional[int] = Field(default=None, primary_key=True) - zip_code: str = Field(..., unique=True, description="Not null") - - -class County(SQLModel, table=True): - """County lookup.""" - __tablename__ = "counties" - - county_id: Optional[int] = Field(default=None, primary_key=True) - county_name: str = Field(..., unique=True, description="Not null") - - -class FIPS(SQLModel, table=True): - """FIPS code (preserve leading zeros).""" - __tablename__ = "fips" - - fips_id: Optional[int] = Field(default=None, primary_key=True) - fips_description: Optional[str] = Field(default=None) - - -class State(SQLModel, table=True): - """State lookup.""" - __tablename__ = "states" - - state_id: Optional[int] = Field(default=None, primary_key=True) - state_name: str = Field(..., unique=True, description="Not null") - - -class Region(SQLModel, table=True): - """Region lookup.""" - __tablename__ = "regions" - - region_id: Optional[int] = Field(default=None, primary_key=True) - region_name: str = Field(..., unique=True, description="Not null") - - -class LocationResolution(SQLModel, table=True): - """Resolution of a location (e.g., GPS, county, state).""" - __tablename__ = "location_resolutions" - - location_resolution_id: Optional[int] = Field(default=None, primary_key=True) - resolution_type: str = Field(..., unique=True, - description="region, state, city, county, etc") diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml index f3d26ede..2cc58cf0 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml @@ -38,8 +38,6 @@ classes: PrimaryCrop: is_a: LookupBase description: Primary crop definition. - slots: - - note ResourceAvailability: is_a: BaseEntity diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/metadata_samples.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/metadata_samples.py deleted file mode 100644 index 7ab750e7..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/metadata_samples.py +++ /dev/null @@ -1,79 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - - -class Metadata(SQLModel, table=True): - """Additional metadata linked to a field sample.""" - __tablename__ = "metadata" - - metadata_id: Optional[int] = Field(default=None, primary_key=True) - sample_id: Optional[int] = Field(default=None, - description="Reference to field_samples.sample_id") - # foreign_key="field_samples.sample_id") - ag_treatment_id: Optional[int] = Field(default=None, - description="Reference to ag_treatments.ag_treatment_id") - # foreign_key="ag_treatments.ag_treatment_id") - last_application_date: Optional[date] = Field(default=None, - description="if applicable") - treatment_amount_per_acre: Optional[Decimal] = Field(default=None, - description="if applicable") - soil_type: Optional[int] = Field(default=None, - description="Reference to soil_type.soil_type_id") - # foreign_key="soil_type.soil_type_id") - - -class ParticleSize(SQLModel, table=True): - """Particle‑size measurements for a sample.""" - __tablename__ = "particle_size" - - particle_size_id: Optional[int] = Field(default=None, primary_key=True) - sample_id: Optional[int] = Field(default=None, - description="Reference to field_samples.sample_id") - # foreign_key="field_samples.sample_id") - particle_length: Optional[int] = Field(default=None) - particle_width: Optional[int] = Field(default=None) - particle_height: Optional[int] = Field(default=None) - particle_units: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - - -class SoilType(SQLModel, table=True): - """Soil classification.""" - __tablename__ = "soil_type" - - soil_type_id: Optional[int] = Field(default=None, primary_key=True) - soil_type: Optional[str] = Field(default=None, unique=True) - soil_location: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id") - # foreign_key="geographic_locations.location_id") - - -class AgTreatment(SQLModel, table=True): - """Agricultural treatment (e.g., pesticide, herbicide).""" - __tablename__ = "ag_treatments" - - ag_treatment_id: Optional[int] = Field(default=None, primary_key=True) - ag_treatment_name: Optional[str] = Field(default=None, - description="pesticide, herbicade") - - -class Taxonomy(SQLModel, table=True): - """Taxonomic hierarchy for a biomass.""" - __tablename__ = "taxonomy" - - taxonomy_id: Optional[int] = Field(default=None, primary_key=True) - kingdom: Optional[str] = Field(default=None) - phylum: Optional[str] = Field(default=None) - class_: Optional[str] = Field(default=None, alias="class") - order: Optional[str] = Field(default=None) - family: Optional[str] = Field(default=None) - genus: Optional[str] = Field(default=None) - species: Optional[str] = Field(default=None) - variety_subspecies_cultivar: Optional[str] = Field(default=None) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/organizations.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/organizations.py deleted file mode 100644 index 2db06cbb..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/organizations.py +++ /dev/null @@ -1,46 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - - -# ---------------------------------------------------------------------- -# Organizational tables -# ---------------------------------------------------------------------- - - -class Affiliation(SQLModel, table=True): - """Affiliation (e.g., university, company).""" - __tablename__ = "affiliations" - - affiliation_id: Optional[int] = Field(default=None, primary_key=True) - affiliation_name: str = Field(..., unique=True, description="Not null") - - -class Building(SQLModel, table=True): - """Building that can house rooms / equipment.""" - __tablename__ = "buildings" - - building_id: Optional[int] = Field(default=None, primary_key=True) - building_name: Optional[str] = Field(default=None, unique=True) - location_id: Optional[int] = Field(default=None, - description="Reference to geographic_locations.location_id") - # foreign_key="geographic_locations.location_id") - affiliation_id: Optional[int] = Field(default=None, - description="Reference to affiliations.affiliation_id") - # foreign_key="affiliations.affiliation_id") - - -class Room(SQLModel, table=True): - """Room inside a building.""" - __tablename__ = "rooms" - - room_id: Optional[int] = Field(default=None, primary_key=True) - room_number: Optional[str] = Field(default=None, unique=True) - building_id: Optional[int] = Field(default=None, - description="Reference to buildings.building_id") - # foreign_key="buildings.building_id") diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/people_contacts.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/people_contacts.py deleted file mode 100644 index 9775edf0..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/people_contacts.py +++ /dev/null @@ -1,59 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# People / contacts -# ---------------------------------------------------------------------- - - -class AnalystContact(SQLModel, table=True): - """Analyst or data‑entry contact.""" - __tablename__ = "analyst_contact" - - analyst_id: Optional[int] = Field(default=None, primary_key=True) - analyst_first_name: Optional[str] = Field(default=None) - analyst_last_name: Optional[str] = Field(default=None) - analyst_email: Optional[str] = Field(default=None) - analyst_affiliation: Optional[int] = Field(default=None, - description="Reference to affiliations.affiliation_id") - # foreign_key="affiliations.affiliation_id") - - -class Provider(SQLModel, table=True): - """Provider of samples / data.""" - __tablename__ = "providers" - - provider_id: Optional[int] = Field(default=None, primary_key=True) - provider_name: str = Field(..., unique=True, description="Not null") - provider_affiliation: Optional[int] = Field(default=None, - description="Reference to affiliations.affiliation_id") - # foreign_key="affiliations.affiliation_id") - provider_type_id: Optional[int] = Field(default=None, - description="Reference to provider_types.provider_type_id") - # foreign_key="provider_types.provider_type_id") - anonymous: Optional[bool] = Field(default=None) - - -class ProviderType(SQLModel, table=True): - """Category of provider (facility, farm, processor, etc.).""" - __tablename__ = "provider_types" - - provider_type_id: Optional[int] = Field(default=None, primary_key=True) - provider_type: Optional[str] = Field(default=None) - - -class Collector(SQLModel, table=True): - """Collector of field samples.""" - __tablename__ = "collectors" - - collector_id: Optional[int] = Field(default=None, primary_key=True) - collector_name: str = Field(..., unique=True, description="Not null") - collector_affiliation: Optional[int] = Field(default=None, - description="Reference to affiliations.affiliation_id") - # foreign_key="affiliations.affiliation_id") diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/sample_preprocessing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/sample_preprocessing.py deleted file mode 100644 index 769001f6..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/sample_preprocessing.py +++ /dev/null @@ -1,68 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# Sample preprocessing / processing -# ---------------------------------------------------------------------- - - -class PreprocessingMethod(SQLModel, table=True): - """Method used to pre‑process a sample.""" - __tablename__ = "preprocessing_methods" - - prepro_method_id: Optional[int] = Field(default=None, primary_key=True) - prepro_method: Optional[str] = Field(default=None, - description="As Is, Knife Mill (2mm), Oven Dry") - prepro_method_abbrev_id: Optional[int] = Field(default=None, - description="Reference to preprocessing_methods_abbreviations.prepro_methods_abbrev_id",) - # foreign_key="preprocessing_methods_abbreviations.prepro_methods_abbrev_id") - prepro_temp_c: Optional[Decimal] = Field(default=None) - drying_step: Optional[bool] = Field(default=None) - method_ref_id: Optional[int] = Field(default=None, - description="Reference to references.reference_id",) - # foreign_key="references.reference_id") - - -class PreprocessingMethodAbbreviation(SQLModel, table=True): - """Abbreviation for a preprocessing method.""" - __tablename__ = "preprocessing_methods_abbreviations" - - prepro_methods_abbrev_id: Optional[int] = Field(default=None, primary_key=True) - prepro_method_abbrev: Optional[str] = Field(default=None, unique=True) - - -class PreprocessedSample(SQLModel, table=True): - """Result of a preprocessing step.""" - __tablename__ = "preprocessed_samples" - - prepro_material_id: Optional[int] = Field(default=None, primary_key=True) - prepro_material_name: Optional[str] = Field(default=None) - biomass_sample_id: Optional[int] = Field(default=None, - description="Reference to field_samples.sample_id",) - # foreign_key="field_samples.sample_id") - prepro_method_id: Optional[int] = Field(default=None, - description="Reference to preprocessing_methods.prepro_method_id",) - # foreign_key="preprocessing_methods.prepro_method_id") - amount_before_drying_g: Optional[Decimal] = Field(default=None) - amount_after_drying: Optional[Decimal] = Field(default=None) - processing_date: Optional[date] = Field(default=None) - storage_building: Optional[int] = Field(default=None, - description="Reference to buildings.building_id",) - # foreign_key="buildings.building_id") - amount_remaining_g: Optional[Decimal] = Field(default=None) - amount_as_of_date: Optional[date] = Field(default=None) - prepro_analyst_id: Optional[int] = Field(default=None, - description="Reference to analyst_contact.analyst_id",) - # foreign_key="analyst_contact.analyst_id") - prepro_note: Optional[str] = Field(default=None) - - __table_args__ = ( - Index("idx_preprocessed_samples_biomass_sample_id", "biomass_sample_id"), - Index("idx_preprocessed_samples_prepro_method_id", "prepro_method_id"), - ) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/specific_aalysis_results.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/specific_aalysis_results.py deleted file mode 100644 index f416bdf2..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/specific_aalysis_results.py +++ /dev/null @@ -1,199 +0,0 @@ -from __future__ import annotations - -from datetime import datetime, date -from decimal import Decimal -from typing import Optional - -from sqlmodel import SQLModel, Field -from sqlalchemy import Index - -# ---------------------------------------------------------------------- -# Specific analysis result tables -# ---------------------------------------------------------------------- - - -class ProximateAnalysis(SQLModel, table=True): - """Proximate analysis results (e.g., moisture, ash).""" - __tablename__ = "proximate_analysis" - - prox_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - notes: Optional[str] = Field(default=None) - - -class ICPAnalysis(SQLModel, table=True): - """ICP (Inductively Coupled Plasma) analysis.""" - __tablename__ = "icp_analysis" - - icp_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - concentration_calculation_url_id: Optional[int] = Field(default=None, - description="Reference to url.url_id") - # foreign_key="url.url_id") - result_wavelength: Optional[Decimal] = Field(default=None) - raw_url: Optional[str] = Field(default=None) - notes: Optional[str] = Field(default=None) - - -class CompositionalAnalysis(SQLModel, table=True): - """Compositional analysis (derived parameters).""" - __tablename__ = "compositional_analysis" - - cmp_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - calculated_parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - calculated_parameter_value: Optional[Decimal] = Field(default=None) - calculated_parameter_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - notes: Optional[str] = Field(default=None) - - -class XRFAnalysis(SQLModel, table=True): - """X‑Ray Fluorescence analysis.""" - __tablename__ = "xrf_analysis" - - xrf_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - notes: Optional[str] = Field(default=None) - - -class FermentationProfile(SQLModel, table=True): - """Fermentation profile results.""" - __tablename__ = "fermentation_profile" - - fp_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - organism_id: Optional[int] = Field(default=None, - description="Reference to organisms.organism_id") - # foreign_key="organisms.organism_id") - product_type_id: Optional[int] = Field(default=None, - description="Reference to product_type.product_type_id") - # foreign_key="product_type.product_type_id") - product_value: Optional[Decimal] = Field(default=None) - product_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - notes: Optional[str] = Field(default=None) - - -class Organism(SQLModel, table=True): - """Organism used in a fermentation.""" - __tablename__ = "organisms" - - organism_id: Optional[int] = Field(default=None, primary_key=True) - organism_name: Optional[str] = Field(default=None) - organism_strain_id: Optional[int] = Field(default=None) - notes: Optional[str] = Field(default=None) - - -class GasificationProfile(SQLModel, table=True): - """Gasification profile results.""" - __tablename__ = "gasification_profile" - - gasification_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - parameter_id: Optional[int] = Field(default=None, - description="Reference to parameters.parameter_id") - # foreign_key="parameters.parameter_id") - value: Optional[Decimal] = Field(default=None) - unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - notes: Optional[str] = Field(default=None) - product_type_id: Optional[int] = Field(default=None, - description="Reference to product_type.product_type_id") - # foreign_key="product_type.product_type_id") - product_value: Optional[Decimal] = Field(default=None) - product_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - - -class AutoclaveProfile(SQLModel, table=True): - """Autoclave experiment results.""" - __tablename__ = "autoclave_profile" - - autoclave_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - product_type_id: Optional[int] = Field(default=None, - description="Reference to product_type.product_type_id") - # foreign_key="product_type.product_type_id") - product_value: Optional[Decimal] = Field(default=None) - product_unit_id: Optional[int] = Field(default=None, - description="Reference to units.unit_id") - # foreign_key="units.unit_id") - - -class AnalysisReplicate(SQLModel, table=True): - """Link between a result and its replicate UUID (used for G‑Sheet tracking).""" - __tablename__ = "analysis_replicate_id" - - analysis_replicate_id: Optional[int] = Field(default=None, primary_key=True) - result_id: Optional[int] = Field(default=None, - description="Reference to analysis_results.result_id") - # foreign_key="analysis_results.result_id") - analysis_types_id: Optional[int] = Field(default=None, - description="Reference to analysis_types.analysis_type_id") - # foreign_key="analysis_types.analysis_type_id") - analysis_replicate_uuid: Optional[str] = Field(default=None) - - -class ProductType(SQLModel, table=True): - """Product type produced in a process (e.g., Butyric, Biochar).""" - __tablename__ = "product_type" - - product_type_id: Optional[int] = Field(default=None, primary_key=True) - product: Optional[str] = Field(default=None, - description="e.g., Butyric, Iso‑Butyric, Propionic, Hydrogen, Syngas, Biochar, Indigoidine, 3HP, etc") diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/user.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/user.py deleted file mode 100644 index 7864a64c..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/user.py +++ /dev/null @@ -1,13 +0,0 @@ -from typing import Optional -from sqlmodel import SQLModel, Field - -class User(SQLModel, table=True): - __tablename__ = 'testusers2' - - id: Optional[int] = Field(default=None, primary_key=True) - name: Optional[str] = Field(default=None) - fullname: Optional[str] = Field(default=None) - nickname: Optional[str] = Field(default=None) - - def __repr__(self): - return f"" From ec6f7414e6cd0e8d201311834880200e79a352db Mon Sep 17 00:00:00 2001 From: mglbleta Date: Fri, 12 Dec 2025 12:32:57 -0800 Subject: [PATCH 56/81] changes to pixi.toml and some comments on linkml schema --- docs/README.md | 2 +- docs/datamodels/README.md | 2 +- docs/deployment/README.md | 2 +- docs/pipeline/README.md | 2 +- docs/resources/README.md | 2 +- docs/webservice/README.md | 2 +- pixi.toml | 2 +- .../linkml/modules/aim1_records.yaml | 3 ++ .../datamodels/linkml/modules/core.yaml | 6 +++ .../linkml/modules/data_sources_metadata.yaml | 18 ++++++++- .../linkml/modules/field_sampling.yaml | 40 +++++++++---------- 11 files changed, 53 insertions(+), 28 deletions(-) diff --git a/docs/README.md b/docs/README.md index 32d46ee8..94389aee 120000 --- a/docs/README.md +++ b/docs/README.md @@ -1 +1 @@ -../README.md \ No newline at end of file +../README.md diff --git a/docs/datamodels/README.md b/docs/datamodels/README.md index b62101ad..f3c7aa23 120000 --- a/docs/datamodels/README.md +++ b/docs/datamodels/README.md @@ -1 +1 @@ -../../src/ca_biositing/datamodels/README.md \ No newline at end of file +../../src/ca_biositing/datamodels/README.md diff --git a/docs/deployment/README.md b/docs/deployment/README.md index d5c46ad4..5159bcfe 120000 --- a/docs/deployment/README.md +++ b/docs/deployment/README.md @@ -1 +1 @@ -../../deployment/README.md \ No newline at end of file +../../deployment/README.md diff --git a/docs/pipeline/README.md b/docs/pipeline/README.md index 82a8c831..544d50b1 120000 --- a/docs/pipeline/README.md +++ b/docs/pipeline/README.md @@ -1 +1 @@ -../../src/ca_biositing/pipeline/README.md \ No newline at end of file +../../src/ca_biositing/pipeline/README.md diff --git a/docs/resources/README.md b/docs/resources/README.md index 9f21ec35..ea34ca59 120000 --- a/docs/resources/README.md +++ b/docs/resources/README.md @@ -1 +1 @@ -../../resources/README.md \ No newline at end of file +../../resources/README.md diff --git a/docs/webservice/README.md b/docs/webservice/README.md index 749a635e..24ea2883 120000 --- a/docs/webservice/README.md +++ b/docs/webservice/README.md @@ -1 +1 @@ -../../src/ca_biositing/webservice/README.md \ No newline at end of file +../../src/ca_biositing/webservice/README.md diff --git a/pixi.toml b/pixi.toml index 4f48ca56..9f1deb56 100644 --- a/pixi.toml +++ b/pixi.toml @@ -259,7 +259,7 @@ args = [ { "arg" = "env_file", "default" = "../docker/.env" }, ] cwd = "resources/prefect" -cmd = "./deploy.py --env-file {{ env_file }} {{ deployment_name }}" +cmd = ["python", "deploy.py", "--env-file", "{{ env_file }}", "{{ deployment_name }}"] description = "Deploy the ETL pipeline to Prefect." depends-on = [{ task = "start-services" }] diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml index fc2ae1ff..c3d5aae7 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml @@ -125,3 +125,6 @@ slots: sample_id: range: integer description: Reference to PreparedSample. +#How are slots above determined? I see the 6 slots that were defined outside of the Aim1RecordBase class, +#but I don't see why the other slots listed (technical_replicate_no, technical_replicate_total, qc_pass, raw_data_id, sample_id) are highlighted. +#Should the remaining slots in the base class be included in these slots as well? diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml index 234b9b4f..eec6318b 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml @@ -35,6 +35,8 @@ classes: - uri slots: + ##Slots from BaseEntity + id: identifier: true range: integer @@ -56,6 +58,8 @@ slots: range: integer description: Reference to the lineage group. + ##Slots from LookupBase + name: range: string description: Name of the entity. @@ -68,6 +72,8 @@ slots: range: uri description: URI for the entity. + ##Slots for other ETL related fields + note: range: string description: Additional notes. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index cc20fe83..ce6e04be 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -31,6 +31,22 @@ classes: - license - note + #missing fields compared to DBdiagram. Was this a purposeful paring down of fields? + #data_source_type_id + #full_title + #creator + #subject + #publisher + #date + #types + #biocirv + #format + #language + #relation + #temporal_coverage + #location_coverage + #rights + FileObjectMetadata: is_a: BaseEntity description: Metadata for a file object. @@ -44,7 +60,7 @@ classes: DataSourceType: is_a: BaseEntity - description: Type of data source. + description: Type of data source (e.g. database, literature). slots: - source_type_id diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml index 9eaedfd7..74ab00d6 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml @@ -43,6 +43,26 @@ classes: - field_sample_storage_location_id - note + PhysicalCharacteristic: + is_a: BaseEntity + description: Physical characteristics of a sample. + slots: + - field_sample_id + - particle_length + - particle_width + - particle_height + - particle_unit_id + + FieldSampleCondition: + is_a: BaseEntity + description: Condition of the field sample. + slots: + - field_sample_id + - ag_treatment_id + - last_application_date + - treatment_amount_per_acre + - processing_method_id + FieldStorageMethod: is_a: LookupBase description: Method of field storage. @@ -59,16 +79,6 @@ classes: is_a: LookupBase description: Method of processing. - PhysicalCharacteristic: - is_a: BaseEntity - description: Physical characteristics of a sample. - slots: - - field_sample_id - - particle_length - - particle_width - - particle_height - - particle_unit_id - SoilType: is_a: LookupBase description: Type of soil. @@ -77,16 +87,6 @@ classes: is_a: LookupBase description: Agricultural treatment. - FieldSampleCondition: - is_a: BaseEntity - description: Condition of the field sample. - slots: - - field_sample_id - - ag_treatment_id - - last_application_date - - treatment_amount_per_acre - - processing_method_id - LocationSoilType: is_a: BaseEntity description: Soil type at a location. From 9a533504ba988299805e3c8479110ba2cb4152bd Mon Sep 17 00:00:00 2001 From: mglbleta Date: Fri, 12 Dec 2025 18:30:11 -0800 Subject: [PATCH 57/81] added some comments to organize and ask questions --- .../linkml/modules/aim1_records.yaml | 22 +++-- .../linkml/modules/aim2_records.yaml | 8 +- .../datamodels/linkml/modules/analysis.yaml | 4 + .../linkml/modules/data_sources_metadata.yaml | 2 +- .../linkml/modules/external_data.yaml | 87 ++++++++++--------- .../linkml/modules/general_analysis.yaml | 4 + .../datamodels/linkml/modules/geography.yaml | 11 --- .../modules/methods_parameters_units.yaml | 8 ++ .../linkml/modules/resource_information.yaml | 6 ++ 9 files changed, 89 insertions(+), 63 deletions(-) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml index c3d5aae7..85028218 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml @@ -82,6 +82,19 @@ classes: description: RGB analysis record. slots: + #Slots imported + #dataset_id: from general_analysis.yaml + #experiment_id: from experiments.yaml + #resource_id: from resource_information.yaml + #method_id: from experiments.yaml + #note: from core.yaml + + #New slots defined in Aim1RecordBase class + + sample_id: + range: integer + description: Reference to PreparedSample. + technical_replicate_no: range: integer description: Replicate number. @@ -98,6 +111,8 @@ slots: range: boolean description: Whether the record passed QC. + #Potential slots for XrfRecord and XrdRecords + maybe_wavelength_nm: range: decimal description: Wavelength in nm. @@ -121,10 +136,3 @@ slots: maybe_scan_high_nm: range: integer description: High scan range in nm. - - sample_id: - range: integer - description: Reference to PreparedSample. -#How are slots above determined? I see the 6 slots that were defined outside of the Aim1RecordBase class, -#but I don't see why the other slots listed (technical_replicate_no, technical_replicate_total, qc_pass, raw_data_id, sample_id) are highlighted. -#Should the remaining slots in the base class be included in these slots as well? diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml index 8eabaa1f..2fdcda17 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml @@ -31,12 +31,12 @@ classes: - experiment_id - resource_id - sample_id + - technical_replicate_total + - technical_replicate_no - analyst_id - raw_data_id - qc_pass - note - - technical_replicate_total - - technical_replicate_no PretreatmentRecord: is_a: Aim2RecordBase @@ -47,7 +47,7 @@ classes: - reaction_block_id - block_position - temperature - - replicate_no + - replicate_no #delete bc redundancy with technical_replicate_no in aim2recordbase entity? FermentationRecord: is_a: Aim2RecordBase @@ -56,7 +56,7 @@ classes: - strain_id - pretreatment_method_id - eh_method_id - - replicate_no + - replicate_no #delete bc redundancy with technical_replicate_no in aim2recordbase entity? - well_position - temperature - agitation_rpm diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml index 456b876d..83292024 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml @@ -60,6 +60,10 @@ classes: description: Type of analysis. slots: + #Slots imported + #parameter_id: from methods.yaml + #note: from core.yaml + dataset_id: range: integer description: Reference to Dataset. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index ce6e04be..5710afd3 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -31,7 +31,7 @@ classes: - license - note - #missing fields compared to DBdiagram. Was this a purposeful paring down of fields? + #missing fields compared to DBdiagram. #data_source_type_id #full_title #creator diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml index cfca5168..4f80ac2d 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml @@ -33,6 +33,33 @@ classes: is_a: LookupBase description: USDA survey program. + UsdaCensusRecord: + is_a: BaseEntity + description: USDA census record. + slots: + - dataset_id + - geoid + - commodity_code + - year + - source_reference + - note + + UsdaSurveyRecord: + is_a: BaseEntity + description: USDA survey record. + slots: + - dataset_id + - geoid + - commodity_code + - year + - survey_program_id + - survey_period + - reference_month + - seasonal_flag + - note + + #RESOURCE ONTOLOGY MAPPING + UsdaCommodity: is_a: LookupBase description: USDA commodity. @@ -62,30 +89,7 @@ classes: - match_tier - note - UsdaCensusRecord: - is_a: BaseEntity - description: USDA census record. - slots: - - dataset_id - - geoid - - commodity_code - - year - - source_reference - - note - - UsdaSurveyRecord: - is_a: BaseEntity - description: USDA survey record. - slots: - - dataset_id - - geoid - - commodity_code - - year - - survey_program_id - - survey_period - - reference_month - - seasonal_flag - - note + #USDA MARKET DATA UsdaMarketReport: is_a: BaseEntity @@ -111,9 +115,9 @@ classes: - report_date - commodity_id - market_type_id - - market_type_catagory + - market_type_category - grp - - market_catagory_id + - market_category_id - class_ - grade - variety @@ -125,6 +129,8 @@ classes: - freight - trans_mode + #LANDIQ DATA + LandiqRecord: is_a: BaseEntity description: LandIQ record. @@ -140,7 +146,19 @@ classes: - acres - version - note - - test + + Polygon: + description: Geospatial polygon. + slots: + - id + - geoid + - geom + slot_usage: + id: + identifier: true + range: integer + + #BILLION TON DATA BillionTon2023Record: is_a: BaseEntity @@ -161,17 +179,6 @@ classes: - product_density_dtpersqmi - land_source - Polygon: - description: Geospatial polygon. - slots: - - id - - geoid - - geom - slot_usage: - id: - identifier: true - range: integer - slots: usda_source: range: string @@ -289,7 +296,7 @@ slots: range: integer description: ID of the market type. - market_type_catagory: + market_type_category: range: string description: Category of the market type. @@ -297,7 +304,7 @@ slots: range: string description: Group. - market_catagory_id: + market_category_id: range: integer description: ID of the market category. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml index cc8a195a..6f9db701 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml @@ -53,6 +53,10 @@ classes: - note slots: + #Slots imported + #parameter_id: from methods.yaml + #note: from core.yaml + record_type: range: string description: Type of record. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml index 32a8a880..0b6ec0eb 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml @@ -43,17 +43,6 @@ classes: - lon - is_anonymous - Polygon: - description: Geospatial polygon definition. - slots: - - id - - geoid - - geom - slot_usage: - id: - identifier: true - range: integer - slots: geoid: range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml index 1f4b0c5d..579609c2 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml @@ -81,6 +81,8 @@ classes: range: integer slots: + #Method slots + method_abbrev_id: range: integer description: Reference to MethodAbbrev. @@ -101,6 +103,8 @@ slots: range: integer description: Reference to DataSource. + #Parameter slots + standard_unit_id: range: integer description: Reference to Unit. @@ -109,6 +113,8 @@ slots: range: boolean description: Whether the parameter is calculated. + #ParameterCategoryParameter slots + parameter_id: range: integer description: Reference to Parameter. @@ -117,6 +123,8 @@ slots: range: integer description: Reference to ParameterCategory. + #ParameterUnit slots + alternate_unit_id: range: integer description: Reference to Unit. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml index 28d31e47..eb2ca5ed 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml @@ -86,6 +86,8 @@ classes: range: integer slots: + #Resource slots + primary_crop_id: range: integer description: Reference to PrimaryCrop. @@ -98,6 +100,8 @@ slots: range: integer description: Reference to ResourceSubclass. + #ResourceAvailability slots + resource_id: range: integer description: Reference to Resource. @@ -118,6 +122,8 @@ slots: range: boolean description: Whether available year-round. + #ResourceCounterfactual slots + counterfactual_description: range: string description: Description of counterfactual scenario. From 7c62775d99a433b5d0e6e2b106941ae6696dddf2 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Mon, 15 Dec 2025 18:35:32 -0800 Subject: [PATCH 58/81] Add and edit revisions to schema (untested) --- .../linkml/modules/aim1_records.yaml | 6 +- .../linkml/modules/aim2_records.yaml | 3 +- .../datamodels/linkml/modules/core.yaml | 30 +---- .../linkml/modules/data_sources_metadata.yaml | 121 ++++++++++++------ .../linkml/modules/external_data.yaml | 4 + .../datamodels/linkml/modules/lineage.yaml | 33 +++++ 6 files changed, 126 insertions(+), 71 deletions(-) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml index 85028218..8328faec 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml @@ -33,6 +33,7 @@ classes: - technical_replicate_no - technical_replicate_total - method_id + - analyst_id - raw_data_id - qc_pass - note @@ -84,9 +85,10 @@ classes: slots: #Slots imported #dataset_id: from general_analysis.yaml - #experiment_id: from experiments.yaml + #experiment_id: from experiments_equipment.yaml + #analyst_id: from experiments_equipment.yaml #resource_id: from resource_information.yaml - #method_id: from experiments.yaml + #method_id: from experiments_equipment.yaml #note: from core.yaml #New slots defined in Aim1RecordBase class diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml index 2fdcda17..670c40b4 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml @@ -33,7 +33,8 @@ classes: - sample_id - technical_replicate_total - technical_replicate_no - - analyst_id + - calc_method_id #differentiated from method in the experiment, optional + - calc_analyst_id #differentiated from analyst in the experiment, optional - raw_data_id - qc_pass - note diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml index eec6318b..870eb513 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml @@ -72,36 +72,8 @@ slots: range: uri description: URI for the entity. - ##Slots for other ETL related fields + ##Slots for other basic fields used across the schema note: range: string description: Additional notes. - - source_table: - range: string - description: Source table name. - - source_row_id: - range: string - description: Source row identifier. - - started_at: - range: datetime - description: Start time of the ETL run. - - completed_at: - range: datetime - description: Completion time of the ETL run. - - pipeline_name: - range: string - description: Name of the pipeline. - - status: - range: string - description: Status of the ETL run. - - records_ingested: - range: integer - description: Number of records ingested. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index 5710afd3..32ae773d 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -23,30 +23,25 @@ classes: slots: - name - description - - uri - - publication_date - - version + - data_source_type_id + - full_title + - creator + - subject - publisher - - author + - contributor + - date + - type + - biocirv + - format + - language + - relation + - temporal_coverage + - location_coverage + - rights - license + - uri - note - #missing fields compared to DBdiagram. - #data_source_type_id - #full_title - #creator - #subject - #publisher - #date - #types - #biocirv - #format - #language - #relation - #temporal_coverage - #location_coverage - #rights - FileObjectMetadata: is_a: BaseEntity description: Metadata for a file object. @@ -73,25 +68,7 @@ classes: description: Type of source (e.g. database, literature). slots: - publication_date: - range: date - description: Date of publication. - - version: - range: string - description: Version of the data source. - - publisher: - range: string - description: Publisher of the data source. - - author: - range: string - description: Author of the data source. - - license: - range: string - description: License of the data source. + #FileObjectMetadata slots data_source_id: range: integer @@ -117,6 +94,72 @@ slots: range: string description: SHA256 checksum of the file. + #DataSourceType slots + source_type_id: range: integer description: Reference to SourceType. + + #DataSource slots + + data_source_type_id: + range: integer + description: Reference to DataSourceType. + + full_title: + range: string + description: Full title of the data source. + + creator: + range: string + description: Entity primarily responsible for making the resource. + + subject: + range: string + description: The topic of the resource. + + publisher: + range: string + description: Publisher of the data source. + + contributor: + range: string + description: Entity responsible for making contributions to the resource. + + date: + range: datetime + description: + Point or period of time associated with an event in the lifecycle of the + resource. + + type: + range: string + description: The nature or genre of the resource. + + biocirv: + range: boolean + description: Internal data flag (FALSE=External, TRUE=Internal). + + format: + range: string + description: File format, physical medium, or dimensions of the resource. + + language: + range: string + description: A language of the resource. + + relation: + range: string + description: A related resource. + + temporal_coverage: + range: string + description: The temporal topic of the resource (Daterange). + + location_coverage_id: + range: integer + description: Reference to LocationResolution. + + rights: + range: string + description: Information about rights held in and over the resource. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml index 4f80ac2d..3321a2f4 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml @@ -380,6 +380,10 @@ slots: range: float description: Number of acres. + version: + range: string + description: Version of the data source. + subclass_id: range: integer description: Reference to ResourceSubclass. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml index 6d0fd301..ed0d6c99 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml @@ -53,3 +53,36 @@ classes: slot_usage: id: identifier: true + +slots: + #Slots for EntityLineage class + + source_table: + range: string + description: Source table name. + + source_row_id: + range: string + description: Source row identifier. + + #Slots for EtlRun class + + started_at: + range: datetime + description: Start time of the ETL run. + + completed_at: + range: datetime + description: Completion time of the ETL run. + + pipeline_name: + range: string + description: Name of the pipeline. + + status: + range: string + description: Status of the ETL run. + + records_ingested: + range: integer + description: Number of records ingested. From 61fcf80b0869e763d5b7a76711cc09e96af04e71 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Mon, 15 Dec 2025 18:48:10 -0800 Subject: [PATCH 59/81] Making people group full of base entity --- .../ca_biositing/datamodels/linkml/modules/people.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml index 818bce18..94f0f42e 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml @@ -16,6 +16,7 @@ imports: classes: Contact: + is_a: BaseEntity description: Contact information for a person. slots: - id @@ -29,6 +30,7 @@ classes: range: integer Provider: + is_a: BaseEntity description: Provider information. slots: - id From 942b4d4ef5dacf069aa07def80fecdba17d5df02 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Mon, 15 Dec 2025 21:47:39 -0800 Subject: [PATCH 60/81] made changes to try to make an alembic migration to represent the changes in the database. think there was an issue with the LinkML --> alembic --- .../27a733f8f5fb_sync_linkml_changes.py | 32 + .../5632747ee5fe_initial_migration.py | 32 + .../linkml/modules/aim2_records.yaml | 12 +- .../linkml/modules/data_sources_metadata.yaml | 6 +- .../schemas/generated/aim1_records.py | 227 +- .../schemas/generated/aim2_records.py | 242 +- .../schemas/generated/analysis_records.py | 118 +- .../schemas/generated/ca_biositing.py | 2404 ----------------- .../generated/data_sources_metadata.py | 231 +- .../schemas/generated/experiment_equipment.py | 197 +- .../schemas/generated/experiments.py | 118 +- .../schemas/generated/external_data.py | 346 +-- .../schemas/generated/field_sampling.py | 221 +- .../schemas/generated/general_analysis.py | 231 +- .../datamodels/schemas/generated/geography.py | 19 - .../schemas/generated/infrastructure.py | 231 +- .../generated/methods_parameters_units.py | 231 +- .../datamodels/schemas/generated/people.py | 44 - .../datamodels/schemas/generated/places.py | 106 - .../schemas/generated/resource_information.py | 307 --- .../datamodels/schemas/generated/resources.py | 326 --- .../schemas/generated/sample_preparation.py | 1089 -------- .../datamodels/schemas/generated/sampling.py | 964 ------- 23 files changed, 1411 insertions(+), 6323 deletions(-) create mode 100644 alembic/versions/27a733f8f5fb_sync_linkml_changes.py create mode 100644 alembic/versions/5632747ee5fe_initial_migration.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py diff --git a/alembic/versions/27a733f8f5fb_sync_linkml_changes.py b/alembic/versions/27a733f8f5fb_sync_linkml_changes.py new file mode 100644 index 00000000..18492f4a --- /dev/null +++ b/alembic/versions/27a733f8f5fb_sync_linkml_changes.py @@ -0,0 +1,32 @@ +"""Sync LinkML changes + +Revision ID: 27a733f8f5fb +Revises: 5632747ee5fe +Create Date: 2025-12-16 05:25:21.214170 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '27a733f8f5fb' +down_revision: Union[str, Sequence[str], None] = '5632747ee5fe' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/alembic/versions/5632747ee5fe_initial_migration.py b/alembic/versions/5632747ee5fe_initial_migration.py new file mode 100644 index 00000000..043c57bb --- /dev/null +++ b/alembic/versions/5632747ee5fe_initial_migration.py @@ -0,0 +1,32 @@ +"""Initial migration + +Revision ID: 5632747ee5fe +Revises: 1e9784d75e62 +Create Date: 2025-12-16 04:39:20.946195 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '5632747ee5fe' +down_revision: Union[str, Sequence[str], None] = '1e9784d75e62' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column('landiq_record', 'test') + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('landiq_record', sa.Column('test', sa.TEXT(), autoincrement=False, nullable=True)) + # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml index 670c40b4..8e20f1c9 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml @@ -33,8 +33,8 @@ classes: - sample_id - technical_replicate_total - technical_replicate_no - - calc_method_id #differentiated from method in the experiment, optional - - calc_analyst_id #differentiated from analyst in the experiment, optional + - calc_method_id + - calc_analyst_id - raw_data_id - qc_pass - note @@ -158,5 +158,13 @@ slots: range: integer description: Replicate number. + calc_method_id: + range: integer + description: Reference to Method used in calculation. + + calc_analyst_id: + range: integer + description: Reference to Analyst who performed calculation. + technical_replicate_total: range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml index 32ae773d..1eeb2f53 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml @@ -36,7 +36,7 @@ classes: - language - relation - temporal_coverage - - location_coverage + - location_coverage_id - rights - license - uri @@ -163,3 +163,7 @@ slots: rights: range: string description: Information about rights held in and over the resource. + + license: + range: string + description: License of the resource. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py index 6a5fd758..834aaa45 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py @@ -206,45 +206,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class Aim1RecordBase(BaseEntity): """ @@ -258,6 +219,7 @@ class Aim1RecordBase(BaseEntity): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -269,7 +231,7 @@ class Aim1RecordBase(BaseEntity): def __repr__(self): - return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -718,12 +680,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -733,7 +706,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -779,7 +752,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -1138,6 +1111,68 @@ def __repr__(self): +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class FieldStorageMethod(LookupBase): """ Method of field storage. @@ -1238,26 +1273,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class SoilType(LookupBase): """ - Physical characteristics of a sample. + Type of soil. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'soil_type' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1269,11 +1298,11 @@ def __repr__(self): -class SoilType(LookupBase): +class AgTreatment(LookupBase): """ - Type of soil. + Agricultural treatment. """ - __tablename__ = 'soil_type' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1282,7 +1311,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1294,20 +1323,23 @@ def __repr__(self): -class AgTreatment(LookupBase): +class LocationSoilType(BaseEntity): """ - Agricultural treatment. + Soil type at a location. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'location_soil_type' + location_id = Column(Integer()) + soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1319,18 +1351,17 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class Contact(BaseEntity): """ - Condition of the field sample. + Contact information for a person. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'contact' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1338,7 +1369,7 @@ class FieldSampleCondition(BaseEntity): def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1350,15 +1381,14 @@ def __repr__(self): -class LocationSoilType(BaseEntity): +class Provider(BaseEntity): """ - Soil type at a location. + Provider information. """ - __tablename__ = 'location_soil_type' + __tablename__ = 'provider' - location_id = Column(Integer()) - soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1366,7 +1396,7 @@ class LocationSoilType(BaseEntity): def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1391,6 +1421,7 @@ class ProximateRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1402,7 +1433,7 @@ class ProximateRecord(Aim1RecordBase): def __repr__(self): - return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1427,6 +1458,7 @@ class UltimateRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1438,7 +1470,7 @@ class UltimateRecord(Aim1RecordBase): def __repr__(self): - return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1463,6 +1495,7 @@ class CompositionalRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1474,7 +1507,7 @@ class CompositionalRecord(Aim1RecordBase): def __repr__(self): - return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1499,6 +1532,7 @@ class IcpRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1510,7 +1544,7 @@ class IcpRecord(Aim1RecordBase): def __repr__(self): - return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1539,6 +1573,7 @@ class XrfRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1550,7 +1585,7 @@ class XrfRecord(Aim1RecordBase): def __repr__(self): - return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1577,6 +1612,7 @@ class XrdRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1588,7 +1624,7 @@ class XrdRecord(Aim1RecordBase): def __repr__(self): - return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1613,6 +1649,7 @@ class CalorimetryRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1624,7 +1661,7 @@ class CalorimetryRecord(Aim1RecordBase): def __repr__(self): - return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1649,6 +1686,7 @@ class FtnirRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1660,7 +1698,7 @@ class FtnirRecord(Aim1RecordBase): def __repr__(self): - return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1685,6 +1723,7 @@ class RgbRecord(Aim1RecordBase): technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) method_id = Column(Integer()) + analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) @@ -1696,7 +1735,7 @@ class RgbRecord(Aim1RecordBase): def __repr__(self): - return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py index b282c9da..9315f884 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py @@ -206,45 +206,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class Aim2RecordBase(BaseEntity): """ @@ -255,12 +216,13 @@ class Aim2RecordBase(BaseEntity): experiment_id = Column(Integer()) resource_id = Column(Integer()) sample_id = Column(Integer()) - analyst_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -269,7 +231,7 @@ class Aim2RecordBase(BaseEntity): def __repr__(self): - return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -744,12 +706,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -759,7 +732,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -805,7 +778,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -1164,6 +1137,68 @@ def __repr__(self): +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class FieldStorageMethod(LookupBase): """ Method of field storage. @@ -1264,26 +1299,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class SoilType(LookupBase): """ - Physical characteristics of a sample. + Type of soil. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'soil_type' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1295,11 +1324,11 @@ def __repr__(self): -class SoilType(LookupBase): +class AgTreatment(LookupBase): """ - Type of soil. + Agricultural treatment. """ - __tablename__ = 'soil_type' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1308,7 +1337,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1320,20 +1349,23 @@ def __repr__(self): -class AgTreatment(LookupBase): +class LocationSoilType(BaseEntity): """ - Agricultural treatment. + Soil type at a location. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'location_soil_type' + location_id = Column(Integer()) + soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1345,18 +1377,17 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class Contact(BaseEntity): """ - Condition of the field sample. + Contact information for a person. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'contact' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1364,7 +1395,7 @@ class FieldSampleCondition(BaseEntity): def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1376,15 +1407,14 @@ def __repr__(self): -class LocationSoilType(BaseEntity): +class Provider(BaseEntity): """ - Soil type at a location. + Provider information. """ - __tablename__ = 'location_soil_type' + __tablename__ = 'provider' - location_id = Column(Integer()) - soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1392,7 +1422,7 @@ class LocationSoilType(BaseEntity): def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1420,12 +1450,13 @@ class PretreatmentRecord(Aim2RecordBase): experiment_id = Column(Integer()) resource_id = Column(Integer()) sample_id = Column(Integer()) - analyst_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1434,7 +1465,7 @@ class PretreatmentRecord(Aim2RecordBase): def __repr__(self): - return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1465,12 +1496,13 @@ class FermentationRecord(Aim2RecordBase): experiment_id = Column(Integer()) resource_id = Column(Integer()) sample_id = Column(Integer()) - analyst_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1479,7 +1511,7 @@ class FermentationRecord(Aim2RecordBase): def __repr__(self): - return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1504,12 +1536,13 @@ class GasificationRecord(Aim2RecordBase): experiment_id = Column(Integer()) resource_id = Column(Integer()) sample_id = Column(Integer()) - analyst_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1518,7 +1551,7 @@ class GasificationRecord(Aim2RecordBase): def __repr__(self): - return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1540,12 +1573,13 @@ class AutoclaveRecord(Aim2RecordBase): experiment_id = Column(Integer()) resource_id = Column(Integer()) sample_id = Column(Integer()) - analyst_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) raw_data_id = Column(Integer()) qc_pass = Column(Boolean()) note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1554,7 +1588,7 @@ class AutoclaveRecord(Aim2RecordBase): def __repr__(self): - return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py index b8968702..35158f30 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py @@ -150,64 +150,6 @@ def __repr__(self): -class Polygon(Base): - """ - Geospatial polygon definition. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ParameterCategoryParameter(Base): """ Link between parameter and category. @@ -869,6 +811,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Unit(LookupBase): """ Unit of measurement. @@ -1601,7 +1600,6 @@ class PrimaryCrop(LookupBase): """ __tablename__ = 'primary_crop' - note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) description = Column(Text()) @@ -1609,7 +1607,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py deleted file mode 100644 index 87fb054a..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py +++ /dev/null @@ -1,2404 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - -class LineageGroup(Base): - """ - Grouping for lineage information. - """ - __tablename__ = 'lineage_group' - - id = Column(Integer(), primary_key=True, nullable=False ) - etl_run_id = Column(Text()) - note = Column(Text()) - - - def __repr__(self): - return f"LineageGroup(id={self.id},etl_run_id={self.etl_run_id},note={self.note},)" - - - - - - -class EntityLineage(Base): - """ - Lineage information for a specific entity. - """ - __tablename__ = 'entity_lineage' - - id = Column(Integer(), primary_key=True, nullable=False ) - lineage_group_id = Column(Integer()) - source_table = Column(Text()) - source_row_id = Column(Text()) - note = Column(Text()) - - - def __repr__(self): - return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" - - - - - - -class EtlRun(Base): - """ - Information about an ETL run. - """ - __tablename__ = 'etl_run' - - id = Column(Integer(), primary_key=True, nullable=False ) - started_at = Column(DateTime()) - completed_at = Column(DateTime()) - pipeline_name = Column(Text()) - status = Column(Text()) - records_ingested = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class ExperimentMethod(Base): - """ - Link between Experiment and Method. - """ - __tablename__ = 'experiment_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - method_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" - - - - - - -class ExperimentEquipment(Base): - """ - Link between Experiment and Equipment. - """ - __tablename__ = 'experiment_equipment' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - equipment_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" - - - - - - -class ExperimentAnalysis(Base): - """ - Link between Experiment and AnalysisType. - """ - __tablename__ = 'experiment_analysis' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - analysis_type_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" - - - - - - -class ExperimentPreparedSample(Base): - """ - Link between Experiment and PreparedSample. - """ - __tablename__ = 'experiment_prepared_sample' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - prepared_sample_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" - - - - - - -class Polygon(Base): - """ - Geospatial polygon. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) - publisher = Column(Text()) - author = Column(Text()) - license = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source. - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample that has been prepared. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Experiment(BaseEntity): - """ - Experiment definition. - """ - __tablename__ = 'experiment' - - analyst_id = Column(Integer()) - exper_start_date = Column(Date()) - exper_duration = Column(Numeric()) - exper_duration_unit_id = Column(Integer()) - exper_location_id = Column(Integer()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Equipment(LookupBase): - """ - Equipment used in experiments. - """ - __tablename__ = 'equipment' - - equipment_location_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Dataset(BaseEntity): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(Date()) - end_date = Column(Date()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension. - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Observation(BaseEntity): - """ - Observation data. - """ - __tablename__ = 'observation' - - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Aim1RecordBase(BaseEntity): - """ - - """ - __tablename__ = 'aim1_record_base' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Aim2RecordBase(BaseEntity): - """ - - """ - __tablename__ = 'aim2_record_base' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Strain(LookupBase): - """ - Strain used in fermentation. - """ - __tablename__ = 'strain' - - parent_strain_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaDomain(LookupBase): - """ - USDA domain. - """ - __tablename__ = 'usda_domain' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaDomain(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaStatisticCategory(LookupBase): - """ - USDA statistic category. - """ - __tablename__ = 'usda_statistic_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaStatisticCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaSurveyProgram(LookupBase): - """ - USDA survey program. - """ - __tablename__ = 'usda_survey_program' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaSurveyProgram(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaCommodity(LookupBase): - """ - USDA commodity. - """ - __tablename__ = 'usda_commodity' - - usda_source = Column(Text()) - usda_code = Column(Text()) - parent_commodity_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaTermMap(BaseEntity): - """ - Mapping of raw terms to USDA commodities. - """ - __tablename__ = 'usda_term_map' - - source_system = Column(Text()) - source_context = Column(Text()) - raw_term = Column(Text()) - usda_commodity_id = Column(Integer()) - is_verified = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceUsdaCommodityMap(BaseEntity): - """ - Mapping between resources/crops and USDA commodities. - """ - __tablename__ = 'resource_usda_commodity_map' - - resource_id = Column(Integer()) - primary_crop_id = Column(Integer()) - usda_commodity_id = Column(Integer()) - match_tier = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaCensusRecord(BaseEntity): - """ - USDA census record. - """ - __tablename__ = 'usda_census_record' - - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - source_reference = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaSurveyRecord(BaseEntity): - """ - USDA survey record. - """ - __tablename__ = 'usda_survey_record' - - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - survey_program_id = Column(Integer()) - survey_period = Column(Text()) - reference_month = Column(Text()) - seasonal_flag = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaMarketReport(BaseEntity): - """ - USDA market report. - """ - __tablename__ = 'usda_market_report' - - slug_id = Column(Integer()) - slug_name = Column(Text()) - report_series_title = Column(Text()) - frequency = Column(Text()) - office_name = Column(Text()) - office_city_id = Column(Integer()) - office_state_fips = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaMarketReport(slug_id={self.slug_id},slug_name={self.slug_name},report_series_title={self.report_series_title},frequency={self.frequency},office_name={self.office_name},office_city_id={self.office_city_id},office_state_fips={self.office_state_fips},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaMarketRecord(BaseEntity): - """ - USDA market record. - """ - __tablename__ = 'usda_market_record' - - report_id = Column(Integer()) - dataset_id = Column(Integer()) - report_begin_date = Column(DateTime()) - report_end_date = Column(DateTime()) - report_date = Column(DateTime()) - commodity_id = Column(Integer()) - market_type_id = Column(Integer()) - market_type_catagory = Column(Text()) - grp = Column(Text()) - market_catagory_id = Column(Integer()) - class_ = Column(Text()) - grade = Column(Text()) - variety = Column(Text()) - protein_pct = Column(Numeric()) - application = Column(Text()) - pkg = Column(Text()) - sale_type = Column(Text()) - price_unit_id = Column(Integer()) - freight = Column(Text()) - trans_mode = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_catagory={self.market_type_catagory},grp={self.grp},market_catagory_id={self.market_catagory_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LandiqRecord(BaseEntity): - """ - LandIQ record. - """ - __tablename__ = 'landiq_record' - - dataset_id = Column(Integer()) - polygon_id = Column(Integer()) - main_crop = Column(Integer()) - secondary_crop = Column(Integer()) - tertiary_crop = Column(Integer()) - quaternary_crop = Column(Integer()) - confidence = Column(Integer()) - irrigated = Column(Boolean()) - acres = Column(Float()) - version = Column(Text()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class BillionTon2023Record(BaseEntity): - """ - Billion Ton 2023 record. - """ - __tablename__ = 'billion_ton2023_record' - - subclass_id = Column(Integer()) - resource_id = Column(Integer()) - geoid = Column(Text()) - county_square_miles = Column(Float()) - model_name = Column(Text()) - scenario_name = Column(Text()) - price_offered_usd = Column(Numeric()) - production = Column(Integer()) - production_unit_id = Column(Integer()) - btu_ton = Column(Integer()) - production_energy_content = Column(Integer()) - energy_content_unit_id = Column(Integer()) - product_density_dtpersqmi = Column(Numeric()) - land_source = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BillionTon2023Record(subclass_id={self.subclass_id},resource_id={self.resource_id},geoid={self.geoid},county_square_miles={self.county_square_miles},model_name={self.model_name},scenario_name={self.scenario_name},price_offered_usd={self.price_offered_usd},production={self.production},production_unit_id={self.production_unit_id},btu_ton={self.btu_ton},production_energy_content={self.production_energy_content},energy_content_unit_id={self.energy_content_unit_id},product_density_dtpersqmi={self.product_density_dtpersqmi},land_source={self.land_source},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProximateRecord(Aim1RecordBase): - """ - Proximate analysis record. - """ - __tablename__ = 'proximate_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UltimateRecord(Aim1RecordBase): - """ - Ultimate analysis record. - """ - __tablename__ = 'ultimate_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CompositionalRecord(Aim1RecordBase): - """ - Compositional analysis record. - """ - __tablename__ = 'compositional_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class IcpRecord(Aim1RecordBase): - """ - ICP analysis record. - """ - __tablename__ = 'icp_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class XrfRecord(Aim1RecordBase): - """ - XRF analysis record. - """ - __tablename__ = 'xrf_record' - - maybe_wavelength_nm = Column(Numeric()) - maybe_intensity = Column(Numeric()) - maybe_energy_slope = Column(Numeric()) - maybe_energy_offset = Column(Numeric()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class XrdRecord(Aim1RecordBase): - """ - XRD analysis record. - """ - __tablename__ = 'xrd_record' - - maybe_scan_low_nm = Column(Integer()) - maybe_scan_high_nm = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CalorimetryRecord(Aim1RecordBase): - """ - Calorimetry analysis record. - """ - __tablename__ = 'calorimetry_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FtnirRecord(Aim1RecordBase): - """ - FT-NIR analysis record. - """ - __tablename__ = 'ftnir_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class RgbRecord(Aim1RecordBase): - """ - RGB analysis record. - """ - __tablename__ = 'rgb_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PretreatmentRecord(Aim2RecordBase): - """ - Pretreatment record. - """ - __tablename__ = 'pretreatment_record' - - pretreatment_method_id = Column(Integer()) - eh_method_id = Column(Integer()) - reaction_block_id = Column(Integer()) - block_position = Column(Text()) - temperature = Column(Numeric()) - replicate_no = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FermentationRecord(Aim2RecordBase): - """ - Fermentation record. - """ - __tablename__ = 'fermentation_record' - - strain_id = Column(Integer()) - pretreatment_method_id = Column(Integer()) - eh_method_id = Column(Integer()) - replicate_no = Column(Integer()) - well_position = Column(Text()) - temperature = Column(Numeric()) - agitation_rpm = Column(Numeric()) - vessel_id = Column(Integer()) - analyte_detection_equipment_id = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class GasificationRecord(Aim2RecordBase): - """ - Gasification record. - """ - __tablename__ = 'gasification_record' - - feedstock_mass = Column(Numeric()) - bed_temperature = Column(Numeric()) - gas_flow_rate = Column(Numeric()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AutoclaveRecord(Aim2RecordBase): - """ - Autoclave record. - """ - __tablename__ = 'autoclave_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py index 48fe18d7..964a4575 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py @@ -73,45 +73,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -177,12 +138,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -192,7 +164,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -238,7 +210,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -347,6 +319,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Resource(BaseEntity): """ Biomass resource definition. @@ -761,20 +790,26 @@ def __repr__(self): -class FieldStorageMethod(LookupBase): +class PhysicalCharacteristic(BaseEntity): """ - Method of field storage. + Physical characteristics of a sample. """ - __tablename__ = 'field_storage_method' + __tablename__ = 'physical_characteristic' + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -786,20 +821,26 @@ def __repr__(self): -class CollectionMethod(LookupBase): +class FieldSampleCondition(BaseEntity): """ - Method of collection. + Condition of the field sample. """ - __tablename__ = 'collection_method' + __tablename__ = 'field_sample_condition' + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -811,11 +852,11 @@ def __repr__(self): -class HarvestMethod(LookupBase): +class FieldStorageMethod(LookupBase): """ - Method of harvest. + Method of field storage. """ - __tablename__ = 'harvest_method' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -824,7 +865,7 @@ class HarvestMethod(LookupBase): def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -836,11 +877,11 @@ def __repr__(self): -class ProcessingMethod(LookupBase): +class CollectionMethod(LookupBase): """ - Method of processing. + Method of collection. """ - __tablename__ = 'processing_method' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -849,7 +890,7 @@ class ProcessingMethod(LookupBase): def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -861,26 +902,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class HarvestMethod(LookupBase): """ - Physical characteristics of a sample. + Method of harvest. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'harvest_method' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -892,11 +927,11 @@ def __repr__(self): -class SoilType(LookupBase): +class ProcessingMethod(LookupBase): """ - Type of soil. + Method of processing. """ - __tablename__ = 'soil_type' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -905,7 +940,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -917,11 +952,11 @@ def __repr__(self): -class AgTreatment(LookupBase): +class SoilType(LookupBase): """ - Agricultural treatment. + Type of soil. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -930,7 +965,7 @@ class AgTreatment(LookupBase): def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -942,26 +977,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class AgTreatment(LookupBase): """ - Condition of the field sample. + Agricultural treatment. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'ag_treatment' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py index 3f2ab322..7f0bdd34 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py @@ -187,45 +187,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -569,6 +530,68 @@ def __repr__(self): +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class FieldStorageMethod(LookupBase): """ Method of field storage. @@ -669,26 +692,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class SoilType(LookupBase): """ - Physical characteristics of a sample. + Type of soil. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'soil_type' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -700,11 +717,11 @@ def __repr__(self): -class SoilType(LookupBase): +class AgTreatment(LookupBase): """ - Type of soil. + Agricultural treatment. """ - __tablename__ = 'soil_type' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -713,7 +730,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -725,20 +742,23 @@ def __repr__(self): -class AgTreatment(LookupBase): +class LocationSoilType(BaseEntity): """ - Agricultural treatment. + Soil type at a location. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'location_soil_type' + location_id = Column(Integer()) + soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -750,18 +770,17 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class Contact(BaseEntity): """ - Condition of the field sample. + Contact information for a person. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'contact' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -769,7 +788,7 @@ class FieldSampleCondition(BaseEntity): def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -781,15 +800,14 @@ def __repr__(self): -class LocationSoilType(BaseEntity): +class Provider(BaseEntity): """ - Soil type at a location. + Provider information. """ - __tablename__ = 'location_soil_type' + __tablename__ = 'provider' - location_id = Column(Integer()) - soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -797,7 +815,7 @@ class LocationSoilType(BaseEntity): def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -906,12 +924,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -921,7 +950,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -967,7 +996,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py index 4d5b8097..bc022794 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py @@ -149,64 +149,6 @@ def __repr__(self): -class Polygon(Base): - """ - Geospatial polygon definition. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ParameterCategoryParameter(Base): """ Link between parameter and category. @@ -432,6 +374,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Unit(LookupBase): """ Unit of measurement. @@ -707,7 +706,6 @@ class PrimaryCrop(LookupBase): """ __tablename__ = 'primary_crop' - note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) description = Column(Text()) @@ -715,7 +713,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py index c1e3bad5..2c6e1121 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py @@ -149,45 +149,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class UsdaDomain(LookupBase): """ USDA domain. @@ -263,23 +224,27 @@ def __repr__(self): -class UsdaCommodity(LookupBase): +class UsdaCensusRecord(BaseEntity): """ - USDA commodity. + USDA census record. """ - __tablename__ = 'usda_commodity' + __tablename__ = 'usda_census_record' - usda_source = Column(Text()) - usda_code = Column(Text()) - parent_commodity_id = Column(Integer()) + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + source_reference = Column(Text()) + note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -291,17 +256,20 @@ def __repr__(self): -class UsdaTermMap(BaseEntity): +class UsdaSurveyRecord(BaseEntity): """ - Mapping of raw terms to USDA commodities. + USDA survey record. """ - __tablename__ = 'usda_term_map' + __tablename__ = 'usda_survey_record' - source_system = Column(Text()) - source_context = Column(Text()) - raw_term = Column(Text()) - usda_commodity_id = Column(Integer()) - is_verified = Column(Boolean()) + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + survey_program_id = Column(Integer()) + survey_period = Column(Text()) + reference_month = Column(Text()) + seasonal_flag = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -311,7 +279,7 @@ class UsdaTermMap(BaseEntity): def __repr__(self): - return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -323,26 +291,23 @@ def __repr__(self): -class ResourceUsdaCommodityMap(BaseEntity): +class UsdaCommodity(LookupBase): """ - Mapping between resources/crops and USDA commodities. + USDA commodity. """ - __tablename__ = 'resource_usda_commodity_map' + __tablename__ = 'usda_commodity' - resource_id = Column(Integer()) - primary_crop_id = Column(Integer()) - usda_commodity_id = Column(Integer()) - match_tier = Column(Text()) - note = Column(Text()) + usda_source = Column(Text()) + usda_code = Column(Text()) + parent_commodity_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -354,17 +319,17 @@ def __repr__(self): -class UsdaCensusRecord(BaseEntity): +class UsdaTermMap(BaseEntity): """ - USDA census record. + Mapping of raw terms to USDA commodities. """ - __tablename__ = 'usda_census_record' + __tablename__ = 'usda_term_map' - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - source_reference = Column(Text()) + source_system = Column(Text()) + source_context = Column(Text()) + raw_term = Column(Text()) + usda_commodity_id = Column(Integer()) + is_verified = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -374,7 +339,7 @@ class UsdaCensusRecord(BaseEntity): def __repr__(self): - return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -386,20 +351,16 @@ def __repr__(self): -class UsdaSurveyRecord(BaseEntity): +class ResourceUsdaCommodityMap(BaseEntity): """ - USDA survey record. + Mapping between resources/crops and USDA commodities. """ - __tablename__ = 'usda_survey_record' + __tablename__ = 'resource_usda_commodity_map' - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - survey_program_id = Column(Integer()) - survey_period = Column(Text()) - reference_month = Column(Text()) - seasonal_flag = Column(Boolean()) + resource_id = Column(Integer()) + primary_crop_id = Column(Integer()) + usda_commodity_id = Column(Integer()) + match_tier = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -409,7 +370,7 @@ class UsdaSurveyRecord(BaseEntity): def __repr__(self): - return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -468,9 +429,9 @@ class UsdaMarketRecord(BaseEntity): report_date = Column(DateTime()) commodity_id = Column(Integer()) market_type_id = Column(Integer()) - market_type_catagory = Column(Text()) + market_type_category = Column(Text()) grp = Column(Text()) - market_catagory_id = Column(Integer()) + market_category_id = Column(Integer()) class_ = Column(Text()) grade = Column(Text()) variety = Column(Text()) @@ -489,7 +450,7 @@ class UsdaMarketRecord(BaseEntity): def __repr__(self): - return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_catagory={self.market_type_catagory},grp={self.grp},market_catagory_id={self.market_catagory_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_category={self.market_type_category},grp={self.grp},market_category_id={self.market_category_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -518,7 +479,6 @@ class LandiqRecord(BaseEntity): acres = Column(Float()) version = Column(Text()) note = Column(Text()) - test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -527,7 +487,7 @@ class LandiqRecord(BaseEntity): def __repr__(self): - return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -587,12 +547,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -602,7 +573,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -648,7 +619,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -1245,6 +1216,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class FieldSample(BaseEntity): """ Sample collected from the field. @@ -1289,20 +1317,26 @@ def __repr__(self): -class FieldStorageMethod(LookupBase): +class PhysicalCharacteristic(BaseEntity): """ - Method of field storage. + Physical characteristics of a sample. """ - __tablename__ = 'field_storage_method' + __tablename__ = 'physical_characteristic' + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1314,20 +1348,26 @@ def __repr__(self): -class CollectionMethod(LookupBase): +class FieldSampleCondition(BaseEntity): """ - Method of collection. + Condition of the field sample. """ - __tablename__ = 'collection_method' + __tablename__ = 'field_sample_condition' + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1339,11 +1379,11 @@ def __repr__(self): -class HarvestMethod(LookupBase): +class FieldStorageMethod(LookupBase): """ - Method of harvest. + Method of field storage. """ - __tablename__ = 'harvest_method' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1352,7 +1392,7 @@ class HarvestMethod(LookupBase): def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1364,11 +1404,11 @@ def __repr__(self): -class ProcessingMethod(LookupBase): +class CollectionMethod(LookupBase): """ - Method of processing. + Method of collection. """ - __tablename__ = 'processing_method' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1377,7 +1417,7 @@ class ProcessingMethod(LookupBase): def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1389,26 +1429,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class HarvestMethod(LookupBase): """ - Physical characteristics of a sample. + Method of harvest. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'harvest_method' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1420,11 +1454,11 @@ def __repr__(self): -class SoilType(LookupBase): +class ProcessingMethod(LookupBase): """ - Type of soil. + Method of processing. """ - __tablename__ = 'soil_type' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1433,7 +1467,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1445,11 +1479,11 @@ def __repr__(self): -class AgTreatment(LookupBase): +class SoilType(LookupBase): """ - Agricultural treatment. + Type of soil. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1458,7 +1492,7 @@ class AgTreatment(LookupBase): def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1470,26 +1504,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class AgTreatment(LookupBase): """ - Condition of the field sample. + Agricultural treatment. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'ag_treatment' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py index 6fed28ad..0f1b410a 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py @@ -73,45 +73,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -213,6 +174,68 @@ def __repr__(self): +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class FieldStorageMethod(LookupBase): """ Method of field storage. @@ -313,26 +336,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class SoilType(LookupBase): """ - Physical characteristics of a sample. + Type of soil. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'soil_type' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -344,11 +361,11 @@ def __repr__(self): -class SoilType(LookupBase): +class AgTreatment(LookupBase): """ - Type of soil. + Agricultural treatment. """ - __tablename__ = 'soil_type' + __tablename__ = 'ag_treatment' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -357,7 +374,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -369,20 +386,23 @@ def __repr__(self): -class AgTreatment(LookupBase): +class LocationSoilType(BaseEntity): """ - Agricultural treatment. + Soil type at a location. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'location_soil_type' + location_id = Column(Integer()) + soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -394,17 +414,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class LocationAddress(BaseEntity): """ - Condition of the field sample. + Physical address. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'location_address' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -413,7 +436,7 @@ class FieldSampleCondition(BaseEntity): def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -425,15 +448,17 @@ def __repr__(self): -class LocationSoilType(BaseEntity): +class Contact(BaseEntity): """ - Soil type at a location. + Contact information for a person. """ - __tablename__ = 'location_soil_type' + __tablename__ = 'contact' - location_id = Column(Integer()) - soil_type_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -441,7 +466,7 @@ class LocationSoilType(BaseEntity): def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -453,21 +478,14 @@ def __repr__(self): -class LocationAddress(BaseEntity): +class Provider(BaseEntity): """ - Physical address. + Provider information. """ - __tablename__ = 'location_address' + __tablename__ = 'provider' - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -475,7 +493,7 @@ class LocationAddress(BaseEntity): def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -677,12 +695,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -692,7 +721,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -738,7 +767,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py index 5b4bbd8c..69cd6452 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py @@ -73,45 +73,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -295,12 +256,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -310,7 +282,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -356,7 +328,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -465,6 +437,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Resource(BaseEntity): """ Biomass resource definition. @@ -879,20 +908,26 @@ def __repr__(self): -class FieldStorageMethod(LookupBase): +class PhysicalCharacteristic(BaseEntity): """ - Method of field storage. + Physical characteristics of a sample. """ - __tablename__ = 'field_storage_method' + __tablename__ = 'physical_characteristic' + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -904,20 +939,26 @@ def __repr__(self): -class CollectionMethod(LookupBase): +class FieldSampleCondition(BaseEntity): """ - Method of collection. + Condition of the field sample. """ - __tablename__ = 'collection_method' + __tablename__ = 'field_sample_condition' + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -929,11 +970,11 @@ def __repr__(self): -class HarvestMethod(LookupBase): +class FieldStorageMethod(LookupBase): """ - Method of harvest. + Method of field storage. """ - __tablename__ = 'harvest_method' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -942,7 +983,7 @@ class HarvestMethod(LookupBase): def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -954,11 +995,11 @@ def __repr__(self): -class ProcessingMethod(LookupBase): +class CollectionMethod(LookupBase): """ - Method of processing. + Method of collection. """ - __tablename__ = 'processing_method' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -967,7 +1008,7 @@ class ProcessingMethod(LookupBase): def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -979,26 +1020,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class HarvestMethod(LookupBase): """ - Physical characteristics of a sample. + Method of harvest. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'harvest_method' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1010,11 +1045,11 @@ def __repr__(self): -class SoilType(LookupBase): +class ProcessingMethod(LookupBase): """ - Type of soil. + Method of processing. """ - __tablename__ = 'soil_type' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1023,7 +1058,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1035,11 +1070,11 @@ def __repr__(self): -class AgTreatment(LookupBase): +class SoilType(LookupBase): """ - Agricultural treatment. + Type of soil. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1048,7 +1083,7 @@ class AgTreatment(LookupBase): def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1060,26 +1095,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class AgTreatment(LookupBase): """ - Condition of the field sample. + Agricultural treatment. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'ag_treatment' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py index 2de38d94..349885b9 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py @@ -32,25 +32,6 @@ def __repr__(self): -class Polygon(Base): - """ - Geospatial polygon definition. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - class BaseEntity(Base): """ Base entity included in all main entity tables. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py index 20dfafc8..87a37dab 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py @@ -516,45 +516,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -654,12 +615,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -669,7 +641,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -715,7 +687,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' @@ -824,6 +796,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Resource(BaseEntity): """ Biomass resource definition. @@ -1238,20 +1267,26 @@ def __repr__(self): -class FieldStorageMethod(LookupBase): +class PhysicalCharacteristic(BaseEntity): """ - Method of field storage. + Physical characteristics of a sample. """ - __tablename__ = 'field_storage_method' + __tablename__ = 'physical_characteristic' + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1263,20 +1298,26 @@ def __repr__(self): -class CollectionMethod(LookupBase): +class FieldSampleCondition(BaseEntity): """ - Method of collection. + Condition of the field sample. """ - __tablename__ = 'collection_method' + __tablename__ = 'field_sample_condition' + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1288,11 +1329,11 @@ def __repr__(self): -class HarvestMethod(LookupBase): +class FieldStorageMethod(LookupBase): """ - Method of harvest. + Method of field storage. """ - __tablename__ = 'harvest_method' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1301,7 +1342,7 @@ class HarvestMethod(LookupBase): def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1313,11 +1354,11 @@ def __repr__(self): -class ProcessingMethod(LookupBase): +class CollectionMethod(LookupBase): """ - Method of processing. + Method of collection. """ - __tablename__ = 'processing_method' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1326,7 +1367,7 @@ class ProcessingMethod(LookupBase): def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1338,26 +1379,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class HarvestMethod(LookupBase): """ - Physical characteristics of a sample. + Method of harvest. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'harvest_method' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1369,11 +1404,11 @@ def __repr__(self): -class SoilType(LookupBase): +class ProcessingMethod(LookupBase): """ - Type of soil. + Method of processing. """ - __tablename__ = 'soil_type' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1382,7 +1417,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1394,11 +1429,11 @@ def __repr__(self): -class AgTreatment(LookupBase): +class SoilType(LookupBase): """ - Agricultural treatment. + Type of soil. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1407,7 +1442,7 @@ class AgTreatment(LookupBase): def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1419,26 +1454,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class AgTreatment(LookupBase): """ - Condition of the field sample. + Agricultural treatment. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'ag_treatment' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py index 4e50f484..781ff528 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py @@ -111,45 +111,6 @@ def __repr__(self): -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - class ResourceMorphology(Base): """ Morphology of a resource. @@ -391,6 +352,63 @@ def __repr__(self): +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + id = Column(Integer(), primary_key=True, nullable=False ) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + id = Column(Integer(), primary_key=True, nullable=False ) + codename = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class Resource(BaseEntity): """ Biomass resource definition. @@ -617,20 +635,26 @@ def __repr__(self): -class FieldStorageMethod(LookupBase): +class PhysicalCharacteristic(BaseEntity): """ - Method of field storage. + Physical characteristics of a sample. """ - __tablename__ = 'field_storage_method' + __tablename__ = 'physical_characteristic' + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -642,20 +666,26 @@ def __repr__(self): -class CollectionMethod(LookupBase): +class FieldSampleCondition(BaseEntity): """ - Method of collection. + Condition of the field sample. """ - __tablename__ = 'collection_method' + __tablename__ = 'field_sample_condition' + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -667,11 +697,11 @@ def __repr__(self): -class HarvestMethod(LookupBase): +class FieldStorageMethod(LookupBase): """ - Method of harvest. + Method of field storage. """ - __tablename__ = 'harvest_method' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -680,7 +710,7 @@ class HarvestMethod(LookupBase): def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -692,11 +722,11 @@ def __repr__(self): -class ProcessingMethod(LookupBase): +class CollectionMethod(LookupBase): """ - Method of processing. + Method of collection. """ - __tablename__ = 'processing_method' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -705,7 +735,7 @@ class ProcessingMethod(LookupBase): def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -717,26 +747,20 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class HarvestMethod(LookupBase): """ - Physical characteristics of a sample. + Method of harvest. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'harvest_method' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -748,11 +772,11 @@ def __repr__(self): -class SoilType(LookupBase): +class ProcessingMethod(LookupBase): """ - Type of soil. + Method of processing. """ - __tablename__ = 'soil_type' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -761,7 +785,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -773,11 +797,11 @@ def __repr__(self): -class AgTreatment(LookupBase): +class SoilType(LookupBase): """ - Agricultural treatment. + Type of soil. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -786,7 +810,7 @@ class AgTreatment(LookupBase): def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -798,26 +822,20 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class AgTreatment(LookupBase): """ - Condition of the field sample. + Agricultural treatment. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'ag_treatment' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -865,12 +883,23 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) publisher = Column(Text()) - author = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) license = Column(Text()) + uri = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -880,7 +909,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -926,7 +955,7 @@ def __repr__(self): class DataSourceType(BaseEntity): """ - Type of data source. + Type of data source (e.g. database, literature). """ __tablename__ = 'data_source_type' diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py index 7eacc534..e69de29b 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py @@ -1,44 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py deleted file mode 100644 index 4eccd8ac..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py +++ /dev/null @@ -1,106 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py deleted file mode 100644 index b1d3d70e..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py +++ /dev/null @@ -1,307 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py deleted file mode 100644 index bec06909..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py +++ /dev/null @@ -1,326 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Polygon(Base): - """ - Geospatial polygon definition. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py deleted file mode 100644 index a3da8a03..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py +++ /dev/null @@ -1,1089 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample that has been prepared. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - publication_date = Column(Date()) - version = Column(Text()) - publisher = Column(Text()) - author = Column(Text()) - license = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},uri={self.uri},publication_date={self.publication_date},version={self.version},publisher={self.publisher},author={self.author},license={self.license},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source. - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py deleted file mode 100644 index 63f68798..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py +++ /dev/null @@ -1,964 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Polygon(Base): - """ - Geospatial polygon definition. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - -class Contact(Base): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - id = Column(Integer(), primary_key=True, nullable=False ) - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - - - def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},)" - - - - - - -class Provider(Base): - """ - Provider information. - """ - __tablename__ = 'provider' - - id = Column(Integer(), primary_key=True, nullable=False ) - codename = Column(Text()) - - - def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample prepared for analysis. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } From 4c7d9d7212601914256eafd7fece7d4caa6fc30e Mon Sep 17 00:00:00 2001 From: mglbleta Date: Tue, 16 Dec 2025 16:26:50 -0800 Subject: [PATCH 61/81] hallucinations removed working update --- .../bfa07351a507_remove_hallucinations.py | 138 + .../d82910ff757e_initial_migration.py | 32 + .../datamodels/linkml/modules/people.yaml | 8 +- .../schemas/generated/aim1_records.py | 8 +- .../schemas/generated/aim2_records.py | 8 +- .../schemas/generated/analysis_records.py | 8 +- .../schemas/generated/ca_biositing.py | 2447 +++++++++++++++++ .../generated/data_sources_metadata.py | 8 +- .../schemas/generated/experiment_equipment.py | 8 +- .../schemas/generated/experiments.py | 8 +- .../schemas/generated/external_data.py | 8 +- .../schemas/generated/field_sampling.py | 8 +- .../schemas/generated/general_analysis.py | 8 +- .../schemas/generated/infrastructure.py | 8 +- .../generated/methods_parameters_units.py | 8 +- .../datamodels/schemas/generated/people.py | 106 + .../datamodels/schemas/generated/places.py | 106 + .../schemas/generated/resource_information.py | 307 +++ .../datamodels/schemas/generated/resources.py | 306 +++ .../schemas/generated/sample_preparation.py | 1118 ++++++++ .../datamodels/schemas/generated/sampling.py | 962 +++++++ 21 files changed, 5567 insertions(+), 51 deletions(-) create mode 100644 alembic/versions/bfa07351a507_remove_hallucinations.py create mode 100644 alembic/versions/d82910ff757e_initial_migration.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py diff --git a/alembic/versions/bfa07351a507_remove_hallucinations.py b/alembic/versions/bfa07351a507_remove_hallucinations.py new file mode 100644 index 00000000..6ac8caa9 --- /dev/null +++ b/alembic/versions/bfa07351a507_remove_hallucinations.py @@ -0,0 +1,138 @@ +"""Remove hallucinations\ + +Revision ID: bfa07351a507 +Revises: d82910ff757e +Create Date: 2025-12-17 00:05:46.750313 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'bfa07351a507' +down_revision: Union[str, Sequence[str], None] = 'd82910ff757e' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('aim1_record_base', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('aim2_record_base', sa.Column('calc_method_id', sa.Integer(), nullable=True)) + op.add_column('aim2_record_base', sa.Column('calc_analyst_id', sa.Integer(), nullable=True)) + op.drop_column('aim2_record_base', 'analyst_id') + op.add_column('autoclave_record', sa.Column('calc_method_id', sa.Integer(), nullable=True)) + op.add_column('autoclave_record', sa.Column('calc_analyst_id', sa.Integer(), nullable=True)) + op.drop_column('autoclave_record', 'analyst_id') + op.add_column('calorimetry_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('compositional_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('contact', sa.Column('created_at', sa.DateTime(), nullable=True)) + op.add_column('contact', sa.Column('updated_at', sa.DateTime(), nullable=True)) + op.add_column('contact', sa.Column('etl_run_id', sa.Text(), nullable=True)) + op.add_column('contact', sa.Column('lineage_group_id', sa.Integer(), nullable=True)) + op.add_column('data_source', sa.Column('data_source_type_id', sa.Integer(), nullable=True)) + op.add_column('data_source', sa.Column('full_title', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('creator', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('subject', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('contributor', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('date', sa.DateTime(), nullable=True)) + op.add_column('data_source', sa.Column('type', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('biocirv', sa.Boolean(), nullable=True)) + op.add_column('data_source', sa.Column('format', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('language', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('relation', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('temporal_coverage', sa.Text(), nullable=True)) + op.add_column('data_source', sa.Column('location_coverage_id', sa.Integer(), nullable=True)) + op.add_column('data_source', sa.Column('rights', sa.Text(), nullable=True)) + op.drop_column('data_source', 'publication_date') + op.drop_column('data_source', 'version') + op.drop_column('data_source', 'author') + op.add_column('fermentation_record', sa.Column('calc_method_id', sa.Integer(), nullable=True)) + op.add_column('fermentation_record', sa.Column('calc_analyst_id', sa.Integer(), nullable=True)) + op.drop_column('fermentation_record', 'analyst_id') + op.add_column('ftnir_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('gasification_record', sa.Column('calc_method_id', sa.Integer(), nullable=True)) + op.add_column('gasification_record', sa.Column('calc_analyst_id', sa.Integer(), nullable=True)) + op.drop_column('gasification_record', 'analyst_id') + op.add_column('icp_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('pretreatment_record', sa.Column('calc_method_id', sa.Integer(), nullable=True)) + op.add_column('pretreatment_record', sa.Column('calc_analyst_id', sa.Integer(), nullable=True)) + op.drop_column('pretreatment_record', 'analyst_id') + op.add_column('provider', sa.Column('created_at', sa.DateTime(), nullable=True)) + op.add_column('provider', sa.Column('updated_at', sa.DateTime(), nullable=True)) + op.add_column('provider', sa.Column('etl_run_id', sa.Text(), nullable=True)) + op.add_column('provider', sa.Column('lineage_group_id', sa.Integer(), nullable=True)) + op.add_column('proximate_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('rgb_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('ultimate_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('usda_market_record', sa.Column('market_type_category', sa.Text(), nullable=True)) + op.add_column('usda_market_record', sa.Column('market_category_id', sa.Integer(), nullable=True)) + op.drop_column('usda_market_record', 'market_type_catagory') + op.drop_column('usda_market_record', 'market_catagory_id') + op.add_column('xrd_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + op.add_column('xrf_record', sa.Column('analyst_id', sa.Integer(), nullable=True)) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column('xrf_record', 'analyst_id') + op.drop_column('xrd_record', 'analyst_id') + op.add_column('usda_market_record', sa.Column('market_catagory_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.add_column('usda_market_record', sa.Column('market_type_catagory', sa.TEXT(), autoincrement=False, nullable=True)) + op.drop_column('usda_market_record', 'market_category_id') + op.drop_column('usda_market_record', 'market_type_category') + op.drop_column('ultimate_record', 'analyst_id') + op.drop_column('rgb_record', 'analyst_id') + op.drop_column('proximate_record', 'analyst_id') + op.drop_column('provider', 'lineage_group_id') + op.drop_column('provider', 'etl_run_id') + op.drop_column('provider', 'updated_at') + op.drop_column('provider', 'created_at') + op.add_column('pretreatment_record', sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('pretreatment_record', 'calc_analyst_id') + op.drop_column('pretreatment_record', 'calc_method_id') + op.drop_column('icp_record', 'analyst_id') + op.add_column('gasification_record', sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('gasification_record', 'calc_analyst_id') + op.drop_column('gasification_record', 'calc_method_id') + op.drop_column('ftnir_record', 'analyst_id') + op.add_column('fermentation_record', sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('fermentation_record', 'calc_analyst_id') + op.drop_column('fermentation_record', 'calc_method_id') + op.add_column('data_source', sa.Column('author', sa.TEXT(), autoincrement=False, nullable=True)) + op.add_column('data_source', sa.Column('version', sa.TEXT(), autoincrement=False, nullable=True)) + op.add_column('data_source', sa.Column('publication_date', sa.DATE(), autoincrement=False, nullable=True)) + op.drop_column('data_source', 'rights') + op.drop_column('data_source', 'location_coverage_id') + op.drop_column('data_source', 'temporal_coverage') + op.drop_column('data_source', 'relation') + op.drop_column('data_source', 'language') + op.drop_column('data_source', 'format') + op.drop_column('data_source', 'biocirv') + op.drop_column('data_source', 'type') + op.drop_column('data_source', 'date') + op.drop_column('data_source', 'contributor') + op.drop_column('data_source', 'subject') + op.drop_column('data_source', 'creator') + op.drop_column('data_source', 'full_title') + op.drop_column('data_source', 'data_source_type_id') + op.drop_column('contact', 'lineage_group_id') + op.drop_column('contact', 'etl_run_id') + op.drop_column('contact', 'updated_at') + op.drop_column('contact', 'created_at') + op.drop_column('compositional_record', 'analyst_id') + op.drop_column('calorimetry_record', 'analyst_id') + op.add_column('autoclave_record', sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('autoclave_record', 'calc_analyst_id') + op.drop_column('autoclave_record', 'calc_method_id') + op.add_column('aim2_record_base', sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('aim2_record_base', 'calc_analyst_id') + op.drop_column('aim2_record_base', 'calc_method_id') + op.drop_column('aim1_record_base', 'analyst_id') + # ### end Alembic commands ### diff --git a/alembic/versions/d82910ff757e_initial_migration.py b/alembic/versions/d82910ff757e_initial_migration.py new file mode 100644 index 00000000..d1550e08 --- /dev/null +++ b/alembic/versions/d82910ff757e_initial_migration.py @@ -0,0 +1,32 @@ +"""Initial migration + +Revision ID: d82910ff757e +Revises: 27a733f8f5fb +Create Date: 2025-12-16 22:48:03.561768 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'd82910ff757e' +down_revision: Union[str, Sequence[str], None] = '27a733f8f5fb' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml index 94f0f42e..5f5c59f5 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml @@ -13,13 +13,13 @@ default_range: string imports: - linkml:types + - core classes: Contact: is_a: BaseEntity description: Contact information for a person. slots: - - id - first_name - last_name - email @@ -33,7 +33,6 @@ classes: is_a: BaseEntity description: Provider information. slots: - - id - codename slot_usage: id: @@ -41,11 +40,6 @@ classes: range: integer slots: - id: - identifier: true - range: integer - description: Unique identifier. - first_name: range: string description: First name. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py index 834aaa45..ef08780e 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py @@ -1357,11 +1357,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1369,7 +1369,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1387,8 +1387,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1396,7 +1396,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py index 9315f884..db37c954 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py @@ -1383,11 +1383,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1395,7 +1395,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1413,8 +1413,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1422,7 +1422,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py index 35158f30..53befe22 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py @@ -817,11 +817,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -829,7 +829,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -847,8 +847,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -856,7 +856,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py new file mode 100644 index 00000000..7cdc3fb0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py @@ -0,0 +1,2447 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class LineageGroup(Base): + """ + Grouping for lineage information. + """ + __tablename__ = 'lineage_group' + + id = Column(Integer(), primary_key=True, nullable=False ) + etl_run_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"LineageGroup(id={self.id},etl_run_id={self.etl_run_id},note={self.note},)" + + + + + + +class EntityLineage(Base): + """ + Lineage information for a specific entity. + """ + __tablename__ = 'entity_lineage' + + id = Column(Integer(), primary_key=True, nullable=False ) + lineage_group_id = Column(Integer()) + source_table = Column(Text()) + source_row_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" + + + + + + +class EtlRun(Base): + """ + Information about an ETL run. + """ + __tablename__ = 'etl_run' + + id = Column(Integer(), primary_key=True, nullable=False ) + started_at = Column(DateTime()) + completed_at = Column(DateTime()) + pipeline_name = Column(Text()) + status = Column(Text()) + records_ingested = Column(Integer()) + note = Column(Text()) + + + def __repr__(self): + return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'parameter_category_parameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'parameter_unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ExperimentMethod(Base): + """ + Link between Experiment and Method. + """ + __tablename__ = 'experiment_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + method_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" + + + + + + +class ExperimentEquipment(Base): + """ + Link between Experiment and Equipment. + """ + __tablename__ = 'experiment_equipment' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + equipment_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" + + + + + + +class ExperimentAnalysis(Base): + """ + Link between Experiment and AnalysisType. + """ + __tablename__ = 'experiment_analysis' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + analysis_type_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + + + + + + +class ExperimentPreparedSample(Base): + """ + Link between Experiment and PreparedSample. + """ + __tablename__ = 'experiment_prepared_sample' + + id = Column(Integer(), primary_key=True, nullable=False ) + experiment_id = Column(Integer()) + prepared_sample_id = Column(Integer()) + + + def __repr__(self): + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + + + + + + +class Polygon(Base): + """ + Geospatial polygon. + """ + __tablename__ = 'polygon' + + id = Column(Integer(), primary_key=True, nullable=False ) + geoid = Column(Text()) + geom = Column(Text()) + + + def __repr__(self): + return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'primary_crop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'field_sample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'field_storage_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'collection_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'harvest_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'processing_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'soil_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'ag_treatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'location_soil_type' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'data_source' + + name = Column(Text()) + description = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) + publisher = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) + license = Column(Text()) + uri = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'file_object_metadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source (e.g. database, literature). + """ + __tablename__ = 'data_source_type' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'location_resolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'source_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'preparation_method' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'preparation_method_abbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'prepared_sample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'method_abbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'method_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'method_standard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'parameter_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Experiment(BaseEntity): + """ + Experiment definition. + """ + __tablename__ = 'experiment' + + analyst_id = Column(Integer()) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer()) + exper_location_id = Column(Integer()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Equipment(LookupBase): + """ + Equipment used in experiments. + """ + __tablename__ = 'equipment' + + equipment_location_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AnalysisType(LookupBase): + """ + Type of analysis. + """ + __tablename__ = 'analysis_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Dataset(BaseEntity): + """ + Dataset definition. + """ + __tablename__ = 'dataset' + + name = Column(Text()) + record_type = Column(Text()) + source_id = Column(Integer()) + start_date = Column(Date()) + end_date = Column(Date()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DimensionType(LookupBase): + """ + Type of dimension. + """ + __tablename__ = 'dimension_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Observation(BaseEntity): + """ + Observation data. + """ + __tablename__ = 'observation' + + dataset_id = Column(Integer()) + record_type = Column(Text()) + record_id = Column(Integer()) + parameter_id = Column(Integer()) + value = Column(Numeric()) + unit_id = Column(Integer()) + dimension_type_id = Column(Integer()) + dimension_value = Column(Numeric()) + dimension_unit_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Aim1RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'aim1_record_base' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Aim2RecordBase(BaseEntity): + """ + + """ + __tablename__ = 'aim2_record_base' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Strain(LookupBase): + """ + Strain used in fermentation. + """ + __tablename__ = 'strain' + + parent_strain_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaDomain(LookupBase): + """ + USDA domain. + """ + __tablename__ = 'usda_domain' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaDomain(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaStatisticCategory(LookupBase): + """ + USDA statistic category. + """ + __tablename__ = 'usda_statistic_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaStatisticCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyProgram(LookupBase): + """ + USDA survey program. + """ + __tablename__ = 'usda_survey_program' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaSurveyProgram(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCensusRecord(BaseEntity): + """ + USDA census record. + """ + __tablename__ = 'usda_census_record' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + source_reference = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaSurveyRecord(BaseEntity): + """ + USDA survey record. + """ + __tablename__ = 'usda_survey_record' + + dataset_id = Column(Integer()) + geoid = Column(Text()) + commodity_code = Column(Integer()) + year = Column(Integer()) + survey_program_id = Column(Integer()) + survey_period = Column(Text()) + reference_month = Column(Text()) + seasonal_flag = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaCommodity(LookupBase): + """ + USDA commodity. + """ + __tablename__ = 'usda_commodity' + + usda_source = Column(Text()) + usda_code = Column(Text()) + parent_commodity_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaTermMap(BaseEntity): + """ + Mapping of raw terms to USDA commodities. + """ + __tablename__ = 'usda_term_map' + + source_system = Column(Text()) + source_context = Column(Text()) + raw_term = Column(Text()) + usda_commodity_id = Column(Integer()) + is_verified = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceUsdaCommodityMap(BaseEntity): + """ + Mapping between resources/crops and USDA commodities. + """ + __tablename__ = 'resource_usda_commodity_map' + + resource_id = Column(Integer()) + primary_crop_id = Column(Integer()) + usda_commodity_id = Column(Integer()) + match_tier = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketReport(BaseEntity): + """ + USDA market report. + """ + __tablename__ = 'usda_market_report' + + slug_id = Column(Integer()) + slug_name = Column(Text()) + report_series_title = Column(Text()) + frequency = Column(Text()) + office_name = Column(Text()) + office_city_id = Column(Integer()) + office_state_fips = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketReport(slug_id={self.slug_id},slug_name={self.slug_name},report_series_title={self.report_series_title},frequency={self.frequency},office_name={self.office_name},office_city_id={self.office_city_id},office_state_fips={self.office_state_fips},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UsdaMarketRecord(BaseEntity): + """ + USDA market record. + """ + __tablename__ = 'usda_market_record' + + report_id = Column(Integer()) + dataset_id = Column(Integer()) + report_begin_date = Column(DateTime()) + report_end_date = Column(DateTime()) + report_date = Column(DateTime()) + commodity_id = Column(Integer()) + market_type_id = Column(Integer()) + market_type_category = Column(Text()) + grp = Column(Text()) + market_category_id = Column(Integer()) + class_ = Column(Text()) + grade = Column(Text()) + variety = Column(Text()) + protein_pct = Column(Numeric()) + application = Column(Text()) + pkg = Column(Text()) + sale_type = Column(Text()) + price_unit_id = Column(Integer()) + freight = Column(Text()) + trans_mode = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_category={self.market_type_category},grp={self.grp},market_category_id={self.market_category_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LandiqRecord(BaseEntity): + """ + LandIQ record. + """ + __tablename__ = 'landiq_record' + + dataset_id = Column(Integer()) + polygon_id = Column(Integer()) + main_crop = Column(Integer()) + secondary_crop = Column(Integer()) + tertiary_crop = Column(Integer()) + quaternary_crop = Column(Integer()) + confidence = Column(Integer()) + irrigated = Column(Boolean()) + acres = Column(Float()) + version = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class BillionTon2023Record(BaseEntity): + """ + Billion Ton 2023 record. + """ + __tablename__ = 'billion_ton2023_record' + + subclass_id = Column(Integer()) + resource_id = Column(Integer()) + geoid = Column(Text()) + county_square_miles = Column(Float()) + model_name = Column(Text()) + scenario_name = Column(Text()) + price_offered_usd = Column(Numeric()) + production = Column(Integer()) + production_unit_id = Column(Integer()) + btu_ton = Column(Integer()) + production_energy_content = Column(Integer()) + energy_content_unit_id = Column(Integer()) + product_density_dtpersqmi = Column(Numeric()) + land_source = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BillionTon2023Record(subclass_id={self.subclass_id},resource_id={self.resource_id},geoid={self.geoid},county_square_miles={self.county_square_miles},model_name={self.model_name},scenario_name={self.scenario_name},price_offered_usd={self.price_offered_usd},production={self.production},production_unit_id={self.production_unit_id},btu_ton={self.btu_ton},production_energy_content={self.production_energy_content},energy_content_unit_id={self.energy_content_unit_id},product_density_dtpersqmi={self.product_density_dtpersqmi},land_source={self.land_source},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProximateRecord(Aim1RecordBase): + """ + Proximate analysis record. + """ + __tablename__ = 'proximate_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class UltimateRecord(Aim1RecordBase): + """ + Ultimate analysis record. + """ + __tablename__ = 'ultimate_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CompositionalRecord(Aim1RecordBase): + """ + Compositional analysis record. + """ + __tablename__ = 'compositional_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class IcpRecord(Aim1RecordBase): + """ + ICP analysis record. + """ + __tablename__ = 'icp_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrfRecord(Aim1RecordBase): + """ + XRF analysis record. + """ + __tablename__ = 'xrf_record' + + maybe_wavelength_nm = Column(Numeric()) + maybe_intensity = Column(Numeric()) + maybe_energy_slope = Column(Numeric()) + maybe_energy_offset = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class XrdRecord(Aim1RecordBase): + """ + XRD analysis record. + """ + __tablename__ = 'xrd_record' + + maybe_scan_low_nm = Column(Integer()) + maybe_scan_high_nm = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CalorimetryRecord(Aim1RecordBase): + """ + Calorimetry analysis record. + """ + __tablename__ = 'calorimetry_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FtnirRecord(Aim1RecordBase): + """ + FT-NIR analysis record. + """ + __tablename__ = 'ftnir_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class RgbRecord(Aim1RecordBase): + """ + RGB analysis record. + """ + __tablename__ = 'rgb_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer()) + analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PretreatmentRecord(Aim2RecordBase): + """ + Pretreatment record. + """ + __tablename__ = 'pretreatment_record' + + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + reaction_block_id = Column(Integer()) + block_position = Column(Text()) + temperature = Column(Numeric()) + replicate_no = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FermentationRecord(Aim2RecordBase): + """ + Fermentation record. + """ + __tablename__ = 'fermentation_record' + + strain_id = Column(Integer()) + pretreatment_method_id = Column(Integer()) + eh_method_id = Column(Integer()) + replicate_no = Column(Integer()) + well_position = Column(Text()) + temperature = Column(Numeric()) + agitation_rpm = Column(Numeric()) + vessel_id = Column(Integer()) + analyte_detection_equipment_id = Column(Integer()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class GasificationRecord(Aim2RecordBase): + """ + Gasification record. + """ + __tablename__ = 'gasification_record' + + feedstock_mass = Column(Numeric()) + bed_temperature = Column(Numeric()) + gas_flow_rate = Column(Numeric()) + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AutoclaveRecord(Aim2RecordBase): + """ + Autoclave record. + """ + __tablename__ = 'autoclave_record' + + dataset_id = Column(Integer()) + experiment_id = Column(Integer()) + resource_id = Column(Integer()) + sample_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) + raw_data_id = Column(Integer()) + qc_pass = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py index 964a4575..975b6bd5 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py @@ -325,11 +325,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -337,7 +337,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -355,8 +355,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -364,7 +364,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py index 7f0bdd34..b93abd1f 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py @@ -776,11 +776,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -788,7 +788,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -806,8 +806,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -815,7 +815,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py index bc022794..c953a83a 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py @@ -380,11 +380,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -392,7 +392,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -410,8 +410,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -419,7 +419,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py index 2c6e1121..d86817b3 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py @@ -1222,11 +1222,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1234,7 +1234,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1252,8 +1252,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -1261,7 +1261,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py index 0f1b410a..f699dc79 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py @@ -454,11 +454,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -466,7 +466,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -484,8 +484,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -493,7 +493,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py index 69cd6452..88195134 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py @@ -443,11 +443,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -455,7 +455,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -473,8 +473,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -482,7 +482,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py index 87a37dab..833b7951 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py @@ -802,11 +802,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -814,7 +814,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -832,8 +832,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -841,7 +841,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py index 781ff528..61f06d91 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py @@ -358,11 +358,11 @@ class Contact(BaseEntity): """ __tablename__ = 'contact' - id = Column(Integer(), primary_key=True, nullable=False ) first_name = Column(Text()) last_name = Column(Text()) email = Column(Text()) affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -370,7 +370,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(id={self.id},first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -388,8 +388,8 @@ class Provider(BaseEntity): """ __tablename__ = 'provider' - id = Column(Integer(), primary_key=True, nullable=False ) codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) etl_run_id = Column(Text()) @@ -397,7 +397,7 @@ class Provider(BaseEntity): def __repr__(self): - return f"Provider(id={self.id},codename={self.codename},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py index e69de29b..8219be89 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py @@ -0,0 +1,106 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py new file mode 100644 index 00000000..4eccd8ac --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py @@ -0,0 +1,106 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py new file mode 100644 index 00000000..b1d3d70e --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py @@ -0,0 +1,307 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'primary_crop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py new file mode 100644 index 00000000..41d9b229 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py @@ -0,0 +1,306 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'primary_crop' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py new file mode 100644 index 00000000..db5d6386 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py @@ -0,0 +1,1118 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'parameter_category_parameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'parameter_unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'preparation_method' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'preparation_method_abbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample that has been prepared. + """ + __tablename__ = 'prepared_sample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'primary_crop' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'field_sample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'field_storage_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'collection_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'harvest_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'processing_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'soil_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'ag_treatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'location_soil_type' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'data_source' + + name = Column(Text()) + description = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) + publisher = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) + license = Column(Text()) + uri = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'file_object_metadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source (e.g. database, literature). + """ + __tablename__ = 'data_source_type' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'location_resolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'source_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'method_abbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'method_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'method_standard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'parameter_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py new file mode 100644 index 00000000..78c99d62 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py @@ -0,0 +1,962 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic region definition (e.g. county, state). + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer()) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between parameter and category. + """ + __tablename__ = 'parameter_category_parameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between parameter and alternate units. + """ + __tablename__ = 'parameter_unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'field_sample' + + name = Column(Text()) + resource_id = Column(Integer()) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'field_storage_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'collection_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'harvest_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'processing_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'soil_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'ag_treatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'location_soil_type' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethod(BaseEntity): + """ + Method of sample preparation. + """ + __tablename__ = 'preparation_method' + + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer()) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparationMethodAbbreviation(LookupBase): + """ + Abbreviation for preparation method. + """ + __tablename__ = 'preparation_method_abbreviation' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PreparedSample(BaseEntity): + """ + Sample prepared for analysis. + """ + __tablename__ = 'prepared_sample' + + name = Column(Text()) + field_sample_id = Column(Integer()) + prep_method_id = Column(Integer()) + prep_date = Column(Date()) + preparer_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Specific physical location. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_crop_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryCrop(LookupBase): + """ + Primary crop definition. + """ + __tablename__ = 'primary_crop' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer()) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer()) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for a method. + """ + __tablename__ = 'method_abbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of a method. + """ + __tablename__ = 'method_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with a method. + """ + __tablename__ = 'method_standard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter measured. + """ + __tablename__ = 'parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of a parameter. + """ + __tablename__ = 'parameter_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } From f78d9bb0ae9d7b13b5ee181ed9208479a1963756 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Tue, 16 Dec 2025 17:14:22 -0800 Subject: [PATCH 62/81] removed useless alembic versions and fixed the revision path --- .../27a733f8f5fb_sync_linkml_changes.py | 32 ------------------- .../5632747ee5fe_initial_migration.py | 32 ------------------- .../bfa07351a507_remove_hallucinations.py | 2 +- .../d82910ff757e_initial_migration.py | 32 ------------------- 4 files changed, 1 insertion(+), 97 deletions(-) delete mode 100644 alembic/versions/27a733f8f5fb_sync_linkml_changes.py delete mode 100644 alembic/versions/5632747ee5fe_initial_migration.py delete mode 100644 alembic/versions/d82910ff757e_initial_migration.py diff --git a/alembic/versions/27a733f8f5fb_sync_linkml_changes.py b/alembic/versions/27a733f8f5fb_sync_linkml_changes.py deleted file mode 100644 index 18492f4a..00000000 --- a/alembic/versions/27a733f8f5fb_sync_linkml_changes.py +++ /dev/null @@ -1,32 +0,0 @@ -"""Sync LinkML changes - -Revision ID: 27a733f8f5fb -Revises: 5632747ee5fe -Create Date: 2025-12-16 05:25:21.214170 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '27a733f8f5fb' -down_revision: Union[str, Sequence[str], None] = '5632747ee5fe' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### diff --git a/alembic/versions/5632747ee5fe_initial_migration.py b/alembic/versions/5632747ee5fe_initial_migration.py deleted file mode 100644 index 043c57bb..00000000 --- a/alembic/versions/5632747ee5fe_initial_migration.py +++ /dev/null @@ -1,32 +0,0 @@ -"""Initial migration - -Revision ID: 5632747ee5fe -Revises: 1e9784d75e62 -Create Date: 2025-12-16 04:39:20.946195 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = '5632747ee5fe' -down_revision: Union[str, Sequence[str], None] = '1e9784d75e62' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.drop_column('landiq_record', 'test') - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - op.add_column('landiq_record', sa.Column('test', sa.TEXT(), autoincrement=False, nullable=True)) - # ### end Alembic commands ### diff --git a/alembic/versions/bfa07351a507_remove_hallucinations.py b/alembic/versions/bfa07351a507_remove_hallucinations.py index 6ac8caa9..68d853dd 100644 --- a/alembic/versions/bfa07351a507_remove_hallucinations.py +++ b/alembic/versions/bfa07351a507_remove_hallucinations.py @@ -13,7 +13,7 @@ # revision identifiers, used by Alembic. revision: str = 'bfa07351a507' -down_revision: Union[str, Sequence[str], None] = 'd82910ff757e' +down_revision: Union[str, Sequence[str], None] = '1e9784d75e62' branch_labels: Union[str, Sequence[str], None] = None depends_on: Union[str, Sequence[str], None] = None diff --git a/alembic/versions/d82910ff757e_initial_migration.py b/alembic/versions/d82910ff757e_initial_migration.py deleted file mode 100644 index d1550e08..00000000 --- a/alembic/versions/d82910ff757e_initial_migration.py +++ /dev/null @@ -1,32 +0,0 @@ -"""Initial migration - -Revision ID: d82910ff757e -Revises: 27a733f8f5fb -Create Date: 2025-12-16 22:48:03.561768 - -""" -from typing import Sequence, Union - -from alembic import op -import sqlalchemy as sa - - -# revision identifiers, used by Alembic. -revision: str = 'd82910ff757e' -down_revision: Union[str, Sequence[str], None] = '27a733f8f5fb' -branch_labels: Union[str, Sequence[str], None] = None -depends_on: Union[str, Sequence[str], None] = None - - -def upgrade() -> None: - """Upgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### - - -def downgrade() -> None: - """Downgrade schema.""" - # ### commands auto generated by Alembic - please adjust! ### - pass - # ### end Alembic commands ### From e074d3c09e121a1ae955d0bf417bb0eefe55f322 Mon Sep 17 00:00:00 2001 From: mglbleta Date: Wed, 17 Dec 2025 11:20:52 -0800 Subject: [PATCH 63/81] removed duplicate .yaml files --- ...4417c6d044_deleted_duplicate_yaml_files.py | 32 + .../datamodels/linkml/modules/analysis.yaml | 109 -- .../linkml/modules/analysis_records.yaml | 233 --- .../linkml/modules/experiments.yaml | 138 -- .../datamodels/linkml/modules/methods.yaml | 120 -- .../datamodels/linkml/modules/resources.yaml | 176 -- .../datamodels/linkml/modules/sampling.yaml | 250 --- .../datamodels/schemas/generated/analysis.py | 375 ---- .../schemas/generated/analysis_records.py | 1693 ----------------- .../schemas/generated/experiments.py | 1222 ------------ .../datamodels/schemas/generated/methods.py | 275 --- .../datamodels/schemas/generated/resources.py | 306 --- .../datamodels/schemas/generated/sampling.py | 962 ---------- 13 files changed, 32 insertions(+), 5859 deletions(-) create mode 100644 alembic/versions/184417c6d044_deleted_duplicate_yaml_files.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py diff --git a/alembic/versions/184417c6d044_deleted_duplicate_yaml_files.py b/alembic/versions/184417c6d044_deleted_duplicate_yaml_files.py new file mode 100644 index 00000000..1afa0f71 --- /dev/null +++ b/alembic/versions/184417c6d044_deleted_duplicate_yaml_files.py @@ -0,0 +1,32 @@ +"""Deleted duplicate .yaml files + +Revision ID: 184417c6d044 +Revises: bfa07351a507 +Create Date: 2025-12-17 19:03:32.278635 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '184417c6d044' +down_revision: Union[str, Sequence[str], None] = 'bfa07351a507' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml deleted file mode 100644 index 83292024..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis.yaml +++ /dev/null @@ -1,109 +0,0 @@ -id: https://w3id.org/ca_biositing/analysis -name: analysis -title: Analysis Definitions -description: Datasets and observations. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - methods - -classes: - Dataset: - description: Dataset definition. - slots: - - id - - name - - record_type - - source_id - - start_date - - end_date - - description - slot_usage: - id: - identifier: true - range: integer - - Observation: - description: Observation data. - slots: - - id - - dataset_id - - record_type - - record_id - - parameter_id - - value - - unit_id - - dimension_type_id - - dimension_value - - dimension_unit_id - - note - slot_usage: - id: - identifier: true - range: integer - - DimensionType: - is_a: LookupBase - description: Type of dimension (e.g. timepoint, wavelength). - - AnalysisType: - is_a: LookupBase - description: Type of analysis. - -slots: - #Slots imported - #parameter_id: from methods.yaml - #note: from core.yaml - - dataset_id: - range: integer - description: Reference to Dataset. - - record_type: - range: string - description: Type of record. - - record_id: - range: integer - description: ID of the record. - - value: - range: decimal - description: Value of the observation. - - unit_id: - range: integer - description: Reference to Unit. - - dimension_type_id: - range: integer - description: Reference to DimensionType. - - dimension_value: - range: decimal - description: Value of the dimension. - - dimension_unit_id: - range: integer - description: Reference to Unit (dimension). - - source_id: - range: integer - description: Reference to Source. - - start_date: - range: datetime - description: Start date of the dataset. - - end_date: - range: datetime - description: End date of the dataset. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml deleted file mode 100644 index 4ec92ee7..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/analysis_records.yaml +++ /dev/null @@ -1,233 +0,0 @@ -id: https://w3id.org/ca_biositing/analysis_records -name: analysis_records -title: Analysis Records -description: Specific analysis record types. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - analysis - - experiments - - methods - - sampling - - resources - -classes: - # Base Record Class (Mixin) - RecordBase: - mixin: true - slots: - - id - - dataset_id - - experiment_id - - resource_id - - sample_id - - technical_replicate_no - - technical_replicate_total - - method_id - - raw_data_id - - qc_pass - - note - slot_usage: - id: - identifier: true - range: integer - - ProximateRecord: - is_a: RecordBase - description: Proximate analysis record. - - UltimateRecord: - is_a: RecordBase - description: Ultimate analysis record. - - CompositionalRecord: - is_a: RecordBase - description: Compositional analysis record. - - IcpRecord: - is_a: RecordBase - description: ICP analysis record. - - XrfRecord: - is_a: RecordBase - description: XRF analysis record. - slots: - - maybe_wavelength_nm - - maybe_intensity - - maybe_energy_slope - - maybe_energy_offset - - XrdRecord: - is_a: RecordBase - description: XRD analysis record. - slots: - - maybe_scan_low_nm - - maybe_scan_high_nm - - CalorimetryRecord: - is_a: RecordBase - description: Calorimetry analysis record. - - FtnirRecord: - is_a: RecordBase - description: FT-NIR analysis record. - - RgbRecord: - is_a: RecordBase - description: RGB analysis record. - - PretreatmentRecord: - is_a: RecordBase - description: Pretreatment record. - slots: - - pretreatment_method - - eh_method_id - - reaction_block_id - - block_position - - temperature - - replicate_no - - analyst_id - - FermentationRecord: - is_a: RecordBase - description: Fermentation record. - slots: - - strain_id - - pretreatement_method_id - - eh_method_id - - replicate_no - - well_position - - temperature - - agitation_rpm - - vessel_id - - analyte_detection_equipment_id - - analyst_id - - GasificationRecord: - is_a: RecordBase - description: Gasification record. - slots: - - feedstock_mass - - bed_temperature - - gas_flow_rate - - analyst_id - - AutoclaveRecord: - is_a: RecordBase - description: Autoclave record. - slots: - - analyst_id - -slots: - technical_replicate_no: - range: integer - description: Technical replicate number. - - technical_replicate_total: - range: integer - description: Total technical replicates. - - raw_data_id: - range: integer - description: Reference to FileObjectMetadata. - - qc_pass: - range: boolean - description: Whether QC passed. - - maybe_wavelength_nm: - range: decimal - description: Wavelength in nm. - - maybe_intensity: - range: decimal - description: Intensity. - - maybe_energy_slope: - range: decimal - description: Energy slope. - - maybe_energy_offset: - range: decimal - description: Energy offset. - - maybe_scan_low_nm: - range: integer - description: Scan low nm. - - maybe_scan_high_nm: - range: integer - description: Scan high nm. - - pretreatment_method: - range: integer - description: Reference to Method (pretreatment). - - eh_method_id: - range: integer - description: Reference to Method (enzymatic hydrolysis). - - reaction_block_id: - range: integer - description: Reaction block ID. - - block_position: - range: string - description: Position in block. - - temperature: - range: decimal - description: Temperature. - - replicate_no: - range: integer - description: Replicate number. - - strain_id: - range: integer - description: Reference to Strain. - - pretreatement_method_id: - range: integer - description: Reference to Method (pretreatment). - - well_position: - range: string - description: Well position. - - agitation_rpm: - range: decimal - description: Agitation RPM. - - vessel_id: - range: integer - description: Reference to Equipment (vessel). - - analyte_detection_equipment_id: - range: integer - description: Reference to Equipment (detection). - - feedstock_mass: - range: decimal - description: Feedstock mass. - - bed_temperature: - range: decimal - description: Bed temperature. - - gas_flow_rate: - range: decimal - description: Gas flow rate. - - sample_id: - range: integer - description: Reference to Sample. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml deleted file mode 100644 index 56bf5322..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiments.yaml +++ /dev/null @@ -1,138 +0,0 @@ -id: https://w3id.org/ca_biositing/experiments -name: experiments -title: Experiment Definitions -description: Experiments, equipment, and analysis. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - geography - - people - - methods - - sampling - - analysis - -classes: - Experiment: - is_a: BaseEntity - description: Experiment definition. - slots: - - analyst_id - - exper_start_date - - exper_duration - - exper_duration_unit_id - - exper_location_id - - description - - Equipment: - is_a: LookupBase - description: Equipment used in experiments. - slots: - - equipment_location_id - - ExperimentEquipment: - description: Link between experiment and equipment. - slots: - - id - - experiment_id - - equipment_id - slot_usage: - id: - identifier: true - range: integer - - ExperimentAnalysis: - description: Link between experiment and analysis type. - slots: - - id - - experiment_id - - analysis_type_id - slot_usage: - id: - identifier: true - range: integer - - ExperimentPreparedSample: - description: Link between experiment and prepared sample. - slots: - - id - - experiment_id - - prepared_sample_id - slot_usage: - id: - identifier: true - range: integer - - ExperimentMethod: - description: Link between experiment and method. - slots: - - id - - experiment_id - - method_id - slot_usage: - id: - identifier: true - range: integer - - Strain: - is_a: LookupBase - description: Strain of organism. - slots: - - parent_strain_id - -slots: - analyst_id: - range: integer - description: Reference to Contact (analyst). - - exper_start_date: - range: date - description: Start date of experiment. - - exper_duration: - range: decimal - description: Duration of experiment. - - exper_duration_unit_id: - range: integer - description: Reference to Unit. - - exper_location_id: - range: integer - description: Reference to LocationAddress. - - equipment_location_id: - range: integer - description: Reference to LocationAddress. - - experiment_id: - range: integer - description: Reference to Experiment. - - equipment_id: - range: integer - description: Reference to Equipment. - - analysis_type_id: - range: integer - description: Reference to AnalysisType. - - prepared_sample_id: - range: integer - description: Reference to PreparedSample. - - method_id: - range: integer - description: Reference to Method. - - parent_strain_id: - range: integer - description: Reference to Strain (parent). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml deleted file mode 100644 index d370f253..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods.yaml +++ /dev/null @@ -1,120 +0,0 @@ -id: https://w3id.org/ca_biositing/methods -name: methods -title: Methods and Parameters -description: Methods, parameters, and units. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - -classes: - Unit: - is_a: LookupBase - description: Unit of measurement. - - Method: - is_a: BaseEntity - description: Analytical method. - slots: - - name - - method_abbrev_id - - method_category_id - - method_standard_id - - description - - detection_limits - - source_id - - MethodAbbrev: - is_a: LookupBase - description: Abbreviation for a method. - - MethodCategory: - is_a: LookupBase - description: Category of a method. - - MethodStandard: - is_a: LookupBase - description: Standard associated with a method. - - Parameter: - is_a: BaseEntity - description: Parameter measured. - slots: - - name - - standard_unit_id - - calculated - - description - - ParameterCategory: - is_a: LookupBase - description: Category of a parameter. - - ParameterCategoryParameter: - description: Link between parameter and category. - slots: - - id - - parameter_id - - parameter_category_id - slot_usage: - id: - identifier: true - range: integer - - ParameterUnit: - description: Link between parameter and alternate units. - slots: - - id - - parameter_id - - alternate_unit_id - slot_usage: - id: - identifier: true - range: integer - -slots: - method_abbrev_id: - range: integer - description: Reference to MethodAbbrev. - - method_category_id: - range: integer - description: Reference to MethodCategory. - - method_standard_id: - range: integer - description: Reference to MethodStandard. - - detection_limits: - range: string - description: Detection limits of the method. - - source_id: - range: integer - description: Reference to DataSource. - - standard_unit_id: - range: integer - description: Reference to Unit (standard). - - calculated: - range: boolean - description: Whether the parameter is calculated. - - parameter_id: - range: integer - description: Reference to Parameter. - - parameter_category_id: - range: integer - description: Reference to ParameterCategory. - - alternate_unit_id: - range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml deleted file mode 100644 index 2cc58cf0..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resources.yaml +++ /dev/null @@ -1,176 +0,0 @@ -id: https://w3id.org/ca_biositing/resources -name: resources -title: Resource Definitions -description: Biomass resources and their classifications. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - geography - -classes: - Resource: - is_a: BaseEntity - description: Biomass resource definition. - slots: - - name - - primary_crop_id - - resource_class_id - - resource_subclass_id - - note - - ResourceClass: - is_a: LookupBase - description: Classification of resources. - - ResourceSubclass: - is_a: LookupBase - description: Sub-classification of resources. - - PrimaryCrop: - is_a: LookupBase - description: Primary crop definition. - - ResourceAvailability: - is_a: BaseEntity - description: Availability of a resource in a location. - slots: - - resource_id - - geoid - - from_month - - to_month - - year_round - - note - - ResourceCounterfactual: - is_a: BaseEntity - description: Counterfactual uses of a resource. - slots: - - geoid - - resource_id - - counterfactual_description - - animal_bedding_percent - - animal_bedding_source_id - - animal_feed_percent - - animal_feed_source_id - - bioelectricty_percent - - bioelectricty_source_id - - burn_percent - - burn_source_id - - compost_percent - - compost_source_id - - landfill_percent - - landfill_source_id - - counterfactual_date - - note - - ResourceMorphology: - description: Morphology of a resource. - slots: - - id - - resource_id - - morphology_uri - slot_usage: - id: - identifier: true - range: integer - -slots: - primary_crop_id: - range: integer - description: Reference to PrimaryCrop. - - resource_class_id: - range: integer - description: Reference to ResourceClass. - - resource_subclass_id: - range: integer - description: Reference to ResourceSubclass. - - resource_id: - range: integer - description: Reference to Resource. - - geoid: - range: string - description: Reference to Geography. - - from_month: - range: integer - description: Start month of availability. - - to_month: - range: integer - description: End month of availability. - - year_round: - range: boolean - description: Whether available year-round. - - counterfactual_description: - range: string - description: Description of counterfactual scenario. - - animal_bedding_percent: - range: decimal - description: Percentage used for animal bedding. - - animal_bedding_source_id: - range: integer - description: Source for animal bedding data. - - animal_feed_percent: - range: decimal - description: Percentage used for animal feed. - - animal_feed_source_id: - range: integer - description: Source for animal feed data. - - bioelectricty_percent: - range: decimal - description: Percentage used for bioelectricity. - - bioelectricty_source_id: - range: integer - description: Source for bioelectricity data. - - burn_percent: - range: decimal - description: Percentage burned. - - burn_source_id: - range: integer - description: Source for burn data. - - compost_percent: - range: decimal - description: Percentage composted. - - compost_source_id: - range: integer - description: Source for compost data. - - landfill_percent: - range: decimal - description: Percentage landfilled. - - landfill_source_id: - range: integer - description: Source for landfill data. - - counterfactual_date: - range: date - description: Date of counterfactual data. - - morphology_uri: - range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml deleted file mode 100644 index 9b449f57..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sampling.yaml +++ /dev/null @@ -1,250 +0,0 @@ -id: https://w3id.org/ca_biositing/sampling -name: sampling -title: Sampling Definitions -description: Field sampling and preparation. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - geography - - people - - resources - - methods - -classes: - FieldSample: - is_a: BaseEntity - description: Sample collected from the field. - slots: - - name - - resource_id - - provider_id - - collector_id - - sample_collection_source - - amount_collected - - amount_collected_unit_id - - sampling_location_id - - field_storage_method_id - - field_storage_duration_value - - field_storage_duration_unit_id - - field_storage_location_id - - collection_timestamp - - collection_method_id - - harvest_method_id - - harvest_date - - field_sample_storage_location_id - - note - - FieldStorageMethod: - is_a: LookupBase - description: Method of field storage. - - CollectionMethod: - is_a: LookupBase - description: Method of collection. - - HarvestMethod: - is_a: LookupBase - description: Method of harvest. - - ProcessingMethod: - is_a: LookupBase - description: Method of processing. - - PhysicalCharacteristic: - is_a: BaseEntity - description: Physical characteristics of a sample. - slots: - - field_sample_id - - particle_length - - particle_width - - particle_height - - particle_unit_id - - SoilType: - is_a: LookupBase - description: Type of soil. - - AgTreatment: - is_a: LookupBase - description: Agricultural treatment. - - FieldSampleCondition: - is_a: BaseEntity - description: Condition of the field sample. - slots: - - field_sample_id - - ag_treatment_id - - last_application_date - - treatment_amount_per_acre - - processing_method_id - - LocationSoilType: - is_a: BaseEntity - description: Soil type at a location. - slots: - - location_id - - soil_type_id - - PreparationMethod: - is_a: BaseEntity - description: Method of sample preparation. - slots: - - name - - description - - prep_method_abbrev_id - - prep_temp_c - - uri - - drying_step - - PreparationMethodAbbreviation: - is_a: LookupBase - description: Abbreviation for preparation method. - - PreparedSample: - is_a: BaseEntity - description: Sample prepared for analysis. - slots: - - name - - field_sample_id - - prep_method_id - - prep_date - - preparer_id - - note - -slots: - provider_id: - range: integer - description: Reference to Provider. - - collector_id: - range: integer - description: Reference to Contact (collector). - - sample_collection_source: - range: string - description: Source of sample collection. - - amount_collected: - range: decimal - description: Amount collected. - - amount_collected_unit_id: - range: integer - description: Reference to Unit. - - sampling_location_id: - range: integer - description: Reference to LocationAddress. - - field_storage_method_id: - range: integer - description: Reference to FieldStorageMethod. - - field_storage_duration_value: - range: decimal - description: Duration of field storage. - - field_storage_duration_unit_id: - range: integer - description: Reference to Unit. - - field_storage_location_id: - range: integer - description: Reference to LocationAddress. - - collection_timestamp: - range: datetime - description: Timestamp of collection. - - collection_method_id: - range: integer - description: Reference to CollectionMethod. - - harvest_method_id: - range: integer - description: Reference to HarvestMethod. - - harvest_date: - range: date - description: Date of harvest. - - field_sample_storage_location_id: - range: integer - description: Reference to LocationAddress. - - field_sample_id: - range: integer - description: Reference to FieldSample. - - particle_length: - range: decimal - description: Length of particle. - - particle_width: - range: decimal - description: Width of particle. - - particle_height: - range: decimal - description: Height of particle. - - particle_unit_id: - range: integer - description: Reference to Unit. - - ag_treatment_id: - range: integer - description: Reference to AgTreatment. - - last_application_date: - range: date - description: Date of last application. - - treatment_amount_per_acre: - range: float - description: Amount of treatment per acre. - - processing_method_id: - range: integer - description: Reference to ProcessingMethod. - - location_id: - range: integer - description: Reference to LocationAddress. - - soil_type_id: - range: integer - description: Reference to SoilType. - - prep_method_abbrev_id: - range: integer - description: Reference to PreparationMethodAbbreviation. - - prep_temp_c: - range: decimal - description: Preparation temperature in Celsius. - - drying_step: - range: boolean - description: Whether drying step was included. - - prep_method_id: - range: integer - description: Reference to PreparationMethod. - - prep_date: - range: date - description: Date of preparation. - - preparer_id: - range: integer - description: Reference to Contact (preparer). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py deleted file mode 100644 index f860432f..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis.py +++ /dev/null @@ -1,375 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class Dataset(Base): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(DateTime()) - end_date = Column(DateTime()) - description = Column(Text()) - - - def __repr__(self): - return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" - - - - - - -class Observation(Base): - """ - Observation data. - """ - __tablename__ = 'observation' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class DimensionType(LookupBase): - """ - Type of dimension (e.g. timepoint, wavelength). - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py deleted file mode 100644 index 53befe22..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/analysis_records.py +++ /dev/null @@ -1,1693 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class RecordBase(Base): - """ - - """ - __tablename__ = 'record_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"RecordBase(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Dataset(Base): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(DateTime()) - end_date = Column(DateTime()) - description = Column(Text()) - - - def __repr__(self): - return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" - - - - - - -class Observation(Base): - """ - Observation data. - """ - __tablename__ = 'observation' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class ExperimentEquipment(Base): - """ - Link between experiment and equipment. - """ - __tablename__ = 'experiment_equipment' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - equipment_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" - - - - - - -class ExperimentAnalysis(Base): - """ - Link between experiment and analysis type. - """ - __tablename__ = 'experiment_analysis' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - analysis_type_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" - - - - - - -class ExperimentPreparedSample(Base): - """ - Link between experiment and prepared sample. - """ - __tablename__ = 'experiment_prepared_sample' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - prepared_sample_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" - - - - - - -class ExperimentMethod(Base): - """ - Link between experiment and method. - """ - __tablename__ = 'experiment_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - method_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ProximateRecord(RecordBase): - """ - Proximate analysis record. - """ - __tablename__ = 'proximate_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"ProximateRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UltimateRecord(RecordBase): - """ - Ultimate analysis record. - """ - __tablename__ = 'ultimate_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"UltimateRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CompositionalRecord(RecordBase): - """ - Compositional analysis record. - """ - __tablename__ = 'compositional_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"CompositionalRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class IcpRecord(RecordBase): - """ - ICP analysis record. - """ - __tablename__ = 'icp_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"IcpRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class XrfRecord(RecordBase): - """ - XRF analysis record. - """ - __tablename__ = 'xrf_record' - - maybe_wavelength_nm = Column(Numeric()) - maybe_intensity = Column(Numeric()) - maybe_energy_slope = Column(Numeric()) - maybe_energy_offset = Column(Numeric()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class XrdRecord(RecordBase): - """ - XRD analysis record. - """ - __tablename__ = 'xrd_record' - - maybe_scan_low_nm = Column(Integer()) - maybe_scan_high_nm = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CalorimetryRecord(RecordBase): - """ - Calorimetry analysis record. - """ - __tablename__ = 'calorimetry_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"CalorimetryRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FtnirRecord(RecordBase): - """ - FT-NIR analysis record. - """ - __tablename__ = 'ftnir_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"FtnirRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class RgbRecord(RecordBase): - """ - RGB analysis record. - """ - __tablename__ = 'rgb_record' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"RgbRecord(id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PretreatmentRecord(RecordBase): - """ - Pretreatment record. - """ - __tablename__ = 'pretreatment_record' - - pretreatment_method = Column(Integer()) - eh_method_id = Column(Integer()) - reaction_block_id = Column(Integer()) - block_position = Column(Text()) - temperature = Column(Numeric()) - replicate_no = Column(Integer()) - analyst_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"PretreatmentRecord(pretreatment_method={self.pretreatment_method},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FermentationRecord(RecordBase): - """ - Fermentation record. - """ - __tablename__ = 'fermentation_record' - - strain_id = Column(Integer()) - pretreatement_method_id = Column(Integer()) - eh_method_id = Column(Integer()) - replicate_no = Column(Integer()) - well_position = Column(Text()) - temperature = Column(Numeric()) - agitation_rpm = Column(Numeric()) - vessel_id = Column(Integer()) - analyte_detection_equipment_id = Column(Integer()) - analyst_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"FermentationRecord(strain_id={self.strain_id},pretreatement_method_id={self.pretreatement_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class GasificationRecord(RecordBase): - """ - Gasification record. - """ - __tablename__ = 'gasification_record' - - feedstock_mass = Column(Numeric()) - bed_temperature = Column(Numeric()) - gas_flow_rate = Column(Numeric()) - analyst_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AutoclaveRecord(RecordBase): - """ - Autoclave record. - """ - __tablename__ = 'autoclave_record' - - analyst_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - - - def __repr__(self): - return f"AutoclaveRecord(analyst_id={self.analyst_id},id={self.id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension (e.g. timepoint, wavelength). - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample prepared for analysis. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Experiment(BaseEntity): - """ - Experiment definition. - """ - __tablename__ = 'experiment' - - analyst_id = Column(Integer()) - exper_start_date = Column(Date()) - exper_duration = Column(Numeric()) - exper_duration_unit_id = Column(Integer()) - exper_location_id = Column(Integer()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Equipment(LookupBase): - """ - Equipment used in experiments. - """ - __tablename__ = 'equipment' - - equipment_location_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Strain(LookupBase): - """ - Strain of organism. - """ - __tablename__ = 'strain' - - parent_strain_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py deleted file mode 100644 index c953a83a..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiments.py +++ /dev/null @@ -1,1222 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ExperimentEquipment(Base): - """ - Link between experiment and equipment. - """ - __tablename__ = 'experiment_equipment' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - equipment_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" - - - - - - -class ExperimentAnalysis(Base): - """ - Link between experiment and analysis type. - """ - __tablename__ = 'experiment_analysis' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - analysis_type_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" - - - - - - -class ExperimentPreparedSample(Base): - """ - Link between experiment and prepared sample. - """ - __tablename__ = 'experiment_prepared_sample' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - prepared_sample_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" - - - - - - -class ExperimentMethod(Base): - """ - Link between experiment and method. - """ - __tablename__ = 'experiment_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - method_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class Dataset(Base): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(DateTime()) - end_date = Column(DateTime()) - description = Column(Text()) - - - def __repr__(self): - return f"Dataset(id={self.id},name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},)" - - - - - - -class Observation(Base): - """ - Observation data. - """ - __tablename__ = 'observation' - - id = Column(Integer(), primary_key=True, nullable=False ) - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"Observation(id={self.id},dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},)" - - - - - - -class Experiment(BaseEntity): - """ - Experiment definition. - """ - __tablename__ = 'experiment' - - analyst_id = Column(Integer()) - exper_start_date = Column(Date()) - exper_duration = Column(Numeric()) - exper_duration_unit_id = Column(Integer()) - exper_location_id = Column(Integer()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Equipment(LookupBase): - """ - Equipment used in experiments. - """ - __tablename__ = 'equipment' - - equipment_location_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Strain(LookupBase): - """ - Strain of organism. - """ - __tablename__ = 'strain' - - parent_strain_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample prepared for analysis. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension (e.g. timepoint, wavelength). - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py deleted file mode 100644 index 5a5c33e9..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods.py +++ /dev/null @@ -1,275 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py deleted file mode 100644 index 41d9b229..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resources.py +++ /dev/null @@ -1,306 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py deleted file mode 100644 index 78c99d62..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sampling.py +++ /dev/null @@ -1,962 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between parameter and category. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between parameter and alternate units. - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample prepared for analysis. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_crop_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryCrop(LookupBase): - """ - Primary crop definition. - """ - __tablename__ = 'primary_crop' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryCrop(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for a method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of a method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with a method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of a parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } From 4f9f7596689985df21bf6b97b87f82b2d13b5eeb Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Fri, 19 Dec 2025 11:35:56 -0700 Subject: [PATCH 64/81] cleaning up a last few things before merge --- .../datamodels/utils/database_joins.ipynb | 570 ++++++++++++++++++ .../utils/query_landiq_observation.py | 22 + 2 files changed, 592 insertions(+) create mode 100644 src/ca_biositing/datamodels/utils/database_joins.ipynb create mode 100644 src/ca_biositing/datamodels/utils/query_landiq_observation.py diff --git a/src/ca_biositing/datamodels/utils/database_joins.ipynb b/src/ca_biositing/datamodels/utils/database_joins.ipynb new file mode 100644 index 00000000..dbb836f2 --- /dev/null +++ b/src/ca_biositing/datamodels/utils/database_joins.ipynb @@ -0,0 +1,570 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Database Joins and Denormalized Views\n", + "\n", + "This notebook demonstrates how to use SQLAlchemy to perform complex joins on the project's data models and create denormalized views suitable for API endpoints.\n", + "\n", + "It replaces the older `database_interaction.ipynb` and uses the new generated data models.\n", + "\n", + "**Note:** Ensure you are running this notebook in the project's Pixi environment where `ca-biositing-datamodels` is installed." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Python Executable: /Users/pjsmitty301/ca-biositing/.pixi/envs/default/bin/python\n", + "✅ You are running in a Pixi environment.\n" + ] + } + ], + "source": [ + "# Verify Kernel\n", + "import sys\n", + "print(f\"Python Executable: {sys.executable}\")\n", + "\n", + "# Check if we are in the pixi environment (path should contain .pixi)\n", + "if \".pixi\" in sys.executable:\n", + " print(\"✅ You are running in a Pixi environment.\")\n", + "else:\n", + " print(\"⚠️ You might be running in the wrong kernel. Please select the 'default' kernel created by Pixi.\")" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Libraries and models imported successfully.\n" + ] + } + ], + "source": [ + "import pandas as pd\n", + "from sqlalchemy import create_engine, select\n", + "from sqlalchemy.orm import Session\n", + "\n", + "# Import models from ca_biositing.py as the source of truth\n", + "from ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", + "\n", + "print(\"Libraries and models imported successfully.\")" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Connected to database.\n" + ] + } + ], + "source": [ + "# Database Connection\n", + "DATABASE_URL = \"postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db\"\n", + "engine = create_engine(DATABASE_URL)\n", + "print(f\"Connected to database.\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## 1. Join LandIQ Record and Observation\n", + "\n", + "We will join `LandiqRecord` and `Observation` tables on `observation.record_id = landiq_record.id`." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [ + { + "ename": "TypeError", + "evalue": " is not a generic class", + "output_type": "error", + "traceback": [ + "\u001b[31m---------------------------------------------------------------------------\u001b[39m", + "\u001b[31mTypeError\u001b[39m Traceback (most recent call last)", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[34]\u001b[39m\u001b[32m, line 2\u001b[39m\n\u001b[32m 1\u001b[39m stmt2 = select(LandiqRecord, PrimaryCrop).join(\n\u001b[32m----> \u001b[39m\u001b[32m2\u001b[39m \u001b[43mPrimaryCrop\u001b[49m\u001b[43m[\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mname\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m]\u001b[49m, \n\u001b[32m 3\u001b[39m LandiqRecord.main_crop == PrimaryCrop.id).limit(\u001b[32m10\u001b[39m)\n\u001b[32m 5\u001b[39m \u001b[38;5;28mprint\u001b[39m(stmt2)\n\u001b[32m 7\u001b[39m df2 = pd.read_sql(stmt2, engine)\n", + "\u001b[36mFile \u001b[39m\u001b[32m~/ca-biositing/.pixi/envs/default/lib/python3.12/typing.py:398\u001b[39m, in \u001b[36m_tp_cache..decorator..inner\u001b[39m\u001b[34m(*args, **kwds)\u001b[39m\n\u001b[32m 396\u001b[39m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m:\n\u001b[32m 397\u001b[39m \u001b[38;5;28;01mpass\u001b[39;00m \u001b[38;5;66;03m# All real errors (not unhashable args) are raised below.\u001b[39;00m\n\u001b[32m--> \u001b[39m\u001b[32m398\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[43m*\u001b[49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43m*\u001b[49m\u001b[43mkwds\u001b[49m\u001b[43m)\u001b[49m\n", + "\u001b[36mFile \u001b[39m\u001b[32m~/ca-biositing/.pixi/envs/default/lib/python3.12/typing.py:1110\u001b[39m, in \u001b[36m_generic_class_getitem\u001b[39m\u001b[34m(cls, params)\u001b[39m\n\u001b[32m 1108\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m prepare \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[32m 1109\u001b[39m params = prepare(\u001b[38;5;28mcls\u001b[39m, params)\n\u001b[32m-> \u001b[39m\u001b[32m1110\u001b[39m \u001b[43m_check_generic\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparams\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mlen\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m__parameters__\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 1112\u001b[39m new_args = []\n\u001b[32m 1113\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m param, new_arg \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mzip\u001b[39m(\u001b[38;5;28mcls\u001b[39m.__parameters__, params):\n", + "\u001b[36mFile \u001b[39m\u001b[32m~/ca-biositing/.pixi/envs/default/lib/python3.12/site-packages/typing_extensions.py:3111\u001b[39m, in \u001b[36m_check_generic\u001b[39m\u001b[34m(cls, parameters, elen)\u001b[39m\n\u001b[32m 3106\u001b[39m \u001b[38;5;250m\u001b[39m\u001b[33;03m\"\"\"Check correct count for parameters of a generic cls (internal helper).\u001b[39;00m\n\u001b[32m 3107\u001b[39m \n\u001b[32m 3108\u001b[39m \u001b[33;03mThis gives a nice error message in case of count mismatch.\u001b[39;00m\n\u001b[32m 3109\u001b[39m \u001b[33;03m\"\"\"\u001b[39;00m\n\u001b[32m 3110\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m elen:\n\u001b[32m-> \u001b[39m\u001b[32m3111\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(\u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mcls\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m is not a generic class\u001b[39m\u001b[33m\"\u001b[39m)\n\u001b[32m 3112\u001b[39m alen = \u001b[38;5;28mlen\u001b[39m(parameters)\n\u001b[32m 3113\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m alen != elen:\n", + "\u001b[31mTypeError\u001b[39m: is not a generic class" + ] + } + ], + "source": [ + "stmt2 = select(LandiqRecord, PrimaryCrop).join(\n", + " PrimaryCrop, \n", + " LandiqRecord.main_crop == PrimaryCrop.id).limit(10)\n", + "\n", + "print(stmt2)\n", + "\n", + "df2 = pd.read_sql(stmt2, engine)\n", + "\n", + "df2.columns\n" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "SQL Query:\n", + "SELECT landiq_record.dataset_id, landiq_record.polygon_id, landiq_record.main_crop, landiq_record.secondary_crop, landiq_record.tertiary_crop, landiq_record.quaternary_crop, landiq_record.confidence, landiq_record.irrigated, landiq_record.acres, landiq_record.version, landiq_record.note, landiq_record.test, landiq_record.id, landiq_record.created_at, landiq_record.updated_at, landiq_record.etl_run_id, landiq_record.lineage_group_id, observation.dataset_id AS dataset_id_1, observation.record_type, observation.record_id, observation.parameter_id, observation.value, observation.unit_id, observation.dimension_type_id, observation.dimension_value, observation.dimension_unit_id, observation.note AS note_1, observation.id AS id_1, observation.created_at AS created_at_1, observation.updated_at AS updated_at_1, observation.etl_run_id AS etl_run_id_1, observation.lineage_group_id AS lineage_group_id_1 \n", + "FROM landiq_record JOIN observation ON observation.record_id = landiq_record.id\n" + ] + } + ], + "source": [ + "# Create the join query\n", + "stmt = select(LandiqRecord, Observation).join(\n", + " Observation,\n", + " Observation.record_id == LandiqRecord.id\n", + ")\n", + "\n", + "print(\"SQL Query:\")\n", + "print(stmt)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Loaded 0 rows.\n" + ] + }, + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "index", + "rawType": "int64", + "type": "integer" + }, + { + "name": "dataset_id", + "rawType": "object", + "type": "string" + }, + { + "name": "polygon_id", + "rawType": "object", + "type": "string" + }, + { + "name": "main_crop", + "rawType": "object", + "type": "string" + }, + { + "name": "secondary_crop", + "rawType": "object", + "type": "string" + }, + { + "name": "tertiary_crop", + "rawType": "object", + "type": "string" + }, + { + "name": "quaternary_crop", + "rawType": "object", + "type": "string" + }, + { + "name": "confidence", + "rawType": "object", + "type": "string" + }, + { + "name": "irrigated", + "rawType": "object", + "type": "string" + }, + { + "name": "acres", + "rawType": "object", + "type": "string" + }, + { + "name": "version", + "rawType": "object", + "type": "string" + }, + { + "name": "note", + "rawType": "object", + "type": "string" + }, + { + "name": "test", + "rawType": "object", + "type": "string" + }, + { + "name": "id", + "rawType": "object", + "type": "string" + }, + { + "name": "created_at", + "rawType": "object", + "type": "string" + }, + { + "name": "updated_at", + "rawType": "object", + "type": "string" + }, + { + "name": "etl_run_id", + "rawType": "object", + "type": "string" + }, + { + "name": "lineage_group_id", + "rawType": "object", + "type": "string" + }, + { + "name": "dataset_id_1", + "rawType": "object", + "type": "string" + }, + { + "name": "record_type", + "rawType": "object", + "type": "string" + }, + { + "name": "record_id", + "rawType": "object", + "type": "string" + }, + { + "name": "parameter_id", + "rawType": "object", + "type": "string" + }, + { + "name": "value", + "rawType": "object", + "type": "string" + }, + { + "name": "unit_id", + "rawType": "object", + "type": "string" + }, + { + "name": "dimension_type_id", + "rawType": "object", + "type": "string" + }, + { + "name": "dimension_value", + "rawType": "object", + "type": "string" + }, + { + "name": "dimension_unit_id", + "rawType": "object", + "type": "string" + }, + { + "name": "note_1", + "rawType": "object", + "type": "string" + }, + { + "name": "id_1", + "rawType": "object", + "type": "string" + }, + { + "name": "created_at_1", + "rawType": "object", + "type": "string" + }, + { + "name": "updated_at_1", + "rawType": "object", + "type": "string" + }, + { + "name": "etl_run_id_1", + "rawType": "object", + "type": "string" + }, + { + "name": "lineage_group_id_1", + "rawType": "object", + "type": "string" + } + ], + "ref": "edc059e1-7169-4eb9-ad76-c55b46d93053", + "rows": [], + "shape": { + 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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [dataset_id, polygon_id, main_crop, secondary_crop, tertiary_crop, quaternary_crop, confidence, irrigated, acres, version, note, test, id, created_at, updated_at, etl_run_id, lineage_group_id, dataset_id_1, record_type, record_id, parameter_id, value, unit_id, dimension_type_id, dimension_value, dimension_unit_id, note_1, id_1, created_at_1, updated_at_1, etl_run_id_1, lineage_group_id_1]\n", + "Index: []\n", + "\n", + "[0 rows x 32 columns]" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# Execute and load into DataFrame\n", + "try:\n", + " with Session(engine) as session:\n", + " # Using pandas read_sql to execute the statement and fetch results\n", + " # Note: Columns with same names (like 'id') might be duplicated or suffixed automatically by pandas.\n", + " df = pd.read_sql(stmt, session.bind)\n", + " \n", + " print(f\"Loaded {len(df)} rows.\")\n", + " display(df.head())\n", + "except Exception as e:\n", + " print(f\"Error executing query: {e}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "Index(['dataset_id', 'polygon_id', 'main_crop', 'secondary_crop',\n", + " 'tertiary_crop', 'quaternary_crop', 'confidence', 'irrigated', 'acres',\n", + " 'version', 'note', 'test', 'id', 'created_at', 'updated_at',\n", + " 'etl_run_id', 'lineage_group_id', 'dataset_id_1', 'record_type',\n", + " 'record_id', 'parameter_id', 'value', 'unit_id', 'dimension_type_id',\n", + " 'dimension_value', 'dimension_unit_id', 'note_1', 'id_1',\n", + " 'created_at_1', 'updated_at_1', 'etl_run_id_1', 'lineage_group_id_1'],\n", + " dtype='object')" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.columns" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "index", + "rawType": "int64", + "type": "integer" + }, + { + "name": "id", + "rawType": "object", + "type": "string" + }, + { + "name": "dataset_id", + "rawType": "object", + "type": "string" + }, + { + "name": "record_id", + "rawType": "object", + "type": "string" + }, + { + "name": "main_crop", + "rawType": "object", + "type": "string" + }, + { + "name": "parameter_id", + "rawType": "object", + "type": "string" + }, + { + "name": "value", + "rawType": "object", + "type": "string" + }, + { + "name": "unit_id", + "rawType": "object", + "type": "string" + } + ], + "ref": "5c95c323-56ec-4546-ad20-84e7b50c7748", + "rows": [], + "shape": { + "columns": 7, + "rows": 0 + } + }, + "text/html": [ + "
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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [id, dataset_id, record_id, main_crop, parameter_id, value, unit_id]\n", + "Index: []" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df[[\"id\", \"dataset_id\", \"record_id\", \"main_crop\", \"parameter_id\", \"value\", \"unit_id\"]]" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.0" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/src/ca_biositing/datamodels/utils/query_landiq_observation.py b/src/ca_biositing/datamodels/utils/query_landiq_observation.py new file mode 100644 index 00000000..6a7a0ee4 --- /dev/null +++ b/src/ca_biositing/datamodels/utils/query_landiq_observation.py @@ -0,0 +1,22 @@ +from sqlalchemy import select +from ca_biositing.datamodels.schemas.generated.ca_biositing import LandiqRecord, Observation + +def generate_query(): + """ + Generates a SQL query joining LandiqRecord and Observation tables. + """ + # Create the select statement + # We select from LandiqRecord and join Observation + # The join condition is explicitly specified as requested: + # observation.record_id = landiq_record.id + stmt = select(LandiqRecord, Observation).join( + Observation, + Observation.record_id == LandiqRecord.id + ) + + return stmt + +if __name__ == "__main__": + query = generate_query() + print("Generated SQL Query:") + print(query) From eb90e0fcee29b03836e1ebb1766eaf3836a9488a Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Mon, 22 Dec 2025 14:16:32 -0700 Subject: [PATCH 65/81] adding database.py and config.py to datamodels folder. modifying ca_biositing.yaml to include the infrastructure models --- ...668dac367_added_test_column_to_resource.py | 34 ++ ...22d3d9ea6_adding_infrastructure_i_think.py | 346 +++++++++++++ census.survey.mmd | 53 -- .../ca_biositing/datamodels/config.py | 34 ++ .../ca_biositing/datamodels/database.py | 26 + .../datamodels/linkml/ca_biositing.yaml | 2 + .../linkml/modules/resource_information.yaml | 5 + .../schemas/generated/aim1_records.py | 3 +- .../schemas/generated/aim2_records.py | 3 +- .../schemas/generated/ca_biositing.py | 480 +++++++++++++++++- .../generated/data_sources_metadata.py | 3 +- .../schemas/generated/experiment_equipment.py | 3 +- .../schemas/generated/external_data.py | 3 +- .../schemas/generated/field_sampling.py | 3 +- .../schemas/generated/general_analysis.py | 3 +- .../schemas/generated/infrastructure.py | 3 +- .../generated/methods_parameters_units.py | 3 +- .../schemas/generated/resource_information.py | 3 +- .../schemas/generated/sample_preparation.py | 3 +- 19 files changed, 948 insertions(+), 65 deletions(-) create mode 100644 alembic/versions/5a6668dac367_added_test_column_to_resource.py create mode 100644 alembic/versions/fc422d3d9ea6_adding_infrastructure_i_think.py delete mode 100644 census.survey.mmd create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/config.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/database.py diff --git a/alembic/versions/5a6668dac367_added_test_column_to_resource.py b/alembic/versions/5a6668dac367_added_test_column_to_resource.py new file mode 100644 index 00000000..1b30aa8e --- /dev/null +++ b/alembic/versions/5a6668dac367_added_test_column_to_resource.py @@ -0,0 +1,34 @@ +"""added test column to Resource + +Revision ID: 5a6668dac367 +Revises: 184417c6d044 +Create Date: 2025-12-22 17:49:18.175092 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '5a6668dac367' +down_revision: Union[str, Sequence[str], None] = '184417c6d044' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column('landiq_record', 'test') + op.add_column('resource', sa.Column('test', sa.Text(), nullable=True)) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_column('resource', 'test') + op.add_column('landiq_record', sa.Column('test', sa.TEXT(), autoincrement=False, nullable=True)) + # ### end Alembic commands ### diff --git a/alembic/versions/fc422d3d9ea6_adding_infrastructure_i_think.py b/alembic/versions/fc422d3d9ea6_adding_infrastructure_i_think.py new file mode 100644 index 00000000..68b1bd0f --- /dev/null +++ b/alembic/versions/fc422d3d9ea6_adding_infrastructure_i_think.py @@ -0,0 +1,346 @@ +"""adding infrastructure I think + +Revision ID: fc422d3d9ea6 +Revises: 5a6668dac367 +Create Date: 2025-12-22 21:13:56.161244 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'fc422d3d9ea6' +down_revision: Union[str, Sequence[str], None] = '5a6668dac367' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('facility_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('facility_name', sa.Text(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('capacity_mw', sa.Numeric(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('operator', sa.Text(), nullable=True), + sa.Column('start_year', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('infrastructure_biodiesel_plants', + sa.Column('biodiesel_plant_id', sa.Integer(), nullable=False), + sa.Column('company', sa.Text(), nullable=True), + sa.Column('bbi_index', sa.Integer(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('capacity_mmg_per_y', sa.Integer(), nullable=True), + sa.Column('feedstock', sa.Text(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('address', sa.Text(), nullable=True), + sa.Column('coordinates', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('biodiesel_plant_id') + ) + op.create_table('infrastructure_biosolids_facilities', + sa.Column('biosolid_facility_id', sa.Integer(), nullable=False), + sa.Column('report_submitted_date', sa.Date(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('facility', sa.Text(), nullable=True), + sa.Column('authority', sa.Text(), nullable=True), + sa.Column('plant_type', sa.Text(), nullable=True), + sa.Column('aqmd', sa.Text(), nullable=True), + sa.Column('facility_address', sa.Text(), nullable=True), + sa.Column('facility_city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('facility_zip', sa.Text(), nullable=True), + sa.Column('facility_county', sa.Text(), nullable=True), + sa.Column('mailing_street_1', sa.Text(), nullable=True), + sa.Column('mailing_city', sa.Text(), nullable=True), + sa.Column('mailing_state', sa.Text(), nullable=True), + sa.Column('mailing_zip', sa.Text(), nullable=True), + sa.Column('biosolids_number', sa.Text(), nullable=True), + sa.Column('biosolids_contact', sa.Text(), nullable=True), + sa.Column('biosolids_contact_phone', sa.Text(), nullable=True), + sa.Column('biosolids_contact_email', sa.Text(), nullable=True), + sa.Column('adwf', sa.Numeric(), nullable=True), + sa.Column('potw_biosolids_generated', sa.Integer(), nullable=True), + sa.Column('twtds_biosolids_treated', sa.Integer(), nullable=True), + sa.Column('class_b_land_app', sa.Integer(), nullable=True), + sa.Column('class_b_applier', sa.Text(), nullable=True), + sa.Column('class_a_compost', sa.Integer(), nullable=True), + sa.Column('class_a_heat_dried', sa.Integer(), nullable=True), + sa.Column('class_a_other', sa.Integer(), nullable=True), + sa.Column('class_a_other_applier', sa.Text(), nullable=True), + sa.Column('twtds_transfer_to_second_preparer', sa.Integer(), nullable=True), + sa.Column('twtds_second_preparer_name', sa.Text(), nullable=True), + sa.Column('adc_or_final_c', sa.Integer(), nullable=True), + sa.Column('landfill', sa.Integer(), nullable=True), + sa.Column('landfill_name', sa.Text(), nullable=True), + sa.Column('surface_disposal', sa.Integer(), nullable=True), + sa.Column('deepwell_injection', sa.Text(), nullable=True), + sa.Column('stored', sa.Integer(), nullable=True), + sa.Column('longterm_treatment', sa.Integer(), nullable=True), + sa.Column('other', sa.Integer(), nullable=True), + sa.Column('name_of_other', sa.Text(), nullable=True), + sa.Column('incineration', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('biosolid_facility_id') + ) + op.create_table('infrastructure_cafo_manure_locations', + sa.Column('cafo_manure_id', sa.Integer(), nullable=False), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('owner_name', sa.Text(), nullable=True), + sa.Column('facility_name', sa.Text(), nullable=True), + sa.Column('address', sa.Text(), nullable=True), + sa.Column('town', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('zip', sa.Text(), nullable=True), + sa.Column('animal', sa.Text(), nullable=True), + sa.Column('animal_feed_operation_type', sa.Text(), nullable=True), + sa.Column('animal_units', sa.Integer(), nullable=True), + sa.Column('animal_count', sa.Integer(), nullable=True), + sa.Column('manure_total_solids', sa.Numeric(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('date_accessed', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('cafo_manure_id') + ) + op.create_table('infrastructure_combustion_plants', + sa.Column('combustion_fid', sa.Integer(), nullable=False), + sa.Column('objectid', sa.Integer(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('county', sa.Text(), nullable=True), + sa.Column('equivalent_generation', sa.Numeric(), nullable=True), + sa.Column('np_mw', sa.Numeric(), nullable=True), + sa.Column('cf', sa.Numeric(), nullable=True), + sa.Column('yearload', sa.Integer(), nullable=True), + sa.Column('fuel', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('wkt_geom', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('combustion_fid') + ) + op.create_table('infrastructure_district_energy_systems', + sa.Column('des_fid', sa.Integer(), nullable=False), + sa.Column('cbg_id', sa.Integer(), nullable=True), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('system', sa.Text(), nullable=True), + sa.Column('object_id', sa.Integer(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('primary_fuel', sa.Text(), nullable=True), + sa.Column('secondary_fuel', sa.Text(), nullable=True), + sa.Column('usetype', sa.Text(), nullable=True), + sa.Column('cap_st', sa.Numeric(), nullable=True), + sa.Column('cap_hw', sa.Numeric(), nullable=True), + sa.Column('cap_cw', sa.Numeric(), nullable=True), + sa.Column('chpcg_cap', sa.Numeric(), nullable=True), + sa.Column('excess_c', sa.Numeric(), nullable=True), + sa.Column('excess_h', sa.Numeric(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('wkt_geom', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('des_fid') + ) + op.create_table('infrastructure_ethanol_biorefineries', + sa.Column('ethanol_biorefinery_id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('address', sa.Text(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('capacity_mgy', sa.Integer(), nullable=True), + sa.Column('production_mgy', sa.Integer(), nullable=True), + sa.Column('constr_exp', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('ethanol_biorefinery_id') + ) + op.create_table('infrastructure_food_processing_facilities', + sa.Column('processing_facility_id', sa.Integer(), nullable=False), + sa.Column('address', sa.Text(), nullable=True), + sa.Column('county', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('company', sa.Text(), nullable=True), + sa.Column('join_count', sa.Integer(), nullable=True), + sa.Column('master_type', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('subtype', sa.Text(), nullable=True), + sa.Column('target_fid', sa.Integer(), nullable=True), + sa.Column('processing_type', sa.Text(), nullable=True), + sa.Column('zip', sa.Text(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('wkt_geom', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('processing_facility_id') + ) + op.create_table('infrastructure_landfills', + sa.Column('project_id', sa.Text(), nullable=False), + sa.Column('project_int_id', sa.Integer(), nullable=True), + sa.Column('ghgrp_id', sa.Text(), nullable=True), + sa.Column('landfill_id', sa.Integer(), nullable=True), + sa.Column('landfill_name', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('physical_address', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('county', sa.Text(), nullable=True), + sa.Column('zip_code', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('ownership_type', sa.Text(), nullable=True), + sa.Column('landfill_owner_orgs', sa.Text(), nullable=True), + sa.Column('landfill_opened_year', sa.Date(), nullable=True), + sa.Column('landfill_closure_year', sa.Date(), nullable=True), + sa.Column('landfill_status', sa.Text(), nullable=True), + sa.Column('waste_in_place', sa.Integer(), nullable=True), + sa.Column('waste_in_place_year', sa.Date(), nullable=True), + sa.Column('lfg_system_in_place', sa.Boolean(), nullable=True), + sa.Column('lfg_collected', sa.Numeric(), nullable=True), + sa.Column('lfg_flared', sa.Numeric(), nullable=True), + sa.Column('project_status', sa.Text(), nullable=True), + sa.Column('project_name', sa.Text(), nullable=True), + sa.Column('project_start_date', sa.Date(), nullable=True), + sa.Column('project_shutdown_date', sa.Date(), nullable=True), + sa.Column('project_type_category', sa.Text(), nullable=True), + sa.Column('lfg_energy_project_type', sa.Text(), nullable=True), + sa.Column('rng_delivery_method', sa.Text(), nullable=True), + sa.Column('actual_mw_generation', sa.Numeric(), nullable=True), + sa.Column('rated_mw_capacity', sa.Numeric(), nullable=True), + sa.Column('lfg_flow_to_project', sa.Numeric(), nullable=True), + sa.Column('direct_emission_reductions', sa.Numeric(), nullable=True), + sa.Column('avoided_emission_reductions', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('project_id') + ) + op.create_table('infrastructure_livestock_anaerobic_digesters', + sa.Column('digester_id', sa.Integer(), nullable=False), + sa.Column('project_name', sa.Text(), nullable=True), + sa.Column('project_type', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('digester_type', sa.Text(), nullable=True), + sa.Column('profile', sa.Text(), nullable=True), + sa.Column('year_operational', sa.Date(), nullable=True), + sa.Column('animal_type_class', sa.Text(), nullable=True), + sa.Column('animal_types', sa.Text(), nullable=True), + sa.Column('pop_feeding_digester', sa.Text(), nullable=True), + sa.Column('total_pop_feeding_digester', sa.Integer(), nullable=True), + sa.Column('cattle', sa.Integer(), nullable=True), + sa.Column('dairy', sa.Integer(), nullable=True), + sa.Column('poultry', sa.Integer(), nullable=True), + sa.Column('swine', sa.Integer(), nullable=True), + sa.Column('codigestion', sa.Text(), nullable=True), + sa.Column('biogas_generation_estimate', sa.Integer(), nullable=True), + sa.Column('electricity_generated', sa.Integer(), nullable=True), + sa.Column('biogas_end_uses', sa.Text(), nullable=True), + sa.Column('methane_emission_reductions', sa.Integer(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('digester_id') + ) + op.create_table('infrastructure_msw_to_energy_anaerobic_digesters', + sa.Column('wte_id', sa.Integer(), nullable=False), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('county', sa.Text(), nullable=True), + sa.Column('equivalent_generation', sa.Numeric(), nullable=True), + sa.Column('feedstock', sa.Text(), nullable=True), + sa.Column('dayload', sa.Numeric(), nullable=True), + sa.Column('dayload_bdt', sa.Numeric(), nullable=True), + sa.Column('facility_type', sa.Text(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('wkt_geom', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('wte_id') + ) + op.create_table('infrastructure_saf_and_renewable_diesel_plants', + sa.Column('ibcc_index', sa.Integer(), nullable=False), + sa.Column('company', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('country', sa.Text(), nullable=True), + sa.Column('capacity', sa.Text(), nullable=True), + sa.Column('feedstock', sa.Text(), nullable=True), + sa.Column('products', sa.Text(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('address', sa.Text(), nullable=True), + sa.Column('coordinates', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('ibcc_index') + ) + op.create_table('infrastructure_wastewater_treatment_plants', + sa.Column('plant_id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('codigestion', sa.Text(), nullable=True), + sa.Column('flow_design_adjusted', sa.Numeric(), nullable=True), + sa.Column('flow_average', sa.Numeric(), nullable=True), + sa.Column('biosolids', sa.Numeric(), nullable=True), + sa.Column('excess_flow', sa.Numeric(), nullable=True), + sa.Column('biogas_utilized', sa.Boolean(), nullable=True), + sa.Column('flaring', sa.Boolean(), nullable=True), + sa.Column('excess_mass_loading_rate', sa.Numeric(), nullable=True), + sa.Column('excess_mass_loading_rate_wet', sa.Numeric(), nullable=True), + sa.Column('methane_production', sa.Numeric(), nullable=True), + sa.Column('energy_content', sa.Numeric(), nullable=True), + sa.Column('electric_kw', sa.Numeric(), nullable=True), + sa.Column('thermal_mmbtu_d', sa.Numeric(), nullable=True), + sa.Column('electric_kwh', sa.Numeric(), nullable=True), + sa.Column('thermal_annual_mmbtu_y', sa.Numeric(), nullable=True), + sa.Column('anaerobic_digestion_facility', sa.Text(), nullable=True), + sa.Column('county', sa.Text(), nullable=True), + sa.Column('dayload_bdt', sa.Numeric(), nullable=True), + sa.Column('dayload', sa.Numeric(), nullable=True), + sa.Column('equivalent_generation', sa.Numeric(), nullable=True), + sa.Column('facility_type', sa.Text(), nullable=True), + sa.Column('feedstock', sa.Text(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('zipcode', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('plant_id') + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('infrastructure_wastewater_treatment_plants') + op.drop_table('infrastructure_saf_and_renewable_diesel_plants') + op.drop_table('infrastructure_msw_to_energy_anaerobic_digesters') + op.drop_table('infrastructure_livestock_anaerobic_digesters') + op.drop_table('infrastructure_landfills') + op.drop_table('infrastructure_food_processing_facilities') + op.drop_table('infrastructure_ethanol_biorefineries') + op.drop_table('infrastructure_district_energy_systems') + op.drop_table('infrastructure_combustion_plants') + op.drop_table('infrastructure_cafo_manure_locations') + op.drop_table('infrastructure_biosolids_facilities') + op.drop_table('infrastructure_biodiesel_plants') + op.drop_table('facility_record') + # ### end Alembic commands ### diff --git a/census.survey.mmd b/census.survey.mmd deleted file mode 100644 index 8ff952c9..00000000 --- a/census.survey.mmd +++ /dev/null @@ -1,53 +0,0 @@ -erDiagram -CensusRecord { - integer year - CropEnum crop - VariableEnum variable - UnitEnum unit - float value - BearingStatusEnum bearing_status - string class_desc - string domain_desc - string source - string notes -} -Geography { - string state_name - string state_fips - string county_name - string county_fips - string geoid - string region_name - string agg_level_desc -} -SurveyRecord { - string period_desc - string freq_desc - string program_desc - integer year - CropEnum crop - VariableEnum variable - UnitEnum unit - float value - BearingStatusEnum bearing_status - string class_desc - string domain_desc - string source - string notes -} -UsdaRecord { - integer year - CropEnum crop - VariableEnum variable - UnitEnum unit - float value - BearingStatusEnum bearing_status - string class_desc - string domain_desc - string source - string notes -} - -CensusRecord ||--|o Geography : "geography" -SurveyRecord ||--|o Geography : "geography" -UsdaRecord ||--|o Geography : "geography" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/config.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/config.py new file mode 100644 index 00000000..9ea419ec --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/config.py @@ -0,0 +1,34 @@ +from pydantic_settings import BaseSettings, SettingsConfigDict +from typing import Optional + +class Settings(BaseSettings): + """ + Application settings and configuration for the datamodels package. + + Uses Pydantic Settings to load configuration from environment variables + and .env files. + """ + POSTGRES_USER: str = "postgres" + POSTGRES_PASSWORD: str = "postgres" + POSTGRES_DB: str = "biositing" + POSTGRES_HOST: str = "db" + POSTGRES_PORT: int = 5432 + DATABASE_URL: Optional[str] = None + + model_config = SettingsConfigDict( + env_file=".env", + env_file_encoding="utf-8", + extra="ignore", + case_sensitive=True + ) + + @property + def database_url(self) -> str: + """ + Constructs the database URL from components if not explicitly set. + """ + if self.DATABASE_URL: + return self.DATABASE_URL + return f"postgresql://{self.POSTGRES_USER}:{self.POSTGRES_PASSWORD}@{self.POSTGRES_HOST}:{self.POSTGRES_PORT}/{self.POSTGRES_DB}" + +settings = Settings() diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py new file mode 100644 index 00000000..00dc9b3c --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py @@ -0,0 +1,26 @@ +from sqlmodel import SQLModel, create_engine, Session +from .config import settings + +# Create engine using the database URL from settings +# echo=False by default to avoid verbose SQL logging +engine = create_engine(settings.database_url, echo=False) + +def get_session(): + """ + Dependency that yields a database session. + Useful for FastAPI dependencies. + """ + with Session(engine) as session: + yield session + +def create_db_and_tables(): + """ + Create all tables defined in SQLModel metadata. + """ + SQLModel.metadata.create_all(engine) + +def get_engine(): + """ + Returns the database engine. + """ + return engine diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml index 94d9f8d2..fed17afb 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml @@ -30,3 +30,5 @@ imports: - modules/aim1_records - modules/aim2_records - modules/external_data + - modules/infrastructure + - modules/geography diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml index eb2ca5ed..f06fa29d 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml @@ -26,6 +26,7 @@ classes: - resource_class_id - resource_subclass_id - note + - test ResourceClass: is_a: LookupBase @@ -100,6 +101,10 @@ slots: range: integer description: Reference to ResourceSubclass. + test: + range: string + description: Test field. + #ResourceAvailability slots resource_id: diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py index ef08780e..075f0de2 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py @@ -896,6 +896,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -904,7 +905,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py index db37c954..45edb52c 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py @@ -922,6 +922,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -930,7 +931,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py index 7cdc3fb0..734d1d17 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py @@ -288,6 +288,449 @@ def __repr__(self): +class InfrastructureBiodieselPlants(Base): + """ + Biodiesel plants infrastructure. + """ + __tablename__ = 'infrastructure_biodiesel_plants' + + biodiesel_plant_id = Column(Integer(), primary_key=True, nullable=False ) + company = Column(Text()) + bbi_index = Column(Integer()) + city = Column(Text()) + state = Column(Text()) + capacity_mmg_per_y = Column(Integer()) + feedstock = Column(Text()) + status = Column(Text()) + address = Column(Text()) + coordinates = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + source = Column(Text()) + + + def __repr__(self): + return f"InfrastructureBiodieselPlants(biodiesel_plant_id={self.biodiesel_plant_id},company={self.company},bbi_index={self.bbi_index},city={self.city},state={self.state},capacity_mmg_per_y={self.capacity_mmg_per_y},feedstock={self.feedstock},status={self.status},address={self.address},coordinates={self.coordinates},latitude={self.latitude},longitude={self.longitude},source={self.source},)" + + + + + + +class InfrastructureBiosolidsFacilities(Base): + """ + Biosolids facilities infrastructure. + """ + __tablename__ = 'infrastructure_biosolids_facilities' + + biosolid_facility_id = Column(Integer(), primary_key=True, nullable=False ) + report_submitted_date = Column(Date()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + facility = Column(Text()) + authority = Column(Text()) + plant_type = Column(Text()) + aqmd = Column(Text()) + facility_address = Column(Text()) + facility_city = Column(Text()) + state = Column(Text()) + facility_zip = Column(Text()) + facility_county = Column(Text()) + mailing_street_1 = Column(Text()) + mailing_city = Column(Text()) + mailing_state = Column(Text()) + mailing_zip = Column(Text()) + biosolids_number = Column(Text()) + biosolids_contact = Column(Text()) + biosolids_contact_phone = Column(Text()) + biosolids_contact_email = Column(Text()) + adwf = Column(Numeric()) + potw_biosolids_generated = Column(Integer()) + twtds_biosolids_treated = Column(Integer()) + class_b_land_app = Column(Integer()) + class_b_applier = Column(Text()) + class_a_compost = Column(Integer()) + class_a_heat_dried = Column(Integer()) + class_a_other = Column(Integer()) + class_a_other_applier = Column(Text()) + twtds_transfer_to_second_preparer = Column(Integer()) + twtds_second_preparer_name = Column(Text()) + adc_or_final_c = Column(Integer()) + landfill = Column(Integer()) + landfill_name = Column(Text()) + surface_disposal = Column(Integer()) + deepwell_injection = Column(Text()) + stored = Column(Integer()) + longterm_treatment = Column(Integer()) + other = Column(Integer()) + name_of_other = Column(Text()) + incineration = Column(Integer()) + + + def __repr__(self): + return f"InfrastructureBiosolidsFacilities(biosolid_facility_id={self.biosolid_facility_id},report_submitted_date={self.report_submitted_date},latitude={self.latitude},longitude={self.longitude},facility={self.facility},authority={self.authority},plant_type={self.plant_type},aqmd={self.aqmd},facility_address={self.facility_address},facility_city={self.facility_city},state={self.state},facility_zip={self.facility_zip},facility_county={self.facility_county},mailing_street_1={self.mailing_street_1},mailing_city={self.mailing_city},mailing_state={self.mailing_state},mailing_zip={self.mailing_zip},biosolids_number={self.biosolids_number},biosolids_contact={self.biosolids_contact},biosolids_contact_phone={self.biosolids_contact_phone},biosolids_contact_email={self.biosolids_contact_email},adwf={self.adwf},potw_biosolids_generated={self.potw_biosolids_generated},twtds_biosolids_treated={self.twtds_biosolids_treated},class_b_land_app={self.class_b_land_app},class_b_applier={self.class_b_applier},class_a_compost={self.class_a_compost},class_a_heat_dried={self.class_a_heat_dried},class_a_other={self.class_a_other},class_a_other_applier={self.class_a_other_applier},twtds_transfer_to_second_preparer={self.twtds_transfer_to_second_preparer},twtds_second_preparer_name={self.twtds_second_preparer_name},adc_or_final_c={self.adc_or_final_c},landfill={self.landfill},landfill_name={self.landfill_name},surface_disposal={self.surface_disposal},deepwell_injection={self.deepwell_injection},stored={self.stored},longterm_treatment={self.longterm_treatment},other={self.other},name_of_other={self.name_of_other},incineration={self.incineration},)" + + + + + + +class InfrastructureCafoManureLocations(Base): + """ + CAFO manure locations infrastructure. + """ + __tablename__ = 'infrastructure_cafo_manure_locations' + + cafo_manure_id = Column(Integer(), primary_key=True, nullable=False ) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + owner_name = Column(Text()) + facility_name = Column(Text()) + address = Column(Text()) + town = Column(Text()) + state = Column(Text()) + zip = Column(Text()) + animal = Column(Text()) + animal_feed_operation_type = Column(Text()) + animal_units = Column(Integer()) + animal_count = Column(Integer()) + manure_total_solids = Column(Numeric()) + source = Column(Text()) + date_accessed = Column(Date()) + + + def __repr__(self): + return f"InfrastructureCafoManureLocations(cafo_manure_id={self.cafo_manure_id},latitude={self.latitude},longitude={self.longitude},owner_name={self.owner_name},facility_name={self.facility_name},address={self.address},town={self.town},state={self.state},zip={self.zip},animal={self.animal},animal_feed_operation_type={self.animal_feed_operation_type},animal_units={self.animal_units},animal_count={self.animal_count},manure_total_solids={self.manure_total_solids},source={self.source},date_accessed={self.date_accessed},)" + + + + + + +class InfrastructureEthanolBiorefineries(Base): + """ + Ethanol biorefineries infrastructure. + """ + __tablename__ = 'infrastructure_ethanol_biorefineries' + + ethanol_biorefinery_id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + city = Column(Text()) + state = Column(Text()) + address = Column(Text()) + type = Column(Text()) + capacity_mgy = Column(Integer()) + production_mgy = Column(Integer()) + constr_exp = Column(Integer()) + + + def __repr__(self): + return f"InfrastructureEthanolBiorefineries(ethanol_biorefinery_id={self.ethanol_biorefinery_id},name={self.name},city={self.city},state={self.state},address={self.address},type={self.type},capacity_mgy={self.capacity_mgy},production_mgy={self.production_mgy},constr_exp={self.constr_exp},)" + + + + + + +class InfrastructureLandfills(Base): + """ + Landfills infrastructure. + """ + __tablename__ = 'infrastructure_landfills' + + project_id = Column(Text(), primary_key=True, nullable=False ) + project_int_id = Column(Integer()) + ghgrp_id = Column(Text()) + landfill_id = Column(Integer()) + landfill_name = Column(Text()) + state = Column(Text()) + physical_address = Column(Text()) + city = Column(Text()) + county = Column(Text()) + zip_code = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + ownership_type = Column(Text()) + landfill_owner_orgs = Column(Text()) + landfill_opened_year = Column(Date()) + landfill_closure_year = Column(Date()) + landfill_status = Column(Text()) + waste_in_place = Column(Integer()) + waste_in_place_year = Column(Date()) + lfg_system_in_place = Column(Boolean()) + lfg_collected = Column(Numeric()) + lfg_flared = Column(Numeric()) + project_status = Column(Text()) + project_name = Column(Text()) + project_start_date = Column(Date()) + project_shutdown_date = Column(Date()) + project_type_category = Column(Text()) + lfg_energy_project_type = Column(Text()) + rng_delivery_method = Column(Text()) + actual_mw_generation = Column(Numeric()) + rated_mw_capacity = Column(Numeric()) + lfg_flow_to_project = Column(Numeric()) + direct_emission_reductions = Column(Numeric()) + avoided_emission_reductions = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureLandfills(project_id={self.project_id},project_int_id={self.project_int_id},ghgrp_id={self.ghgrp_id},landfill_id={self.landfill_id},landfill_name={self.landfill_name},state={self.state},physical_address={self.physical_address},city={self.city},county={self.county},zip_code={self.zip_code},latitude={self.latitude},longitude={self.longitude},ownership_type={self.ownership_type},landfill_owner_orgs={self.landfill_owner_orgs},landfill_opened_year={self.landfill_opened_year},landfill_closure_year={self.landfill_closure_year},landfill_status={self.landfill_status},waste_in_place={self.waste_in_place},waste_in_place_year={self.waste_in_place_year},lfg_system_in_place={self.lfg_system_in_place},lfg_collected={self.lfg_collected},lfg_flared={self.lfg_flared},project_status={self.project_status},project_name={self.project_name},project_start_date={self.project_start_date},project_shutdown_date={self.project_shutdown_date},project_type_category={self.project_type_category},lfg_energy_project_type={self.lfg_energy_project_type},rng_delivery_method={self.rng_delivery_method},actual_mw_generation={self.actual_mw_generation},rated_mw_capacity={self.rated_mw_capacity},lfg_flow_to_project={self.lfg_flow_to_project},direct_emission_reductions={self.direct_emission_reductions},avoided_emission_reductions={self.avoided_emission_reductions},)" + + + + + + +class InfrastructureLivestockAnaerobicDigesters(Base): + """ + Livestock anaerobic digesters infrastructure. + """ + __tablename__ = 'infrastructure_livestock_anaerobic_digesters' + + digester_id = Column(Integer(), primary_key=True, nullable=False ) + project_name = Column(Text()) + project_type = Column(Text()) + city = Column(Text()) + state = Column(Text()) + digester_type = Column(Text()) + profile = Column(Text()) + year_operational = Column(Date()) + animal_type_class = Column(Text()) + animal_types = Column(Text()) + pop_feeding_digester = Column(Text()) + total_pop_feeding_digester = Column(Integer()) + cattle = Column(Integer()) + dairy = Column(Integer()) + poultry = Column(Integer()) + swine = Column(Integer()) + codigestion = Column(Text()) + biogas_generation_estimate = Column(Integer()) + electricity_generated = Column(Integer()) + biogas_end_uses = Column(Text()) + methane_emission_reductions = Column(Integer()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureLivestockAnaerobicDigesters(digester_id={self.digester_id},project_name={self.project_name},project_type={self.project_type},city={self.city},state={self.state},digester_type={self.digester_type},profile={self.profile},year_operational={self.year_operational},animal_type_class={self.animal_type_class},animal_types={self.animal_types},pop_feeding_digester={self.pop_feeding_digester},total_pop_feeding_digester={self.total_pop_feeding_digester},cattle={self.cattle},dairy={self.dairy},poultry={self.poultry},swine={self.swine},codigestion={self.codigestion},biogas_generation_estimate={self.biogas_generation_estimate},electricity_generated={self.electricity_generated},biogas_end_uses={self.biogas_end_uses},methane_emission_reductions={self.methane_emission_reductions},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureSafAndRenewableDieselPlants(Base): + """ + SAF and renewable diesel plants infrastructure. + """ + __tablename__ = 'infrastructure_saf_and_renewable_diesel_plants' + + ibcc_index = Column(Integer(), primary_key=True, nullable=False ) + company = Column(Text()) + city = Column(Text()) + state = Column(Text()) + country = Column(Text()) + capacity = Column(Text()) + feedstock = Column(Text()) + products = Column(Text()) + status = Column(Text()) + address = Column(Text()) + coordinates = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureSafAndRenewableDieselPlants(ibcc_index={self.ibcc_index},company={self.company},city={self.city},state={self.state},country={self.country},capacity={self.capacity},feedstock={self.feedstock},products={self.products},status={self.status},address={self.address},coordinates={self.coordinates},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureWastewaterTreatmentPlants(Base): + """ + Wastewater treatment plants infrastructure. + """ + __tablename__ = 'infrastructure_wastewater_treatment_plants' + + plant_id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + state = Column(Text()) + codigestion = Column(Text()) + flow_design_adjusted = Column(Numeric()) + flow_average = Column(Numeric()) + biosolids = Column(Numeric()) + excess_flow = Column(Numeric()) + biogas_utilized = Column(Boolean()) + flaring = Column(Boolean()) + excess_mass_loading_rate = Column(Numeric()) + excess_mass_loading_rate_wet = Column(Numeric()) + methane_production = Column(Numeric()) + energy_content = Column(Numeric()) + electric_kw = Column(Numeric()) + thermal_mmbtu_d = Column(Numeric()) + electric_kwh = Column(Numeric()) + thermal_annual_mmbtu_y = Column(Numeric()) + anaerobic_digestion_facility = Column(Text()) + county = Column(Text()) + dayload_bdt = Column(Numeric()) + dayload = Column(Numeric()) + equivalent_generation = Column(Numeric()) + facility_type = Column(Text()) + feedstock = Column(Text()) + type = Column(Text()) + city = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + zipcode = Column(Text()) + + + def __repr__(self): + return f"InfrastructureWastewaterTreatmentPlants(plant_id={self.plant_id},name={self.name},state={self.state},codigestion={self.codigestion},flow_design_adjusted={self.flow_design_adjusted},flow_average={self.flow_average},biosolids={self.biosolids},excess_flow={self.excess_flow},biogas_utilized={self.biogas_utilized},flaring={self.flaring},excess_mass_loading_rate={self.excess_mass_loading_rate},excess_mass_loading_rate_wet={self.excess_mass_loading_rate_wet},methane_production={self.methane_production},energy_content={self.energy_content},electric_kw={self.electric_kw},thermal_mmbtu_d={self.thermal_mmbtu_d},electric_kwh={self.electric_kwh},thermal_annual_mmbtu_y={self.thermal_annual_mmbtu_y},anaerobic_digestion_facility={self.anaerobic_digestion_facility},county={self.county},dayload_bdt={self.dayload_bdt},dayload={self.dayload},equivalent_generation={self.equivalent_generation},facility_type={self.facility_type},feedstock={self.feedstock},type={self.type},city={self.city},latitude={self.latitude},longitude={self.longitude},zipcode={self.zipcode},)" + + + + + + +class InfrastructureCombustionPlants(Base): + """ + Combustion plants infrastructure. + """ + __tablename__ = 'infrastructure_combustion_plants' + + combustion_fid = Column(Integer(), primary_key=True, nullable=False ) + objectid = Column(Integer()) + status = Column(Text()) + city = Column(Text()) + name = Column(Text()) + county = Column(Text()) + equivalent_generation = Column(Numeric()) + np_mw = Column(Numeric()) + cf = Column(Numeric()) + yearload = Column(Integer()) + fuel = Column(Text()) + notes = Column(Text()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureCombustionPlants(combustion_fid={self.combustion_fid},objectid={self.objectid},status={self.status},city={self.city},name={self.name},county={self.county},equivalent_generation={self.equivalent_generation},np_mw={self.np_mw},cf={self.cf},yearload={self.yearload},fuel={self.fuel},notes={self.notes},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureDistrictEnergySystems(Base): + """ + District energy systems infrastructure. + """ + __tablename__ = 'infrastructure_district_energy_systems' + + des_fid = Column(Integer(), primary_key=True, nullable=False ) + cbg_id = Column(Integer()) + name = Column(Text()) + system = Column(Text()) + object_id = Column(Integer()) + city = Column(Text()) + state = Column(Text()) + primary_fuel = Column(Text()) + secondary_fuel = Column(Text()) + usetype = Column(Text()) + cap_st = Column(Numeric()) + cap_hw = Column(Numeric()) + cap_cw = Column(Numeric()) + chpcg_cap = Column(Numeric()) + excess_c = Column(Numeric()) + excess_h = Column(Numeric()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureDistrictEnergySystems(des_fid={self.des_fid},cbg_id={self.cbg_id},name={self.name},system={self.system},object_id={self.object_id},city={self.city},state={self.state},primary_fuel={self.primary_fuel},secondary_fuel={self.secondary_fuel},usetype={self.usetype},cap_st={self.cap_st},cap_hw={self.cap_hw},cap_cw={self.cap_cw},chpcg_cap={self.chpcg_cap},excess_c={self.excess_c},excess_h={self.excess_h},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureFoodProcessingFacilities(Base): + """ + Food processing facilities infrastructure. + """ + __tablename__ = 'infrastructure_food_processing_facilities' + + processing_facility_id = Column(Integer(), primary_key=True, nullable=False ) + address = Column(Text()) + county = Column(Text()) + city = Column(Text()) + company = Column(Text()) + join_count = Column(Integer()) + master_type = Column(Text()) + state = Column(Text()) + subtype = Column(Text()) + target_fid = Column(Integer()) + processing_type = Column(Text()) + zip = Column(Text()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureFoodProcessingFacilities(processing_facility_id={self.processing_facility_id},address={self.address},county={self.county},city={self.city},company={self.company},join_count={self.join_count},master_type={self.master_type},state={self.state},subtype={self.subtype},target_fid={self.target_fid},processing_type={self.processing_type},zip={self.zip},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureMswToEnergyAnaerobicDigesters(Base): + """ + MSW to energy anaerobic digesters infrastructure. + """ + __tablename__ = 'infrastructure_msw_to_energy_anaerobic_digesters' + + wte_id = Column(Integer(), primary_key=True, nullable=False ) + city = Column(Text()) + county = Column(Text()) + equivalent_generation = Column(Numeric()) + feedstock = Column(Text()) + dayload = Column(Numeric()) + dayload_bdt = Column(Numeric()) + facility_type = Column(Text()) + status = Column(Text()) + notes = Column(Text()) + source = Column(Text()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureMswToEnergyAnaerobicDigesters(wte_id={self.wte_id},city={self.city},county={self.county},equivalent_generation={self.equivalent_generation},feedstock={self.feedstock},dayload={self.dayload},dayload_bdt={self.dayload_bdt},facility_type={self.facility_type},status={self.status},notes={self.notes},source={self.source},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + class Resource(BaseEntity): """ Biomass resource definition. @@ -299,6 +742,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -307,7 +751,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1943,6 +2387,40 @@ def __repr__(self): +class FacilityRecord(BaseEntity): + """ + Facility record. + """ + __tablename__ = 'facility_record' + + dataset_id = Column(Integer()) + facility_name = Column(Text()) + location_id = Column(Integer()) + capacity_mw = Column(Numeric()) + resource_id = Column(Integer()) + operator = Column(Text()) + start_year = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FacilityRecord(dataset_id={self.dataset_id},facility_name={self.facility_name},location_id={self.location_id},capacity_mw={self.capacity_mw},resource_id={self.resource_id},operator={self.operator},start_year={self.start_year},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + class ProximateRecord(Aim1RecordBase): """ Proximate analysis record. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py index 975b6bd5..9183431c 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py @@ -387,6 +387,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -395,7 +396,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py index b93abd1f..ae56a768 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py @@ -1082,6 +1082,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1090,7 +1091,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py index d86817b3..d854df67 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py @@ -1045,6 +1045,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1053,7 +1054,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py index f699dc79..822de073 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py @@ -516,6 +516,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -524,7 +525,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py index 88195134..6470faba 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py @@ -505,6 +505,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -513,7 +514,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py index 833b7951..796558e4 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py @@ -864,6 +864,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -872,7 +873,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py index 61f06d91..6be929f8 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py @@ -420,6 +420,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -428,7 +429,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py index b1d3d70e..bc84a0af 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py @@ -103,6 +103,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -111,7 +112,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py index db5d6386..b543fbaa 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py @@ -321,6 +321,7 @@ class Resource(BaseEntity): resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) + test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -329,7 +330,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" From 5574630951e0d6a65d0bbdadda22308f444d122f Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Mon, 22 Dec 2025 14:55:55 -0700 Subject: [PATCH 66/81] adding comment to init.py to try to solve CI CD issues --- .../datamodels/ca_biositing/datamodels/schemas/__init__.py | 1 + .../ca_biositing/datamodels/schemas/generated/__init__.py | 1 + 2 files changed, 2 insertions(+) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py index dbb70e85..6279548e 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/__init__.py @@ -1 +1,2 @@ # This file makes this a Python package. +# Schemas package. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py index dbb70e85..73de05be 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/__init__.py @@ -1 +1,2 @@ # This file makes this a Python package. +# Generated schemas. From e0947fc73d0de22736c4a7c117719f7a7df9a42c Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Tue, 23 Dec 2025 10:12:53 -0700 Subject: [PATCH 67/81] fixed primary_ag_product etl pipeline, modified master flow script and docs --- AGENTS.md | 2 +- ...28_changing_primary_crop_to_primary_ag_.py | 56 +++++++++++++++++++ docs/README.md | 2 +- docs/datamodels/README.md | 2 +- docs/deployment/README.md | 2 +- docs/pipeline/README.md | 2 +- docs/resources/README.md | 2 +- docs/webservice/README.md | 2 +- resources/prefect/run_prefect_flow.py | 30 ++++++---- .../linkml/modules/external_data.yaml | 10 ++-- .../linkml/modules/resource_information.yaml | 10 ++-- .../schemas/generated/aim1_records.py | 12 ++-- .../schemas/generated/aim2_records.py | 12 ++-- .../schemas/generated/ca_biositing.py | 16 +++--- .../generated/data_sources_metadata.py | 12 ++-- .../schemas/generated/experiment_equipment.py | 12 ++-- .../schemas/generated/external_data.py | 16 +++--- .../schemas/generated/field_sampling.py | 12 ++-- .../schemas/generated/general_analysis.py | 12 ++-- .../schemas/generated/infrastructure.py | 12 ++-- .../generated/methods_parameters_units.py | 12 ++-- .../schemas/generated/resource_information.py | 12 ++-- .../schemas/generated/sample_preparation.py | 12 ++-- src/ca_biositing/pipeline/AGENTS.md | 24 +++++--- src/ca_biositing/pipeline/README.md | 35 ++++++------ ...imary_product.py => primary_ag_product.py} | 24 ++++---- .../transform/products/primary_ag_product.py | 41 ++++++++++++++ .../etl/transform/products/primary_product.py | 38 ------------- .../pipeline/flows/primary_ag_product.py | 26 +++++++++ .../pipeline/flows/primary_product.py | 26 --------- 30 files changed, 280 insertions(+), 206 deletions(-) create mode 100644 alembic/versions/e84690898528_changing_primary_crop_to_primary_ag_.py rename src/ca_biositing/pipeline/ca_biositing/pipeline/etl/load/products/{primary_product.py => primary_ag_product.py} (61%) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/transform/products/primary_ag_product.py delete mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/transform/products/primary_product.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/flows/primary_ag_product.py delete mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/flows/primary_product.py diff --git a/AGENTS.md b/AGENTS.md index 45e1e109..f65c5373 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -404,7 +404,7 @@ ca-biositing/ │ │ │ │ ├── transform/ # Transform tasks │ │ │ │ └── load/ # Load tasks │ │ │ ├── flows/ # Prefect flows -│ │ │ │ ├── primary_product.py +│ │ │ │ ├── primary_ag_product.py │ │ │ │ ├── analysis_type.py │ │ │ │ └── ... │ │ │ └── utils/ # Utilities diff --git a/alembic/versions/e84690898528_changing_primary_crop_to_primary_ag_.py b/alembic/versions/e84690898528_changing_primary_crop_to_primary_ag_.py new file mode 100644 index 00000000..d7efd056 --- /dev/null +++ b/alembic/versions/e84690898528_changing_primary_crop_to_primary_ag_.py @@ -0,0 +1,56 @@ +"""changing primary crop to primary_ag_product + +Revision ID: e84690898528 +Revises: fc422d3d9ea6 +Create Date: 2025-12-23 16:04:40.644736 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'e84690898528' +down_revision: Union[str, Sequence[str], None] = 'fc422d3d9ea6' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('primary_ag_product', + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.drop_table('primary_crop') + op.add_column('resource', sa.Column('primary_ag_product_id', sa.Integer(), nullable=True)) + op.drop_column('resource', 'primary_crop_id') + op.add_column('resource_usda_commodity_map', sa.Column('primary_ag_product_id', sa.Integer(), nullable=True)) + op.drop_column('resource_usda_commodity_map', 'primary_crop_id') + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.add_column('resource_usda_commodity_map', sa.Column('primary_crop_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('resource_usda_commodity_map', 'primary_ag_product_id') + op.add_column('resource', sa.Column('primary_crop_id', sa.INTEGER(), autoincrement=False, nullable=True)) + op.drop_column('resource', 'primary_ag_product_id') + op.create_table('primary_crop', + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('primary_crop_pkey')) + ) + op.drop_table('primary_ag_product') + # ### end Alembic commands ### diff --git a/docs/README.md b/docs/README.md index 94389aee..32d46ee8 120000 --- a/docs/README.md +++ b/docs/README.md @@ -1 +1 @@ -../README.md +../README.md \ No newline at end of file diff --git a/docs/datamodels/README.md b/docs/datamodels/README.md index f3c7aa23..b62101ad 120000 --- a/docs/datamodels/README.md +++ b/docs/datamodels/README.md @@ -1 +1 @@ -../../src/ca_biositing/datamodels/README.md +../../src/ca_biositing/datamodels/README.md \ No newline at end of file diff --git a/docs/deployment/README.md b/docs/deployment/README.md index 5159bcfe..d5c46ad4 120000 --- a/docs/deployment/README.md +++ b/docs/deployment/README.md @@ -1 +1 @@ -../../deployment/README.md +../../deployment/README.md \ No newline at end of file diff --git a/docs/pipeline/README.md b/docs/pipeline/README.md index 544d50b1..82a8c831 120000 --- a/docs/pipeline/README.md +++ b/docs/pipeline/README.md @@ -1 +1 @@ -../../src/ca_biositing/pipeline/README.md +../../src/ca_biositing/pipeline/README.md \ No newline at end of file diff --git a/docs/resources/README.md b/docs/resources/README.md index ea34ca59..9f21ec35 120000 --- a/docs/resources/README.md +++ b/docs/resources/README.md @@ -1 +1 @@ -../../resources/README.md +../../resources/README.md \ No newline at end of file diff --git a/docs/webservice/README.md b/docs/webservice/README.md index 24ea2883..749a635e 120000 --- a/docs/webservice/README.md +++ b/docs/webservice/README.md @@ -1 +1 @@ -../../src/ca_biositing/webservice/README.md +../../src/ca_biositing/webservice/README.md \ No newline at end of file diff --git a/resources/prefect/run_prefect_flow.py b/resources/prefect/run_prefect_flow.py index b350f382..03f5e926 100644 --- a/resources/prefect/run_prefect_flow.py +++ b/resources/prefect/run_prefect_flow.py @@ -1,24 +1,32 @@ import sys -from prefect import flow -from ca_biositing.pipeline.flows.primary_product import primary_product_flow -from ca_biositing.pipeline.flows.analysis_type import analysis_type_flow +import traceback +from prefect import flow, get_run_logger +from prefect.utilities.importtools import import_object -# A dictionary mapping flow names to their function objects +# A dictionary mapping flow names to their import paths AVAILABLE_FLOWS = { - "primary_product": primary_product_flow, - "analysis_type": analysis_type_flow, + "primary_ag_product": "ca_biositing.pipeline.flows.primary_ag_product.primary_ag_product_flow", + "analysis_type": "ca_biositing.pipeline.flows.analysis_type.analysis_type_flow", } @flow(name="Master ETL Flow", log_prints=True) def master_flow(): """ A master flow to orchestrate all ETL pipelines. + This flow dynamically imports and runs sub-flows, allowing it to continue + even if some sub-flows fail to import or run. """ - print("Running master ETL flow...") - for flow_name, flow_func in AVAILABLE_FLOWS.items(): - print(f"--- Running sub-flow: {flow_name} ---") - flow_func() - print("Master ETL flow completed.") + logger = get_run_logger() + logger.info("Running master ETL flow...") + for flow_name, flow_path in AVAILABLE_FLOWS.items(): + try: + logger.info(f"--- Running sub-flow: {flow_name} ---") + flow_func = import_object(flow_path) + flow_func() + except Exception as e: + logger.error(f"Flow '{flow_name}' failed with error: {e}") + logger.error(traceback.format_exc()) + logger.info("Master ETL flow completed.") if __name__ == "__main__": # This script is a placeholder for running flows directly. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml index 3321a2f4..679a5f4a 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml @@ -84,7 +84,7 @@ classes: description: Mapping between resources/crops and USDA commodities. slots: - resource_id - - primary_crop_id + - primary_ag_product_id - usda_commodity_id - match_tier - note @@ -354,19 +354,19 @@ slots: main_crop: range: integer - description: Reference to PrimaryCrop. + description: Reference to PrimaryAgProduct. secondary_crop: range: integer - description: Reference to PrimaryCrop. + description: Reference to PrimaryAgProduct. tertiary_crop: range: integer - description: Reference to PrimaryCrop. + description: Reference to PrimaryAgProduct. quaternary_crop: range: integer - description: Reference to PrimaryCrop. + description: Reference to PrimaryAgProduct. confidence: range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml index f06fa29d..82237cae 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml @@ -22,7 +22,7 @@ classes: description: Biomass resource definition. slots: - name - - primary_crop_id + - primary_ag_product_id - resource_class_id - resource_subclass_id - note @@ -36,9 +36,9 @@ classes: is_a: LookupBase description: Sub-classification of resources. - PrimaryCrop: + PrimaryAgProduct: is_a: LookupBase - description: Primary crop definition. + description: Primary agricultural product definition. slots: - note @@ -89,9 +89,9 @@ classes: slots: #Resource slots - primary_crop_id: + primary_ag_product_id: range: integer - description: Reference to PrimaryCrop. + description: Reference to PrimaryAgProduct. resource_class_id: range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py index 075f0de2..85b02306 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py @@ -892,7 +892,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -905,7 +905,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -967,11 +967,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -981,7 +981,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py index 45edb52c..374bbf8b 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py @@ -918,7 +918,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -931,7 +931,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -993,11 +993,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1007,7 +1007,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py index 734d1d17..6fc7680f 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py @@ -738,7 +738,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -751,7 +751,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -813,11 +813,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -827,7 +827,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -2206,7 +2206,7 @@ class ResourceUsdaCommodityMap(BaseEntity): __tablename__ = 'resource_usda_commodity_map' resource_id = Column(Integer()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) usda_commodity_id = Column(Integer()) match_tier = Column(Text()) note = Column(Text()) @@ -2218,7 +2218,7 @@ class ResourceUsdaCommodityMap(BaseEntity): def __repr__(self): - return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_ag_product_id={self.primary_ag_product_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py index 9183431c..10206eab 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py @@ -383,7 +383,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -396,7 +396,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -458,11 +458,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -472,7 +472,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py index ae56a768..d27ecc16 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py @@ -1078,7 +1078,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -1091,7 +1091,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1153,11 +1153,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1167,7 +1167,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py index d854df67..deaaf7e6 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py @@ -358,7 +358,7 @@ class ResourceUsdaCommodityMap(BaseEntity): __tablename__ = 'resource_usda_commodity_map' resource_id = Column(Integer()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) usda_commodity_id = Column(Integer()) match_tier = Column(Text()) note = Column(Text()) @@ -370,7 +370,7 @@ class ResourceUsdaCommodityMap(BaseEntity): def __repr__(self): - return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_crop_id={self.primary_crop_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_ag_product_id={self.primary_ag_product_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1041,7 +1041,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -1054,7 +1054,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1116,11 +1116,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1130,7 +1130,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py index 822de073..0e5c3b47 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py @@ -512,7 +512,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -525,7 +525,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -587,11 +587,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -601,7 +601,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py index 6470faba..5e8fd492 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py @@ -501,7 +501,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -514,7 +514,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -576,11 +576,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -590,7 +590,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py index 796558e4..021a9423 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py @@ -860,7 +860,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -873,7 +873,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -935,11 +935,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -949,7 +949,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py index 6be929f8..85ddde97 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py @@ -416,7 +416,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -429,7 +429,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -491,11 +491,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -505,7 +505,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py index bc84a0af..627f9124 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py @@ -99,7 +99,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -112,7 +112,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -174,11 +174,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -188,7 +188,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py index b543fbaa..ae68592c 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py @@ -317,7 +317,7 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_crop_id = Column(Integer()) + primary_ag_product_id = Column(Integer()) resource_class_id = Column(Integer()) resource_subclass_id = Column(Integer()) note = Column(Text()) @@ -330,7 +330,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_crop_id={self.primary_crop_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -392,11 +392,11 @@ def __repr__(self): -class PrimaryCrop(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Primary crop definition. + Primary agricultural product definition. """ - __tablename__ = 'primary_crop' + __tablename__ = 'primary_ag_product' note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -406,7 +406,7 @@ class PrimaryCrop(LookupBase): def __repr__(self): - return f"PrimaryCrop(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/pipeline/AGENTS.md b/src/ca_biositing/pipeline/AGENTS.md index 16b5e29a..1b9fc453 100644 --- a/src/ca_biositing/pipeline/AGENTS.md +++ b/src/ca_biositing/pipeline/AGENTS.md @@ -109,11 +109,13 @@ Located in `ca_biositing/pipeline/etl/`: - Pattern: Prefect `@task` decorated functions that return DataFrames 2. **`transform/`** - Data transformation tasks - - `products/primary_product.py`: Transform primary product data + - `products/primary_ag_product.py`: Transform primary agricultural product + data - Pattern: Prefect `@task` functions that accept and return DataFrames 3. **`load/`** - Data loading tasks - - `products/primary_product.py`: Load primary products to database + - `products/primary_ag_product.py`: Load primary agricultural products to + database - `analysis/`: Analysis-related load functions - Pattern: Prefect `@task` functions that insert data via SQLModel session @@ -126,7 +128,7 @@ Located in `ca_biositing/pipeline/etl/`: Located in `ca_biositing/pipeline/flows/`: -- **`primary_product.py`**: Primary product ETL flow +- **`primary_ag_product.py`**: Primary agricultural product ETL flow - **`analysis_type.py`**: Analysis type ETL flow - Pattern: Prefect `@flow` decorated functions that orchestrate tasks @@ -141,8 +143,10 @@ Located in `ca_biositing/pipeline/utils/`: 2. **`gsheet_to_pandas.py`** - Google Sheets to DataFrame conversion - `gsheet_to_df()`: Main extraction function -3. **`run_pipeline.py`** - Master pipeline orchestrator - - Runs all ETL flows in sequence +3. **`../../resources/prefect/run_prefect_flow.py`** - Master pipeline + orchestrator + - A resilient master flow that dynamically imports and runs all ETL flows, + catching errors from individual flows. 4. **`clear_alembic.py`** - Database migration cleanup utility @@ -442,7 +446,8 @@ def test_lookup_utility(session): 4. **Create flow** in `flows/my_flow.py`: - Use `@flow` decorator - Orchestrate extract → transform → load - - Add to master orchestrator in `utils/run_pipeline.py` + - Add the flow's import path to the `AVAILABLE_FLOWS` dictionary in + `resources/prefect/run_prefect_flow.py` 5. **Write tests** in `tests/test_my_pipeline.py`: - Mock external dependencies @@ -634,10 +639,11 @@ Run flows from command line or Python: ```bash # Run specific flow -python -m ca_biositing.pipeline.flows.primary_product +python -m ca_biositing.pipeline.flows.primary_ag_product -# Run all flows (master orchestrator) -python -m ca_biositing.pipeline.utils.run_pipeline +# Run all flows via the main project's pixi task +# This executes the master flow defined in resources/prefect/run_prefect_flow.py +pixi run run-etl ``` ### Usage with Docker diff --git a/src/ca_biositing/pipeline/README.md b/src/ca_biositing/pipeline/README.md index ac9c59e1..e0514b5f 100644 --- a/src/ca_biositing/pipeline/README.md +++ b/src/ca_biositing/pipeline/README.md @@ -33,20 +33,20 @@ src/ca_biositing/pipeline/ │ │ │ └── experiments.py │ │ ├── transform/ # Data transformation tasks │ │ │ └── products/ -│ │ │ └── primary_product.py +│ │ │ └── primary_ag_product.py │ │ ├── load/ # Data loading tasks │ │ │ ├── analysis/ │ │ │ └── products/ -│ │ │ └── primary_product.py +│ │ │ └── primary_ag_product.py │ │ └── templates/ # ETL module templates │ ├── flows/ # Prefect flow definitions │ │ ├── analysis_type.py -│ │ └── primary_product.py +│ │ └── primary_ag_product.py │ └── utils/ # Utility functions │ ├── __init__.py │ ├── gsheet_to_pandas.py │ ├── lookup_utils.py -│ └── run_pipeline.py +│ └── ../../resources/prefect/run_prefect_flow.py ├── tests/ # Test suite │ ├── __init__.py │ ├── conftest.py # Pytest fixtures @@ -89,15 +89,12 @@ directory: on SQLModel changes - **Note:** Database models are now in the shared `ca-biositing-datamodels` package -- **[See: docs/ALEMBIC_WORKFLOW.md](./ALEMBIC_WORKFLOW.md)** ### 3. ETL Pipeline Development (Prefect) - **Purpose:** Running the ETL pipeline and adding new data pipelines - **Details:** Using Prefect's flow orchestration with extract, transform, and load tasks -- **[See: docs/ETL_WORKFLOW.md](./ETL_WORKFLOW.md)** -- **[See: docs/PREFECT_WORKFLOW.md](./PREFECT_WORKFLOW.md)** ### 4. Google Cloud Setup @@ -162,7 +159,7 @@ See `tests/README.md` for detailed information about the test suite. ```python from ca_biositing.pipeline.etl.extract.basic_sample_info import extract_basic_sample_info -from ca_biositing.pipeline.flows.primary_product import primary_product_flow +from ca_biositing.pipeline.flows.primary_ag_product import primary_ag_product_flow from ca_biositing.pipeline.utils.lookup_utils import replace_name_with_id_df # Use in your code @@ -172,10 +169,10 @@ from ca_biositing.pipeline.utils.lookup_utils import replace_name_with_id_df ### Running Prefect Flows ```python -from ca_biositing.pipeline.flows.primary_product import primary_product_flow +from ca_biositing.pipeline.flows.primary_ag_product import primary_ag_product_flow # Run the flow -primary_product_flow() +primary_ag_product_flow() ``` ### Using Utility Functions @@ -232,7 +229,8 @@ docker-compose exec app alembic upgrade head **5. Run ETL Pipeline:** ```bash -docker-compose exec app python utils/run_pipeline.py +# This executes the master flow defined in resources/prefect/run_prefect_flow.py +pixi run run-etl ``` See `docs/DOCKER_WORKFLOW.md` and `docs/ETL_WORKFLOW.md` for detailed @@ -249,17 +247,19 @@ instructions. **Transform:** Data cleaning and transformation using pandas -- `transform/products/primary_product.py`: Transform primary product data +- `transform/products/primary_ag_product.py`: Transform primary agricultural + product data **Load:** Load transformed data into PostgreSQL -- `load/products/primary_product.py`: Load primary products into database +- `load/products/primary_ag_product.py`: Load primary agricultural products into + database ### Prefect Flows Orchestrated workflows that combine ETL tasks: -- `flows/primary_product.py`: Primary product ETL flow +- `flows/primary_ag_product.py`: Primary agricultural product ETL flow - `flows/analysis_type.py`: Analysis type ETL flow ### Utility Functions @@ -271,7 +271,9 @@ Orchestrated workflows that combine ETL tasks: **`gsheet_to_pandas.py`**: Google Sheets to pandas DataFrame conversion -**`run_pipeline.py`**: Master script to run all ETL flows +**`../../resources/prefect/run_prefect_flow.py`**: A resilient master flow that +dynamically imports and runs all ETL flows, catching errors from individual +flows. ## Dependencies @@ -304,8 +306,7 @@ pixi run pre-commit run --files src/ca_biositing/pipeline/**/* 5. **Tests:** Add tests in `tests/` 6. **Run:** Execute the flow -See `etl/templates/` for template files and `docs/ETL_WORKFLOW.md` for detailed -instructions. +See `etl/templates/` for template files ### Adding Database Models diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/load/products/primary_product.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/load/products/primary_ag_product.py similarity index 61% rename from src/ca_biositing/pipeline/ca_biositing/pipeline/etl/load/products/primary_product.py rename to src/ca_biositing/pipeline/ca_biositing/pipeline/etl/load/products/primary_ag_product.py index 57d0d6d3..0508d3a3 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/load/products/primary_product.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/load/products/primary_ag_product.py @@ -2,37 +2,37 @@ from prefect import task, get_run_logger from sqlmodel import Session, select from ca_biositing.datamodels.database import engine -from ca_biositing.datamodels.biomass import PrimaryProduct +from ca_biositing.datamodels.schemas.generated.ca_biositing import PrimaryAgProduct @task -def load_products_primary_product(primary_product_df: pd.DataFrame): +def load_products_primary_ag_product(primary_ag_product_df: pd.DataFrame): """ - Loads the data from the primary products DataFrame into the database. + Loads the data from the primary ag products DataFrame into the database. - Iterates over a DataFrame and inserts each product name from the 'Primary_crop' column - into the PrimaryProduct table. + Iterates over a DataFrame and inserts each product name from the 'name' column + into the PrimaryAgProduct table. """ logger = get_run_logger() - if primary_product_df is None or primary_product_df.empty: + if primary_ag_product_df is None or primary_ag_product_df.empty: logger.info("No data to load. Skipping database insertion.") return - column_name = 'Primary_crop' - if column_name not in primary_product_df.columns: + column_name = 'name' + if column_name not in primary_ag_product_df.columns: logger.error(f"Column '{column_name}' not found in the DataFrame. Aborting load.") return - logger.info(f"Attempting to load {len(primary_product_df)} products into the database...") + logger.info(f"Attempting to load {len(primary_ag_product_df)} products into the database...") with Session(engine) as session: - statement = select(PrimaryProduct.primary_product_name) + statement = select(PrimaryAgProduct.name) existing_products = session.exec(statement).all() existing_product_names = set(existing_products) records_to_add = [] - for product_name in primary_product_df[column_name]: + for product_name in primary_ag_product_df[column_name]: if product_name not in existing_product_names: - product = PrimaryProduct(primary_product_name=product_name) + product = PrimaryAgProduct(name=product_name) records_to_add.append(product) existing_product_names.add(product_name) # Add to set to avoid re-adding in same batch diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/transform/products/primary_ag_product.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/transform/products/primary_ag_product.py new file mode 100644 index 00000000..25182c62 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/transform/products/primary_ag_product.py @@ -0,0 +1,41 @@ +from typing import Optional, Dict +import pandas as pd +from prefect import task, get_run_logger + +EXTRACT_SOURCES = ["basic_sample_info"] + +@task +def transform_products_primary_ag_product(data_sources: Dict[str, pd.DataFrame]) -> Optional[pd.DataFrame]: + """ + Transforms the raw data to extract unique primary agricultural products. + + This function is purely for transformation (the 'T' in ETL). It takes the + raw DataFrame and performs the specific transformations needed for the + 'primary_ag_product' table. + + Args: + data_sources: A dictionary of DataFrames from the extraction step. + + Returns: + A transformed DataFrame with a single 'name' column containing + unique product names, or None if an error occurs. + """ + logger = get_run_logger() + logger.info("Transforming raw data for primary ag products...") + + raw_df = data_sources["basic_sample_info"] + + #Step 1: Convert column names to lowercase for consistency + raw_df.columns = [col.lower() for col in raw_df.columns] + + # Step 2: Check if the required column exists + if 'primary_ag_product' not in raw_df.columns: + logger.error("'primary_ag_product' column not found in the raw data.") + return None + + # Step 3: Get unique product names and create the final DataFrame + primary_ag_product= raw_df['primary_ag_product'].unique() + transformed_df = pd.DataFrame(primary_ag_product, columns=["name"]) + + logger.info(f"Successfully transformed data, found {len(transformed_df)} unique primary_ag_products.") + return transformed_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/transform/products/primary_product.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/transform/products/primary_product.py deleted file mode 100644 index 237435cd..00000000 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/transform/products/primary_product.py +++ /dev/null @@ -1,38 +0,0 @@ -from typing import Optional, Dict -import pandas as pd -from prefect import task, get_run_logger - -EXTRACT_SOURCES = ["basic_sample_info"] - -@task -def transform_products_primary_product(data_sources: Dict[str, pd.DataFrame]) -> Optional[pd.DataFrame]: - """ - Transforms the raw data to extract unique primary products. - - This function is purely for transformation (the 'T' in ETL). It takes the - raw DataFrame and performs the specific transformations needed for the - 'primary_product' table. - - Args: - data_sources: A dictionary of DataFrames from the extraction step. - - Returns: - A transformed DataFrame with a single 'Primary_crop' column containing - unique product names, or None if an error occurs. - """ - logger = get_run_logger() - logger.info("Transforming raw data for primary products...") - - raw_df = data_sources["basic_sample_info"] - - # Step 1: Check if the required column exists - if 'Primary_crop' not in raw_df.columns: - logger.error("'Primary_crop' column not found in the raw data.") - return None - - # Step 2: Get unique product names and create the final DataFrame - primary_product_names = raw_df['Primary_crop'].unique() - transformed_df = pd.DataFrame(primary_product_names, columns=["Primary_crop"]) - - logger.info(f"Successfully transformed data, found {len(transformed_df)} unique primary products.") - return transformed_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/flows/primary_ag_product.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/flows/primary_ag_product.py new file mode 100644 index 00000000..7ae5cf9b --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/flows/primary_ag_product.py @@ -0,0 +1,26 @@ +from prefect import flow +from ca_biositing.pipeline.etl.extract.basic_sample_info import extract_basic_sample_info +from ca_biositing.pipeline.etl.transform.products.primary_ag_product import transform_products_primary_ag_product +from ca_biositing.pipeline.etl.load.products.primary_ag_product import load_products_primary_ag_product + +@flow(name="Primary Ag Product ETL", log_prints=True) +def primary_ag_product_flow(): + """ + ETL flow for processing primary agricultural products data. + + This flow extracts basic sample information, transforms it to identify + unique primary agricultural products, and loads them into the database. + """ + print("Running Primary Ag Product ETL flow...") + + # Extract + basic_sample_info_df = extract_basic_sample_info() + + # Transform + # The transform function expects a dictionary of data sources. + primary_ag_product_df = transform_products_primary_ag_product({"basic_sample_info": basic_sample_info_df}) + + # Load + load_products_primary_ag_product(primary_ag_product_df) + + print("Primary Ag Product ETL flow completed successfully.") diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/flows/primary_product.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/flows/primary_product.py deleted file mode 100644 index 8e6a1524..00000000 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/flows/primary_product.py +++ /dev/null @@ -1,26 +0,0 @@ -from prefect import flow -from ca_biositing.pipeline.etl.extract.basic_sample_info import extract_basic_sample_info -from ca_biositing.pipeline.etl.transform.products.primary_product import transform_products_primary_product -from ca_biositing.pipeline.etl.load.products.primary_product import load_products_primary_product - -@flow(name="Primary Product ETL", log_prints=True) -def primary_product_flow(): - """ - ETL flow for processing primary products. - - This flow extracts basic sample information, transforms it to identify - unique primary products, and loads them into the database. - """ - print("Running Primary Product ETL flow...") - - # Extract - basic_sample_info_df = extract_basic_sample_info() - - # Transform - # The transform function expects a dictionary of data sources. - primary_product_df = transform_products_primary_product({"basic_sample_info": basic_sample_info_df}) - - # Load - load_products_primary_product(primary_product_df) - - print("Primary Product ETL flow completed successfully.") From fd235be591c59c3b50d6a28c1d8af3566f896075 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Tue, 30 Dec 2025 08:55:42 -0700 Subject: [PATCH 68/81] holiday work. New notebook for importing gsheeets to pandas and playing around --- .../15467b7f2f3d_test_after_revert.py | 32 + .../linkml/modules/primary_ag_product.yaml | 23 + .../linkml/modules/resource_availability.yaml | 35 + .../linkml/modules/resource_class.yaml | 21 + .../modules/resource_counterfactual.yaml | 47 + .../linkml/modules/resource_morphology.yaml | 34 + .../linkml/modules/resource_subclass.yaml | 21 + .../schemas/generated/primary_ag_product.py | 75 ++ .../generated/resource_availability.py | 308 +++++ .../schemas/generated/resource_class.py | 74 ++ .../generated/resource_counterfactual.py | 1030 +++++++++++++++++ .../schemas/generated/resource_morphology.py | 308 +++++ .../schemas/generated/resource_subclass.py | 74 ++ .../datamodels/utils/database_joins.ipynb | 491 +------- .../pipeline/etl/extract/experiments.py | 2 +- .../pipeline/etl/extract/proximate.py | 59 + .../utils/gsheet_extraction_notebook.ipynb | 179 +++ 17 files changed, 2376 insertions(+), 437 deletions(-) create mode 100644 alembic/versions/15467b7f2f3d_test_after_revert.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/primary_ag_product.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_availability.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_class.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_counterfactual.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_morphology.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_subclass.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/primary_ag_product.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_availability.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_class.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_counterfactual.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_morphology.py create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_subclass.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/proximate.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb diff --git a/alembic/versions/15467b7f2f3d_test_after_revert.py b/alembic/versions/15467b7f2f3d_test_after_revert.py new file mode 100644 index 00000000..38dddb9d --- /dev/null +++ b/alembic/versions/15467b7f2f3d_test_after_revert.py @@ -0,0 +1,32 @@ +"""test after revert + +Revision ID: 15467b7f2f3d +Revises: e84690898528 +Create Date: 2025-12-25 05:02:50.212384 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '15467b7f2f3d' +down_revision: Union[str, Sequence[str], None] = 'e84690898528' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/primary_ag_product.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/primary_ag_product.yaml new file mode 100644 index 00000000..2c5c9b4c --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/primary_ag_product.yaml @@ -0,0 +1,23 @@ +id: https://w3id.org/ca_biositing/primary_ag_product +name: primary_ag_product +title: Primary Agricultural Product +description: Core definitions for primary agricultural products. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + PrimaryAgProduct: + is_a: LookupBase + description: Primary agricultural product definition. + slots: + - note diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_availability.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_availability.yaml new file mode 100644 index 00000000..9bf95246 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_availability.yaml @@ -0,0 +1,35 @@ +id: https://w3id.org/ca_biositing/resource_availability +name: resource_availability +title: Resource Availability +description: Availability of a resource in a location. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - places + - resource_information + +classes: + ResourceAvailability: + is_a: BaseEntity + description: Availability of a resource in a location. + slots: + - resource_id + - geoid + - from_month + - to_month + - year_round + - note + +slots: + resource_id: + range: Resource + description: Reference to Resource. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_class.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_class.yaml new file mode 100644 index 00000000..cc39fe4e --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_class.yaml @@ -0,0 +1,21 @@ +id: https://w3id.org/ca_biositing/resource_class +name: resource_class +title: Resource Class +description: Classification of resources. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + ResourceClass: + is_a: LookupBase + description: Classification of resources. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_counterfactual.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_counterfactual.yaml new file mode 100644 index 00000000..d346b197 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_counterfactual.yaml @@ -0,0 +1,47 @@ +id: https://w3id.org/ca_biositing/resource_counterfactual +name: resource_counterfactual +title: Resource Counterfactual +description: Counterfactual uses of a resource. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - places + - resource_information + - data_sources_metadata + +classes: + ResourceCounterfactual: + is_a: BaseEntity + description: Counterfactual uses of a resource. + slots: + - geoid + - resource_id + - counterfactual_description + - animal_bedding_percent + - animal_bedding_source_id + - animal_feed_percent + - animal_feed_source_id + - bioelectricty_percent + - bioelectricty_source_id + - burn_percent + - burn_source_id + - compost_percent + - compost_source_id + - landfill_percent + - landfill_source_id + - counterfactual_date + - note + +slots: + resource_id: + range: Resource + description: Reference to Resource. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_morphology.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_morphology.yaml new file mode 100644 index 00000000..f9d93c67 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_morphology.yaml @@ -0,0 +1,34 @@ +id: https://w3id.org/ca_biositing/resource_morphology +name: resource_morphology +title: Resource Morphology +description: Morphology of a resource. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + - resource_information + +classes: + ResourceMorphology: + description: Morphology of a resource. + slots: + - id + - resource_id + - morphology_uri + slot_usage: + id: + identifier: true + range: integer + +slots: + resource_id: + range: Resource + description: Reference to Resource. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_subclass.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_subclass.yaml new file mode 100644 index 00000000..0236bca8 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_subclass.yaml @@ -0,0 +1,21 @@ +id: https://w3id.org/ca_biositing/resource_subclass +name: resource_subclass +title: Resource Subclass +description: Sub-classification of resources. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - core + +classes: + ResourceSubclass: + is_a: LookupBase + description: Sub-classification of resources. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/primary_ag_product.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/primary_ag_product.py new file mode 100644 index 00000000..dfa0f14f --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/primary_ag_product.py @@ -0,0 +1,75 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class PrimaryAgProduct(LookupBase): + """ + Primary agricultural product definition. + """ + __tablename__ = 'primary_ag_product' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_availability.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_availability.py new file mode 100644 index 00000000..c02c738f --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_availability.py @@ -0,0 +1,308 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer(), ForeignKey('Resource.id')) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_ag_product_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + test = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryAgProduct(LookupBase): + """ + Primary agricultural product definition. + """ + __tablename__ = 'primary_ag_product' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_class.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_class.py new file mode 100644 index 00000000..b47201f8 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_class.py @@ -0,0 +1,74 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_counterfactual.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_counterfactual.py new file mode 100644 index 00000000..4568cca1 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_counterfactual.py @@ -0,0 +1,1030 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class ParameterCategoryParameter(Base): + """ + Link between Parameter and ParameterCategory. + """ + __tablename__ = 'parameter_category_parameter' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + parameter_category_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + + + + + + +class ParameterUnit(Base): + """ + Link between Parameter and Unit (alternate units). + """ + __tablename__ = 'parameter_unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer()) + alternate_unit_id = Column(Integer()) + + + def __repr__(self): + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + + + + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_ag_product_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + test = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryAgProduct(LookupBase): + """ + Primary agricultural product definition. + """ + __tablename__ = 'primary_ag_product' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer(), ForeignKey('Resource.id')) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Contact(BaseEntity): + """ + Contact information for a person. + """ + __tablename__ = 'contact' + + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Provider(BaseEntity): + """ + Provider information. + """ + __tablename__ = 'provider' + + codename = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSource(BaseEntity): + """ + Source of data. + """ + __tablename__ = 'data_source' + + name = Column(Text()) + description = Column(Text()) + data_source_type_id = Column(Integer()) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) + publisher = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer()) + rights = Column(Text()) + license = Column(Text()) + uri = Column(Text()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FileObjectMetadata(BaseEntity): + """ + Metadata for a file object. + """ + __tablename__ = 'file_object_metadata' + + data_source_id = Column(Integer()) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class DataSourceType(BaseEntity): + """ + Type of data source (e.g. database, literature). + """ + __tablename__ = 'data_source_type' + + source_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'location_resolution' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SourceType(LookupBase): + """ + Type of source (e.g. database, literature). + """ + __tablename__ = 'source_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Unit(LookupBase): + """ + Unit of measurement. + """ + __tablename__ = 'unit' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Method(BaseEntity): + """ + Analytical method. + """ + __tablename__ = 'method' + + name = Column(Text()) + method_abbrev_id = Column(Integer()) + method_category_id = Column(Integer()) + method_standard_id = Column(Integer()) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodAbbrev(LookupBase): + """ + Abbreviation for method. + """ + __tablename__ = 'method_abbrev' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodCategory(LookupBase): + """ + Category of method. + """ + __tablename__ = 'method_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class MethodStandard(LookupBase): + """ + Standard associated with the method. + """ + __tablename__ = 'method_standard' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Parameter(BaseEntity): + """ + Parameter being measured. + """ + __tablename__ = 'parameter' + + name = Column(Text()) + standard_unit_id = Column(Integer()) + calculated = Column(Boolean()) + description = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ParameterCategory(LookupBase): + """ + Category of parameter. + """ + __tablename__ = 'parameter_category' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSample(BaseEntity): + """ + Sample collected from the field. + """ + __tablename__ = 'field_sample' + + name = Column(Text()) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + provider_id = Column(Integer()) + collector_id = Column(Integer()) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer()) + sampling_location_id = Column(Integer()) + field_storage_method_id = Column(Integer()) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer()) + field_storage_location_id = Column(Integer()) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer()) + harvest_method_id = Column(Integer()) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PhysicalCharacteristic(BaseEntity): + """ + Physical characteristics of a sample. + """ + __tablename__ = 'physical_characteristic' + + field_sample_id = Column(Integer()) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldSampleCondition(BaseEntity): + """ + Condition of the field sample. + """ + __tablename__ = 'field_sample_condition' + + field_sample_id = Column(Integer()) + ag_treatment_id = Column(Integer()) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class FieldStorageMethod(LookupBase): + """ + Method of field storage. + """ + __tablename__ = 'field_storage_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class CollectionMethod(LookupBase): + """ + Method of collection. + """ + __tablename__ = 'collection_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class HarvestMethod(LookupBase): + """ + Method of harvest. + """ + __tablename__ = 'harvest_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ProcessingMethod(LookupBase): + """ + Method of processing. + """ + __tablename__ = 'processing_method' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class SoilType(LookupBase): + """ + Type of soil. + """ + __tablename__ = 'soil_type' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class AgTreatment(LookupBase): + """ + Agricultural treatment. + """ + __tablename__ = 'ag_treatment' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationSoilType(BaseEntity): + """ + Soil type at a location. + """ + __tablename__ = 'location_soil_type' + + location_id = Column(Integer()) + soil_type_id = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_morphology.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_morphology.py new file mode 100644 index 00000000..0b9bcf94 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_morphology.py @@ -0,0 +1,308 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ResourceMorphology(Base): + """ + Morphology of a resource. + """ + __tablename__ = 'resource_morphology' + + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + morphology_uri = Column(Text()) + + + def __repr__(self): + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" + + + + + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class Geography(Base): + """ + Geographic location. + """ + __tablename__ = 'geography' + + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) + + + def __repr__(self): + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" + + + + + + +class LocationAddress(BaseEntity): + """ + Physical address. + """ + __tablename__ = 'location_address' + + geography_id = Column(Text()) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class Resource(BaseEntity): + """ + Biomass resource definition. + """ + __tablename__ = 'resource' + + name = Column(Text()) + primary_ag_product_id = Column(Integer()) + resource_class_id = Column(Integer()) + resource_subclass_id = Column(Integer()) + note = Column(Text()) + test = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceClass(LookupBase): + """ + Classification of resources. + """ + __tablename__ = 'resource_class' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class PrimaryAgProduct(LookupBase): + """ + Primary agricultural product definition. + """ + __tablename__ = 'primary_ag_product' + + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceAvailability(BaseEntity): + """ + Availability of a resource in a location. + """ + __tablename__ = 'resource_availability' + + resource_id = Column(Integer(), ForeignKey('Resource.id')) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class ResourceCounterfactual(BaseEntity): + """ + Counterfactual uses of a resource. + """ + __tablename__ = 'resource_counterfactual' + + geoid = Column(Text()) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + counterfactual_description = Column(Text()) + animal_bedding_percent = Column(Numeric()) + animal_bedding_source_id = Column(Integer()) + animal_feed_percent = Column(Numeric()) + animal_feed_source_id = Column(Integer()) + bioelectricty_percent = Column(Numeric()) + bioelectricty_source_id = Column(Integer()) + burn_percent = Column(Numeric()) + burn_source_id = Column(Integer()) + compost_percent = Column(Numeric()) + compost_source_id = Column(Integer()) + landfill_percent = Column(Numeric()) + landfill_source_id = Column(Integer()) + counterfactual_date = Column(Date()) + note = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_subclass.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_subclass.py new file mode 100644 index 00000000..a3919852 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_subclass.py @@ -0,0 +1,74 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class BaseEntity(Base): + """ + Base entity included in all main entity tables. + """ + __tablename__ = 'base_entity' + + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + + +class LookupBase(Base): + """ + Base class for enum/ontology-like tables. + """ + __tablename__ = 'lookup_base' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + + +class ResourceSubclass(LookupBase): + """ + Sub-classification of resources. + """ + __tablename__ = 'resource_subclass' + + id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) + + + def __repr__(self): + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } diff --git a/src/ca_biositing/datamodels/utils/database_joins.ipynb b/src/ca_biositing/datamodels/utils/database_joins.ipynb index dbb836f2..e4a9b9a5 100644 --- a/src/ca_biositing/datamodels/utils/database_joins.ipynb +++ b/src/ca_biositing/datamodels/utils/database_joins.ipynb @@ -15,21 +15,13 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Python Executable: /Users/pjsmitty301/ca-biositing/.pixi/envs/default/bin/python\n", - "✅ You are running in a Pixi environment.\n" - ] - } - ], + "outputs": [], "source": [ "# Verify Kernel\n", "import sys\n", + "\n", "print(f\"Python Executable: {sys.executable}\")\n", "\n", "# Check if we are in the pixi environment (path should contain .pixi)\n", @@ -41,17 +33,9 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Libraries and models imported successfully.\n" - ] - } - ], + "outputs": [], "source": [ "import pandas as pd\n", "from sqlalchemy import create_engine, select\n", @@ -65,17 +49,9 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Connected to database.\n" - ] - } - ], + "outputs": [], "source": [ "# Database Connection\n", "DATABASE_URL = \"postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db\"\n", @@ -96,22 +72,23 @@ "cell_type": "code", "execution_count": null, "metadata": {}, - "outputs": [ - { - "ename": "TypeError", - "evalue": " is not a generic class", - "output_type": "error", - "traceback": [ - "\u001b[31m---------------------------------------------------------------------------\u001b[39m", - "\u001b[31mTypeError\u001b[39m Traceback (most recent call last)", - "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[34]\u001b[39m\u001b[32m, line 2\u001b[39m\n\u001b[32m 1\u001b[39m stmt2 = select(LandiqRecord, PrimaryCrop).join(\n\u001b[32m----> \u001b[39m\u001b[32m2\u001b[39m \u001b[43mPrimaryCrop\u001b[49m\u001b[43m[\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mname\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m]\u001b[49m, \n\u001b[32m 3\u001b[39m LandiqRecord.main_crop == PrimaryCrop.id).limit(\u001b[32m10\u001b[39m)\n\u001b[32m 5\u001b[39m \u001b[38;5;28mprint\u001b[39m(stmt2)\n\u001b[32m 7\u001b[39m df2 = pd.read_sql(stmt2, engine)\n", - "\u001b[36mFile \u001b[39m\u001b[32m~/ca-biositing/.pixi/envs/default/lib/python3.12/typing.py:398\u001b[39m, in \u001b[36m_tp_cache..decorator..inner\u001b[39m\u001b[34m(*args, **kwds)\u001b[39m\n\u001b[32m 396\u001b[39m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m:\n\u001b[32m 397\u001b[39m \u001b[38;5;28;01mpass\u001b[39;00m \u001b[38;5;66;03m# All real errors (not unhashable args) are raised below.\u001b[39;00m\n\u001b[32m--> \u001b[39m\u001b[32m398\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfunc\u001b[49m\u001b[43m(\u001b[49m\u001b[43m*\u001b[49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43m*\u001b[49m\u001b[43mkwds\u001b[49m\u001b[43m)\u001b[49m\n", - "\u001b[36mFile \u001b[39m\u001b[32m~/ca-biositing/.pixi/envs/default/lib/python3.12/typing.py:1110\u001b[39m, in \u001b[36m_generic_class_getitem\u001b[39m\u001b[34m(cls, params)\u001b[39m\n\u001b[32m 1108\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m prepare \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[32m 1109\u001b[39m params = prepare(\u001b[38;5;28mcls\u001b[39m, params)\n\u001b[32m-> \u001b[39m\u001b[32m1110\u001b[39m \u001b[43m_check_generic\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparams\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mlen\u001b[39;49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mcls\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m__parameters__\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 1112\u001b[39m new_args = []\n\u001b[32m 1113\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m param, new_arg \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mzip\u001b[39m(\u001b[38;5;28mcls\u001b[39m.__parameters__, params):\n", - "\u001b[36mFile \u001b[39m\u001b[32m~/ca-biositing/.pixi/envs/default/lib/python3.12/site-packages/typing_extensions.py:3111\u001b[39m, in \u001b[36m_check_generic\u001b[39m\u001b[34m(cls, parameters, elen)\u001b[39m\n\u001b[32m 3106\u001b[39m \u001b[38;5;250m\u001b[39m\u001b[33;03m\"\"\"Check correct count for parameters of a generic cls (internal helper).\u001b[39;00m\n\u001b[32m 3107\u001b[39m \n\u001b[32m 3108\u001b[39m \u001b[33;03mThis gives a nice error message in case of count mismatch.\u001b[39;00m\n\u001b[32m 3109\u001b[39m \u001b[33;03m\"\"\"\u001b[39;00m\n\u001b[32m 3110\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m elen:\n\u001b[32m-> \u001b[39m\u001b[32m3111\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m(\u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mcls\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m is not a generic class\u001b[39m\u001b[33m\"\u001b[39m)\n\u001b[32m 3112\u001b[39m alen = \u001b[38;5;28mlen\u001b[39m(parameters)\n\u001b[32m 3113\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m alen != elen:\n", - "\u001b[31mTypeError\u001b[39m: is not a generic class" - ] - } - ], + "outputs": [], + "source": [ + "# Create the join query\n", + "stmt = select(LandiqRecord, Observation).join(\n", + " Observation,\n", + " Observation.record_id == LandiqRecord.id\n", + ")\n", + "\n", + "print(\"SQL Query:\")\n", + "print(stmt)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "stmt2 = select(LandiqRecord, PrimaryCrop).join(\n", " PrimaryCrop, \n", @@ -124,281 +101,11 @@ "df2.columns\n" ] }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "SQL Query:\n", - "SELECT landiq_record.dataset_id, landiq_record.polygon_id, landiq_record.main_crop, landiq_record.secondary_crop, landiq_record.tertiary_crop, landiq_record.quaternary_crop, landiq_record.confidence, landiq_record.irrigated, landiq_record.acres, landiq_record.version, landiq_record.note, landiq_record.test, landiq_record.id, landiq_record.created_at, landiq_record.updated_at, landiq_record.etl_run_id, landiq_record.lineage_group_id, observation.dataset_id AS dataset_id_1, observation.record_type, observation.record_id, observation.parameter_id, observation.value, observation.unit_id, observation.dimension_type_id, observation.dimension_value, observation.dimension_unit_id, observation.note AS note_1, observation.id AS id_1, observation.created_at AS created_at_1, observation.updated_at AS updated_at_1, observation.etl_run_id AS etl_run_id_1, observation.lineage_group_id AS lineage_group_id_1 \n", - "FROM landiq_record JOIN observation ON observation.record_id = landiq_record.id\n" - ] - } - ], - "source": [ - "# Create the join query\n", - "stmt = select(LandiqRecord, Observation).join(\n", - " Observation,\n", - " Observation.record_id == LandiqRecord.id\n", - ")\n", - "\n", - "print(\"SQL Query:\")\n", - "print(stmt)" - ] - }, { "cell_type": "code", "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - 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" - ], - "text/plain": [ - "Empty DataFrame\n", - "Columns: [dataset_id, polygon_id, main_crop, secondary_crop, tertiary_crop, quaternary_crop, confidence, irrigated, acres, version, note, test, id, created_at, updated_at, etl_run_id, lineage_group_id, dataset_id_1, record_type, record_id, parameter_id, value, unit_id, dimension_type_id, dimension_value, dimension_unit_id, note_1, id_1, created_at_1, updated_at_1, etl_run_id_1, lineage_group_id_1]\n", - "Index: []\n", - "\n", - "[0 rows x 32 columns]" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "# Execute and load into DataFrame\n", "try:\n", @@ -415,135 +122,47 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "Index(['dataset_id', 'polygon_id', 'main_crop', 'secondary_crop',\n", - " 'tertiary_crop', 'quaternary_crop', 'confidence', 'irrigated', 'acres',\n", - " 'version', 'note', 'test', 'id', 'created_at', 'updated_at',\n", - " 'etl_run_id', 'lineage_group_id', 'dataset_id_1', 'record_type',\n", - " 'record_id', 'parameter_id', 'value', 'unit_id', 'dimension_type_id',\n", - " 'dimension_value', 'dimension_unit_id', 'note_1', 'id_1',\n", - " 'created_at_1', 'updated_at_1', 'etl_run_id_1', 'lineage_group_id_1'],\n", - " dtype='object')" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "df.columns" ] }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.microsoft.datawrangler.viewer.v0+json": { - "columns": [ - { - "name": "index", - "rawType": "int64", - "type": "integer" - }, - { - "name": "id", - "rawType": "object", - "type": "string" - }, - { - "name": "dataset_id", - "rawType": "object", - "type": "string" - }, - { - "name": "record_id", - "rawType": "object", - "type": "string" - }, - { - "name": "main_crop", - "rawType": "object", - "type": "string" - }, - { - "name": "parameter_id", - "rawType": "object", - "type": "string" - }, - { - "name": "value", - "rawType": "object", - "type": "string" - }, - { - "name": "unit_id", - "rawType": "object", - "type": "string" - } - ], - "ref": "5c95c323-56ec-4546-ad20-84e7b50c7748", - "rows": [], - "shape": { - "columns": 7, - "rows": 0 - } - }, - "text/html": [ - "
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iddataset_idrecord_idmain_cropparameter_idvalueunit_id
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" - ], - "text/plain": [ - "Empty DataFrame\n", - "Columns: [id, dataset_id, record_id, main_crop, parameter_id, value, unit_id]\n", - "Index: []" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "df[[\"id\", \"dataset_id\", \"record_id\", \"main_crop\", \"parameter_id\", \"value\", \"unit_id\"]]" ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "query = select(Observation, LandiqRecord, PrimaryCrop).join(\n", + " Observation,\n", + " Observation.record_id == LandiqRecord.id).join(\n", + " PrimaryCrop,\n", + " LandiqRecord.main_crop == PrimaryCrop.id).limit(10)\n", + "\n", + "df3 = pd.read_sql(query, engine)\n", + "\n", + "df3.columns" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pd.read_sql(select(LandiqRecord), engine)" + ] } ], "metadata": { diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/experiments.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/experiments.py index 25a6d194..9a74e350 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/experiments.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/experiments.py @@ -1,7 +1,7 @@ from typing import Optional import pandas as pd from prefect import task, get_run_logger -from ca_biositing.pipeline.utils.gsheet_to_pandas import gsheet_to_df +from ...utils.gsheet_to_pandas import gsheet_to_df @task def extract_experiments() -> Optional[pd.DataFrame]: diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/proximate.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/proximate.py new file mode 100644 index 00000000..9bbaf910 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/proximate.py @@ -0,0 +1,59 @@ +""" +ETL Extract Template +--- + +This module provides a template for extracting data from a Google Sheet. + +To use this template: +1. Copy this file to the appropriate subdirectory in `src/etl/extract/`. + For example: `src/etl/extract/new_module/new_data.py` +2. Update the configuration constants (`GSHEET_NAME`, `WORKSHEET_NAME`). +3. Ensure the `CREDENTIALS_PATH` is correct. +""" + +from typing import Optional +import os +import pandas as pd +from prefect import task, get_run_logger +from ...utils.gsheet_to_pandas import gsheet_to_df + +# --- CONFIGURATION --- +# TODO: Replace with the name of the Google Sheet file. +GSHEET_NAME = "Aim 1-Feedstock Collection and Processing Data-BioCirV" + +# TODO: Replace with the exact name of the worksheet/tab to extract data from. +WORKSHEET_NAME = "03.1-Proximate" + +# The path to the credentials file. This is typically kept in the project root. +CREDENTIALS_PATH = "credentials.json" + + +@task +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: + """ + Extracts raw data from the specified Google Sheet worksheet. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + logger.info(f"Extracting raw data from '{WORKSHEET_NAME}' in '{GSHEET_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + + # The gsheet_to_df function handles authentication, data fetching, and error handling. + raw_df = gsheet_to_df(GSHEET_NAME, WORKSHEET_NAME, credentials_path) + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb new file mode 100644 index 00000000..b098f40d --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb @@ -0,0 +1,179 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "import sys\n", + "import pandas as pd\n", + "import janitor as jn\n", + "from IPython.display import display\n", + "\n", + "# --- Robustly find the project root ---\n", + "# The project root is the directory containing the 'pixi.toml' file.\n", + "path = os.getcwd()\n", + "project_root = None\n", + "while path != os.path.dirname(path): # Stop at the filesystem root\n", + " if 'pixi.toml' in os.listdir(path):\n", + " project_root = path\n", + " break\n", + " path = os.path.dirname(path)\n", + "\n", + "if not project_root:\n", + " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", + "\n", + "# --- Add project root to sys.path ---\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + " print(f\"Added project root '{project_root}' to sys.path\")\n", + "else:\n", + " print(f\"Project root '{project_root}' is already in sys.path\")\n", + "\n", + "# --- Import the module ---\n", + "try:\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate\n", + " print(\"Successfully imported 'proximate' module.\")\n", + "except ImportError as e:\n", + " print(f\"Failed to import 'proximate' module: {e}\")\n", + " print(f\"\\nFull sys.path: {sys.path}\")\n", + "\n", + "# --- Run the extraction ---\n", + "if 'proximate' in locals():\n", + " try:\n", + " # Pass the project_root to the extract function\n", + " df = proximate.extract(project_root=project_root)\n", + " if df is not None:\n", + " print(\"\\nSuccessfully extracted data.\")\n", + " display(df.head())\n", + " else:\n", + " print(\"\\nExtraction returned no data. Check the logs above for errors.\")\n", + " except Exception as e:\n", + " print(f\"\\nAn error occurred during extraction: {e}\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "df.clean_names()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "df[['Record_ID', 'Source_codename', 'Prepared_sample']]" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "## Convert 'Value' column to numeric\n", + "pv_df = df[['Parameter', 'Value']]\n", + "\n", + "pv_df['Value'] = pd.to_numeric(pv_df['Value'], errors='coerce')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "pv_df\n", + "\n", + "if pv_df.groupby('Parameter').mean() is not None:\n", + " print(\"Mean values by Parameter:\")\n", + " display(pv_df.groupby('Parameter').mean())\n", + "else:\n", + " print(\"No numeric values available to compute means.\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "df2 = df[['Resource', 'Parameter', 'Value', 'Unit']]\n", + "\n", + "df2['Value'] = pd.to_numeric(df2['Value'], errors='coerce')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "df2" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "df2 = df2.dropna(subset=['Value'])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "summary_stats = df2.groupby(['Resource', 'Parameter'])['Value'].agg(['mean', 'median', 'min', 'max', 'std', 'count'])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "summary_stats" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "name": "python", + "version": "3.12" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} From 907686ba1ca492efd578895d1eb825ea9e7ea961 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Fri, 2 Jan 2026 21:41:29 -0700 Subject: [PATCH 69/81] feat: notebook for gsheets extraction, data playground, and pk id lookup insertion. --- .../pipeline/etl/extract/cmpana.py | 59 + .../pipeline/etl/extract/ultimate.py | 59 + .../ca_biositing/pipeline/utils/engine.py | 6 + .../utils/gsheet_extraction_notebook.ipynb | 4100 ++++++++++++++++- .../pipeline/utils/name_id_swap.py | 81 + .../pipeline/utils/seed_biomass.sql | 15 - 6 files changed, 4272 insertions(+), 48 deletions(-) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/cmpana.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ultimate.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/engine.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py delete mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/seed_biomass.sql diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/cmpana.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/cmpana.py new file mode 100644 index 00000000..b34a39ca --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/cmpana.py @@ -0,0 +1,59 @@ +""" +ETL Extract Template +--- + +This module provides a template for extracting data from a Google Sheet. + +To use this template: +1. Copy this file to the appropriate subdirectory in `src/etl/extract/`. + For example: `src/etl/extract/new_module/new_data.py` +2. Update the configuration constants (`GSHEET_NAME`, `WORKSHEET_NAME`). +3. Ensure the `CREDENTIALS_PATH` is correct. +""" + +from typing import Optional +import os +import pandas as pd +from prefect import task, get_run_logger +from ...utils.gsheet_to_pandas import gsheet_to_df + +# --- CONFIGURATION --- +# TODO: Replace with the name of the Google Sheet file. +GSHEET_NAME = "Aim 1-Feedstock Collection and Processing Data-BioCirV" + +# TODO: Replace with the exact name of the worksheet/tab to extract data from. +WORKSHEET_NAME = "03.3-CmpAna" + +# The path to the credentials file. This is typically kept in the project root. +CREDENTIALS_PATH = "credentials.json" + + +@task +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: + """ + Extracts raw data from the specified Google Sheet worksheet. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + logger.info(f"Extracting raw data from '{WORKSHEET_NAME}' in '{GSHEET_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + + # The gsheet_to_df function handles authentication, data fetching, and error handling. + raw_df = gsheet_to_df(GSHEET_NAME, WORKSHEET_NAME, credentials_path) + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ultimate.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ultimate.py new file mode 100644 index 00000000..c7495876 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ultimate.py @@ -0,0 +1,59 @@ +""" +ETL Extract Template +--- + +This module provides a template for extracting data from a Google Sheet. + +To use this template: +1. Copy this file to the appropriate subdirectory in `src/etl/extract/`. + For example: `src/etl/extract/new_module/new_data.py` +2. Update the configuration constants (`GSHEET_NAME`, `WORKSHEET_NAME`). +3. Ensure the `CREDENTIALS_PATH` is correct. +""" + +from typing import Optional +import os +import pandas as pd +from prefect import task, get_run_logger +from ...utils.gsheet_to_pandas import gsheet_to_df + +# --- CONFIGURATION --- +# TODO: Replace with the name of the Google Sheet file. +GSHEET_NAME = "Aim 1-Feedstock Collection and Processing Data-BioCirV" + +# TODO: Replace with the exact name of the worksheet/tab to extract data from. +WORKSHEET_NAME = "03.7-Ultimate" + +# The path to the credentials file. This is typically kept in the project root. +CREDENTIALS_PATH = "credentials.json" + + +@task +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: + """ + Extracts raw data from the specified Google Sheet worksheet. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + logger.info(f"Extracting raw data from '{WORKSHEET_NAME}' in '{GSHEET_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + + # The gsheet_to_df function handles authentication, data fetching, and error handling. + raw_df = gsheet_to_df(GSHEET_NAME, WORKSHEET_NAME, credentials_path) + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/engine.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/engine.py new file mode 100644 index 00000000..a24e92a0 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/engine.py @@ -0,0 +1,6 @@ +from sqlmodel import create_engine, Session + +DATABASE_URL = "postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db" +engine = create_engine(DATABASE_URL) + +db_session = Session(engine) diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb index b098f40d..9d27799e 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb @@ -2,13 +2,1522 @@ "cells": [ { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Added project root '/Users/pjsmitty301/ca-biositing' to sys.path\n", + "Successfully imported all module.\n" + ] + }, + { + "data": { + "text/html": [ + "
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20:54:45.631 | INFO    | Task run 'extract' - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n",
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20:54:47.211 | INFO    | Task run 'extract' - Successfully extracted raw data.\n",
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" + ], + "text/plain": [ + " Cmp_UUID_033 Record_ID Prepared_sample \\\n", + "0 3EE2993D-86E3-1F16-C7EA-F8D555E114 (85)E114 Oak-TmPm01O(85) \n", + "1 46878EF9-1226-22A0-D5D8-CF65E241CB (85)41CB Oak-TmPm01O(85) \n", + "2 76A7A2F4-C4E4-E60F-1187-DEC6E02246 (85)2246 Oak-TmPm01O(85) \n", + "3 7A136832-286B-07CB-62DE-ACF52F9311 (85)9311 Oak-TmPm01O(85) \n", + "4 B709ECEE-F9A6-A55D-A59E-93B7B863D7 (85)63D7 Oak-TmPm01O(85) \n", + "\n", + " Resource Preparation_method Storage_cond Exper_abbrev Repl_no \\\n", + "0 Tomato pomace Oven dry RT vacuum sealed Cmp04xk 1 \n", + "1 Tomato pomace Oven dry RT vacuum sealed Cmp04xk 2 \n", + "2 Tomato pomace Oven dry RT vacuum sealed Cmp04xk 3 \n", + "3 Tomato pomace Oven dry RT vacuum sealed Cmp04xk 1 \n", + "4 Tomato pomace Oven dry RT vacuum sealed Cmp04xk 2 \n", + "\n", + " Repl_ID Parameter ... Unit Created_at Updated_at \\\n", + "0 Cmp04xk(85)1 Glucan ... % dry weight 1/23/2025 9:00:01 \n", + "1 Cmp04xk(85)2 Glucan ... % dry weight 1/23/2025 9:00:16 \n", + "2 Cmp04xk(85)3 Glucan ... % dry weight 1/23/2025 9:00:31 \n", + "3 Cmp04xk(85)1 Glucose ... % dry weight 1/23/2025 9:00:46 \n", + "4 Cmp04xk(85)2 Glucose ... % dry weight 1/23/2025 9:01:01 \n", + "\n", + " QC_result Note Analysis_type Equipment Raw_data_URL Analyst_email \\\n", + "0 pass Chemical composition xkang2@lbl.gov \n", + "1 pass Chemical composition xkang2@lbl.gov \n", + "2 pass Chemical composition xkang2@lbl.gov \n", + "3 pass Chemical composition xkang2@lbl.gov \n", + "4 pass Chemical composition xkang2@lbl.gov \n", + "\n", + " Upload_status \n", + "0 ready \n", + "1 ready \n", + "2 ready \n", + "3 ready \n", + "4 ready \n", + "\n", + "[5 rows x 21 columns]" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "Cmp Ana extraction process completed.\n" + ] + } + ], "source": [ "import os\n", "import sys\n", "import pandas as pd\n", + "import numpy as np\n", "import janitor as jn\n", "from IPython.display import display\n", "\n", @@ -34,10 +1543,10 @@ "\n", "# --- Import the module ---\n", "try:\n", - " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate\n", - " print(\"Successfully imported 'proximate' module.\")\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate, ultimate, cmpana\n", + " print(\"Successfully imported all module.\")\n", "except ImportError as e:\n", - " print(f\"Failed to import 'proximate' module: {e}\")\n", + " print(f\"Failed to import modules: {e}\")\n", " print(f\"\\nFull sys.path: {sys.path}\")\n", "\n", "# --- Run the extraction ---\n", @@ -46,21 +1555,67 @@ " # Pass the project_root to the extract function\n", " df = proximate.extract(project_root=project_root)\n", " if df is not None:\n", - " print(\"\\nSuccessfully extracted data.\")\n", + " print(\"\\nSuccessfully extracted proximate data.\")\n", " display(df.head())\n", " else:\n", - " print(\"\\nExtraction returned no data. Check the logs above for errors.\")\n", + " print(\"\\n Prox extraction returned no data. Check the logs above for errors.\")\n", + " except Exception as e:\n", + " print(f\"\\nAn error occurred during prox extraction: {e}\")\n", + "\n", + "if 'ultimate' in locals():\n", + " try:\n", + " df2 = ultimate.extract(project_root=project_root)\n", + " if df is not None:\n", + " print(\"\\nSuccessfully extracted Ultimate data.\")\n", + " display(df2.head())\n", + " else:\n", + " print(\"\\n Ultimate extraction returned no data. Check the logs above for errors.\")\n", " except Exception as e:\n", - " print(f\"\\nAn error occurred during extraction: {e}\")" + " print(f\"\\nAn error occurred during extraction: {e}\")\n", + "\n", + "if 'cmpana' in locals():\n", + " try:\n", + " df3 = cmpana.extract(project_root=project_root)\n", + " if df is not None:\n", + " print(\"\\nSuccessfully extracted CmpAna data.\")\n", + " display(df3.head())\n", + " else:\n", + " print(\"\\nCmpAna extraction returned no data. Check the logs above for errors.\")\n", + " except Exception as e:\n", + " print(f\"\\nAn error occurred during cmp ana extraction: {e}\")\n", + " finally:\n", + " print(\"\\nCmp Ana extraction process completed.\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### This function seeks to clean the incoming gsheet dataframes and coerce the types" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ - "df.clean_names()" + "def clean_the_gsheets(df):\n", + " # 1. Clean names and drop rows\n", + " df = df.clean_names().dropna(subset=['repl_no', 'value'])\n", + "\n", + " # 2. Coerce types (using errors='coerce' handles messy string data)\n", + " df['repl_no'] = pd.to_numeric(df['repl_no'], errors='coerce').astype('Int32') # Capital 'I' handles NaNs\n", + " df['value'] = pd.to_numeric(df['value'], errors='coerce').astype(np.float32)\n", + "\n", + " # 3. Dates\n", + " df['created_at'] = pd.to_datetime(df['created_at'], errors='coerce')\n", + " df['updated_at'] = pd.to_datetime(df['updated_at'], errors='coerce')\n", + "\n", + " # 4. Convert remaining objects to best possible types (like strings)\n", + " df = df.convert_dtypes()\n", + " \n", + " return df # Return the FULL dataframe, not just .head()" ] }, { @@ -69,7 +1624,11 @@ "metadata": {}, "outputs": [], "source": [ - "df[['Record_ID', 'Source_codename', 'Prepared_sample']]" + "dataframes = [df, df2, df3]\n", + "\n", + "clean_dataframes = [clean_the_gsheets(df) for df in dataframes]\n", + "\n", + "clean_dataframes[2].head()\n" ] }, { @@ -78,10 +1637,11 @@ "metadata": {}, "outputs": [], "source": [ - "## Convert 'Value' column to numeric\n", - "pv_df = df[['Parameter', 'Value']]\n", + "summary_stats = clean_dataframes[0].\\\n", + " groupby(['resource', 'parameter'])['value'].\\\n", + " agg(['mean', 'median', 'min', 'max', 'std', 'count'])\n", "\n", - "pv_df['Value'] = pd.to_numeric(pv_df['Value'], errors='coerce')" + "summary_stats" ] }, { @@ -90,13 +1650,12 @@ "metadata": {}, "outputs": [], "source": [ - "pv_df\n", - "\n", - "if pv_df.groupby('Parameter').mean() is not None:\n", - " print(\"Mean values by Parameter:\")\n", - " display(pv_df.groupby('Parameter').mean())\n", - "else:\n", - " print(\"No numeric values available to compute means.\")" + "clean_dataframes[0][['resource', 'parameter', 'value', 'unit']].\\\n", + " groupby(['resource', 'parameter', 'unit'], as_index=False).\\\n", + " agg({'value': 'mean'}).\\\n", + " query('value > 30').\\\n", + " sort_values(by='value', ascending=False).\\\n", + " round({'value': 1})\n" ] }, { @@ -105,9 +1664,18 @@ "metadata": {}, "outputs": [], "source": [ - "df2 = df[['Resource', 'Parameter', 'Value', 'Unit']]\n", + "list_of_param = (\"Moisture\", \"Total solids\", \"Ash\")\n", + "\n", + "def is_it_volatile_solids(df):\n", + " df['check'] = \"VS\"\n", + "\n", + " df.loc[df['parameter'].isin(list_of_param), 'check'] = \"In list\"\n", + " return df\n", "\n", - "df2['Value'] = pd.to_numeric(df2['Value'], errors='coerce')" + "is_it_volatile_solids(df)\n", + "\n", + "df[['check', 'parameter']]\n", + "\n" ] }, { @@ -116,7 +1684,17 @@ "metadata": {}, "outputs": [], "source": [ - "df2" + "\n", + "#This defines a function to calculate the square root of the 'value' column in a DataFrame\n", + "def sqrtvalue(df):\n", + " df = df.assign(sqrtvalue = df['value'] ** 0.5)\n", + " return df\n", + "\n", + "#List comprehension to apply sqrtvalue to each DataFrame\n", + "clean_rooted_df = [sqrtvalue(df) for df in clean_dataframes]\n", + "\n", + "# Display the head of the third DataFrame\n", + "clean_rooted_df[2].head()" ] }, { @@ -125,25 +1703,2462 @@ "metadata": {}, "outputs": [], "source": [ - "df2 = df2.dropna(subset=['Value'])" + "cmpana_raw = cmpana.extract(project_root=project_root)\n", + "\n", + "cmpana_raw.head()" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Connected to database.\n" + ] + }, + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "index", + "rawType": "int64", + "type": "integer" + }, + { + "name": "id", + "rawType": "int64", + "type": "integer" + }, + { + "name": "name", + "rawType": "object", + "type": "string" + }, + { + "name": "note", + "rawType": "object", + "type": "unknown" + }, + { + "name": "description", + "rawType": "object", + "type": "unknown" + }, + { + "name": "uri", + "rawType": "object", + "type": "unknown" + } + ], + "ref": "0dabe9e2-728a-486d-9dd1-c1edd094e9c2", + "rows": [ + [ + "0", + "1", + "Tomatoes for processing", + null, + null, + null + ], + [ + "1", + "2", + "Grapes", + null, + null, + null + ], + [ + "2", + "3", + "Almonds", + null, + null, + null + ], + [ + "3", + "4", + "Walnuts", + null, + null, + null + ], + [ + "4", + "5", + "Sweet potatoes", + null, + null, + null + ], + [ + "5", + "6", + "Algae", + null, + null, + null + ], + [ + "6", + "7", + "Olives - processing", + null, + null, + null + ], + [ + "7", + "8", + "Corn - all", + null, + null, + null + ], + [ + "8", + "9", + "Hay - alfalfa", + null, + null, + null + ], + [ + "9", + "10", + "Silage - wheat", + null, + null, + null + ], + [ + "10", + "11", + "Rice", + null, + null, + null + ], + [ + "11", + "12", + "Peaches", + null, + null, + null + ], + [ + "12", + "13", + "Potatoes", + null, + null, + null + ], + [ + "13", + "14", + "Cucumbers and pickles", + null, + null, + null + ], + [ + "14", + "15", + "Pistachios", + null, + null, + null + ], + [ + "15", + "16", + "Cotton", + null, + null, + null + ], + [ + "16", + "17", + "Olives - market", + null, + null, + null + ], + [ + "17", + "18", + "", + null, + null, + null + ] + ], + "shape": { + "columns": 5, + "rows": 18 + } + }, + "text/html": [ + "
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" + ], + "text/plain": [ + " id name note description uri\n", + "0 1 Tomatoes for processing None None None\n", + "1 2 Grapes None None None\n", + "2 3 Almonds None None None\n", + "3 4 Walnuts None None None\n", + "4 5 Sweet potatoes None None None\n", + "5 6 Algae None None None\n", + "6 7 Olives - processing None None None\n", + "7 8 Corn - all None None None\n", + "8 9 Hay - alfalfa None None None\n", + "9 10 Silage - wheat None None None\n", + "10 11 Rice None None None\n", + "11 12 Peaches None None None\n", + "12 13 Potatoes None None None\n", + "13 14 Cucumbers and pickles None None None\n", + "14 15 Pistachios None None None\n", + "15 16 Cotton None None None\n", + "16 17 Olives - market None None None\n", + "17 18 None None None" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ - "summary_stats = df2.groupby(['Resource', 'Parameter'])['Value'].agg(['mean', 'median', 'min', 'max', 'std', 'count'])" + "from sqlmodel import Session, select, create_engine\n", + "import pandas as pd\n", + "import os\n", + "import sys\n", + "\n", + "\n", + "# Database Connection\n", + "DATABASE_URL = \"postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db\"\n", + "engine = create_engine(DATABASE_URL)\n", + "print(f\"Connected to database.\")\n", + "\n", + "primary_ag_product = pd.read_sql(\"SELECT * FROM primary_ag_product;\", con=engine)\n", + "\n", + "#reorders columns so id and name are first\n", + "cols = ['id', 'name'] + [c for c in primary_ag_product.columns if c not in ['id', 'name']]\n", + "\n", + "primary_ag_product = primary_ag_product[[*cols]]\n", + "\n", + "primary_ag_product\n" ] }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "index", + "rawType": "int64", + "type": "integer" + }, + { + "name": "description", + "rawType": "object", + "type": "unknown" + }, + { + "name": "id", + "rawType": "int64", + "type": "integer" + }, + { + "name": "name", + "rawType": "object", + "type": "string" + }, + { + "name": "note", + "rawType": "object", + "type": "unknown" + }, + { + "name": "uri", + "rawType": "object", + "type": "unknown" + } + ], + "ref": "52090a35-9379-4dc9-b918-583b23513ddd", + "rows": [ + [ + "0", + null, + "1", + "Tomatoes for processing", + null, + null + ], + [ + "1", + null, + "2", + "Grapes", + null, + null + ], + [ + "2", + null, + "3", + "Almonds", + null, + null + ], + [ + "3", + null, + "4", + "Walnuts", + null, + null + ], + [ + "4", + null, + "5", + "Sweet potatoes", + null, + null + ] + ], + "shape": { + "columns": 5, + "rows": 5 + } + }, + "text/html": [ + "
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" + ], + "text/plain": [ + " description id name note uri\n", + "0 None 1 Tomatoes for processing None None\n", + "1 None 2 Grapes None None\n", + "2 None 3 Almonds None None\n", + "3 None 4 Walnuts None None\n", + "4 None 5 Sweet potatoes None None" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from sqlalchemy.orm import Session\n", + "from sqlalchemy import select\n", + "import pandas as pd\n", + "import os\n", + "import sys\n", + "\n", + "# --- project root discovery (unchanged) ---\n", + "path = os.getcwd()\n", + "project_root = None\n", + "while path != os.path.dirname(path):\n", + " if 'pixi.toml' in os.listdir(path):\n", + " project_root = path\n", + " break\n", + " path = os.path.dirname(path)\n", + "\n", + "if not project_root:\n", + " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", + "\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + "\n", + "# --- imports ---\n", + "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", + "from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import PrimaryAgProduct\n", + "\n", + "# --- query + dataframe ---\n", + "with Session(engine) as db:\n", + " stmt = select(*PrimaryAgProduct.__table__.columns)\n", + " rows = db.execute(stmt).mappings().all()\n", + "\n", + "df = pd.DataFrame(rows)\n", + "\n", + "df.head()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
21:07:54.222 | INFO    | Task run 'extract' - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n",
+       "
\n" + ], + "text/plain": [ + "21:07:54.222 | \u001b[36mINFO\u001b[0m | Task run 'extract' - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
21:07:59.598 | INFO    | Task run 'extract' - Successfully extracted raw data.\n",
+       "
\n" + ], + "text/plain": [ + "21:07:59.598 | \u001b[36mINFO\u001b[0m | Task run 'extract' - Successfully extracted raw data.\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
21:07:59.601 | INFO    | Task run 'extract' - Finished in state Completed()\n",
+       "
\n" + ], + "text/plain": [ + "21:07:59.601 | \u001b[36mINFO\u001b[0m | Task run 'extract' - Finished in state \u001b[32mCompleted\u001b[0m()\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "from sqlalchemy.orm import Session\n", + "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", + "from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", + "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import (\n", + " replace_name_with_id_df,\n", + ") \n", + "\n", + "#This extractst the raw proximate data\n", + "df = cmpana.extract(project_root=project_root)\n", + "\n", + "#this cleans the names to lowercase and parses data into a standard format. Also renames the column to match with what will be in the database\n", + "test_df = clean_the_gsheets(df).rename(columns={'parameter': 'name'})\n", + "\n", + "#this replaces the names with IDs\n", + "with Session(engine) as db:\n", + " parameter_ids = replace_name_with_id_df(\n", + " db=db,\n", + " df=test_df,\n", + " ref_model=Parameter,\n", + " name_column_name=\"name\", # column in df + table\n", + " id_column_name=\"id\", # PK column in table\n", + " final_column_name=\"parameter_id\"\n", + " )\n", + "\n", + "##I EVENTUALLY WANT SOME LOGS ABOUT HOW MANY WERE ADDED, HOW MANY RETRIEVED, ETC. MAYBE PUT THAT IN THE \n", + "#resource_id_mapping = df_with_ids.rename(columns={\"id\": \"resource_id\"})\n", + "\n", + "#resource_id_mapping\n" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "index", + "rawType": "int64", + "type": "integer" + }, + { + "name": "cmp_uuid_033", + "rawType": "string", + "type": "string" + }, + { + "name": "record_id", + "rawType": "string", + "type": "string" + }, + { + "name": "prepared_sample", + "rawType": "string", + "type": "string" + }, + { + "name": "resource", + "rawType": "string", + "type": "string" + }, + { + "name": "preparation_method", + "rawType": "string", + "type": "string" + }, + { + "name": "storage_cond", + "rawType": "string", + "type": "string" + }, + { + "name": "exper_abbrev", + "rawType": "string", + "type": "string" + }, + { + "name": "repl_no", + "rawType": "Int32", + "type": 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cmp_uuid_033record_idprepared_sampleresourcepreparation_methodstorage_condexper_abbrevrepl_norepl_idvalue...created_atupdated_atqc_resultnoteanalysis_typeequipmentraw_data_urlanalyst_emailupload_statusparameter_id
03EE2993D-86E3-1F16-C7EA-F8D555E114(85)E114Oak-TmPm01O(85)Tomato pomaceOven dryRT vacuum sealedCmp04xk1Cmp04xk(85)114.16...2025-01-23 09:00:01NaTpassChemical compositionxkang2@lbl.govready6
146878EF9-1226-22A0-D5D8-CF65E241CB(85)41CBOak-TmPm01O(85)Tomato pomaceOven dryRT vacuum sealedCmp04xk2Cmp04xk(85)214.18...2025-01-23 09:00:16NaTpassChemical compositionxkang2@lbl.govready6
276A7A2F4-C4E4-E60F-1187-DEC6E02246(85)2246Oak-TmPm01O(85)Tomato pomaceOven dryRT vacuum sealedCmp04xk3Cmp04xk(85)314.12...2025-01-23 09:00:31NaTpassChemical compositionxkang2@lbl.govready6
37A136832-286B-07CB-62DE-ACF52F9311(85)9311Oak-TmPm01O(85)Tomato pomaceOven dryRT vacuum sealedCmp04xk1Cmp04xk(85)115.74...2025-01-23 09:00:46NaTpassChemical compositionxkang2@lbl.govready4
4B709ECEE-F9A6-A55D-A59E-93B7B863D7(85)63D7Oak-TmPm01O(85)Tomato pomaceOven dryRT vacuum sealedCmp04xk2Cmp04xk(85)215.75...2025-01-23 09:01:01NaTpassChemical compositionxkang2@lbl.govready4
..................................................................
38579799601-0E25-3832-3BBF-F4BD9EE973(A0)E973Hum-AlmBr024KM2(A0)Almond BranchesKnife Mill (2mm)RT vacuum sealedCmp17xk2Cmp17xk(A0)217.290001...2025-03-04 09:55:00NaTpassChemical compositionxkang2@lbl.govnot ready5
386A4E3393F-72C3-A0ED-C041-105A33031A(A0)031AHum-AlmBr024KM2(A0)Almond BranchesKnife Mill (2mm)RT vacuum sealedCmp17xk3Cmp17xk(A0)317.5...2025-03-04 09:55:15NaTpassChemical compositionxkang2@lbl.govnot ready5
3873D5A85F8-31A2-0CC2-74E6-05D8197C3A(A0)7C3AHum-AlmBr024KM2(A0)Almond BranchesKnife Mill (2mm)RT vacuum sealedCmp17xk1Cmp17xk(A0)135.970001...2025-03-04 09:55:30NaTpassChemical compositionxkang2@lbl.govnot ready3
388C7AE456E-4DCD-AE34-A0D0-BD39D04E42(A0)4E42Hum-AlmBr024KM2(A0)Almond BranchesKnife Mill (2mm)RT vacuum sealedCmp17xk2Cmp17xk(A0)235.279999...2025-03-04 09:55:45NaTpassChemical compositionxkang2@lbl.govnot ready3
389A5E617A2-9831-3E9F-7072-6C5FB8129B(A0)129BHum-AlmBr024KM2(A0)Almond BranchesKnife Mill (2mm)RT vacuum sealedCmp17xk3Cmp17xk(A0)334.990002...2025-03-04 09:56:00NaTpassChemical compositionxkang2@lbl.govnot ready3
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390 rows × 21 columns

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" + ], + "text/plain": [ + " cmp_uuid_033 record_id prepared_sample \\\n", + "0 3EE2993D-86E3-1F16-C7EA-F8D555E114 (85)E114 Oak-TmPm01O(85) \n", + "1 46878EF9-1226-22A0-D5D8-CF65E241CB (85)41CB Oak-TmPm01O(85) \n", + "2 76A7A2F4-C4E4-E60F-1187-DEC6E02246 (85)2246 Oak-TmPm01O(85) \n", + "3 7A136832-286B-07CB-62DE-ACF52F9311 (85)9311 Oak-TmPm01O(85) \n", + "4 B709ECEE-F9A6-A55D-A59E-93B7B863D7 (85)63D7 Oak-TmPm01O(85) \n", + ".. ... ... ... \n", + "385 79799601-0E25-3832-3BBF-F4BD9EE973 (A0)E973 Hum-AlmBr024KM2(A0) \n", + "386 A4E3393F-72C3-A0ED-C041-105A33031A (A0)031A Hum-AlmBr024KM2(A0) \n", + "387 3D5A85F8-31A2-0CC2-74E6-05D8197C3A (A0)7C3A Hum-AlmBr024KM2(A0) \n", + "388 C7AE456E-4DCD-AE34-A0D0-BD39D04E42 (A0)4E42 Hum-AlmBr024KM2(A0) \n", + "389 A5E617A2-9831-3E9F-7072-6C5FB8129B (A0)129B Hum-AlmBr024KM2(A0) \n", + "\n", + " resource preparation_method storage_cond exper_abbrev \\\n", + "0 Tomato pomace Oven dry RT vacuum sealed Cmp04xk \n", + "1 Tomato pomace Oven dry RT vacuum sealed Cmp04xk \n", + "2 Tomato pomace Oven dry RT vacuum sealed Cmp04xk \n", + "3 Tomato pomace Oven dry RT vacuum sealed Cmp04xk \n", + "4 Tomato pomace Oven dry RT vacuum sealed Cmp04xk \n", + ".. ... ... ... ... \n", + "385 Almond Branches Knife Mill (2mm) RT vacuum sealed Cmp17xk \n", + "386 Almond Branches Knife Mill (2mm) RT vacuum sealed Cmp17xk \n", + "387 Almond Branches Knife Mill (2mm) RT vacuum sealed Cmp17xk \n", + "388 Almond Branches Knife Mill (2mm) RT vacuum sealed Cmp17xk \n", + "389 Almond Branches Knife Mill (2mm) RT vacuum sealed Cmp17xk \n", + "\n", + " repl_no repl_id value ... created_at updated_at \\\n", + "0 1 Cmp04xk(85)1 14.16 ... 2025-01-23 09:00:01 NaT \n", + "1 2 Cmp04xk(85)2 14.18 ... 2025-01-23 09:00:16 NaT \n", + "2 3 Cmp04xk(85)3 14.12 ... 2025-01-23 09:00:31 NaT \n", + "3 1 Cmp04xk(85)1 15.74 ... 2025-01-23 09:00:46 NaT \n", + "4 2 Cmp04xk(85)2 15.75 ... 2025-01-23 09:01:01 NaT \n", + ".. ... ... ... ... ... ... \n", + "385 2 Cmp17xk(A0)2 17.290001 ... 2025-03-04 09:55:00 NaT \n", + "386 3 Cmp17xk(A0)3 17.5 ... 2025-03-04 09:55:15 NaT \n", + "387 1 Cmp17xk(A0)1 35.970001 ... 2025-03-04 09:55:30 NaT \n", + "388 2 Cmp17xk(A0)2 35.279999 ... 2025-03-04 09:55:45 NaT \n", + "389 3 Cmp17xk(A0)3 34.990002 ... 2025-03-04 09:56:00 NaT \n", + "\n", + " qc_result note analysis_type equipment raw_data_url \\\n", + "0 pass Chemical composition \n", + "1 pass Chemical composition \n", + "2 pass Chemical composition \n", + "3 pass Chemical composition \n", + "4 pass Chemical composition \n", + ".. ... ... ... ... ... \n", + "385 pass Chemical composition \n", + "386 pass Chemical composition \n", + "387 pass Chemical composition \n", + "388 pass Chemical composition \n", + "389 pass Chemical composition \n", + "\n", + " analyst_email upload_status parameter_id \n", + "0 xkang2@lbl.gov ready 6 \n", + "1 xkang2@lbl.gov ready 6 \n", + "2 xkang2@lbl.gov ready 6 \n", + "3 xkang2@lbl.gov ready 4 \n", + "4 xkang2@lbl.gov ready 4 \n", + ".. ... ... ... \n", + "385 xkang2@lbl.gov not ready 5 \n", + "386 xkang2@lbl.gov not ready 5 \n", + "387 xkang2@lbl.gov not ready 3 \n", + "388 xkang2@lbl.gov not ready 3 \n", + "389 xkang2@lbl.gov not ready 3 \n", + "\n", + "[390 rows x 21 columns]" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "parameter_ids\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ - "summary_stats" + "import numpy as np\n", + "from prefect import get_run_logger\n", + "\n", + "resource = pd.read_sql(\"SELECT id, name FROM resource\", con=engine)\n", + "\n", + "resource['name'] = resource['name'].str.lower()\n", + "\n", + "resource['name'] = resource['name'].replace('', np.nan)\n", + "resource.dropna(subset=['name'], inplace=True)\n", + "\n", + "\n", + "resource\n" ] }, { @@ -152,7 +4167,12 @@ "metadata": {}, "outputs": [], "source": [ - "\n" + "resource = pd.read_sql(\"SELECT id, name FROM resource\", con=engine)\n", + "\n", + "#this converts the entire dataframe to lowercase\n", + "df = df.map(lambda x: x.lower() if isinstance(x, str) else x)\n", + "\n", + "print(df)" ] }, { @@ -160,18 +4180,32 @@ "execution_count": null, "metadata": {}, "outputs": [], - "source": [] + "source": [ + "field_sample = pd.read_sql_query(\"SELECT * FROM field_sample\", con=engine)\n", + "\n", + "field_sample = field_sample[['id', 'name', 'resource_id']]\n", + "\n", + "field_sample" + ] } ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "default", "language": "python", "name": "python3" }, "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", "name": "python", - "version": "3.12" + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.13.11" } }, "nbformat": 4, diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py new file mode 100644 index 00000000..6c92cb4f --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py @@ -0,0 +1,81 @@ +from typing import Type, TypeVar, Any + +import pandas as pd +from sqlalchemy.orm import Session +from sqlalchemy import select + +ModelType = TypeVar("ModelType", bound=Any) + +def replace_id_with_name_df( + db: Session, + df: pd.DataFrame, + ref_model: Type[ModelType], + id_column_name: str, + name_column_name: str, +) -> pd.DataFrame: + # Fetch reference table rows as mappings + rows = db.execute( + select(*ref_model.__table__.columns) + ).mappings().all() + + # Build ID → name map + id_to_name_map = { + row[id_column_name]: row[name_column_name] + for row in rows + } + + df_copy = df.copy() + df_copy[name_column_name] = df_copy[id_column_name].map(id_to_name_map) + df_copy = df_copy.drop(columns=[id_column_name]) + + return df_copy + + +def replace_name_with_id_df( + db: Session, + df: pd.DataFrame, + ref_model: Type[ModelType], + name_column_name: str, + id_column_name: str, + final_column_name: str +) -> pd.DataFrame: + # Fetch reference table rows + rows = db.execute( + select(*ref_model.__table__.columns) + ).mappings().all() + + name_to_id_map = { + row[name_column_name]: row[id_column_name] + for row in rows + } + + df_copy = df.copy() + + unique_names = set(df_copy[name_column_name].dropna().unique()) + new_names = unique_names - set(name_to_id_map.keys()) + + if new_names: + for name in new_names: + new_record = ref_model(**{name_column_name: name}) + db.add(new_record) + + # Commit once, not per row + db.commit() + + # Refresh and update lookup + refreshed = db.execute( + select(ref_model).where( + getattr(ref_model, name_column_name).in_(new_names) + ) + ).scalars().all() + + for record in refreshed: + name_to_id_map[getattr(record, name_column_name)] = getattr( + record, id_column_name + ) + + df_copy[id_column_name] = df_copy[name_column_name].map(name_to_id_map) + df_copy = df_copy.drop(columns=[name_column_name]) + df_copy = df_copy.rename(columns={id_column_name: final_column_name}) + + return df_copy diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/seed_biomass.sql b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/seed_biomass.sql deleted file mode 100644 index c0d3337d..00000000 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/seed_biomass.sql +++ /dev/null @@ -1,15 +0,0 @@ --- This script inserts 10 sample rows into the biomass table. --- Note: This assumes that valid records exist in the primary_product, taxonomy, and biomass_type tables --- for the foreign key IDs used below. - -INSERT INTO biomass (biomass_name, primary_product_id, taxonomy_id, biomass_type_id, biomass_notes) VALUES -('Corn Stover', 1, 101, 1, 'Lignocellulosic biomass from corn stalks and leaves.'), -('Switchgrass', 2, 102, 1, 'Perennial grass used as a dedicated energy crop.'), -('Pine Wood Chips', 3, 103, 2, 'Woody biomass from pine trees, chipped for processing.'), -('Algae Culture', 4, 104, 3, 'Aquatic biomass grown for biofuel production.'), -('Municipal Solid Waste (MSW)', 5, 105, 4, 'Organic fraction of household waste.'), -('Food Waste', 6, 106, 4, 'Post-consumer food scraps from restaurants.'), -('Manure Slurry', 7, 107, 5, 'Animal waste from dairy farms, used in anaerobic digestion.'), -('Miscanthus Giganteus', 2, 108, 1, 'High-yield sterile hybrid grass for bioenergy.'), -('Willow Coppice', 3, 109, 2, 'Short-rotation coppice willow for biomass energy.'), -('Sugarcane Bagasse', 1, 110, 1, 'Fibrous residue left after sugarcane crushing.'); From 5e961aa19d87a1df708b83051e01a15efeb1fd8c Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Sat, 3 Jan 2026 08:39:43 -0700 Subject: [PATCH 70/81] modifying name_id_swap_function --- .../pipeline/utils/name_id_swap.py | 53 +++++++++++-------- 1 file changed, 31 insertions(+), 22 deletions(-) diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py index 6c92cb4f..d9290968 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py @@ -31,51 +31,60 @@ def replace_id_with_name_df( return df_copy + def replace_name_with_id_df( db: Session, df: pd.DataFrame, - ref_model: Type[ModelType], - name_column_name: str, + ref_model, + df_name_column: str, + model_name_attr: str, id_column_name: str, - final_column_name: str + final_column_name: str, ) -> pd.DataFrame: - # Fetch reference table rows + """ + Replace a DataFrame name column with foreign key IDs from a SQLAlchemy table. + Creates missing reference records if needed. + """ + + # 1. Fetch existing reference rows (name + id only) rows = db.execute( - select(*ref_model.__table__.columns) - ).mappings().all() + select( + getattr(ref_model, model_name_attr), + getattr(ref_model, id_column_name), + ) + ).all() - name_to_id_map = { - row[name_column_name]: row[id_column_name] - for row in rows - } + name_to_id_map = {name: id_ for name, id_ in rows} df_copy = df.copy() - unique_names = set(df_copy[name_column_name].dropna().unique()) + # 2. Determine which names are new + unique_names = set(df_copy[df_name_column].dropna().unique()) new_names = unique_names - set(name_to_id_map.keys()) + # 3. Insert missing reference rows if new_names: for name in new_names: - new_record = ref_model(**{name_column_name: name}) + new_record = ref_model(**{model_name_attr: name}) db.add(new_record) - # Commit once, not per row - db.commit() + # Flush to get IDs without ending the transaction + db.flush() - # Refresh and update lookup + # Re-query just-created rows refreshed = db.execute( select(ref_model).where( - getattr(ref_model, name_column_name).in_(new_names) + getattr(ref_model, model_name_attr).in_(new_names) ) ).scalars().all() for record in refreshed: - name_to_id_map[getattr(record, name_column_name)] = getattr( - record, id_column_name - ) + name_to_id_map[ + getattr(record, model_name_attr) + ] = getattr(record, id_column_name) - df_copy[id_column_name] = df_copy[name_column_name].map(name_to_id_map) - df_copy = df_copy.drop(columns=[name_column_name]) - df_copy = df_copy.rename(columns={id_column_name: final_column_name}) + # 4. Replace name column with ID column + df_copy[final_column_name] = df_copy[df_name_column].map(name_to_id_map) + df_copy = df_copy.drop(columns=[df_name_column]) return df_copy From 6d7990b252f7f86b948946ce958cc48bbb830f2c Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Sun, 4 Jan 2026 20:06:00 -0700 Subject: [PATCH 71/81] was trying to fix dev container kernel issue. Did not succeed. Also made new ETL notebook and modified some of the gsheet extraction notebook --- pixi.lock | 1606 +++++- pixi.toml | 1 + .../pipeline/utils/etl_notebook.ipynb | 1787 ++++++ .../utils/gsheet_extraction_notebook.ipynb | 4929 ++++------------- .../pipeline/utils/name_id_swap.py | 8 +- 5 files changed, 4407 insertions(+), 3924 deletions(-) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb diff --git a/pixi.lock b/pixi.lock index faeb4843..5581bcfd 100644 --- a/pixi.lock +++ b/pixi.lock @@ -10,13 +10,25 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - conda: https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/anyio-4.12.0-pyhcf101f3_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-25.1.0-pyhd8ed1ab_0.conda + - 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It is designed for interactive development and exploration before migrating logic into the production pipeline.\n", + "\n", + "It covers:\n", + "\n", + "1. **Setup**: Importing necessary libraries and establishing a connection to the database.\n", + "2. **Extraction**: Pulling raw data from Google Sheets.\n", + "3. **Cleaning**: Standardizing data types, handling missing values, and cleaning column names.\n", + "4. **Normalization**: Replacing human-readable names (e.g., \"Corn\") with database foreign key IDs (e.g., `resource_id: 1`).\n", + "5. **Utilities**: Common functions for data manipulation and analysis.\n", + "6. **Deployment Plan**: A step-by-step guide for moving the code from this notebook into the production ETL modules." + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2026-01-04 08:53:57,422 - INFO - Project root '/Users/pjsmitty301/ca-biositing' is already in sys.path\n", + "2026-01-04 08:53:57,423 - INFO - Successfully imported all project modules.\n" + ] + } + ], + "source": [ + "import os\n", + "import sys\n", + "import pandas as pd\n", + "import numpy as np\n", + "import janitor as jn\n", + "import logging\n", + "from IPython.display import display\n", + "from sqlalchemy.orm import Session\n", + "from sqlalchemy import select\n", + "\n", + "# --- Basic Logging Configuration for Notebook ---\n", + "# When running in a notebook, we use Python's standard logging.\n", + "# In the production pipeline, this will be replaced by Prefect's `get_run_logger()`\n", + "logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')\n", + "logger = logging.getLogger()\n", + "\n", + "# --- Robustly find the project root ---\n", + "# This ensures that the notebook can be run from any directory within the project.\n", + "path = os.getcwd()\n", + "project_root = None\n", + "while path != os.path.dirname(path):\n", + " if 'pixi.toml' in os.listdir(path):\n", + " project_root = path\n", + " break\n", + " path = os.path.dirname(path)\n", + "\n", + "if not project_root:\n", + " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", + "\n", + "# Add the project root to the Python path to allow for module imports\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + " logger.info(f\"Added project root '{project_root}' to sys.path\")\n", + "else:\n", + " logger.info(f\"Project root '{project_root}' is already in sys.path\")\n", + "\n", + "# --- Import project modules ---\n", + "try:\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", + " from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import replace_name_with_id_df\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate, ultimate, cmpana\n", + " logger.info('Successfully imported all project modules.')\n", + "except ImportError as e:\n", + " logger.error(f'Failed to import project modules: {e}', exc_info=True)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Data Cleaning Function" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [], + "source": [ + "def clean_the_gsheets(df):\n", + " \"\"\"Cleans and standardizes a DataFrame extracted from Google Sheets.\n", + "\n", + " This function performs several key operations:\n", + " 1. Cleans column names to a standard format (snake_case).\n", + " 2. Drops rows where essential columns ('repl_no', 'value') are empty.\n", + " 3. Coerces data types for numeric and datetime columns, handling errors gracefully.\n", + " 4. Converts remaining columns to the best possible data types.\n", + "\n", + " Args:\n", + " df (pd.DataFrame): The raw DataFrame.\n", + "\n", + " Returns:\n", + " pd.DataFrame: The cleaned DataFrame.\n", + " \"\"\"\n", + " logger.info('Starting DataFrame cleaning process.')\n", + " if not isinstance(df, pd.DataFrame):\n", + " logger.error('Input is not a pandas DataFrame.')\n", + " return None\n", + " \n", + " try:\n", + " # 1. Clean names and drop rows with missing essential data\n", + " df_cleaned = df.clean_names().dropna(subset=['repl_no', 'value'])\n", + " logger.info(f'Dropped {len(df) - len(df_cleaned)} rows with missing values.')\n", + "\n", + " # 2. Coerce numeric types\n", + " df_cleaned['repl_no'] = pd.to_numeric(df_cleaned['repl_no'], errors='coerce').astype('Int32')\n", + " df_cleaned['value'] = pd.to_numeric(df_cleaned['value'], errors='coerce').astype(np.float32)\n", + "\n", + " # 3. Coerce datetime types\n", + " if 'created_at' in df_cleaned.columns:\n", + " df_cleaned['created_at'] = pd.to_datetime(df_cleaned['created_at'], errors='coerce')\n", + " if 'updated_at' in df_cleaned.columns:\n", + " df_cleaned['updated_at'] = pd.to_datetime(df_cleaned['updated_at'], errors='coerce')\n", + "\n", + " # 4. Convert other dtypes to best possible\n", + " df_cleaned = df_cleaned.convert_dtypes()\n", + " logger.info('Successfully cleaned DataFrame.')\n", + " \n", + " \n", + " # 5. Convert all string data to lowercase\n", + " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + " logger.info('Converted all string data to lowercase.')\n", + " return df_cleaned\n", + "\n", + " except Exception as e:\n", + " logger.error(f'An error occurred during DataFrame cleaning: {e}', exc_info=True)\n", + " return None\n", + "\n", + " " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Data Normalization Function" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [], + "source": [ + "def normalize_dataframes(dataframes, normalize_columns):\n", + " \"\"\"Normalizes a list of DataFrames by replacing name columns with foreign key IDs.\n", + "\n", + " This function iterates through a list of dataframes and, for each one, iterates\n", + " through a dictionary of columns that need to be normalized. It uses the \n", + " `replace_name_with_id_df` utility to look up or create the corresponding ID\n", + " in the database.\n", + "\n", + " Args:\n", + " dataframes (list[pd.DataFrame]): A list of DataFrames to normalize.\n", + " normalize_columns (dict): A dictionary mapping column names to SQLModel classes and attributes.\n", + "\n", + " Returns:\n", + " list[pd.DataFrame]: The list of normalized DataFrames.\n", + " \"\"\"\n", + " logger.info(f'Starting normalization process for {len(dataframes)} dataframes.')\n", + " normalized_dfs = []\n", + " try:\n", + " with Session(engine) as db:\n", + " for i, df in enumerate(dataframes):\n", + " if not isinstance(df, pd.DataFrame):\n", + " logger.warning(f'Item {i+1} is not a DataFrame, skipping.')\n", + " continue\n", + " \n", + " logger.info(f'Processing DataFrame #{i+1} with {len(df)} rows.')\n", + " df_normalized = df.copy()\n", + "\n", + " for df_col, (model, model_name_attr) in normalize_columns.items():\n", + " if df_col not in df_normalized.columns:\n", + " logger.warning(f\"Column '{df_col}' not in DataFrame #{i+1}. Skipping normalization for this column.\")\n", + " continue\n", + " \n", + " try:\n", + " logger.info(f\"Normalizing column '{df_col}' using model '{model.__name__}'.\")\n", + " df_normalized = replace_name_with_id_df(\n", + " db=db,\n", + " df=df_normalized,\n", + " ref_model=model,\n", + " df_name_column=df_col,\n", + " model_name_attr=model_name_attr,\n", + " id_column_name='id',\n", + " final_column_name=f'{df_col}_id'\n", + " )\n", + " new_col_name = f'{df_col}_id'\n", + " num_nulls = df_normalized[new_col_name].isnull().sum()\n", + " logger.info(f\"Successfully normalized '{df_col}'. New column '{new_col_name}' contains {num_nulls} null values.\")\n", + " except Exception as e:\n", + " logger.error(f\"Error normalizing column '{df_col}' in DataFrame #{i+1}: {e}\", exc_info=True)\n", + " continue # Continue to the next column\n", + " \n", + " normalized_dfs.append(df_normalized)\n", + " logger.info(f'Finished processing DataFrame #{i+1}.')\n", + " \n", + " logger.info('Committing database session.')\n", + " db.commit()\n", + " logger.info('Database commit successful.')\n", + " except Exception as e:\n", + " logger.error(f'A critical error occurred during the database session: {e}', exc_info=True)\n", + " db.rollback()\n", + " logger.info('Database session rolled back.')\n", + " \n", + " return normalized_dfs" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### ETL Execution Example" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2026-01-04 08:58:52,849 - INFO - Starting data extraction...\n", + "2026-01-04 08:58:52,865 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-04 08:58:52,877 - INFO - Extracting raw data from '03.1-Proximate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", + "2026-01-04 08:58:54,699 - INFO - Successfully extracted raw data.\n", + "2026-01-04 08:58:54,703 - INFO - Finished in state Completed()\n", + "2026-01-04 08:58:54,724 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-04 08:58:54,736 - INFO - Extracting raw data from '03.7-Ultimate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", + "2026-01-04 08:58:55,992 - INFO - Successfully extracted raw data.\n", + "2026-01-04 08:58:55,996 - INFO - Finished in state Completed()\n", + "2026-01-04 08:58:56,016 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-04 08:58:56,029 - INFO - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", + "2026-01-04 08:58:57,291 - INFO - Successfully extracted raw data.\n", + "2026-01-04 08:58:57,294 - INFO - Finished in state Completed()\n", + "2026-01-04 08:58:57,296 - INFO - Data extraction complete.\n", + "2026-01-04 08:58:57,299 - INFO - Starting data cleaning...\n", + "2026-01-04 08:58:57,299 - INFO - Starting DataFrame cleaning process.\n", + "2026-01-04 08:58:57,302 - INFO - Dropped 0 rows with missing values.\n", + "2026-01-04 08:58:57,309 - INFO - Successfully cleaned DataFrame.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_25314/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "2026-01-04 08:58:57,314 - INFO - Converted all string data to lowercase.\n", + "2026-01-04 08:58:57,315 - INFO - Starting DataFrame cleaning process.\n", + "2026-01-04 08:58:57,316 - INFO - Dropped 0 rows with missing values.\n", + "2026-01-04 08:58:57,319 - INFO - Successfully cleaned DataFrame.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_25314/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "2026-01-04 08:58:57,320 - INFO - Converted all string data to lowercase.\n", + "2026-01-04 08:58:57,321 - INFO - Starting DataFrame cleaning process.\n", + "2026-01-04 08:58:57,325 - INFO - Dropped 0 rows with missing values.\n", + "2026-01-04 08:58:57,335 - INFO - Successfully cleaned DataFrame.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_25314/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "2026-01-04 08:58:57,340 - INFO - Converted all string data to lowercase.\n", + "2026-01-04 08:58:57,342 - INFO - Data cleaning complete.\n", + "2026-01-04 08:58:57,342 - INFO - Starting data normalization...\n", + "2026-01-04 08:58:57,343 - INFO - Starting normalization process for 3 dataframes.\n", + "2026-01-04 08:58:57,343 - INFO - Processing DataFrame #1 with 759 rows.\n", + "2026-01-04 08:58:57,344 - INFO - Normalizing column 'resource' using model 'Resource'.\n", + "2026-01-04 08:58:57,355 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", + "2026-01-04 08:58:57,356 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", + "2026-01-04 08:58:57,367 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", + "2026-01-04 08:58:57,367 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", + "2026-01-04 08:58:57,369 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", + "2026-01-04 08:58:57,369 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", + "2026-01-04 08:58:57,372 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", + "2026-01-04 08:58:57,372 - INFO - Normalizing column 'unit' using model 'Unit'.\n", + "2026-01-04 08:58:57,374 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", + "2026-01-04 08:58:57,374 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", + "2026-01-04 08:58:57,375 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", + "2026-01-04 08:58:57,375 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", + "2026-01-04 08:58:57,379 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", + "2026-01-04 08:58:57,379 - WARNING - Column 'primary_ag_product' not in DataFrame #1. Skipping normalization for this column.\n", + "2026-01-04 08:58:57,379 - INFO - Finished processing DataFrame #1.\n", + "2026-01-04 08:58:57,379 - INFO - Processing DataFrame #2 with 64 rows.\n", + "2026-01-04 08:58:57,380 - INFO - Normalizing column 'resource' using model 'Resource'.\n", + "2026-01-04 08:58:57,384 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", + "2026-01-04 08:58:57,384 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", + "2026-01-04 08:58:57,388 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", + "2026-01-04 08:58:57,388 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", + "2026-01-04 08:58:57,392 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", + "2026-01-04 08:58:57,392 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", + "2026-01-04 08:58:57,396 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", + "2026-01-04 08:58:57,396 - INFO - Normalizing column 'unit' using model 'Unit'.\n", + "2026-01-04 08:58:57,398 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", + "2026-01-04 08:58:57,398 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", + "2026-01-04 08:58:57,399 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", + "2026-01-04 08:58:57,400 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", + "2026-01-04 08:58:57,403 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", + "2026-01-04 08:58:57,403 - WARNING - Column 'primary_ag_product' not in DataFrame #2. Skipping normalization for this column.\n", + "2026-01-04 08:58:57,403 - INFO - Finished processing DataFrame #2.\n", + "2026-01-04 08:58:57,403 - INFO - Processing DataFrame #3 with 390 rows.\n", + "2026-01-04 08:58:57,404 - INFO - Normalizing column 'resource' using model 'Resource'.\n", + "2026-01-04 08:58:57,406 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", + "2026-01-04 08:58:57,406 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", + "2026-01-04 08:58:57,408 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", + "2026-01-04 08:58:57,408 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", + "2026-01-04 08:58:57,409 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", + "2026-01-04 08:58:57,410 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", + "2026-01-04 08:58:57,411 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", + "2026-01-04 08:58:57,411 - INFO - Normalizing column 'unit' using model 'Unit'.\n", + "2026-01-04 08:58:57,413 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", + "2026-01-04 08:58:57,413 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", + "2026-01-04 08:58:57,415 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", + "2026-01-04 08:58:57,415 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", + "2026-01-04 08:58:57,416 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", + "2026-01-04 08:58:57,416 - WARNING - Column 'primary_ag_product' not in DataFrame #3. Skipping normalization for this column.\n", + "2026-01-04 08:58:57,417 - INFO - Finished processing DataFrame #3.\n", + "2026-01-04 08:58:57,417 - INFO - Committing database session.\n", + "2026-01-04 08:58:57,418 - INFO - Database commit successful.\n", + "2026-01-04 08:58:57,418 - INFO - Data normalization complete.\n", + "2026-01-04 08:58:57,418 - INFO - Displaying results of normalization...\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "--- Normalized DataFrame 1 ---\n" + ] + }, + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "index", + "rawType": "int64", + "type": "integer" + }, + { + "name": "prox_uuid_031", + "rawType": "object", + "type": "string" + }, + { + "name": "record_id", + "rawType": "object", + "type": "string" + }, + { + "name": "source_codename", + "rawType": "object", + "type": "string" + }, + { + "name": "storage_cond", + "rawType": "object", + "type": "string" + }, + { + "name": "exper_abbrev", + "rawType": "object", + "type": "string" + }, + { + "name": "repl_no", + "rawType": "float64", + "type": "float" + }, + { + "name": "repl_id", + "rawType": "object", + "type": "string" + }, + { + "name": "value", + "rawType": "float64", + "type": "float" + }, + { + "name": "created_at", + "rawType": "datetime64[ns]", + "type": "datetime" + }, + { + "name": "updated_at", + "rawType": "datetime64[ns]", + "type": "datetime" + }, + { + "name": "qc_result", + "rawType": "object", + "type": "string" + }, + { + "name": "upload_status", + "rawType": "object", + "type": "string" + }, + { + "name": "note", + "rawType": "object", + "type": "string" + }, + { + "name": "resource_id", + "rawType": "int64", + "type": "integer" + }, + { + "name": "prepared_sample_id", + "rawType": "int64", + "type": "integer" + }, + { + "name": "preparation_method_id", + "rawType": "int64", + "type": "integer" + }, + { + "name": "parameter_id", + "rawType": "int64", + "type": "integer" + }, + { + "name": "unit_id", + "rawType": "int64", + "type": "integer" + }, + { + "name": "analyst_email_id", + "rawType": "int64", + "type": "integer" + }, + { + "name": "analysis_type_id", + "rawType": "int64", + "type": "integer" + } + ], + "ref": "e2d8eb1c-3fc8-4b97-99b0-df76b598d9df", + "rows": [ + [ + "0", + "d7965110-407f-e356-d41d-b3b9a2b7b7", + "(73)b7b7", + "oakleaf", + "4c", + "prox01xk", + "1.0", + "prox01xk(73)1", + "61.849998474121094", + "2024-10-02 10:31:01", + null, + "pass", + "not ready", + "", + "24", + "109", + "7", + "25", + "1", + "1", + "6" + ], + [ + "1", + "c8fea984-2e9a-8def-55fb-1a9d7d9ba8", + "(73)9ba8", + "oakleaf", + "4c", + "prox01xk", + "2.0", + "prox01xk(73)2", + "63.209999084472656", + "2024-10-02 10:31:31", + null, + "pass", + "ready", + "", + "24", + "109", + "7", + "25", + "1", + "1", + "6" + ], + [ + "2", + "df304d5d-3a85-4881-7142-6d4e5f957d", + "(73)957d", + "oakleaf", + "4c", + "prox01xk", + "3.0", + "prox01xk(73)3", + "63.27000045776367", + "2024-10-02 10:32:01", + null, + "pass", + "imported", + "", + "24", + "109", + "7", + "25", + "1", + "1", + "6" + ], + [ + "3", + "01c6c5be-cea6-54af-3924-b0bad69335", + "(73)9335", + "oakleaf", + "4c", + "prox01xk", + "1.0", + "prox01xk(73)1", + "0.6899999976158142", + "2024-10-03 10:31:01", + null, + "pass", + "import failed", + "", + "24", + "109", + "7", + "23", + "1", + "1", + "6" + ], + [ + "4", + "126745c7-dd41-2f6d-0dc5-28dbca415f", + "(73)415f", + "oakleaf", + "4c", + "prox01xk", + "2.0", + "prox01xk(73)2", + "0.8899999856948853", + "2024-10-03 10:31:31", + null, + "pass", + "", + "", + "24", + "109", + "7", + "23", + "1", + "1", + "6" + ] + ], + "shape": { + "columns": 20, + "rows": 5 + } + }, + "text/html": [ + "
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cmp_uuid_033record_idstorage_condexper_abbrevrepl_norepl_idvaluecreated_atupdated_atqc_result...equipmentraw_data_urlupload_statusresource_idprepared_sample_idpreparation_method_idparameter_idunit_idanalyst_email_idanalysis_type_id
03ee2993d-86e3-1f16-c7ea-f8d555e114(85)e114rt vacuum sealedcmp04xk1cmp04xk(85)114.162025-01-23 09:00:01NaTpass...ready2492812213
146878ef9-1226-22a0-d5d8-cf65e241cb(85)41cbrt vacuum sealedcmp04xk2cmp04xk(85)214.182025-01-23 09:00:16NaTpass...ready2492812213
276a7a2f4-c4e4-e60f-1187-dec6e02246(85)2246rt vacuum sealedcmp04xk3cmp04xk(85)314.122025-01-23 09:00:31NaTpass...ready2492812213
37a136832-286b-07cb-62de-acf52f9311(85)9311rt vacuum sealedcmp04xk1cmp04xk(85)115.742025-01-23 09:00:46NaTpass...ready2492814213
4b709ecee-f9a6-a55d-a59e-93b7b863d7(85)63d7rt vacuum sealedcmp04xk2cmp04xk(85)215.752025-01-23 09:01:01NaTpass...ready2492814213
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5 rows × 21 columns

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" + ], + "text/plain": [ + " cmp_uuid_033 record_id storage_cond \\\n", + "0 3ee2993d-86e3-1f16-c7ea-f8d555e114 (85)e114 rt vacuum sealed \n", + "1 46878ef9-1226-22a0-d5d8-cf65e241cb (85)41cb rt vacuum sealed \n", + "2 76a7a2f4-c4e4-e60f-1187-dec6e02246 (85)2246 rt vacuum sealed \n", + "3 7a136832-286b-07cb-62de-acf52f9311 (85)9311 rt vacuum sealed \n", + "4 b709ecee-f9a6-a55d-a59e-93b7b863d7 (85)63d7 rt vacuum sealed \n", + "\n", + " exper_abbrev repl_no repl_id value created_at updated_at \\\n", + "0 cmp04xk 1 cmp04xk(85)1 14.16 2025-01-23 09:00:01 NaT \n", + "1 cmp04xk 2 cmp04xk(85)2 14.18 2025-01-23 09:00:16 NaT \n", + "2 cmp04xk 3 cmp04xk(85)3 14.12 2025-01-23 09:00:31 NaT \n", + "3 cmp04xk 1 cmp04xk(85)1 15.74 2025-01-23 09:00:46 NaT \n", + "4 cmp04xk 2 cmp04xk(85)2 15.75 2025-01-23 09:01:01 NaT \n", + "\n", + " qc_result ... equipment raw_data_url upload_status resource_id \\\n", + "0 pass ... ready 24 \n", + "1 pass ... ready 24 \n", + "2 pass ... ready 24 \n", + "3 pass ... ready 24 \n", + "4 pass ... ready 24 \n", + "\n", + " prepared_sample_id preparation_method_id parameter_id unit_id \\\n", + "0 92 8 12 2 \n", + "1 92 8 12 2 \n", + "2 92 8 12 2 \n", + "3 92 8 14 2 \n", + "4 92 8 14 2 \n", + "\n", + " analyst_email_id analysis_type_id \n", + "0 1 3 \n", + "1 1 3 \n", + "2 1 3 \n", + "3 1 3 \n", + "4 1 3 \n", + "\n", + "[5 rows x 21 columns]" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "# --- 1. Extraction ---\n", + "# In a real Prefect flow, each extraction would be a separate task.\n", + "logger.info('Starting data extraction...')\n", + "prox_df = proximate.extract(project_root=project_root)\n", + "ult_df = ultimate.extract(project_root=project_root)\n", + "cmp_df = cmpana.extract(project_root=project_root)\n", + "dataframes = [prox_df, ult_df, cmp_df]\n", + "logger.info('Data extraction complete.')\n", + "\n", + "# --- 2. Cleaning ---\n", + "# This list comprehension applies the cleaning function to each extracted dataframe.\n", + "logger.info('Starting data cleaning...')\n", + "clean_dataframes = [clean_the_gsheets(df) for df in dataframes if df is not None]\n", + "logger.info('Data cleaning complete.')\n", + "\n", + "# --- 3. Normalization ---\n", + "# This dictionary defines the columns to be normalized. \n", + "# The key is the column name in the DataFrame.\n", + "# The value is a tuple containing the corresponding SQLAlchemy model and the name of the attribute on the model to match against.\n", + "NORMALIZE_COLUMNS = {\n", + " 'resource': (Resource, 'name'),\n", + " 'prepared_sample': (PreparedSample, 'name'),\n", + " 'preparation_method': (PreparationMethod, 'name'),\n", + " 'parameter': (Parameter, 'name'),\n", + " 'unit': (Unit, 'name'),\n", + " 'analyst_email': (Contact, 'email'),\n", + " 'analysis_type': (AnalysisType, 'name'),\n", + " 'primary_ag_product': (PrimaryAgProduct, 'name')\n", + "}\n", + "\n", + "logger.info('Starting data normalization...')\n", + "normalized_dataframes = normalize_dataframes(clean_dataframes, NORMALIZE_COLUMNS)\n", + "logger.info('Data normalization complete.')\n", + "\n", + "# --- 4. Display Results ---\n", + "logger.info('Displaying results of normalization...')\n", + "for i, df in enumerate(normalized_dataframes):\n", + " print(f'--- Normalized DataFrame {i+1} ---')\n", + " display(df.head())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Deployment Plan\n", + "\n", + "The code in this notebook will be transitioned to the main ETL pipeline by following these steps:\n", + "\n", + "1. **Function Migration**: The `clean_the_gsheets` and `normalize_dataframes` functions will be moved to a new utility module, for example, `src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_utils.py`. Each function will be decorated with `@task` from Prefect to turn it into a reusable pipeline component.\n", + "2. **Flow Creation**: A new Prefect flow will be created in the `src/ca_biositing/pipeline/ca_biositing/pipeline/flows/` directory (e.g., `master_extraction_flow.py`). This flow will orchestrate the entire ETL process for a given data source.\n", + "3. **Task Integration**: The new flow will be composed of individual tasks. It will call the existing extraction tasks (`proximate.extract`, etc.), and then pass the results to the new cleaning and normalization tasks from `etl_utils.py`.\n", + "4. **Logging**: The `logging` module will be replaced with `get_run_logger()` from Prefect within the tasks to ensure logs are captured by the Prefect UI.\n", + "5. **Configuration**: The `NORMALIZE_COLUMNS` dictionary will be moved to a configuration file or defined within the relevant flow to make it easier to manage and modify without changing the code.\n", + "6. **Testing**: Unit tests will be written for the new utility functions in `etl_utils.py`. An integration test will be created for the new Prefect flow to ensure all the tasks work together correctly.\n", + "7. **Deployment**: Once the flow is complete and tested, it will be deployed to the Prefect server using the `pixi run deploy` command, making it available to be run on a schedule or manually via the UI." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Pixi Default Environment", + "language": "python", + "name": "pixi-default" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.13.11" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb index 9d27799e..bfb3c8c4 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gsheet_extraction_notebook.ipynb @@ -2,62 +2,130 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "import sys\n", + "import pandas as pd\n", + "import numpy as np\n", + "import janitor as jn\n", + "from IPython.display import display\n", + "\n", + "# --- Robustly find the project root ---\n", + "# The project root is the directory containing the 'pixi.toml' file.\n", + "path = os.getcwd()\n", + "project_root = None\n", + "while path != os.path.dirname(path): # Stop at the filesystem root\n", + " if 'pixi.toml' in os.listdir(path):\n", + " project_root = path\n", + " break\n", + " path = os.path.dirname(path)\n", + "\n", + "if not project_root:\n", + " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", + "\n", + "# --- Add project root to sys.path ---\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + " print(f\"Added project root '{project_root}' to sys.path\")\n", + "else:\n", + " print(f\"Project root '{project_root}' is already in sys.path\")\n", + "\n", + "# --- Import the module ---\n", + "try:\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate, ultimate, cmpana\n", + " print(\"Successfully imported all module.\")\n", + "except ImportError as e:\n", + " print(f\"Failed to import modules: {e}\")\n", + " print(f\"\\nFull sys.path: {sys.path}\")\n", + "\n", + "# --- Run the extraction ---\n", + "if 'proximate' in locals():\n", + " try:\n", + " # Pass the project_root to the extract function\n", + " df = proximate.extract(project_root=project_root)\n", + " if df is not None:\n", + " print(\"\\nSuccessfully extracted proximate data.\")\n", + " display(df.head())\n", + " else:\n", + " print(\"\\n Prox extraction returned no data. Check the logs above for errors.\")\n", + " except Exception as e:\n", + " print(f\"\\nAn error occurred during prox extraction: {e}\")\n", + "\n", + "if 'ultimate' in locals():\n", + " try:\n", + " df2 = ultimate.extract(project_root=project_root)\n", + " if df is not None:\n", + " print(\"\\nSuccessfully extracted Ultimate data.\")\n", + " display(df2.head())\n", + " else:\n", + " print(\"\\n Ultimate extraction returned no data. Check the logs above for errors.\")\n", + " except Exception as e:\n", + " print(f\"\\nAn error occurred during extraction: {e}\")\n", + "\n", + "if 'cmpana' in locals():\n", + " try:\n", + " df3 = cmpana.extract(project_root=project_root)\n", + " if df is not None:\n", + " print(\"\\nSuccessfully extracted CmpAna data.\")\n", + " display(df3.head())\n", + " else:\n", + " print(\"\\nCmpAna extraction returned no data. Check the logs above for errors.\")\n", + " except Exception as e:\n", + " print(f\"\\nAn error occurred during cmp ana extraction: {e}\")\n", + " finally:\n", + " print(\"\\nCmp Ana extraction process completed.\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### This function seeks to clean the incoming gsheet dataframes and coerce the types" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "def clean_the_gsheets(df):\n", + " # 1. Clean names and drop rows\n", + " df = df.clean_names().dropna(subset=['repl_no', 'value'])\n", + "\n", + " # 2. Coerce types (using errors='coerce' handles messy string data)\n", + " df['repl_no'] = pd.to_numeric(df['repl_no'], errors='coerce').astype('Int32') # Capital 'I' handles NaNs\n", + " df['value'] = pd.to_numeric(df['value'], errors='coerce').astype(np.float32)\n", + "\n", + " # 3. Dates\n", + " df['created_at'] = pd.to_datetime(df['created_at'], errors='coerce')\n", + " df['updated_at'] = pd.to_datetime(df['updated_at'], errors='coerce')\n", + "\n", + " # 4. Convert remaining objects to best possible types (like strings)\n", + " df = df.convert_dtypes()\n", + "\n", + " # 5. Convert all string data to lowercase\n", + " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "\n", + " # 6. Convert empty strings to NaN\n", + " df.replace(\"\", np.nan, inplace=True)\n", + "\n", + " return df # Return the FULL dataframe, not just .head()" + ] + }, + { + "cell_type": "code", + "execution_count": 11, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Added project root '/Users/pjsmitty301/ca-biositing' to sys.path\n", - "Successfully imported all module.\n" - ] - }, - { - "data": { - "text/html": [ - "
20:54:42.753 | INFO    | Task run 'extract' - Extracting raw data from '03.1-Proximate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n",
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\n", @@ -312,3436 +334,527 @@ " \n", " \n", " \n", - " Prox_UUID_031\n", - " Record_ID\n", - " Source_codename\n", - " Prepared_sample\n", - " Resource\n", - " Preparation_method\n", - " Storage_cond\n", - " Exper_abbrev\n", - " Repl_no\n", - " Repl_ID\n", - " Parameter\n", - " Value\n", - " Unit\n", - " Created_at\n", - " Updated_at\n", - " QC_result\n", - " Upload_status\n", - " Note\n", - " Analysis_type\n", - " Analyst_email\n", + " id\n", + " name\n", + " note\n", + " description\n", + " uri\n", " \n", " \n", " \n", " \n", " 0\n", - " D7965110-407F-E356-D41D-B3B9A2B7B7\n", - " (73)B7B7\n", - " Oakleaf\n", - " Oak-TmPm01A(73)\n", - " Tomato pomace\n", - " As Is\n", - " 4C\n", - " Prox01xk\n", " 1\n", - " Prox01xk(73)1\n", - " Moisture\n", - " 61.85\n", - " % total weight\n", - " 2024-10-02 10:31:01\n", - " \n", - " Pass\n", - " not ready\n", - " \n", - " Proximate analysis\n", - " xkang2@lbl.gov\n", + " Tomatoes for processing\n", + " None\n", + " None\n", + " None\n", " \n", " \n", " 1\n", - " C8FEA984-2E9A-8DEF-55FB-1A9D7D9BA8\n", - " (73)9BA8\n", - " Oakleaf\n", - " Oak-TmPm01A(73)\n", - " Tomato pomace\n", - " As Is\n", - " 4C\n", - " Prox01xk\n", " 2\n", - " Prox01xk(73)2\n", - " Moisture\n", - " 63.21\n", - " % total weight\n", - " 2024-10-02 10:31:31\n", - " \n", - " Pass\n", - " ready\n", - " \n", - " Proximate analysis\n", - " xkang2@lbl.gov\n", + " Grapes\n", + " None\n", + " None\n", + " None\n", " \n", " \n", " 2\n", - " DF304D5D-3A85-4881-7142-6D4E5F957D\n", - " (73)957D\n", - " Oakleaf\n", - " Oak-TmPm01A(73)\n", - " Tomato pomace\n", - " As Is\n", - " 4C\n", - " Prox01xk\n", " 3\n", - " Prox01xk(73)3\n", - " Moisture\n", - " 63.27\n", - " % total weight\n", - " 2024-10-02 10:32:01\n", - " \n", - " Pass\n", - " imported\n", - " \n", - " Proximate analysis\n", - " xkang2@lbl.gov\n", + " Almonds\n", + " None\n", + " None\n", + " None\n", " \n", " \n", " 3\n", - " 01C6C5BE-CEA6-54AF-3924-B0BAD69335\n", - " (73)9335\n", - " Oakleaf\n", - " Oak-TmPm01A(73)\n", - " Tomato pomace\n", - " As Is\n", - " 4C\n", - " Prox01xk\n", - " 1\n", - " Prox01xk(73)1\n", - " Ash\n", - " 0.69\n", - " % total weight\n", - " 2024-10-03 10:31:01\n", - " \n", - " Pass\n", - " import failed\n", - " \n", - " Proximate analysis\n", - " xkang2@lbl.gov\n", + " 4\n", + " Walnuts\n", + " None\n", + " None\n", + " None\n", " \n", " \n", " 4\n", - " 126745C7-DD41-2F6D-0DC5-28DBCA415F\n", - " (73)415F\n", - " Oakleaf\n", - " Oak-TmPm01A(73)\n", - " Tomato pomace\n", - " As Is\n", - " 4C\n", - " Prox01xk\n", - " 2\n", - " Prox01xk(73)2\n", - " Ash\n", - " 0.89\n", - " % total weight\n", - " 2024-10-03 10:31:31\n", - " \n", - " Pass\n", - " \n", - " \n", - " Proximate analysis\n", - " xkang2@lbl.gov\n", + " 5\n", + " Sweet potatoes\n", + " None\n", + " None\n", + " None\n", " \n", - " \n", - "\n", - "
" - ], - "text/plain": [ - " Prox_UUID_031 Record_ID Source_codename \\\n", - "0 D7965110-407F-E356-D41D-B3B9A2B7B7 (73)B7B7 Oakleaf \n", - "1 C8FEA984-2E9A-8DEF-55FB-1A9D7D9BA8 (73)9BA8 Oakleaf \n", - "2 DF304D5D-3A85-4881-7142-6D4E5F957D (73)957D Oakleaf \n", - "3 01C6C5BE-CEA6-54AF-3924-B0BAD69335 (73)9335 Oakleaf \n", - "4 126745C7-DD41-2F6D-0DC5-28DBCA415F (73)415F Oakleaf \n", - "\n", - " Prepared_sample Resource Preparation_method Storage_cond \\\n", - "0 Oak-TmPm01A(73) Tomato pomace As Is 4C \n", - "1 Oak-TmPm01A(73) Tomato pomace As Is 4C \n", - "2 Oak-TmPm01A(73) Tomato pomace As Is 4C \n", - "3 Oak-TmPm01A(73) Tomato pomace As Is 4C \n", - "4 Oak-TmPm01A(73) Tomato pomace As Is 4C \n", - "\n", - " Exper_abbrev Repl_no Repl_ID Parameter Value Unit \\\n", - "0 Prox01xk 1 Prox01xk(73)1 Moisture 61.85 % total weight \n", - "1 Prox01xk 2 Prox01xk(73)2 Moisture 63.21 % total weight \n", - "2 Prox01xk 3 Prox01xk(73)3 Moisture 63.27 % total weight \n", - "3 Prox01xk 1 Prox01xk(73)1 Ash 0.69 % total weight \n", - "4 Prox01xk 2 Prox01xk(73)2 Ash 0.89 % total weight \n", - "\n", - " Created_at Updated_at QC_result Upload_status Note \\\n", - "0 2024-10-02 10:31:01 Pass not ready \n", - "1 2024-10-02 10:31:31 Pass ready \n", - "2 2024-10-02 10:32:01 Pass imported \n", - "3 2024-10-03 10:31:01 Pass import failed \n", - "4 2024-10-03 10:31:31 Pass \n", - "\n", - " Analysis_type Analyst_email \n", - "0 Proximate analysis xkang2@lbl.gov \n", - "1 Proximate analysis xkang2@lbl.gov \n", - "2 Proximate analysis xkang2@lbl.gov \n", - "3 Proximate analysis xkang2@lbl.gov \n", - "4 Proximate analysis xkang2@lbl.gov " - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/html": [ - "
20:54:44.272 | INFO    | Task run 'extract' - Extracting raw data from '03.7-Ultimate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n",
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20:54:45.595 | INFO    | Task run 'extract' - Finished in state Completed()\n",
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"type": "string" - }, - { - "name": "Exper_abbrev", - "rawType": "object", - "type": "string" - }, - { - "name": "Repl_no", - "rawType": "object", - "type": "string" - }, - { - "name": "Repl_ID", - "rawType": "object", - "type": "string" - }, + " \n", + " 5\n", + " 6\n", + " Algae\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 6\n", + " 7\n", + " Olives - processing\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 7\n", + " 8\n", + " Corn - all\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 8\n", + " 9\n", + " Hay - alfalfa\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 9\n", + " 10\n", + " Silage - wheat\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 10\n", + " 11\n", + " Rice\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 11\n", + " 12\n", + " Peaches\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 12\n", + " 13\n", + " Potatoes\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 13\n", + " 14\n", + " Cucumbers and pickles\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 14\n", + " 15\n", + " Pistachios\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 15\n", + " 16\n", + " Cotton\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 16\n", + " 17\n", + " Olives - market\n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + " 17\n", + " 18\n", + " \n", + " None\n", + " None\n", + " None\n", + " \n", + " \n", + "\n", + "" + ], + "text/plain": [ + " id name note description uri\n", + "0 1 Tomatoes for processing None None None\n", + "1 2 Grapes None None None\n", + "2 3 Almonds None None None\n", + "3 4 Walnuts None None None\n", + "4 5 Sweet potatoes None None None\n", + "5 6 Algae None None None\n", + "6 7 Olives - processing None None None\n", + "7 8 Corn - all None None None\n", + "8 9 Hay - alfalfa None None None\n", + "9 10 Silage - wheat None None None\n", + "10 11 Rice None None None\n", + "11 12 Peaches None None None\n", + "12 13 Potatoes None None None\n", + "13 14 Cucumbers and pickles None None None\n", + "14 15 Pistachios None None None\n", + "15 16 Cotton None None None\n", + "16 17 Olives - market None None None\n", + "17 18 None None None" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from sqlmodel import Session, select, create_engine\n", + "import pandas as pd\n", + "import os\n", + "import sys\n", + "\n", + "#This module queries the db via the ORM\n", + "\n", + "# Database Connection\n", + "DATABASE_URL = \"postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db\"\n", + "engine = create_engine(DATABASE_URL)\n", + "print(f\"Connected to database.\")\n", + "\n", + "primary_ag_product = pd.read_sql(\"SELECT * FROM primary_ag_product;\", con=engine)\n", + "\n", + "#reorders columns so id and name are first\n", + "cols = ['id', 'name'] + [c for c in primary_ag_product.columns if c not in ['id', 'name']]\n", + "\n", + "primary_ag_product = primary_ag_product[[*cols]]\n", + "\n", + "primary_ag_product\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "#This is a get_or_create type module for data normalization.\n", + "\n", + "# Extract a df from a gsheet\n", + "df = cmpana.extract(project_root=project_root)\n", + "\n", + "# Cleans the df names and coerces data types\n", + "df = clean_the_gsheets(df)\n", + "\n", + "# Replace empty strings with NaN\n", + "df.replace(r'^\\s*$', np.nan, regex=True, inplace=True)\n", + "\n", + "\n", + "# These are columns that need to be normalized, AKA replaced with IDs.\n", + "# This is a mapping that has first, what it is called in pandas \"resource\"\n", + "# then, the SQLAlchemy model \"Resource\", and then what it is called in the\n", + "# database \"name\"\n", + "\n", + "\n", + "NORMALIZE_COLUMNS = {\n", + " \"resource\": (Resource, \"name\"),\n", + " \"prepared_sample\": (PreparedSample, \"name\"),\n", + " \"preparation_method\": (PreparationMethod, \"name\"),\n", + " \"parameter\": (Parameter, \"name\"),\n", + " \"unit\": (Unit, \"name\"),\n", + " \"analyst_email\": (Contact, \"email\"),\n", + " \"analysis_type\": (AnalysisType, \"name\"),\n", + " \"primary_ag_product\": (PrimaryAgProduct, \"name\")\n", + "}\n", + "\n", + "df_normalized = df.copy()\n", + "\n", + "with Session(engine) as db:\n", + " for df_col, (model, model_name_attr) in NORMALIZE_COLUMNS.items():\n", + " if df_col not in df_normalized.columns:\n", + " continue\n", + "\n", + " df_normalized = replace_name_with_id_df(\n", + " db=db,\n", + " df=df_normalized,\n", + " ref_model=model,\n", + " df_name_column=df_col,\n", + " model_name_attr=model_name_attr,\n", + " id_column_name=\"id\",\n", + " final_column_name=f\"{df_col}_id\",\n", + " )\n", + "\n", + " db.commit()\n", + "\n", + "df_normalized.head()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_9286/3648773749.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_9286/3648773749.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_9286/3648773749.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n" + ] + }, + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "index", + "rawType": "int64", + "type": "integer" + }, + { + "name": "cmp_uuid_033", + "rawType": "object", + "type": "string" + }, + { + "name": "record_id", + "rawType": "object", + "type": "string" + }, + { + "name": "prepared_sample", + "rawType": "object", + "type": "string" + }, + { + "name": "resource", + "rawType": "object", + "type": "string" + }, { - "name": "Parameter", + "name": "preparation_method", + "rawType": "object", + "type": "string" + }, + { + "name": "storage_cond", "rawType": "object", "type": "string" }, { - "name": "Value", + "name": "exper_abbrev", "rawType": "object", "type": "string" }, { - "name": "Unit", + "name": "repl_no", + "rawType": "int64", + "type": "integer" + }, + { + "name": "repl_id", "rawType": "object", "type": "string" }, { - "name": "Created_at", + "name": "parameter", "rawType": "object", "type": "string" }, { - "name": "Updated_at", + "name": "value", + "rawType": "float64", + "type": "float" + }, + { + "name": "unit", "rawType": "object", "type": "string" }, { - "name": "QC_result", + "name": "created_at", + "rawType": "datetime64[ns]", + "type": "datetime" + }, + { + "name": "updated_at", + "rawType": "datetime64[ns]", + "type": "datetime" + }, + { + "name": "qc_result", "rawType": "object", "type": "string" }, { - "name": "Note", + "name": "note", "rawType": "object", "type": "string" }, { - "name": "Analysis_type", + "name": "analysis_type", "rawType": "object", "type": "string" }, { - "name": "Equipment", + "name": "equipment", "rawType": "object", "type": "string" }, { - "name": "Raw_data_URL", + "name": "raw_data_url", "rawType": "object", "type": "string" }, { - "name": "Analyst_email", + "name": "analyst_email", "rawType": "object", "type": "string" }, { - "name": "Upload_status", + "name": "upload_status", "rawType": "object", "type": "string" } ], - "ref": "61714e59-0541-4b74-9d38-a37794cbd34d", - "rows": [ - [ - "0", - "421617A5-E50E-9642-2974-B3275FE822", - ")U22E822", - "Hum-AlmHu023KM2(15)U22", - "Hum-AlmHu023KM2(15)", - "Almond Hulls", - "Knife Mill (2mm)", - "RT vacuum sealed", - "Ult26kh", - "1", - "Ult26kh(15)1", - "DM", - "8.86E+01", - "pc", - "", - "", - "Pass", - "1", - "Ultimate analysis", - "", - "", - "", - "" - ], - [ - "1", - "7E7919C2-5DB4-6BEF-75E2-7E51321200", - ")U001200", - "Hum-AlmHu023KM2(15)U00", - "Hum-AlmHu023KM2(15)", - "Almond Hulls", - "Knife Mill (2mm)", - "RT vacuum sealed", - "Ult26kh", - "1", - "Ult26kh(15)1", - "DM", - "", - "pc", - "", - "", - "Fail", - " 1 dup", - "Ultimate analysis", - "", - "", - "", - "" - ], - [ - "2", - "3AA85881-1185-642F-C44B-41AD2275D2", - ")UD275D2", - "Hum-AlmSh022KM2(13)UD2", - "Hum-AlmSh022KM2(13)", - "Almond Shells", - "Knife Mill (2mm)", - "RT vacuum sealed", - "Ult26kh", - "1", - "Ult26kh(13)1", - "DM", - "8.13E+01", - "pc", - "", - "", - "Pass", - "2", - "Ultimate analysis", - "", - "", - "", - "" - ], - [ - "3", - "FA418804-6C4F-4C90-D78F-84D7DF54D3", - ")UD354D3", - "Ene-WaSh017OKM2(82)UD3", - "Ene-WaSh017OKM2(82)", - "Walnut Shells", - "Oven Dry + Knife Mill (2mm)", - "RT vacuum sealed", - "Ult26kh", - "1", - "Ult26kh(82)1", - "DM", - "9.22E+01", - "pc", - "", - "", - "Pass", - "3", - "Ultimate analysis", - "", - "", - "", - "" - ], - [ - "4", - "6FDACBFC-7E0B-473B-444F-85B7650267", - ")U670267", - "Ebo-GpPm010OKM2(1B)U67", - "Ebo-GpPm010OKM2(1B)", - "Grape pomace", - "Oven Dry + Knife Mill (2mm)", - "RT vacuum sealed", - "Ult26kh", - "1", - "Ult26kh(1B)1", - "DM", - "9.38E+01", - "pc", - "", - "", - "Pass", - "4", - "Ultimate analysis", - "", - "", - "", - "" - ] - ], - "shape": { - "columns": 22, - "rows": 5 - } - }, - "text/html": [ - "
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Ult_UUID_037Record_IDUlt_sample_namePrepared_sampleResourcePreparation_methodStorage_condExper_abbrevRepl_noRepl_ID...UnitCreated_atUpdated_atQC_resultNoteAnalysis_typeEquipmentRaw_data_URLAnalyst_emailUpload_status
0421617A5-E50E-9642-2974-B3275FE822)U22E822Hum-AlmHu023KM2(15)U22Hum-AlmHu023KM2(15)Almond HullsKnife Mill (2mm)RT vacuum sealedUlt26kh1Ult26kh(15)1...pcPass1Ultimate analysis
17E7919C2-5DB4-6BEF-75E2-7E51321200)U001200Hum-AlmHu023KM2(15)U00Hum-AlmHu023KM2(15)Almond HullsKnife Mill (2mm)RT vacuum sealedUlt26kh1Ult26kh(15)1...pcFail1 dupUltimate analysis
23AA85881-1185-642F-C44B-41AD2275D2)UD275D2Hum-AlmSh022KM2(13)UD2Hum-AlmSh022KM2(13)Almond ShellsKnife Mill (2mm)RT vacuum sealedUlt26kh1Ult26kh(13)1...pcPass2Ultimate analysis
3FA418804-6C4F-4C90-D78F-84D7DF54D3)UD354D3Ene-WaSh017OKM2(82)UD3Ene-WaSh017OKM2(82)Walnut ShellsOven Dry + Knife Mill (2mm)RT vacuum sealedUlt26kh1Ult26kh(82)1...pcPass3Ultimate analysis
46FDACBFC-7E0B-473B-444F-85B7650267)U670267Ebo-GpPm010OKM2(1B)U67Ebo-GpPm010OKM2(1B)Grape pomaceOven Dry + Knife Mill (2mm)RT vacuum sealedUlt26kh1Ult26kh(1B)1...pcPass4Ultimate analysis
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20:54:45.631 | INFO    | Task run 'extract' - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n",
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20:54:47.211 | INFO    | Task run 'extract' - Successfully extracted raw data.\n",
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20:54:47.214 | INFO    | Task run 'extract' - Finished in state Completed()\n",
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Cmp_UUID_033Record_IDPrepared_sampleResourcePreparation_methodStorage_condExper_abbrevRepl_noRepl_IDParameter...UnitCreated_atUpdated_atQC_resultNoteAnalysis_typeEquipmentRaw_data_URLAnalyst_emailUpload_status
03EE2993D-86E3-1F16-C7EA-F8D555E114(85)E114Oak-TmPm01O(85)Tomato pomaceOven dryRT vacuum sealedCmp04xk1Cmp04xk(85)1Glucan...% dry weight1/23/2025 9:00:01passChemical compositionxkang2@lbl.govready
146878EF9-1226-22A0-D5D8-CF65E241CB(85)41CBOak-TmPm01O(85)Tomato pomaceOven dryRT vacuum sealedCmp04xk2Cmp04xk(85)2Glucan...% dry weight1/23/2025 9:00:16passChemical compositionxkang2@lbl.govready
276A7A2F4-C4E4-E60F-1187-DEC6E02246(85)2246Oak-TmPm01O(85)Tomato pomaceOven dryRT vacuum sealedCmp04xk3Cmp04xk(85)3Glucan...% dry weight1/23/2025 9:00:31passChemical compositionxkang2@lbl.govready
37A136832-286B-07CB-62DE-ACF52F9311(85)9311Oak-TmPm01O(85)Tomato pomaceOven dryRT vacuum sealedCmp04xk1Cmp04xk(85)1Glucose...% dry weight1/23/2025 9:00:46passChemical compositionxkang2@lbl.govready
4B709ECEE-F9A6-A55D-A59E-93B7B863D7(85)63D7Oak-TmPm01O(85)Tomato pomaceOven dryRT vacuum sealedCmp04xk2Cmp04xk(85)2Glucose...% dry weight1/23/2025 9:01:01passChemical compositionxkang2@lbl.govready
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Unit Created_at Updated_at \\\n", - "0 Cmp04xk(85)1 Glucan ... % dry weight 1/23/2025 9:00:01 \n", - "1 Cmp04xk(85)2 Glucan ... % dry weight 1/23/2025 9:00:16 \n", - "2 Cmp04xk(85)3 Glucan ... % dry weight 1/23/2025 9:00:31 \n", - "3 Cmp04xk(85)1 Glucose ... % dry weight 1/23/2025 9:00:46 \n", - "4 Cmp04xk(85)2 Glucose ... % dry weight 1/23/2025 9:01:01 \n", - "\n", - " QC_result Note Analysis_type Equipment Raw_data_URL Analyst_email \\\n", - "0 pass Chemical composition xkang2@lbl.gov \n", - "1 pass Chemical composition xkang2@lbl.gov \n", - "2 pass Chemical composition xkang2@lbl.gov \n", - "3 pass Chemical composition xkang2@lbl.gov \n", - "4 pass Chemical composition xkang2@lbl.gov \n", - "\n", - " Upload_status \n", - "0 ready \n", - "1 ready \n", - "2 ready \n", - "3 ready \n", - "4 ready \n", - "\n", - "[5 rows x 21 columns]" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n", - "Cmp Ana extraction process completed.\n" - ] - } - ], - "source": [ - "import os\n", - "import sys\n", - "import pandas as pd\n", - "import numpy as np\n", - "import janitor as jn\n", - "from IPython.display import display\n", - "\n", - "# --- Robustly find the project root ---\n", - "# The project root is the directory containing the 'pixi.toml' file.\n", - "path = os.getcwd()\n", - "project_root = None\n", - "while path != os.path.dirname(path): # Stop at the filesystem root\n", - " if 'pixi.toml' in os.listdir(path):\n", - " project_root = path\n", - " break\n", - " path = os.path.dirname(path)\n", - "\n", - "if not project_root:\n", - " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", - "\n", - "# --- Add project root to sys.path ---\n", - "if project_root not in sys.path:\n", - " sys.path.insert(0, project_root)\n", - " print(f\"Added project root '{project_root}' to sys.path\")\n", - "else:\n", - " print(f\"Project root '{project_root}' is already in sys.path\")\n", - "\n", - "# --- Import the module ---\n", - "try:\n", - " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate, ultimate, cmpana\n", - " print(\"Successfully imported all module.\")\n", - "except ImportError as e:\n", - " print(f\"Failed to import modules: {e}\")\n", - " print(f\"\\nFull sys.path: {sys.path}\")\n", - "\n", - "# --- Run the extraction ---\n", - "if 'proximate' in locals():\n", - " try:\n", - " # Pass the project_root to the extract function\n", - " df = proximate.extract(project_root=project_root)\n", - " if df is not None:\n", - " print(\"\\nSuccessfully extracted proximate data.\")\n", - " display(df.head())\n", - " else:\n", - " print(\"\\n Prox extraction returned no data. Check the logs above for errors.\")\n", - " except Exception as e:\n", - " print(f\"\\nAn error occurred during prox extraction: {e}\")\n", - "\n", - "if 'ultimate' in locals():\n", - " try:\n", - " df2 = ultimate.extract(project_root=project_root)\n", - " if df is not None:\n", - " print(\"\\nSuccessfully extracted Ultimate data.\")\n", - " display(df2.head())\n", - " else:\n", - " print(\"\\n Ultimate extraction returned no data. Check the logs above for errors.\")\n", - " except Exception as e:\n", - " print(f\"\\nAn error occurred during extraction: {e}\")\n", - "\n", - "if 'cmpana' in locals():\n", - " try:\n", - " df3 = cmpana.extract(project_root=project_root)\n", - " if df is not None:\n", - " print(\"\\nSuccessfully extracted CmpAna data.\")\n", - " display(df3.head())\n", - " else:\n", - " print(\"\\nCmpAna extraction returned no data. Check the logs above for errors.\")\n", - " except Exception as e:\n", - " print(f\"\\nAn error occurred during cmp ana extraction: {e}\")\n", - " finally:\n", - " print(\"\\nCmp Ana extraction process completed.\")" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "#### This function seeks to clean the incoming gsheet dataframes and coerce the types" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [], - "source": [ - "def clean_the_gsheets(df):\n", - " # 1. Clean names and drop rows\n", - " df = df.clean_names().dropna(subset=['repl_no', 'value'])\n", - "\n", - " # 2. Coerce types (using errors='coerce' handles messy string data)\n", - " df['repl_no'] = pd.to_numeric(df['repl_no'], errors='coerce').astype('Int32') # Capital 'I' handles NaNs\n", - " df['value'] = pd.to_numeric(df['value'], errors='coerce').astype(np.float32)\n", - "\n", - " # 3. Dates\n", - " df['created_at'] = pd.to_datetime(df['created_at'], errors='coerce')\n", - " df['updated_at'] = pd.to_datetime(df['updated_at'], errors='coerce')\n", - "\n", - " # 4. Convert remaining objects to best possible types (like strings)\n", - " df = df.convert_dtypes()\n", - " \n", - " return df # Return the FULL dataframe, not just .head()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "dataframes = [df, df2, df3]\n", - "\n", - "clean_dataframes = [clean_the_gsheets(df) for df in dataframes]\n", - "\n", - "clean_dataframes[2].head()\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "summary_stats = clean_dataframes[0].\\\n", - " groupby(['resource', 'parameter'])['value'].\\\n", - " agg(['mean', 'median', 'min', 'max', 'std', 'count'])\n", - "\n", - "summary_stats" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "clean_dataframes[0][['resource', 'parameter', 'value', 'unit']].\\\n", - " groupby(['resource', 'parameter', 'unit'], as_index=False).\\\n", - " agg({'value': 'mean'}).\\\n", - " query('value > 30').\\\n", - " sort_values(by='value', ascending=False).\\\n", - " round({'value': 1})\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "list_of_param = (\"Moisture\", \"Total solids\", \"Ash\")\n", - "\n", - "def is_it_volatile_solids(df):\n", - " df['check'] = \"VS\"\n", - "\n", - " df.loc[df['parameter'].isin(list_of_param), 'check'] = \"In list\"\n", - " return df\n", - "\n", - "is_it_volatile_solids(df)\n", - "\n", - "df[['check', 'parameter']]\n", - "\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "\n", - "#This defines a function to calculate the square root of the 'value' column in a DataFrame\n", - "def sqrtvalue(df):\n", - " df = df.assign(sqrtvalue = df['value'] ** 0.5)\n", - " return df\n", - "\n", - "#List comprehension to apply sqrtvalue to each DataFrame\n", - "clean_rooted_df = [sqrtvalue(df) for df in clean_dataframes]\n", - "\n", - "# Display the head of the third DataFrame\n", - "clean_rooted_df[2].head()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "cmpana_raw = cmpana.extract(project_root=project_root)\n", - "\n", - "cmpana_raw.head()" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Connected to database.\n" - ] - }, - { - "data": { - "application/vnd.microsoft.datawrangler.viewer.v0+json": { - "columns": [ - { - "name": "index", - "rawType": "int64", - "type": "integer" - }, - { - "name": "id", - "rawType": "int64", - "type": "integer" - }, - { - "name": "name", - "rawType": "object", - "type": "string" - }, - { - "name": "note", - "rawType": "object", - "type": "unknown" - }, - { - "name": "description", - "rawType": "object", - "type": "unknown" - }, - { - "name": "uri", - "rawType": "object", - "type": "unknown" - } - ], - "ref": "0dabe9e2-728a-486d-9dd1-c1edd094e9c2", - "rows": [ - [ - "0", - "1", - "Tomatoes for processing", - null, - null, - null - ], - [ - "1", - "2", - "Grapes", - null, - null, - null - ], - [ - "2", - "3", - "Almonds", - null, - null, - null - ], - [ - "3", - "4", - "Walnuts", - null, - null, - null - ], - [ - "4", - "5", - "Sweet potatoes", - null, - null, - null - ], - [ - "5", - "6", - "Algae", - null, - null, - null - ], - [ - "6", - "7", - "Olives - processing", - null, - null, - null - ], - [ - "7", - "8", - "Corn - all", - null, - null, - null - ], - [ - "8", - "9", - "Hay - alfalfa", - null, - null, - null - ], - [ - "9", - "10", - "Silage - wheat", - null, - null, - null - ], - [ - "10", - "11", - "Rice", - null, - null, - null - ], - [ - "11", - "12", - "Peaches", - null, - null, - null - ], - [ - "12", - "13", - "Potatoes", - null, - null, - null - ], - [ - "13", - "14", - "Cucumbers and pickles", - null, - null, - null - ], - [ - "14", - "15", - "Pistachios", - null, - null, - null - ], - [ - "15", - "16", - "Cotton", - null, - null, - null - ], - [ - "16", - "17", - "Olives - market", - null, - null, - null - ], - [ - "17", - "18", - "", - null, - null, - null - ] - ], - "shape": { - "columns": 5, - "rows": 18 - } - }, - "text/html": [ - "
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idnamenotedescriptionuri
01Tomatoes for processingNoneNoneNone
12GrapesNoneNoneNone
23AlmondsNoneNoneNone
34WalnutsNoneNoneNone
45Sweet potatoesNoneNoneNone
56AlgaeNoneNoneNone
67Olives - processingNoneNoneNone
78Corn - allNoneNoneNone
89Hay - alfalfaNoneNoneNone
910Silage - wheatNoneNoneNone
1011RiceNoneNoneNone
1112PeachesNoneNoneNone
1213PotatoesNoneNoneNone
1314Cucumbers and picklesNoneNoneNone
1415PistachiosNoneNoneNone
1516CottonNoneNoneNone
1617Olives - marketNoneNoneNone
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" - ], - "text/plain": [ - " id name note description uri\n", - "0 1 Tomatoes for processing None None None\n", - "1 2 Grapes None None None\n", - "2 3 Almonds None None None\n", - "3 4 Walnuts None None None\n", - "4 5 Sweet potatoes None None None\n", - "5 6 Algae None None None\n", - "6 7 Olives - processing None None None\n", - "7 8 Corn - all None None None\n", - "8 9 Hay - alfalfa None None None\n", - "9 10 Silage - wheat None None None\n", - "10 11 Rice None None None\n", - "11 12 Peaches None None None\n", - "12 13 Potatoes None None None\n", - "13 14 Cucumbers and pickles None None None\n", - "14 15 Pistachios None None None\n", - "15 16 Cotton None None None\n", - "16 17 Olives - market None None None\n", - "17 18 None None None" - ] - }, - "execution_count": 3, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "from sqlmodel import Session, select, create_engine\n", - "import pandas as pd\n", - "import os\n", - "import sys\n", - "\n", - "\n", - "# Database Connection\n", - "DATABASE_URL = \"postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db\"\n", - "engine = create_engine(DATABASE_URL)\n", - "print(f\"Connected to database.\")\n", - "\n", - "primary_ag_product = pd.read_sql(\"SELECT * FROM primary_ag_product;\", con=engine)\n", - "\n", - "#reorders columns so id and name are first\n", - "cols = ['id', 'name'] + [c for c in primary_ag_product.columns if c not in ['id', 'name']]\n", - "\n", - "primary_ag_product = primary_ag_product[[*cols]]\n", - "\n", - "primary_ag_product\n" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.microsoft.datawrangler.viewer.v0+json": { - "columns": [ - { - "name": "index", - "rawType": "int64", - "type": "integer" - }, - { - "name": "description", - "rawType": "object", - "type": "unknown" - }, - { - "name": "id", - "rawType": "int64", - "type": "integer" - }, - { - "name": "name", - "rawType": "object", - "type": "string" - }, - { - "name": "note", - "rawType": "object", - "type": "unknown" - }, - { - "name": "uri", - "rawType": "object", - "type": "unknown" - } - ], - "ref": "52090a35-9379-4dc9-b918-583b23513ddd", - "rows": [ - [ - "0", - null, - "1", - "Tomatoes for processing", - null, - null - ], - [ - "1", - null, - "2", - "Grapes", - null, - null - ], - [ - "2", - null, - "3", - "Almonds", - null, - null - ], - [ - "3", - null, - "4", - "Walnuts", - null, - null - ], - [ - "4", - null, - "5", - "Sweet potatoes", - null, - null - ] - ], - "shape": { - "columns": 5, - "rows": 5 - } - }, - "text/html": [ - "
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" - ], - "text/plain": [ - " description id name note uri\n", - "0 None 1 Tomatoes for processing None None\n", - "1 None 2 Grapes None None\n", - "2 None 3 Almonds None None\n", - "3 None 4 Walnuts None None\n", - "4 None 5 Sweet potatoes None None" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "from sqlalchemy.orm import Session\n", - "from sqlalchemy import select\n", - "import pandas as pd\n", - "import os\n", - "import sys\n", - "\n", - "# --- project root discovery (unchanged) ---\n", - "path = os.getcwd()\n", - "project_root = None\n", - "while path != os.path.dirname(path):\n", - " if 'pixi.toml' in os.listdir(path):\n", - " project_root = path\n", - " break\n", - " path = os.path.dirname(path)\n", - "\n", - "if not project_root:\n", - " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", - "\n", - "if project_root not in sys.path:\n", - " sys.path.insert(0, project_root)\n", - "\n", - "# --- imports ---\n", - "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", - "from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import PrimaryAgProduct\n", - "\n", - "# --- query + dataframe ---\n", - "with Session(engine) as db:\n", - " stmt = select(*PrimaryAgProduct.__table__.columns)\n", - " rows = db.execute(stmt).mappings().all()\n", - "\n", - "df = pd.DataFrame(rows)\n", - "\n", - "df.head()\n" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
21:07:54.222 | INFO    | Task run 'extract' - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n",
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\n" - ], - "text/plain": [ - "21:07:54.222 | \u001b[36mINFO\u001b[0m | Task run 'extract' - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/html": [ - "
21:07:59.598 | INFO    | Task run 'extract' - Successfully extracted raw data.\n",
-       "
\n" - ], - "text/plain": [ - "21:07:59.598 | \u001b[36mINFO\u001b[0m | Task run 'extract' - Successfully extracted raw data.\n" - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/html": [ - "
21:07:59.601 | INFO    | Task run 'extract' - Finished in state Completed()\n",
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\n" - ], - "text/plain": [ - "21:07:59.601 | \u001b[36mINFO\u001b[0m | Task run 'extract' - Finished in state \u001b[32mCompleted\u001b[0m()\n" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "from sqlalchemy.orm import Session\n", - "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", - "from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", - "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import (\n", - " replace_name_with_id_df,\n", - ") \n", - "\n", - "#This extractst the raw proximate data\n", - "df = cmpana.extract(project_root=project_root)\n", - "\n", - "#this cleans the names to lowercase and parses data into a standard format. Also renames the column to match with what will be in the database\n", - "test_df = clean_the_gsheets(df).rename(columns={'parameter': 'name'})\n", - "\n", - "#this replaces the names with IDs\n", - "with Session(engine) as db:\n", - " parameter_ids = replace_name_with_id_df(\n", - " db=db,\n", - " df=test_df,\n", - " ref_model=Parameter,\n", - " name_column_name=\"name\", # column in df + table\n", - " id_column_name=\"id\", # PK column in table\n", - " final_column_name=\"parameter_id\"\n", - " )\n", - "\n", - "##I EVENTUALLY WANT SOME LOGS ABOUT HOW MANY WERE ADDED, HOW MANY RETRIEVED, ETC. MAYBE PUT THAT IN THE \n", - "#resource_id_mapping = df_with_ids.rename(columns={\"id\": \"resource_id\"})\n", - "\n", - "#resource_id_mapping\n" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.microsoft.datawrangler.viewer.v0+json": { - "columns": [ - { - "name": "index", - "rawType": "int64", - "type": "integer" - }, - { - "name": "cmp_uuid_033", - "rawType": "string", - "type": "string" - }, - { - "name": "record_id", - "rawType": "string", - "type": "string" - }, - { - "name": "prepared_sample", - "rawType": "string", - "type": "string" - }, - { - "name": "resource", - "rawType": "string", - "type": "string" - }, - { - "name": "preparation_method", - "rawType": "string", - "type": "string" - }, - { - "name": "storage_cond", - "rawType": "string", - "type": "string" - }, - { - "name": "exper_abbrev", - "rawType": "string", - "type": "string" - }, - { - "name": "repl_no", - "rawType": "Int32", - "type": "integer" - 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descriptionidnamenoteuri
..................................................................0None1Tomatoes for processingNoneNone
38579799601-0E25-3832-3BBF-F4BD9EE973(A0)E973Hum-AlmBr024KM2(A0)Almond BranchesKnife Mill (2mm)RT vacuum sealedCmp17xk1None2Cmp17xk(A0)217.290001...2025-03-04 09:55:00NaTpassChemical compositionxkang2@lbl.govnot ready5
386A4E3393F-72C3-A0ED-C041-105A33031A(A0)031AHum-AlmBr024KM2(A0)Almond BranchesKnife Mill (2mm)RT vacuum sealedCmp17xk3Cmp17xk(A0)317.5...2025-03-04 09:55:15NaTpassChemical compositionxkang2@lbl.govnot ready5GrapesNoneNone
3873D5A85F8-31A2-0CC2-74E6-05D8197C3A(A0)7C3AHum-AlmBr024KM2(A0)Almond BranchesKnife Mill (2mm)RT vacuum sealedCmp17xk1Cmp17xk(A0)135.970001...2025-03-04 09:55:30NaTpassChemical compositionxkang2@lbl.govnot ready2None3AlmondsNoneNone
388C7AE456E-4DCD-AE34-A0D0-BD39D04E42(A0)4E42Hum-AlmBr024KM2(A0)Almond BranchesKnife Mill (2mm)RT vacuum sealedCmp17xk2Cmp17xk(A0)235.279999...2025-03-04 09:55:45NaTpassChemical compositionxkang2@lbl.govnot ready33None4WalnutsNoneNone
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" ], "text/plain": [ - " cmp_uuid_033 record_id prepared_sample \\\n", - "0 3EE2993D-86E3-1F16-C7EA-F8D555E114 (85)E114 Oak-TmPm01O(85) \n", - "1 46878EF9-1226-22A0-D5D8-CF65E241CB (85)41CB Oak-TmPm01O(85) \n", - "2 76A7A2F4-C4E4-E60F-1187-DEC6E02246 (85)2246 Oak-TmPm01O(85) \n", - "3 7A136832-286B-07CB-62DE-ACF52F9311 (85)9311 Oak-TmPm01O(85) \n", - "4 B709ECEE-F9A6-A55D-A59E-93B7B863D7 (85)63D7 Oak-TmPm01O(85) \n", - ".. ... ... ... \n", - "385 79799601-0E25-3832-3BBF-F4BD9EE973 (A0)E973 Hum-AlmBr024KM2(A0) \n", - "386 A4E3393F-72C3-A0ED-C041-105A33031A (A0)031A Hum-AlmBr024KM2(A0) \n", - "387 3D5A85F8-31A2-0CC2-74E6-05D8197C3A (A0)7C3A Hum-AlmBr024KM2(A0) \n", - "388 C7AE456E-4DCD-AE34-A0D0-BD39D04E42 (A0)4E42 Hum-AlmBr024KM2(A0) \n", - "389 A5E617A2-9831-3E9F-7072-6C5FB8129B (A0)129B Hum-AlmBr024KM2(A0) \n", - "\n", - " resource preparation_method storage_cond exper_abbrev \\\n", - "0 Tomato pomace Oven dry RT vacuum sealed Cmp04xk \n", - "1 Tomato pomace Oven dry RT vacuum sealed Cmp04xk \n", - "2 Tomato pomace Oven dry RT vacuum sealed Cmp04xk \n", - "3 Tomato pomace Oven dry RT vacuum sealed Cmp04xk \n", - "4 Tomato pomace Oven dry RT vacuum sealed Cmp04xk \n", - ".. ... ... ... ... \n", - "385 Almond Branches Knife Mill (2mm) RT vacuum sealed Cmp17xk \n", - "386 Almond Branches Knife Mill (2mm) RT vacuum sealed Cmp17xk \n", - "387 Almond Branches Knife Mill (2mm) RT vacuum sealed Cmp17xk \n", - "388 Almond Branches Knife Mill (2mm) RT vacuum sealed Cmp17xk \n", - "389 Almond Branches Knife Mill (2mm) RT vacuum sealed Cmp17xk \n", - "\n", - " repl_no repl_id value ... created_at updated_at \\\n", - "0 1 Cmp04xk(85)1 14.16 ... 2025-01-23 09:00:01 NaT \n", - "1 2 Cmp04xk(85)2 14.18 ... 2025-01-23 09:00:16 NaT \n", - "2 3 Cmp04xk(85)3 14.12 ... 2025-01-23 09:00:31 NaT \n", - "3 1 Cmp04xk(85)1 15.74 ... 2025-01-23 09:00:46 NaT \n", - "4 2 Cmp04xk(85)2 15.75 ... 2025-01-23 09:01:01 NaT \n", - ".. ... ... ... ... ... ... \n", - "385 2 Cmp17xk(A0)2 17.290001 ... 2025-03-04 09:55:00 NaT \n", - "386 3 Cmp17xk(A0)3 17.5 ... 2025-03-04 09:55:15 NaT \n", - "387 1 Cmp17xk(A0)1 35.970001 ... 2025-03-04 09:55:30 NaT \n", - "388 2 Cmp17xk(A0)2 35.279999 ... 2025-03-04 09:55:45 NaT \n", - "389 3 Cmp17xk(A0)3 34.990002 ... 2025-03-04 09:56:00 NaT \n", - "\n", - " qc_result note analysis_type equipment raw_data_url \\\n", - "0 pass Chemical composition \n", - "1 pass Chemical composition \n", - "2 pass Chemical composition \n", - "3 pass Chemical composition \n", - "4 pass Chemical composition \n", - ".. ... ... ... ... ... \n", - "385 pass Chemical composition \n", - "386 pass Chemical composition \n", - "387 pass Chemical composition \n", - "388 pass Chemical composition \n", - "389 pass Chemical composition \n", - "\n", - " analyst_email upload_status parameter_id \n", - "0 xkang2@lbl.gov ready 6 \n", - "1 xkang2@lbl.gov ready 6 \n", - "2 xkang2@lbl.gov ready 6 \n", - "3 xkang2@lbl.gov ready 4 \n", - "4 xkang2@lbl.gov ready 4 \n", - ".. ... ... ... \n", - "385 xkang2@lbl.gov not ready 5 \n", - "386 xkang2@lbl.gov not ready 5 \n", - "387 xkang2@lbl.gov not ready 3 \n", - "388 xkang2@lbl.gov not ready 3 \n", - "389 xkang2@lbl.gov not ready 3 \n", - "\n", - "[390 rows x 21 columns]" + " description id name note uri\n", + "0 None 1 Tomatoes for processing None None\n", + "1 None 2 Grapes None None\n", + "2 None 3 Almonds None None\n", + "3 None 4 Walnuts None None\n", + "4 None 5 Sweet potatoes None None" ] }, - "execution_count": 15, + "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], + "source": [ + "from sqlalchemy.orm import Session\n", + "from sqlalchemy import select\n", + "import pandas as pd\n", + "import os\n", + "import sys\n", + "\n", + "# --- project root discovery (unchanged) ---\n", + "path = os.getcwd()\n", + "project_root = None\n", + "while path != os.path.dirname(path):\n", + " if 'pixi.toml' in os.listdir(path):\n", + " project_root = path\n", + " break\n", + " path = os.path.dirname(path)\n", + "\n", + "if not project_root:\n", + " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", + "\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + "\n", + "# --- imports ---\n", + "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", + "from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import PrimaryAgProduct\n", + "\n", + "# --- query + dataframe ---\n", + "with Session(engine) as db:\n", + " stmt = select(*PrimaryAgProduct.__table__.columns)\n", + " rows = db.execute(stmt).mappings().all()\n", + "\n", + "df = pd.DataFrame(rows)\n", + "\n", + "df.head()\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "summary_stats = clean_dataframes[0].\\\n", + " groupby(['resource', 'parameter'])['value'].\\\n", + " agg(['mean', 'median', 'min', 'max', 'std', 'count'])\n", + "\n", + "summary_stats" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "clean_dataframes[0][['resource', 'parameter', 'value', 'unit']].\\\n", + " groupby(['resource', 'parameter', 'unit'], as_index=False).\\\n", + " agg({'value': 'mean'}).\\\n", + " query('value > 30').\\\n", + " sort_values(by='value', ascending=False).\\\n", + " round({'value': 1})\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "list_of_param = (\"Moisture\", \"Total solids\", \"Ash\")\n", + "\n", + "def is_it_volatile_solids(df):\n", + " df['check'] = \"VS\"\n", + "\n", + " df.loc[df['parameter'].isin(list_of_param), 'check'] = \"In list\"\n", + " return df\n", + "\n", + "is_it_volatile_solids(df)\n", + "\n", + "df[['check', 'parameter']]\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "#This defines a function to calculate the square root of the 'value' column in a DataFrame\n", + "def sqrtvalue(df):\n", + " df = df.assign(sqrtvalue = df['value'] ** 0.5)\n", + " return df\n", + "\n", + "#List comprehension to apply sqrtvalue to each DataFrame\n", + "clean_rooted_df = [sqrtvalue(df) for df in clean_dataframes]\n", + "\n", + "# Display the head of the third DataFrame\n", + "clean_rooted_df[2].head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "cmpana_raw = cmpana.extract(project_root=project_root)\n", + "\n", + "cmpana_raw.head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from sqlalchemy.orm import Session\n", + "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", + "from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", + "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import (\n", + " replace_name_with_id_df,\n", + ") \n", + "\n", + "#This extractst the raw proximate data\n", + "df = cmpana.extract(project_root=project_root)\n", + "\n", + "#this cleans the names to lowercase and parses data into a standard format. Also renames the column to match with what will be in the database\n", + "test_df = clean_the_gsheets(df).rename(columns={'parameter': 'name'})\n", + "\n", + "#this replaces the names with IDs\n", + "with Session(engine) as db:\n", + " parameter_ids = replace_name_with_id_df(\n", + " db=db,\n", + " df=test_df,\n", + " ref_model=Parameter,\n", + " name_column_name=\"name\", # column in df + table\n", + " id_column_name=\"id\", # PK column in table\n", + " final_column_name=\"parameter_id\"\n", + " )\n", + "\n", + "##I EVENTUALLY WANT SOME LOGS ABOUT HOW MANY WERE ADDED, HOW MANY RETRIEVED, ETC. MAYBE PUT THAT IN THE \n", + "#resource_id_mapping = df_with_ids.rename(columns={\"id\": \"resource_id\"})\n", + "\n", + "#resource_id_mapping\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "parameter_ids\n" ] @@ -4187,6 +1461,63 @@ "\n", "field_sample" ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "#This is a get_or_create type module for data normalization.\n", + "\n", + "# Extract a df from a gsheet\n", + "df = cmpana.extract(project_root=project_root)\n", + "\n", + "# Cleans the df names and coerces data types\n", + "df = clean_the_gsheets(df)\n", + "\n", + "# Replace empty strings with NaN\n", + "df.replace(r'^\\s*$', np.nan, regex=True, inplace=True)\n", + "\n", + "\n", + "# These are columns that need to be normalized, AKA replaced with IDs.\n", + "# This is a mapping that has first, what it is called in pandas \"resource\"\n", + "# then, the SQLAlchemy model \"Resource\", and then what it is called in the\n", + "# database \"name\"\n", + "\n", + "\n", + "NORMALIZE_COLUMNS = {\n", + " \"resource\": (Resource, \"name\"),\n", + " \"prepared_sample\": (PreparedSample, \"name\"),\n", + " \"preparation_method\": (PreparationMethod, \"name\"),\n", + " \"parameter\": (Parameter, \"name\"),\n", + " \"unit\": (Unit, \"name\"),\n", + " \"analyst_email\": (Contact, \"email\"),\n", + " \"analysis_type\": (AnalysisType, \"name\"),\n", + " \"primary_ag_product\": (PrimaryAgProduct, \"name\")\n", + "}\n", + "\n", + "df_normalized = df.copy()\n", + "\n", + "with Session(engine) as db:\n", + " for df_col, (model, model_name_attr) in NORMALIZE_COLUMNS.items():\n", + " if df_col not in df_normalized.columns:\n", + " continue\n", + "\n", + " df_normalized = replace_name_with_id_df(\n", + " db=db,\n", + " df=df_normalized,\n", + " ref_model=model,\n", + " df_name_column=df_col,\n", + " model_name_attr=model_name_attr,\n", + " id_column_name=\"id\",\n", + " final_column_name=f\"{df_col}_id\",\n", + " )\n", + "\n", + " db.commit()\n", + "\n", + "df_normalized.head()\n" + ] } ], "metadata": { diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py index d9290968..5d1d22b7 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/name_id_swap.py @@ -40,10 +40,13 @@ def replace_name_with_id_df( model_name_attr: str, id_column_name: str, final_column_name: str, -) -> pd.DataFrame: +) -> tuple[pd.DataFrame, int]: """ Replace a DataFrame name column with foreign key IDs from a SQLAlchemy table. Creates missing reference records if needed. + + Returns: + A tuple containing the modified DataFrame and the number of new records created. """ # 1. Fetch existing reference rows (name + id only) @@ -61,6 +64,7 @@ def replace_name_with_id_df( # 2. Determine which names are new unique_names = set(df_copy[df_name_column].dropna().unique()) new_names = unique_names - set(name_to_id_map.keys()) + num_new_records = len(new_names) # 3. Insert missing reference rows if new_names: @@ -87,4 +91,4 @@ def replace_name_with_id_df( df_copy[final_column_name] = df_copy[df_name_column].map(name_to_id_map) df_copy = df_copy.drop(columns=[df_name_column]) - return df_copy + return df_copy, num_new_records From f4b06ecae3b7e5f59fdb81f9bd288db4ede249f8 Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Tue, 6 Jan 2026 13:54:03 -0700 Subject: [PATCH 72/81] modified etl_notebook. Db is now running on localhost --- .../pipeline/utils/database_interaction.ipynb | 2 +- .../pipeline/utils/dev_test.ipynb | 53 ++ .../pipeline/utils/etl_notebook.ipynb | 462 +++++++++--------- 3 files changed, 291 insertions(+), 226 deletions(-) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/dev_test.ipynb diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb index 671f288a..c6ba4c99 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/database_interaction.ipynb @@ -347,7 +347,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.13.9" + "version": "3.13.11" } }, "nbformat": 4, diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/dev_test.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/dev_test.ipynb new file mode 100644 index 00000000..c7dfc663 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/dev_test.ipynb @@ -0,0 +1,53 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "d5df752a", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "ca_biositing.datamodels.schemas.generated.ca_biositing.Resource" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import pandas as pd\n", + "import os\n", + "import sys\n", + "from sqlalchemy.orm import Session\n", + "\n", + "from ca_biositing.pipeline.utils.lookup_utils import replace_id_with_name_df\n", + "from ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", + "\n" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "default", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.12" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb index 18fb0314..140d8709 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb @@ -20,15 +20,15 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2026-01-04 08:53:57,422 - INFO - Project root '/Users/pjsmitty301/ca-biositing' is already in sys.path\n", - "2026-01-04 08:53:57,423 - INFO - Successfully imported all project modules.\n" + "2026-01-06 10:31:31,052 - INFO - Added project root '/Users/pjsmitty301/ca-biositing' to sys.path\n", + "2026-01-06 10:31:32,479 - INFO - Successfully imported all project modules.\n" ] } ], @@ -89,7 +89,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -128,12 +128,14 @@ " if 'updated_at' in df_cleaned.columns:\n", " df_cleaned['updated_at'] = pd.to_datetime(df_cleaned['updated_at'], errors='coerce')\n", "\n", - " # 4. Convert other dtypes to best possible\n", + " # 4. Replace empty strings with NaN so they are properly ignored\n", + " df_cleaned = df_cleaned.replace(r'^\\s*$', np.nan, regex=True)\n", + "\n", + " # 5. Convert other dtypes to best possible\n", " df_cleaned = df_cleaned.convert_dtypes()\n", " logger.info('Successfully cleaned DataFrame.')\n", - " \n", - " \n", - " # 5. Convert all string data to lowercase\n", + "\n", + " # 6. Convert all string data to lowercase\n", " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", " logger.info('Converted all string data to lowercase.')\n", " return df_cleaned\n", @@ -154,7 +156,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 5, "metadata": {}, "outputs": [], "source": [ @@ -192,7 +194,7 @@ " \n", " try:\n", " logger.info(f\"Normalizing column '{df_col}' using model '{model.__name__}'.\")\n", - " df_normalized = replace_name_with_id_df(\n", + " df_normalized, num_created = replace_name_with_id_df(\n", " db=db,\n", " df=df_normalized,\n", " ref_model=model,\n", @@ -201,6 +203,8 @@ " id_column_name='id',\n", " final_column_name=f'{df_col}_id'\n", " )\n", + " if num_created > 0:\n", + " logger.info(f\"Created {num_created} new records in '{model.__name__}' table.\")\n", " new_col_name = f'{df_col}_id'\n", " num_nulls = df_normalized[new_col_name].isnull().sum()\n", " logger.info(f\"Successfully normalized '{df_col}'. New column '{new_col_name}' contains {num_nulls} null values.\")\n", @@ -219,7 +223,7 @@ " db.rollback()\n", " logger.info('Database session rolled back.')\n", " \n", - " return normalized_dfs" + " return normalized_dfs\n" ] }, { @@ -231,104 +235,112 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2026-01-04 08:58:52,849 - INFO - Starting data extraction...\n", - "2026-01-04 08:58:52,865 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-04 08:58:52,877 - INFO - Extracting raw data from '03.1-Proximate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", - "2026-01-04 08:58:54,699 - INFO - Successfully extracted raw data.\n", - "2026-01-04 08:58:54,703 - INFO - Finished in state Completed()\n", - "2026-01-04 08:58:54,724 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-04 08:58:54,736 - INFO - Extracting raw data from '03.7-Ultimate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", - "2026-01-04 08:58:55,992 - INFO - Successfully extracted raw data.\n", - "2026-01-04 08:58:55,996 - INFO - Finished in state Completed()\n", - "2026-01-04 08:58:56,016 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-04 08:58:56,029 - INFO - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", - "2026-01-04 08:58:57,291 - INFO - Successfully extracted raw data.\n", - "2026-01-04 08:58:57,294 - INFO - Finished in state Completed()\n", - "2026-01-04 08:58:57,296 - INFO - Data extraction complete.\n", - "2026-01-04 08:58:57,299 - INFO - Starting data cleaning...\n", - "2026-01-04 08:58:57,299 - INFO - Starting DataFrame cleaning process.\n", - "2026-01-04 08:58:57,302 - INFO - Dropped 0 rows with missing values.\n", - "2026-01-04 08:58:57,309 - INFO - Successfully cleaned DataFrame.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_25314/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + "2026-01-06 10:31:40,834 - INFO - Starting data extraction...\n", + "2026-01-06 10:31:40,881 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-06 10:31:40,903 - INFO - Extracting raw data from '03.1-Proximate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", + "2026-01-06 10:31:42,948 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/csrf-token?client=ae9812ec-079b-4fe5-845c-493121391421 \"HTTP/1.1 422 Unprocessable Entity\"\n", + "2026-01-06 10:31:42,966 - INFO - HTTP Request: POST http://127.0.0.1:4200/api/logs/ \"HTTP/1.1 201 Created\"\n", + "2026-01-06 10:31:45,659 - INFO - Successfully extracted raw data.\n", + "2026-01-06 10:31:45,661 - INFO - Finished in state Completed()\n", + "2026-01-06 10:31:45,672 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-06 10:31:45,680 - INFO - Extracting raw data from '03.7-Ultimate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", + "2026-01-06 10:31:46,995 - INFO - HTTP Request: POST http://127.0.0.1:4200/api/logs/ \"HTTP/1.1 201 Created\"\n", + "2026-01-06 10:31:47,292 - INFO - Successfully extracted raw data.\n", + "2026-01-06 10:31:47,296 - INFO - Finished in state Completed()\n", + "2026-01-06 10:31:47,313 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-06 10:31:47,326 - INFO - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", + "2026-01-06 10:31:48,924 - INFO - Successfully extracted raw data.\n", + "2026-01-06 10:31:48,929 - INFO - Finished in state Completed()\n", + "2026-01-06 10:31:48,930 - INFO - Data extraction complete.\n", + "2026-01-06 10:31:48,931 - INFO - Starting data cleaning...\n", + "2026-01-06 10:31:48,933 - INFO - Starting DataFrame cleaning process.\n", + "2026-01-06 10:31:48,939 - INFO - Dropped 0 rows with missing values.\n", + "2026-01-06 10:31:48,950 - INFO - Successfully cleaned DataFrame.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", - "2026-01-04 08:58:57,314 - INFO - Converted all string data to lowercase.\n", - "2026-01-04 08:58:57,315 - INFO - Starting DataFrame cleaning process.\n", - "2026-01-04 08:58:57,316 - INFO - Dropped 0 rows with missing values.\n", - "2026-01-04 08:58:57,319 - INFO - Successfully cleaned DataFrame.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_25314/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + "2026-01-06 10:31:48,958 - INFO - Converted all string data to lowercase.\n", + "2026-01-06 10:31:48,958 - INFO - Starting DataFrame cleaning process.\n", + "2026-01-06 10:31:48,959 - INFO - Dropped 0 rows with missing values.\n", + "2026-01-06 10:31:48,962 - INFO - Successfully cleaned DataFrame.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", - "2026-01-04 08:58:57,320 - INFO - Converted all string data to lowercase.\n", - "2026-01-04 08:58:57,321 - INFO - Starting DataFrame cleaning process.\n", - "2026-01-04 08:58:57,325 - INFO - Dropped 0 rows with missing values.\n", - "2026-01-04 08:58:57,335 - INFO - Successfully cleaned DataFrame.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_25314/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + "2026-01-06 10:31:48,964 - INFO - Converted all string data to lowercase.\n", + "2026-01-06 10:31:48,964 - INFO - Starting DataFrame cleaning process.\n", + "2026-01-06 10:31:48,965 - INFO - Dropped 0 rows with missing values.\n", + "2026-01-06 10:31:48,969 - INFO - Successfully cleaned DataFrame.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", - "2026-01-04 08:58:57,340 - INFO - Converted all string data to lowercase.\n", - "2026-01-04 08:58:57,342 - INFO - Data cleaning complete.\n", - "2026-01-04 08:58:57,342 - INFO - Starting data normalization...\n", - "2026-01-04 08:58:57,343 - INFO - Starting normalization process for 3 dataframes.\n", - "2026-01-04 08:58:57,343 - INFO - Processing DataFrame #1 with 759 rows.\n", - "2026-01-04 08:58:57,344 - INFO - Normalizing column 'resource' using model 'Resource'.\n", - "2026-01-04 08:58:57,355 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", - "2026-01-04 08:58:57,356 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", - "2026-01-04 08:58:57,367 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", - "2026-01-04 08:58:57,367 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", - "2026-01-04 08:58:57,369 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", - "2026-01-04 08:58:57,369 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", - "2026-01-04 08:58:57,372 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", - "2026-01-04 08:58:57,372 - INFO - Normalizing column 'unit' using model 'Unit'.\n", - "2026-01-04 08:58:57,374 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", - "2026-01-04 08:58:57,374 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", - "2026-01-04 08:58:57,375 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", - "2026-01-04 08:58:57,375 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", - "2026-01-04 08:58:57,379 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", - "2026-01-04 08:58:57,379 - WARNING - Column 'primary_ag_product' not in DataFrame #1. Skipping normalization for this column.\n", - "2026-01-04 08:58:57,379 - INFO - Finished processing DataFrame #1.\n", - "2026-01-04 08:58:57,379 - INFO - Processing DataFrame #2 with 64 rows.\n", - "2026-01-04 08:58:57,380 - INFO - Normalizing column 'resource' using model 'Resource'.\n", - "2026-01-04 08:58:57,384 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", - "2026-01-04 08:58:57,384 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", - "2026-01-04 08:58:57,388 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", - "2026-01-04 08:58:57,388 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", - "2026-01-04 08:58:57,392 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", - "2026-01-04 08:58:57,392 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", - "2026-01-04 08:58:57,396 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", - "2026-01-04 08:58:57,396 - INFO - Normalizing column 'unit' using model 'Unit'.\n", - "2026-01-04 08:58:57,398 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", - "2026-01-04 08:58:57,398 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", - "2026-01-04 08:58:57,399 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", - "2026-01-04 08:58:57,400 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", - "2026-01-04 08:58:57,403 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", - "2026-01-04 08:58:57,403 - WARNING - Column 'primary_ag_product' not in DataFrame #2. Skipping normalization for this column.\n", - "2026-01-04 08:58:57,403 - INFO - Finished processing DataFrame #2.\n", - "2026-01-04 08:58:57,403 - INFO - Processing DataFrame #3 with 390 rows.\n", - "2026-01-04 08:58:57,404 - INFO - Normalizing column 'resource' using model 'Resource'.\n", - "2026-01-04 08:58:57,406 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", - "2026-01-04 08:58:57,406 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", - "2026-01-04 08:58:57,408 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", - "2026-01-04 08:58:57,408 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", - "2026-01-04 08:58:57,409 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", - "2026-01-04 08:58:57,410 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", - "2026-01-04 08:58:57,411 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", - "2026-01-04 08:58:57,411 - INFO - Normalizing column 'unit' using model 'Unit'.\n", - "2026-01-04 08:58:57,413 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", - "2026-01-04 08:58:57,413 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", - "2026-01-04 08:58:57,415 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", - "2026-01-04 08:58:57,415 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", - "2026-01-04 08:58:57,416 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", - "2026-01-04 08:58:57,416 - WARNING - Column 'primary_ag_product' not in DataFrame #3. Skipping normalization for this column.\n", - "2026-01-04 08:58:57,417 - INFO - Finished processing DataFrame #3.\n", - "2026-01-04 08:58:57,417 - INFO - Committing database session.\n", - "2026-01-04 08:58:57,418 - INFO - Database commit successful.\n", - "2026-01-04 08:58:57,418 - INFO - Data normalization complete.\n", - "2026-01-04 08:58:57,418 - INFO - Displaying results of normalization...\n" + "2026-01-06 10:31:48,972 - INFO - Converted all string data to lowercase.\n", + "2026-01-06 10:31:48,973 - INFO - Data cleaning complete.\n", + "2026-01-06 10:31:48,973 - INFO - Starting data normalization...\n", + "2026-01-06 10:31:48,974 - INFO - Starting normalization process for 3 dataframes.\n", + "2026-01-06 10:31:48,974 - INFO - Processing DataFrame #1 with 1030 rows.\n", + "2026-01-06 10:31:48,974 - INFO - Normalizing column 'resource' using model 'Resource'.\n", + "2026-01-06 10:31:49,016 - INFO - HTTP Request: POST http://127.0.0.1:4200/api/logs/ \"HTTP/1.1 201 Created\"\n", + "2026-01-06 10:31:49,116 - INFO - Created 35 new records in 'Resource' table.\n", + "2026-01-06 10:31:49,116 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", + "2026-01-06 10:31:49,117 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", + "2026-01-06 10:31:49,120 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", + "2026-01-06 10:31:49,120 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", + "2026-01-06 10:31:49,123 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", + "2026-01-06 10:31:49,124 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", + "2026-01-06 10:31:49,144 - INFO - Created 1 new records in 'Parameter' table.\n", + "2026-01-06 10:31:49,145 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", + "2026-01-06 10:31:49,147 - INFO - Normalizing column 'unit' using model 'Unit'.\n", + "2026-01-06 10:31:49,167 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", + "2026-01-06 10:31:49,176 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", + "2026-01-06 10:31:49,182 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", + "2026-01-06 10:31:49,182 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", + "2026-01-06 10:31:49,189 - INFO - Created 1 new records in 'AnalysisType' table.\n", + "2026-01-06 10:31:49,189 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", + "2026-01-06 10:31:49,189 - WARNING - Column 'primary_ag_product' not in DataFrame #1. Skipping normalization for this column.\n", + "2026-01-06 10:31:49,190 - INFO - Finished processing DataFrame #1.\n", + "2026-01-06 10:31:49,190 - INFO - Processing DataFrame #2 with 64 rows.\n", + "2026-01-06 10:31:49,191 - INFO - Normalizing column 'resource' using model 'Resource'.\n", + "2026-01-06 10:31:49,197 - INFO - Created 1 new records in 'Resource' table.\n", + "2026-01-06 10:31:49,198 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", + "2026-01-06 10:31:49,198 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", + "2026-01-06 10:31:49,201 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", + "2026-01-06 10:31:49,202 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", + "2026-01-06 10:31:49,204 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", + "2026-01-06 10:31:49,204 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", + "2026-01-06 10:31:49,206 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", + "2026-01-06 10:31:49,206 - INFO - Normalizing column 'unit' using model 'Unit'.\n", + "2026-01-06 10:31:49,209 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", + "2026-01-06 10:31:49,209 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", + "2026-01-06 10:31:49,211 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", + "2026-01-06 10:31:49,212 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", + "2026-01-06 10:31:49,213 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", + "2026-01-06 10:31:49,213 - WARNING - Column 'primary_ag_product' not in DataFrame #2. Skipping normalization for this column.\n", + "2026-01-06 10:31:49,214 - INFO - Finished processing DataFrame #2.\n", + "2026-01-06 10:31:49,214 - INFO - Processing DataFrame #3 with 390 rows.\n", + "2026-01-06 10:31:49,215 - INFO - Normalizing column 'resource' using model 'Resource'.\n", + "2026-01-06 10:31:49,217 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", + "2026-01-06 10:31:49,217 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", + "2026-01-06 10:31:49,220 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", + "2026-01-06 10:31:49,220 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", + "2026-01-06 10:31:49,222 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", + "2026-01-06 10:31:49,222 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", + "2026-01-06 10:31:49,224 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", + "2026-01-06 10:31:49,224 - INFO - Normalizing column 'unit' using model 'Unit'.\n", + "2026-01-06 10:31:49,225 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", + "2026-01-06 10:31:49,225 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", + "2026-01-06 10:31:49,228 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", + "2026-01-06 10:31:49,228 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", + "2026-01-06 10:31:49,230 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", + "2026-01-06 10:31:49,230 - WARNING - Column 'primary_ag_product' not in DataFrame #3. Skipping normalization for this column.\n", + "2026-01-06 10:31:49,230 - INFO - Finished processing DataFrame #3.\n", + "2026-01-06 10:31:49,230 - INFO - Committing database session.\n", + "2026-01-06 10:31:49,232 - INFO - Database commit successful.\n", + "2026-01-06 10:31:49,241 - INFO - Data normalization complete.\n", + "2026-01-06 10:31:49,244 - INFO - Displaying results of normalization...\n" ] }, { @@ -448,7 +460,7 @@ "type": "integer" } ], - "ref": "e2d8eb1c-3fc8-4b97-99b0-df76b598d9df", + "ref": "b0e10f3c-2f75-4628-acc4-1c383e10ca93", "rows": [ [ "0", @@ -465,13 +477,13 @@ "pass", "not ready", "", - "24", + "6", "109", "7", - "25", + "3", "1", "1", - "6" + "1" ], [ "1", @@ -488,13 +500,13 @@ "pass", "ready", "", - "24", + "6", "109", "7", - "25", + "3", "1", "1", - "6" + "1" ], [ "2", @@ -511,13 +523,13 @@ "pass", "imported", "", - "24", + "6", "109", "7", - "25", + "3", "1", "1", - "6" + "1" ], [ "3", @@ -534,13 +546,13 @@ "pass", "import failed", "", - "24", + "6", "109", "7", - "23", + "4", "1", "1", - "6" + "1" ], [ "4", @@ -557,13 +569,13 @@ "pass", "", "", - "24", + "6", "109", "7", - "23", + "4", "1", "1", - "6" + "1" ] ], "shape": { @@ -628,13 +640,13 @@ " pass\n", " not ready\n", " \n", - " 24\n", + " 6\n", " 109\n", " 7\n", - " 25\n", + " 3\n", + " 1\n", " 1\n", " 1\n", - " 6\n", " \n", " \n", " 1\n", @@ -651,13 +663,13 @@ " pass\n", " ready\n", " \n", - " 24\n", + " 6\n", " 109\n", " 7\n", - " 25\n", + " 3\n", + " 1\n", " 1\n", " 1\n", - " 6\n", " \n", " \n", " 2\n", @@ -674,13 +686,13 @@ " pass\n", " imported\n", " \n", - " 24\n", + " 6\n", " 109\n", " 7\n", - " 25\n", + " 3\n", + " 1\n", " 1\n", " 1\n", - " 6\n", " \n", " \n", " 3\n", @@ -697,13 +709,13 @@ " pass\n", " import failed\n", " \n", - " 24\n", + " 6\n", " 109\n", " 7\n", - " 23\n", + " 4\n", + " 1\n", " 1\n", " 1\n", - " 6\n", " \n", " \n", " 4\n", @@ -720,13 +732,13 @@ " pass\n", " \n", " \n", - " 24\n", + " 6\n", " 109\n", " 7\n", - " 23\n", + " 4\n", + " 1\n", " 1\n", " 1\n", - " 6\n", " \n", " \n", "\n", @@ -748,25 +760,25 @@ "4 prox01xk 2.0 prox01xk(73)2 0.890000 2024-10-03 10:31:31 \n", "\n", " updated_at qc_result upload_status note resource_id prepared_sample_id \\\n", - "0 NaT pass not ready 24 109 \n", - "1 NaT pass ready 24 109 \n", - "2 NaT pass imported 24 109 \n", - "3 NaT pass import failed 24 109 \n", - "4 NaT pass 24 109 \n", + "0 NaT pass not ready 6 109 \n", + "1 NaT pass ready 6 109 \n", + "2 NaT pass imported 6 109 \n", + "3 NaT pass import failed 6 109 \n", + "4 NaT pass 6 109 \n", "\n", " preparation_method_id parameter_id unit_id analyst_email_id \\\n", - "0 7 25 1 1 \n", - "1 7 25 1 1 \n", - "2 7 25 1 1 \n", - "3 7 23 1 1 \n", - "4 7 23 1 1 \n", + "0 7 3 1 1 \n", + "1 7 3 1 1 \n", + "2 7 3 1 1 \n", + "3 7 4 1 1 \n", + "4 7 4 1 1 \n", "\n", " analysis_type_id \n", - "0 6 \n", - "1 6 \n", - "2 6 \n", - "3 6 \n", - "4 6 " + "0 1 \n", + "1 1 \n", + "2 1 \n", + "3 1 \n", + "4 1 " ] }, "metadata": {}, @@ -899,7 +911,7 @@ "type": "integer" } ], - "ref": "323960ff-b723-432d-b7c9-fa0f9dd8c185", + "ref": "0f732e49-22cb-4b72-a52a-9fade9af05ef", "rows": [ [ "0", @@ -918,13 +930,13 @@ "", "", "", - "8", + "27", "80", "6", - "28", + "8", "3", "2", - "7" + "2" ], [ "1", @@ -943,13 +955,13 @@ "", "", "", - "8", + "27", "80", "6", - "28", + "8", "3", "2", - "7" + "2" ], [ "2", @@ -968,13 +980,13 @@ "", "", "", - "26", + "11", "96", "6", - "28", + "8", "3", "2", - "7" + "2" ], [ "3", @@ -993,13 +1005,13 @@ "", "", "", - "2", + "12", "91", "9", - "28", + "8", "3", "2", - "7" + "2" ], [ "4", @@ -1018,13 +1030,13 @@ "", "", "", - "7", + "21", "153", "9", - "28", + "8", "3", "2", - "7" + "2" ] ], "shape": { @@ -1091,13 +1103,13 @@ " \n", " \n", " \n", - " 8\n", + " 27\n", " 80\n", " 6\n", - " 28\n", + " 8\n", " 3\n", " 2\n", - " 7\n", + " 2\n", " \n", " \n", " 1\n", @@ -1115,13 +1127,13 @@ " \n", " \n", " \n", - " 8\n", + " 27\n", " 80\n", " 6\n", - " 28\n", + " 8\n", " 3\n", " 2\n", - " 7\n", + " 2\n", " \n", " \n", " 2\n", @@ -1139,13 +1151,13 @@ " \n", " \n", " \n", - " 26\n", + " 11\n", " 96\n", " 6\n", - " 28\n", + " 8\n", " 3\n", " 2\n", - " 7\n", + " 2\n", " \n", " \n", " 3\n", @@ -1163,13 +1175,13 @@ " \n", " \n", " \n", - " 2\n", + " 12\n", " 91\n", " 9\n", - " 28\n", + " 8\n", " 3\n", " 2\n", - " 7\n", + " 2\n", " \n", " \n", " 4\n", @@ -1187,13 +1199,13 @@ " \n", " \n", " \n", - " 7\n", + " 21\n", " 153\n", " 9\n", - " 28\n", + " 8\n", " 3\n", " 2\n", - " 7\n", + " 2\n", " \n", " \n", "\n", @@ -1216,25 +1228,25 @@ "4 rt vacuum sealed ult26kh 1 ult26kh(1b)1 93.800003 NaT \n", "\n", " updated_at ... equipment raw_data_url upload_status resource_id \\\n", - "0 NaT ... 8 \n", - "1 NaT ... 8 \n", - "2 NaT ... 26 \n", - "3 NaT ... 2 \n", - "4 NaT ... 7 \n", + "0 NaT ... 27 \n", + "1 NaT ... 27 \n", + "2 NaT ... 11 \n", + "3 NaT ... 12 \n", + "4 NaT ... 21 \n", "\n", " prepared_sample_id preparation_method_id parameter_id unit_id \\\n", - "0 80 6 28 3 \n", - "1 80 6 28 3 \n", - "2 96 6 28 3 \n", - "3 91 9 28 3 \n", - "4 153 9 28 3 \n", + "0 80 6 8 3 \n", + "1 80 6 8 3 \n", + "2 96 6 8 3 \n", + "3 91 9 8 3 \n", + "4 153 9 8 3 \n", "\n", " analyst_email_id analysis_type_id \n", - "0 2 7 \n", - "1 2 7 \n", - "2 2 7 \n", - "3 2 7 \n", - "4 2 7 \n", + "0 2 2 \n", + "1 2 2 \n", + "2 2 2 \n", + "3 2 2 \n", + "4 2 2 \n", "\n", "[5 rows x 22 columns]" ] @@ -1364,7 +1376,7 @@ "type": "integer" } ], - "ref": "31e4fb08-8acb-41fc-bdec-4f79aea24d5f", + "ref": "95361c64-4a65-4fd6-bde6-2efae692d84c", "rows": [ [ "0", @@ -1382,10 +1394,10 @@ "", "", "ready", - "24", + "6", "92", "8", - "12", + "13", "2", "1", "3" @@ -1406,10 +1418,10 @@ "", "", "ready", - "24", + "6", "92", "8", - "12", + "13", "2", "1", "3" @@ -1430,10 +1442,10 @@ "", "", "ready", - "24", + "6", "92", "8", - "12", + "13", "2", "1", "3" @@ -1454,10 +1466,10 @@ "", "", "ready", - "24", + "6", "92", "8", - "14", + "11", "2", "1", "3" @@ -1478,10 +1490,10 @@ "", "", "ready", - "24", + "6", "92", "8", - "14", + "11", "2", "1", "3" @@ -1551,10 +1563,10 @@ " \n", " \n", " ready\n", - " 24\n", + " 6\n", " 92\n", " 8\n", - " 12\n", + " 13\n", " 2\n", " 1\n", " 3\n", @@ -1575,10 +1587,10 @@ " \n", " \n", " ready\n", - " 24\n", + " 6\n", " 92\n", " 8\n", - " 12\n", + " 13\n", " 2\n", " 1\n", " 3\n", @@ -1599,10 +1611,10 @@ " \n", " \n", " ready\n", - " 24\n", + " 6\n", " 92\n", " 8\n", - " 12\n", + " 13\n", " 2\n", " 1\n", " 3\n", @@ -1623,10 +1635,10 @@ " \n", " \n", " ready\n", - " 24\n", + " 6\n", " 92\n", " 8\n", - " 14\n", + " 11\n", " 2\n", " 1\n", " 3\n", @@ -1647,10 +1659,10 @@ " \n", " \n", " ready\n", - " 24\n", + " 6\n", " 92\n", " 8\n", - " 14\n", + " 11\n", " 2\n", " 1\n", " 3\n", @@ -1676,18 +1688,18 @@ "4 cmp04xk 2 cmp04xk(85)2 15.75 2025-01-23 09:01:01 NaT \n", "\n", " qc_result ... equipment raw_data_url upload_status resource_id \\\n", - "0 pass ... ready 24 \n", - "1 pass ... ready 24 \n", - "2 pass ... ready 24 \n", - "3 pass ... ready 24 \n", - "4 pass ... ready 24 \n", + "0 pass ... ready 6 \n", + "1 pass ... ready 6 \n", + "2 pass ... ready 6 \n", + "3 pass ... ready 6 \n", + "4 pass ... ready 6 \n", "\n", " prepared_sample_id preparation_method_id parameter_id unit_id \\\n", - "0 92 8 12 2 \n", - "1 92 8 12 2 \n", - "2 92 8 12 2 \n", - "3 92 8 14 2 \n", - "4 92 8 14 2 \n", + "0 92 8 13 2 \n", + "1 92 8 13 2 \n", + "2 92 8 13 2 \n", + "3 92 8 11 2 \n", + "4 92 8 11 2 \n", "\n", " analyst_email_id analysis_type_id \n", "0 1 3 \n", @@ -1765,9 +1777,9 @@ ], "metadata": { "kernelspec": { - "display_name": "Pixi Default Environment", + "display_name": "default", "language": "python", - "name": "pixi-default" + "name": "python3" }, "language_info": { "codemirror_mode": { From 5f1e0a410a0fd5b5b4f89e21beb96ea1d10738ba Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Wed, 7 Jan 2026 09:32:28 -0700 Subject: [PATCH 73/81] "did the module refactor but may need to mess with the alembic env.py. Committing before that" --- .../datamodels/linkml/ca_biositing.yaml | 112 +- .../linkml/modules/aim1_records.yaml | 140 -- .../aim1_records/aim1_record_base.yaml | 86 + .../aim1_records/calorimetry_record.yaml | 21 + .../aim1_records/compositional_record.yaml | 21 + .../modules/aim1_records/ftnir_record.yaml | 21 + .../icp_record.yaml} | 16 +- .../aim1_records/proximate_record.yaml | 21 + .../modules/aim1_records/rgb_record.yaml | 21 + .../modules/aim1_records/ultimate_record.yaml | 21 + .../modules/aim1_records/xrd_record.yaml | 32 + .../modules/aim1_records/xrf_record.yaml | 40 + .../linkml/modules/aim2_records.yaml | 170 -- .../aim2_records/aim2_record_base.yaml | 60 + .../aim2_records/autoclave_record.yaml | 22 + .../aim2_records/fermentation_record.yaml | 58 + .../aim2_records/gasifcation_record.yaml | 0 .../aim2_records/gasification_record.yaml | 36 + .../aim2_records/pretreatment_record.yaml | 49 + .../linkml/modules/aim2_records/strain.yaml | 27 + .../datamodels/linkml/modules/core.yaml | 79 - .../linkml/modules/core/base_entity.yaml | 40 + .../linkml/modules/core/lookup_base.yaml | 34 + .../datamodels/linkml/modules/core/note.yaml | 12 + .../data_source.yaml} | 83 +- .../data_source_type.yaml | 21 + .../file_object_metadata.yaml | 46 + .../location_resolution.yaml | 13 + .../data_sources_metadata/source_type.yaml | 13 + .../linkml/modules/experiment_equipment.yaml | 127 -- .../experiment_equipment/equipment.yaml | 21 + .../experiment_equipment/experiment.yaml | 44 + .../experiment_analysis.yaml | 30 + .../experiment_equipment.yaml | 30 + .../experiment_method.yaml | 31 + .../experiment_prepared_sample.yaml | 31 + .../linkml/modules/external_data.yaml | 441 ---- .../billion_ton_2023_record.yaml | 89 + .../modules/external_data/landiq_record.yaml | 69 + .../linkml/modules/external_data/polygon.yaml | 30 + .../resource_usda_commodity_map.yaml | 39 + .../external_data/usda_census_record.yaml | 44 + .../modules/external_data/usda_commodity.yaml | 30 + .../modules/external_data/usda_domain.yaml | 13 + .../external_data/usda_market_record.yaml | 119 ++ .../external_data/usda_market_report.yaml | 57 + .../usda_statistic_category.yaml | 13 + .../external_data/usda_survey_program.yaml | 13 + .../external_data/usda_survey_record.yaml | 60 + .../modules/external_data/usda_term_map.yaml | 42 + .../linkml/modules/field_sampling.yaml | 200 -- .../modules/field_sampling/ag_treatment.yaml | 13 + .../field_sampling/collection_method.yaml | 13 + .../modules/field_sampling/field_sample.yaml | 105 + .../field_sample_condition.yaml | 43 + .../field_sampling/field_storage_method.yaml | 13 + .../field_sampling/harvest_method.yaml | 13 + .../field_sampling/location_soil_type.yaml | 27 + .../physical_characteristic.yaml | 42 + .../field_sampling/processing_method.yaml | 13 + .../modules/field_sampling/soil_type.yaml | 13 + .../linkml/modules/general_analysis.yaml | 97 - .../general_analysis/analysis_type.yaml | 13 + .../modules/general_analysis/dataset.yaml | 38 + .../general_analysis/dimension_type.yaml | 13 + .../modules/general_analysis/observation.yaml | 64 + .../datamodels/linkml/modules/geography.yaml | 109 - .../linkml/modules/infrastructure.yaml | 1069 ---------- .../infrastructure/facility_record.yaml | 54 + .../infrastructure_biodiesel_plants.yaml | 83 + .../infrastructure_biosolids_facilities.yaml | 228 +++ .../infrastructure_cafo_manure_locations.yaml | 98 + .../infrastructure_combustion_plants.yaml | 103 + ...nfrastructure_district_energy_systems.yaml | 123 ++ .../infrastructure_ethanol_biorefineries.yaml | 63 + ...astructure_food_processing_facilities.yaml | 103 + .../infrastructure_landfills.yaml | 188 ++ ...ructure_livestock_anaerobic_digesters.yaml | 133 ++ ...ure_msw_to_energy_anaerobic_digesters.yaml | 98 + ...cture_saf_and_renewable_diesel_plants.yaml | 83 + ...structure_wastewater_treatment_plants.yaml | 168 ++ .../datamodels/linkml/modules/lineage.yaml | 88 - .../modules/lineage/entity_lineage.yaml | 36 + .../linkml/modules/lineage/etl_run.yaml | 44 + .../linkml/modules/lineage/lineage_group.yaml | 25 + .../modules/methods_parameters_units.yaml | 130 -- .../methods_parameters_units/method.yaml | 46 + .../method_abbrev.yaml | 13 + .../method_category.yaml | 13 + .../method_standard.yaml | 13 + .../methods_parameters_units/parameter.yaml | 28 + .../parameter_category.yaml | 13 + .../parameter_category_parameter.yaml | 31 + .../parameter_unit.yaml | 31 + .../methods_parameters_units/unit.yaml | 13 + .../{people.yaml => people/contact.yaml} | 30 +- .../linkml/modules/people/provider.yaml | 24 + .../datamodels/linkml/modules/places.yaml | 105 - .../linkml/modules/places/geography.yaml | 52 + .../modules/places/location_address.yaml | 56 + .../linkml/modules/primary_ag_product.yaml | 23 - .../linkml/modules/resource_availability.yaml | 35 - .../modules/resource_counterfactual.yaml | 47 - .../linkml/modules/resource_information.yaml | 189 -- .../primary_ag_product.yaml | 14 + .../resource_information/resource.yaml | 44 + .../resource_availability.yaml | 43 + .../resource_information/resource_class.yaml | 13 + .../resource_counterfactual.yaml | 96 + .../resource_morphology.yaml | 19 +- .../resource_subclass.yaml | 13 + .../linkml/modules/resource_subclass.yaml | 21 - .../linkml/modules/sample_preparation.yaml | 70 - .../preparation_method.yaml | 34 + .../preparation_method_abbreviation.yaml | 13 + .../sample_preparation/prepared_sample.yaml | 40 + .../linkml/test_schemas/schema1.yaml | 18 + .../linkml/test_schemas/schema2.yaml | 22 + .../linkml/test_schemas/schema3.yaml | 26 + .../schemas/generated/aim1_records.py | 1747 ---------------- .../schemas/generated/aim2_records.py | 1600 --------------- .../schemas/generated/ca_biositing.py | 1817 ++++++++--------- .../datamodels/schemas/generated/core.py | 46 - .../generated/data_sources_metadata.py | 1030 ---------- .../schemas/generated/experiment_equipment.py | 1371 ------------- .../schemas/generated/external_data.py | 1557 -------------- .../schemas/generated/field_sampling.py | 1030 ---------- .../schemas/generated/general_analysis.py | 1148 ----------- .../datamodels/schemas/generated/geography.py | 106 - .../schemas/generated/infrastructure.py | 1625 --------------- .../datamodels/schemas/generated/lineage.py | 109 - .../generated/methods_parameters_units.py | 1030 ---------- .../datamodels/schemas/generated/people.py | 106 - .../datamodels/schemas/generated/places.py | 106 - .../schemas/generated/primary_ag_product.py | 75 - .../generated/resource_availability.py | 308 --- .../schemas/generated/resource_class.py | 74 - .../generated/resource_counterfactual.py | 1030 ---------- .../schemas/generated/resource_information.py | 308 --- .../schemas/generated/resource_morphology.py | 308 --- .../schemas/generated/resource_subclass.py | 74 - .../schemas/generated/sample_preparation.py | 1119 ---------- .../schemas/generated_test/schema1.py | 22 + .../schemas/generated_test/schema2.py | 40 + .../schemas/generated_test/schema3.py | 59 + .../datamodels/utils/generate_sqla.py | 25 +- .../datamodels/utils/generate_test_sqla.py | 69 + .../pipeline/utils/etl_notebook.ipynb | 672 +++--- 148 files changed, 5824 insertions(+), 20469 deletions(-) delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/aim1_record_base.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/calorimetry_record.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/compositional_record.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/ftnir_record.yaml rename src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/{resource_class.yaml => aim1_records/icp_record.yaml} (51%) create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/proximate_record.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/rgb_record.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/ultimate_record.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/xrd_record.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/xrf_record.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/aim2_record_base.yaml create mode 100644 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create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema1.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema2.yaml create mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema3.yaml delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py delete mode 100644 src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py delete mode 100644 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src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated_test/schema3.py create mode 100644 src/ca_biositing/datamodels/utils/generate_test_sqla.py diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml index fed17afb..5c2c2bd9 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/ca_biositing.yaml @@ -16,19 +16,99 @@ default_range: string imports: - linkml:types - - modules/core - - modules/resource_information - - modules/field_sampling - - modules/places - - modules/people - - modules/lineage - - modules/data_sources_metadata - - modules/sample_preparation - - modules/methods_parameters_units - - modules/experiment_equipment - - modules/general_analysis - - modules/aim1_records - - modules/aim2_records - - modules/external_data - - modules/infrastructure - - modules/geography + - modules/core/base_entity + - modules/core/lookup_base + - modules/core/note + - modules/data_sources_metadata/data_source + - modules/data_sources_metadata/data_source_type + - modules/data_sources_metadata/file_object_metadata + - modules/data_sources_metadata/location_resolution + - modules/data_sources_metadata/source_type + - modules/experiment_equipment/equipment + - modules/experiment_equipment/experiment + - modules/experiment_equipment/experiment_analysis + - modules/experiment_equipment/experiment_equipment + - modules/experiment_equipment/experiment_method + - modules/experiment_equipment/experiment_prepared_sample + - modules/external_data/billion_ton_2023_record + - modules/external_data/landiq_record + - modules/external_data/polygon + - modules/external_data/resource_usda_commodity_map + - modules/external_data/usda_census_record + - modules/external_data/usda_commodity + - modules/external_data/usda_domain + - modules/external_data/usda_market_record + - modules/external_data/usda_market_report + - modules/external_data/usda_statistic_category + - modules/external_data/usda_survey_program + - modules/external_data/usda_survey_record + - modules/external_data/usda_term_map + - modules/field_sampling/ag_treatment + - modules/field_sampling/collection_method + - modules/field_sampling/field_sample + - modules/field_sampling/field_sample_condition + - modules/field_sampling/field_storage_method + - modules/field_sampling/harvest_method + - modules/field_sampling/location_soil_type + - modules/field_sampling/physical_characteristic + - modules/field_sampling/processing_method + - modules/field_sampling/soil_type + - modules/general_analysis/analysis_type + - modules/general_analysis/dataset + - modules/general_analysis/dimension_type + - modules/general_analysis/observation + - modules/infrastructure/facility_record + - modules/infrastructure/infrastructure_biodiesel_plants + - modules/infrastructure/infrastructure_biosolids_facilities + - modules/infrastructure/infrastructure_cafo_manure_locations + - modules/infrastructure/infrastructure_combustion_plants + - modules/infrastructure/infrastructure_district_energy_systems + - modules/infrastructure/infrastructure_ethanol_biorefineries + - modules/infrastructure/infrastructure_food_processing_facilities + - modules/infrastructure/infrastructure_landfills + - modules/infrastructure/infrastructure_livestock_anaerobic_digesters + - modules/infrastructure/infrastructure_msw_to_energy_anaerobic_digesters + - modules/infrastructure/infrastructure_saf_and_renewable_diesel_plants + - modules/infrastructure/infrastructure_wastewater_treatment_plants + - modules/lineage/entity_lineage + - modules/lineage/etl_run + - modules/lineage/lineage_group + - modules/methods_parameters_units/method + - modules/methods_parameters_units/method_abbrev + - modules/methods_parameters_units/method_category + - modules/methods_parameters_units/method_standard + - modules/methods_parameters_units/parameter + - modules/methods_parameters_units/parameter_category + - modules/methods_parameters_units/parameter_category_parameter + - modules/methods_parameters_units/parameter_unit + - modules/methods_parameters_units/unit + - modules/people/contact + - modules/people/provider + - modules/places/geography + - modules/places/location_address + - modules/aim1_records/aim1_record_base + - modules/aim1_records/proximate_record + - modules/aim1_records/ultimate_record + - modules/aim1_records/compositional_record + - modules/aim1_records/icp_record + - modules/aim1_records/xrf_record + - modules/aim1_records/xrd_record + - modules/aim1_records/calorimetry_record + - modules/aim1_records/ftnir_record + - modules/aim1_records/rgb_record + - modules/aim2_records/aim2_record_base + - modules/aim2_records/pretreatment_record + - modules/aim2_records/fermentation_record + - modules/aim2_records/gasification_record + - modules/aim2_records/autoclave_record + - modules/aim2_records/strain + - modules/resource_information/primary_ag_product + - modules/resource_information/resource + - modules/resource_information/resource_availability + - modules/resource_information/resource_class + #- modules/resource_information/resource_counterfactual + - modules/resource_information/resource_morphology + - modules/resource_information/resource_subclass + - modules/sample_preparation/preparation_method + - modules/sample_preparation/preparation_method_abbreviation + - modules/sample_preparation/prepared_sample diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml deleted file mode 100644 index 8328faec..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records.yaml +++ /dev/null @@ -1,140 +0,0 @@ -id: https://w3id.org/ca_biositing/aim1_records -name: aim1_records -title: Aim 1 Records -description: Records for Aim 1 analysis. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - general_analysis - - experiment_equipment - - resource_information - - sample_preparation - - methods_parameters_units - - data_sources_metadata - -classes: - Aim1RecordBase: - is_a: BaseEntity - abstract: true - slots: - - dataset_id - - experiment_id - - resource_id - - sample_id - - technical_replicate_no - - technical_replicate_total - - method_id - - analyst_id - - raw_data_id - - qc_pass - - note - - ProximateRecord: - is_a: Aim1RecordBase - description: Proximate analysis record. - - UltimateRecord: - is_a: Aim1RecordBase - description: Ultimate analysis record. - - CompositionalRecord: - is_a: Aim1RecordBase - description: Compositional analysis record. - - IcpRecord: - is_a: Aim1RecordBase - description: ICP analysis record. - - XrfRecord: - is_a: Aim1RecordBase - description: XRF analysis record. - slots: - - maybe_wavelength_nm - - maybe_intensity - - maybe_energy_slope - - maybe_energy_offset - - XrdRecord: - is_a: Aim1RecordBase - description: XRD analysis record. - slots: - - maybe_scan_low_nm - - maybe_scan_high_nm - - CalorimetryRecord: - is_a: Aim1RecordBase - description: Calorimetry analysis record. - - FtnirRecord: - is_a: Aim1RecordBase - description: FT-NIR analysis record. - - RgbRecord: - is_a: Aim1RecordBase - description: RGB analysis record. - -slots: - #Slots imported - #dataset_id: from general_analysis.yaml - #experiment_id: from experiments_equipment.yaml - #analyst_id: from experiments_equipment.yaml - #resource_id: from resource_information.yaml - #method_id: from experiments_equipment.yaml - #note: from core.yaml - - #New slots defined in Aim1RecordBase class - - sample_id: - range: integer - description: Reference to PreparedSample. - - technical_replicate_no: - range: integer - description: Replicate number. - - technical_replicate_total: - range: integer - description: Total number of replicates. - - raw_data_id: - range: integer - description: Reference to FileObjectMetadata. - - qc_pass: - range: boolean - description: Whether the record passed QC. - - #Potential slots for XrfRecord and XrdRecords - - maybe_wavelength_nm: - range: decimal - description: Wavelength in nm. - - maybe_intensity: - range: decimal - description: Intensity. - - maybe_energy_slope: - range: decimal - description: Energy slope. - - maybe_energy_offset: - range: decimal - description: Energy offset. - - maybe_scan_low_nm: - range: integer - description: Low scan range in nm. - - maybe_scan_high_nm: - range: integer - description: High scan range in nm. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/aim1_record_base.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/aim1_record_base.yaml new file mode 100644 index 00000000..0a6d0b20 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/aim1_record_base.yaml @@ -0,0 +1,86 @@ +id: https://w3id.org/ca_biositing/aim1_records/aim1_record_base +name: aim1_record_base +title: Aim 1 Record Base +description: Base class for Aim 1 records. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - ../core/base_entity + - ../general_analysis/dataset + - ../experiment_equipment/experiment + - ../resource_information/resource + - ../sample_preparation/prepared_sample + - ../methods_parameters_units/method + - ../people/contact + - ../data_sources_metadata/file_object_metadata + +classes: + Aim1RecordBase: + is_a: BaseEntity + abstract: true + slots: + - dataset_id + + - experiment_id + - resource_id + - sample_id + - technical_replicate_no + - technical_replicate_total + - method_id + - analyst_id + - raw_data_id + - qc_pass + - note + +slots: + sample_id: + range: integer + description: Reference to PreparedSample. + + resource_id: + range: Resource + description: Reference to Resource. + + method_id: + range: Method + description: Reference to Method used in analysis. + + analyst_id: + range: Contact + description: Reference to Analyst who performed analysis. + + raw_data_id: + range: FileObjectMetadata + description: Reference to FileObjectMetadata. + + dataset_id: + range: Dataset + description: Reference to Dataset. + + experiment_id: + range: Experiment + description: Reference to Experiment. + + technical_replicate_no: + range: integer + description: Replicate number. + + technical_replicate_total: + range: integer + description: Total number of replicates. + + qc_pass: + range: boolean + description: Whether the record passed QC. + + note: + range: string + description: Additional notes about the record. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/calorimetry_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/calorimetry_record.yaml new file mode 100644 index 00000000..57de7d67 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/calorimetry_record.yaml @@ -0,0 +1,21 @@ +id: https://w3id.org/ca_biositing/aim1_records/calorimetry_record +name: calorimetry_record +title: Calorimetry Record +description: Calorimetry analysis record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim1_record_base + +classes: + CalorimetryRecord: + is_a: Aim1RecordBase + description: Calorimetry analysis record. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/compositional_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/compositional_record.yaml new file mode 100644 index 00000000..0deffcb2 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/compositional_record.yaml @@ -0,0 +1,21 @@ +id: https://w3id.org/ca_biositing/aim1_records/compositional_record +name: compositional_record +title: Compositional Record +description: Compositional analysis record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim1_record_base + +classes: + CompositionalRecord: + is_a: Aim1RecordBase + description: Compositional analysis record. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/ftnir_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/ftnir_record.yaml new file mode 100644 index 00000000..e9386428 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/ftnir_record.yaml @@ -0,0 +1,21 @@ +id: https://w3id.org/ca_biositing/aim1_records/ftnir_record +name: ftnir_record +title: FT-NIR Record +description: FT-NIR analysis record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim1_record_base + +classes: + FtnirRecord: + is_a: Aim1RecordBase + description: FT-NIR analysis record. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_class.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/icp_record.yaml similarity index 51% rename from src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_class.yaml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/icp_record.yaml index cc39fe4e..db991695 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_class.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/icp_record.yaml @@ -1,7 +1,7 @@ -id: https://w3id.org/ca_biositing/resource_class -name: resource_class -title: Resource Class -description: Classification of resources. +id: https://w3id.org/ca_biositing/aim1_records/icp_record +name: icp_record +title: ICP Record +description: ICP analysis record. license: https://creativecommons.org/publicdomain/zero/1.0/ prefixes: @@ -13,9 +13,9 @@ default_range: string imports: - linkml:types - - core + - aim1_record_base classes: - ResourceClass: - is_a: LookupBase - description: Classification of resources. + IcpRecord: + is_a: Aim1RecordBase + description: ICP analysis record. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/proximate_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/proximate_record.yaml new file mode 100644 index 00000000..57e04b15 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/proximate_record.yaml @@ -0,0 +1,21 @@ +id: https://w3id.org/ca_biositing/aim1_records/proximate_record +name: proximate_record +title: Proximate Record +description: Proximate analysis record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim1_record_base + +classes: + ProximateRecord: + is_a: Aim1RecordBase + description: Proximate analysis record. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/rgb_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/rgb_record.yaml new file mode 100644 index 00000000..11dc81bc --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/rgb_record.yaml @@ -0,0 +1,21 @@ +id: https://w3id.org/ca_biositing/aim1_records/rgb_record +name: rgb_record +title: RGB Record +description: RGB analysis record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim1_record_base + +classes: + RgbRecord: + is_a: Aim1RecordBase + description: RGB analysis record. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/ultimate_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/ultimate_record.yaml new file mode 100644 index 00000000..b03835de --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/ultimate_record.yaml @@ -0,0 +1,21 @@ +id: https://w3id.org/ca_biositing/aim1_records/ultimate_record +name: ultimate_record +title: Ultimate Record +description: Ultimate analysis record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim1_record_base + +classes: + UltimateRecord: + is_a: Aim1RecordBase + description: Ultimate analysis record. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/xrd_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/xrd_record.yaml new file mode 100644 index 00000000..00a69f73 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/xrd_record.yaml @@ -0,0 +1,32 @@ +id: https://w3id.org/ca_biositing/aim1_records/xrd_record +name: xrd_record +title: XRD Record +description: XRD analysis record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim1_record_base + +classes: + XrdRecord: + is_a: Aim1RecordBase + description: XRD analysis record. + slots: + - scan_low_nm + - scan_high_nm + +slots: + scan_low_nm: + range: integer + description: Low scan range in nm. + scan_high_nm: + range: integer + description: High scan range in nm. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/xrf_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/xrf_record.yaml new file mode 100644 index 00000000..df026e1b --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim1_records/xrf_record.yaml @@ -0,0 +1,40 @@ +id: https://w3id.org/ca_biositing/aim1_records/xrf_record +name: xrf_record +title: XRF Record +description: XRF analysis record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim1_record_base + +classes: + XrfRecord: + is_a: Aim1RecordBase + description: XRF analysis record. + slots: + - wavelength_nm + - intensity + - energy_slope + - energy_offset + +slots: + wavelength_nm: + range: decimal + description: Wavelength in nm. + intensity: + range: decimal + description: Intensity. + energy_slope: + range: decimal + description: Energy slope. + energy_offset: + range: decimal + description: Energy offset. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml deleted file mode 100644 index 8e20f1c9..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records.yaml +++ /dev/null @@ -1,170 +0,0 @@ -id: https://w3id.org/ca_biositing/aim2_records -name: aim2_records -title: Aim 2 Records -description: Records for Aim 2 analysis. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - general_analysis - - experiment_equipment - - resource_information - - sample_preparation - - methods_parameters_units - - data_sources_metadata - - people - -classes: - Aim2RecordBase: - is_a: BaseEntity - abstract: true - slots: - - dataset_id - - experiment_id - - resource_id - - sample_id - - technical_replicate_total - - technical_replicate_no - - calc_method_id - - calc_analyst_id - - raw_data_id - - qc_pass - - note - - PretreatmentRecord: - is_a: Aim2RecordBase - description: Pretreatment record. - slots: - - pretreatment_method_id - - eh_method_id - - reaction_block_id - - block_position - - temperature - - replicate_no #delete bc redundancy with technical_replicate_no in aim2recordbase entity? - - FermentationRecord: - is_a: Aim2RecordBase - description: Fermentation record. - slots: - - strain_id - - pretreatment_method_id - - eh_method_id - - replicate_no #delete bc redundancy with technical_replicate_no in aim2recordbase entity? - - well_position - - temperature - - agitation_rpm - - vessel_id - - analyte_detection_equipment_id - - GasificationRecord: - is_a: Aim2RecordBase - description: Gasification record. - slots: - - feedstock_mass - - bed_temperature - - gas_flow_rate - - AutoclaveRecord: - is_a: Aim2RecordBase - description: Autoclave record. - slots: [] - - Strain: - is_a: LookupBase - description: Strain used in fermentation. - slots: - - parent_strain_id - -slots: - pretreatment_method_id: - range: integer - description: Reference to Method (pretreatment). - - eh_method_id: - range: integer - description: Reference to Method (enzymatic hydrolysis). - - reaction_block_id: - range: integer - description: ID of the reaction block. - - block_position: - range: string - description: Position in the block. - - temperature: - range: decimal - description: Temperature. - - replicate_no: - range: integer - description: Replicate number. - - strain_id: - range: integer - description: Reference to Strain. - - well_position: - range: string - description: Position in the well. - - agitation_rpm: - range: decimal - description: Agitation in RPM. - - vessel_id: - range: integer - description: Reference to Equipment (vessel). - - analyte_detection_equipment_id: - range: integer - description: Reference to Equipment (detection). - - feedstock_mass: - range: decimal - description: Mass of feedstock. - - bed_temperature: - range: decimal - description: Bed temperature. - - gas_flow_rate: - range: decimal - description: Gas flow rate. - - parent_strain_id: - range: integer - - sample_id: - range: integer - - raw_data_id: - range: integer - description: Reference to FileObjectMetadata. - - qc_pass: - range: boolean - description: Whether the record passed QC. - - technical_replicate_no: - range: integer - description: Replicate number. - - calc_method_id: - range: integer - description: Reference to Method used in calculation. - - calc_analyst_id: - range: integer - description: Reference to Analyst who performed calculation. - - technical_replicate_total: - range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/aim2_record_base.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/aim2_record_base.yaml new file mode 100644 index 00000000..e614eb3f --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/aim2_record_base.yaml @@ -0,0 +1,60 @@ +id: https://w3id.org/ca_biositing/aim2_records/aim2_record_base +name: aim2_record_base +title: Aim 2 Record Base +description: Base class for Aim 2 records. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - ../core/base_entity + - ../general_analysis/dataset + - ../experiment_equipment/experiment + +classes: + Aim2RecordBase: + is_a: BaseEntity + abstract: true + slots: + - dataset_id + - experiment_id + - resource_id + - sample_id + - technical_replicate_total + - technical_replicate_no + - calc_method_id + - calc_analyst_id + - raw_data_id + - qc_pass + - note + +slots: + experiment_id: + range: integer + description: Reference to Experiment. + resource_id: + range: integer + sample_id: + range: integer + technical_replicate_total: + range: integer + technical_replicate_no: + range: integer + calc_method_id: + range: integer + description: Reference to Method used in calculation. + calc_analyst_id: + range: integer + description: Reference to Analyst who performed calculation. + raw_data_id: + range: integer + description: Reference to FileObjectMetadata. + qc_pass: + range: boolean + description: Whether the record passed QC. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/autoclave_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/autoclave_record.yaml new file mode 100644 index 00000000..d6d96bed --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/autoclave_record.yaml @@ -0,0 +1,22 @@ +id: https://w3id.org/ca_biositing/aim2_records/autoclave_record +name: autoclave_record +title: Autoclave Record +description: Autoclave record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim2_record_base + +classes: + AutoclaveRecord: + is_a: Aim2RecordBase + description: Autoclave record. + slots: [] diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/fermentation_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/fermentation_record.yaml new file mode 100644 index 00000000..f6252706 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/fermentation_record.yaml @@ -0,0 +1,58 @@ +id: https://w3id.org/ca_biositing/aim2_records/fermentation_record +name: fermentation_record +title: Fermentation Record +description: Fermentation record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim2_record_base + - ../methods_parameters_units/method + - ../experiment_equipment/equipment + +classes: + FermentationRecord: + is_a: Aim2RecordBase + description: Fermentation record. + slots: + - strain_id + - pretreatment_method_id + - eh_method_id + - well_position + - temperature + - agitation_rpm + - vessel_id + - analyte_detection_equipment_id + +slots: + strain_id: + range: integer + description: Reference to Strain. + pretreatment_method_id: + range: integer + description: Reference to Method (pretreatment). + eh_method_id: + range: integer + description: Reference to Method (enzymatic hydrolysis). + well_position: + range: string + description: Position in the well. + temperature: + range: decimal + description: Temperature. + agitation_rpm: + range: decimal + description: Agitation in RPM. + vessel_id: + range: integer + description: Reference to Equipment (vessel). + analyte_detection_equipment_id: + range: integer + description: Reference to Equipment (detection). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/gasifcation_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/gasifcation_record.yaml new file mode 100644 index 00000000..e69de29b diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/gasification_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/gasification_record.yaml new file mode 100644 index 00000000..81bc6cfd --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/gasification_record.yaml @@ -0,0 +1,36 @@ +id: https://w3id.org/ca_biositing/aim2_records/gasification_record +name: gasification_record +title: Gasification Record +description: Gasification record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim2_record_base + +classes: + GasificationRecord: + is_a: Aim2RecordBase + description: Gasification record. + slots: + - feedstock_mass + - bed_temperature + - gas_flow_rate + +slots: + feedstock_mass: + range: decimal + description: Mass of feedstock. + bed_temperature: + range: decimal + description: Bed temperature. + gas_flow_rate: + range: decimal + description: Gas flow rate. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/pretreatment_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/pretreatment_record.yaml new file mode 100644 index 00000000..d4309680 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/pretreatment_record.yaml @@ -0,0 +1,49 @@ +id: https://w3id.org/ca_biositing/aim2_records/pretreatment_record +name: pretreatment_record +title: Pretreatment Record +description: Pretreatment record. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - aim2_record_base + - ../methods_parameters_units/method + +classes: + PretreatmentRecord: + is_a: Aim2RecordBase + description: Pretreatment record. + slots: + - pretreatment_method_id + - eh_method_id + - reaction_block_id + - block_position + - temperature + - replicate_no + +slots: + pretreatment_method_id: + range: integer + description: Reference to Method (pretreatment). + eh_method_id: + range: integer + description: Reference to Method (enzymatic hydrolysis). + reaction_block_id: + range: integer + description: ID of the reaction block. + block_position: + range: string + description: Position in the block. + temperature: + range: decimal + description: Temperature. + replicate_no: + range: integer + description: Replicate number. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/strain.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/strain.yaml new file mode 100644 index 00000000..e16307b7 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/aim2_records/strain.yaml @@ -0,0 +1,27 @@ +id: https://w3id.org/ca_biositing/aim2_records/strain +name: strain +title: Strain +description: Strain used in fermentation. +license: https://creativecommons.org/publicdomain/zero/1.0/ + +prefixes: + linkml: https://w3id.org/linkml/ + ca_biositing: https://w3id.org/ca_biositing/ + +default_prefix: ca_biositing +default_range: string + +imports: + - linkml:types + - ../core/lookup_base + +classes: + Strain: + is_a: LookupBase + description: Strain used in fermentation. + slots: + - parent_strain_id + +slots: + parent_strain_id: + range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml deleted file mode 100644 index 870eb513..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core.yaml +++ /dev/null @@ -1,79 +0,0 @@ -id: https://w3id.org/ca_biositing/core -name: core -title: Core Definitions -description: Base classes, lineage, and data source definitions. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - -classes: - BaseEntity: - mixin: true - description: Base entity included in all main entity tables. - slots: - - id - - created_at - - updated_at - - etl_run_id - - lineage_group_id - - LookupBase: - mixin: true - description: Base class for enum/ontology-like tables. - slots: - - id - - name - - description - - uri - -slots: - ##Slots from BaseEntity - - id: - identifier: true - range: integer - description: Unique identifier. - - created_at: - range: datetime - description: Timestamp when the record was created. - - updated_at: - range: datetime - description: Timestamp when the record was last updated. - - etl_run_id: - range: string - description: Identifier of the ETL run. - - lineage_group_id: - range: integer - description: Reference to the lineage group. - - ##Slots from LookupBase - - name: - range: string - description: Name of the entity. - - description: - range: string - description: Description of the entity. - - uri: - range: uri - description: URI for the entity. - - ##Slots for other basic fields used across the schema - - note: - range: string - description: Additional notes. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core/base_entity.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core/base_entity.yaml new file mode 100644 index 00000000..7fcc3d49 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core/base_entity.yaml @@ -0,0 +1,40 @@ +id: https://w3id.org/ca_biositing/core/base_entity +name: base_entity +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types +default_range: string + +classes: + BaseEntity: + mixin: true + description: Base entity included in all main entity tables. + slots: + - id + - created_at + - updated_at + - etl_run_id + - lineage_group_id + +slots: + id: + identifier: true + range: integer + description: Unique identifier. + + created_at: + range: datetime + description: Timestamp when the record was created. + + updated_at: + range: datetime + description: Timestamp when the record was last updated. + + etl_run_id: + range: string + description: Identifier of the ETL run. + + lineage_group_id: + range: integer + description: Reference to the lineage group. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core/lookup_base.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core/lookup_base.yaml new file mode 100644 index 00000000..62932654 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core/lookup_base.yaml @@ -0,0 +1,34 @@ +id: https://w3id.org/ca_biositing/core/lookup_base +name: lookup_base +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types +default_range: string + +classes: + LookupBase: + mixin: true + description: Base class for enum/ontology-like tables. + slots: + - id + - name + - description + - uri + +slots: + id: + identifier: true + range: integer + description: Unique identifier. + name: + range: string + description: Name of the entity. + + description: + range: string + description: Description of the entity. + + uri: + range: uri + description: URI for the entity. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core/note.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core/note.yaml new file mode 100644 index 00000000..91373afd --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/core/note.yaml @@ -0,0 +1,12 @@ +id: https://w3id.org/ca_biositing/core/note +name: note +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types +default_range: string + +slots: + note: + range: string + description: Additional notes. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/data_source.yaml similarity index 55% rename from src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/data_source.yaml index 1eeb2f53..648926b6 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/data_source.yaml @@ -1,20 +1,14 @@ -id: https://w3id.org/ca_biositing/data_sources_metadata -name: data_sources_metadata -title: Data Sources and Metadata -description: Data sources, types, and file metadata. -license: https://creativecommons.org/publicdomain/zero/1.0/ - +id: https://w3id.org/ca_biositing/data_sources_metadata/data_source +name: data_source prefixes: linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - imports: - linkml:types - - core - - field_sampling + - ../core/base_entity + - data_source_type + - location_resolution + - ../core/note +default_range: string classes: DataSource: @@ -42,68 +36,9 @@ classes: - uri - note - FileObjectMetadata: - is_a: BaseEntity - description: Metadata for a file object. - slots: - - data_source_id - - bucket_path - - file_format - - file_size - - checksum_md5 - - checksum_sha256 - - DataSourceType: - is_a: BaseEntity - description: Type of data source (e.g. database, literature). - slots: - - source_type_id - - LocationResolution: - is_a: LookupBase - description: Resolution of the location (e.g. nation, state, county). - - SourceType: - is_a: LookupBase - description: Type of source (e.g. database, literature). - slots: - #FileObjectMetadata slots - - data_source_id: - range: integer - description: Reference to DataSource. - - bucket_path: - range: string - description: Path to the file in the bucket. - - file_format: - range: string - description: Format of the file. - - file_size: - range: integer - description: Size of the file in bytes. - - checksum_md5: - range: string - description: MD5 checksum of the file. - - checksum_sha256: - range: string - description: SHA256 checksum of the file. - - #DataSourceType slots - - source_type_id: - range: integer - description: Reference to SourceType. - - #DataSource slots - data_source_type_id: - range: integer + range: DataSourceType description: Reference to DataSourceType. full_title: @@ -157,7 +92,7 @@ slots: description: The temporal topic of the resource (Daterange). location_coverage_id: - range: integer + range: LocationResolution description: Reference to LocationResolution. rights: diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/data_source_type.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/data_source_type.yaml new file mode 100644 index 00000000..924d9e5f --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/data_source_type.yaml @@ -0,0 +1,21 @@ +id: https://w3id.org/ca_biositing/data_sources_metadata/data_source_type +name: data_source_type +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - source_type +default_range: string + +classes: + DataSourceType: + is_a: BaseEntity + description: Type of data source (e.g. database, literature). + slots: + - source_type_id + +slots: + source_type_id: + range: SourceType + description: Reference to SourceType. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/file_object_metadata.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/file_object_metadata.yaml new file mode 100644 index 00000000..919b6ca1 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/file_object_metadata.yaml @@ -0,0 +1,46 @@ +id: https://w3id.org/ca_biositing/data_sources_metadata/file_object_metadata +name: file_object_metadata +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - data_source +default_range: string + +classes: + FileObjectMetadata: + is_a: BaseEntity + description: Metadata for a file object. + slots: + - data_source_id + - bucket_path + - file_format + - file_size + - checksum_md5 + - checksum_sha256 + +slots: + data_source_id: + range: DataSource + description: Reference to DataSource. + + bucket_path: + range: string + description: Path to the file in the bucket. + + file_format: + range: string + description: Format of the file. + + file_size: + range: integer + description: Size of the file in bytes. + + checksum_md5: + range: string + description: MD5 checksum of the file. + + checksum_sha256: + range: string + description: SHA256 checksum of the file. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/location_resolution.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/location_resolution.yaml new file mode 100644 index 00000000..89c3ccdc --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/location_resolution.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/data_sources_metadata/location_resolution +name: location_resolution +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + LocationResolution: + is_a: LookupBase + description: Resolution of the location (e.g. nation, state, county). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/source_type.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/source_type.yaml new file mode 100644 index 00000000..f4ad79dc --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/data_sources_metadata/source_type.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/data_sources_metadata/source_type +name: source_type +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + SourceType: + is_a: LookupBase + description: Type of source (e.g. database, literature). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml deleted file mode 100644 index bc76394b..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment.yaml +++ /dev/null @@ -1,127 +0,0 @@ -id: https://w3id.org/ca_biositing/experiment_equipment -name: experiment_equipment -title: Experiments and Equipment -description: Experimental data and equipment. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - places - - methods_parameters_units - - sample_preparation - - general_analysis - -classes: - Experiment: - is_a: BaseEntity - description: Experiment definition. - slots: - - analyst_id - - exper_start_date - - exper_duration - - exper_duration_unit_id - - exper_location_id - - description - - Equipment: - is_a: LookupBase - description: Equipment used in experiments. - slots: - - equipment_location_id - - ExperimentMethod: - description: Link between Experiment and Method. - slots: - - id - - experiment_id - - method_id - slot_usage: - id: - identifier: true - range: integer - - ExperimentEquipment: - description: Link between Experiment and Equipment. - slots: - - id - - experiment_id - - equipment_id - slot_usage: - id: - identifier: true - range: integer - - ExperimentAnalysis: - description: Link between Experiment and AnalysisType. - slots: - - id - - experiment_id - - analysis_type_id - slot_usage: - id: - identifier: true - range: integer - - ExperimentPreparedSample: - description: Link between Experiment and PreparedSample. - slots: - - id - - experiment_id - - prepared_sample_id - slot_usage: - id: - identifier: true - range: integer - -slots: - analyst_id: - range: integer - description: Reference to Contact (analyst). - - exper_start_date: - range: date - description: Start date of the experiment. - - exper_duration: - range: decimal - description: Duration of the experiment. - - exper_duration_unit_id: - range: integer - description: Reference to Unit. - - exper_location_id: - range: integer - description: Reference to LocationAddress. - - equipment_location_id: - range: integer - description: Reference to LocationAddress. - - experiment_id: - range: integer - description: Reference to Experiment. - - equipment_id: - range: integer - description: Reference to Equipment. - - analysis_type_id: - range: integer - description: Reference to AnalysisType. - - prepared_sample_id: - range: integer - description: Reference to PreparedSample. - - method_id: - range: integer - description: Reference to Method. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/equipment.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/equipment.yaml new file mode 100644 index 00000000..fb403b50 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/equipment.yaml @@ -0,0 +1,21 @@ +id: https://w3id.org/ca_biositing/experiment_equipment/equipment +name: equipment +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base + - ../places/location_address +default_range: string + +classes: + Equipment: + is_a: LookupBase + description: Equipment used in experiments. + slots: + - equipment_location_id + +slots: + equipment_location_id: + range: LocationAddress + description: Reference to LocationAddress. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment.yaml new file mode 100644 index 00000000..3719fea4 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment.yaml @@ -0,0 +1,44 @@ +id: https://w3id.org/ca_biositing/experiment_equipment/experiment +name: experiment +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../people/contact + - ../places/location_address + - ../methods_parameters_units/unit +default_range: string + +classes: + Experiment: + is_a: BaseEntity + description: Experiment definition. + slots: + - analyst_id + - exper_start_date + - exper_duration + - exper_duration_unit_id + - exper_location_id + - description + +slots: + analyst_id: + range: Contact + description: Reference to Contact (analyst). + + exper_start_date: + range: date + description: Start date of the experiment. + + exper_duration: + range: decimal + description: Duration of the experiment. + + exper_duration_unit_id: + range: Unit + description: Reference to Unit. + + exper_location_id: + range: LocationAddress + description: Reference to LocationAddress. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_analysis.yaml new file mode 100644 index 00000000..f6be8596 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_analysis.yaml @@ -0,0 +1,30 @@ +id: https://w3id.org/ca_biositing/experiment_equipment/experiment_analysis +name: experiment_analysis +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - experiment + - ../general_analysis/analysis_type +default_range: string + +classes: + ExperimentAnalysis: + description: Link between Experiment and AnalysisType. + slots: + - id + - experiment_id + - analysis_type_id + slot_usage: + id: + identifier: true + range: integer + +slots: + experiment_id: + range: Experiment + description: Reference to Experiment. + + analysis_type_id: + range: AnalysisType + description: Reference to AnalysisType. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_equipment.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_equipment.yaml new file mode 100644 index 00000000..7197ebeb --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_equipment.yaml @@ -0,0 +1,30 @@ +id: https://w3id.org/ca_biositing/experiment_equipment/experiment_equipment +name: experiment_equipment +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - experiment + - equipment +default_range: string + +classes: + ExperimentEquipment: + description: Link between Experiment and Equipment. + slots: + - id + - experiment_id + - equipment_id + slot_usage: + id: + identifier: true + range: integer + +slots: + experiment_id: + range: Experiment + description: Reference to Experiment. + + equipment_id: + range: Equipment + description: Reference to Equipment. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_method.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_method.yaml new file mode 100644 index 00000000..e0a9e35d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_method.yaml @@ -0,0 +1,31 @@ +id: https://w3id.org/ca_biositing/experiment_equipment/experiment_method +name: experiment_method +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - experiment + - ../methods_parameters_units/method +default_range: string + +classes: + ExperimentMethod: + description: Link between Experiment and Method. + slots: + - id + - experiment_id + - method_id + slot_usage: + id: + identifier: true + range: integer + +slots: + experiment_id: + range: Experiment + description: Reference to Experiment. + + method_id: + range: Method + description: Reference to Method. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_prepared_sample.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_prepared_sample.yaml new file mode 100644 index 00000000..969e235f --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/experiment_equipment/experiment_prepared_sample.yaml @@ -0,0 +1,31 @@ +id: https://w3id.org/ca_biositing/experiment_equipment/experiment_prepared_sample +name: experiment_prepared_sample +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - experiment + - ../sample_preparation/prepared_sample +default_range: string + +classes: + ExperimentPreparedSample: + description: Link between Experiment and PreparedSample. + slots: + - id + - experiment_id + - prepared_sample_id + slot_usage: + id: + identifier: true + range: integer + +slots: + experiment_id: + range: Experiment + description: Reference to Experiment. + + prepared_sample_id: + range: PreparedSample + description: Reference to PreparedSample. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml deleted file mode 100644 index 679a5f4a..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data.yaml +++ /dev/null @@ -1,441 +0,0 @@ -id: https://w3id.org/ca_biositing/external_data -name: external_data -title: External Data -description: External datasets (USDA, LandIQ, etc.). -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - general_analysis - - places - - resource_information - - methods_parameters_units - - data_sources_metadata - -classes: - UsdaDomain: - is_a: LookupBase - description: USDA domain. - - UsdaStatisticCategory: - is_a: LookupBase - description: USDA statistic category. - - UsdaSurveyProgram: - is_a: LookupBase - description: USDA survey program. - - UsdaCensusRecord: - is_a: BaseEntity - description: USDA census record. - slots: - - dataset_id - - geoid - - commodity_code - - year - - source_reference - - note - - UsdaSurveyRecord: - is_a: BaseEntity - description: USDA survey record. - slots: - - dataset_id - - geoid - - commodity_code - - year - - survey_program_id - - survey_period - - reference_month - - seasonal_flag - - note - - #RESOURCE ONTOLOGY MAPPING - - UsdaCommodity: - is_a: LookupBase - description: USDA commodity. - slots: - - usda_source - - usda_code - - parent_commodity_id - - UsdaTermMap: - is_a: BaseEntity - description: Mapping of raw terms to USDA commodities. - slots: - - source_system - - source_context - - raw_term - - usda_commodity_id - - is_verified - - note - - ResourceUsdaCommodityMap: - is_a: BaseEntity - description: Mapping between resources/crops and USDA commodities. - slots: - - resource_id - - primary_ag_product_id - - usda_commodity_id - - match_tier - - note - - #USDA MARKET DATA - - UsdaMarketReport: - is_a: BaseEntity - description: USDA market report. - slots: - - slug_id - - slug_name - - report_series_title - - frequency - - office_name - - office_city_id - - office_state_fips - - source_id - - UsdaMarketRecord: - is_a: BaseEntity - description: USDA market record. - slots: - - report_id - - dataset_id - - report_begin_date - - report_end_date - - report_date - - commodity_id - - market_type_id - - market_type_category - - grp - - market_category_id - - class_ - - grade - - variety - - protein_pct - - application - - pkg - - sale_type - - price_unit_id - - freight - - trans_mode - - #LANDIQ DATA - - LandiqRecord: - is_a: BaseEntity - description: LandIQ record. - slots: - - dataset_id - - polygon_id - - main_crop - - secondary_crop - - tertiary_crop - - quaternary_crop - - confidence - - irrigated - - acres - - version - - note - - Polygon: - description: Geospatial polygon. - slots: - - id - - geoid - - geom - slot_usage: - id: - identifier: true - range: integer - - #BILLION TON DATA - - BillionTon2023Record: - is_a: BaseEntity - description: Billion Ton 2023 record. - slots: - - subclass_id - - resource_id - - geoid - - county_square_miles - - model_name - - scenario_name - - price_offered_usd - - production - - production_unit_id - - btu_ton - - production_energy_content - - energy_content_unit_id - - product_density_dtpersqmi - - land_source - -slots: - usda_source: - range: string - description: Source of the USDA definition (NASS, AMS). - - usda_code: - range: string - description: Official USDA code. - - parent_commodity_id: - range: integer - description: Reference to parent UsdaCommodity. - - source_system: - range: string - description: Source system (NASS, AMS). - - source_context: - range: string - description: Context of the source (Group, Slug ID). - - raw_term: - range: string - description: Raw term from the source. - - usda_commodity_id: - range: integer - description: Reference to UsdaCommodity. - - is_verified: - range: boolean - description: Whether the mapping is verified. - - match_tier: - range: string - description: Tier of the match. - - commodity_code: - range: integer - description: Reference to UsdaCommodity. - - year: - range: integer - description: Year of the record. - - source_reference: - range: string - description: Reference to the source. - - survey_program_id: - range: integer - description: Reference to UsdaSurveyProgram. - - survey_period: - range: string - description: Period of the survey. - - reference_month: - range: string - description: Reference month. - - seasonal_flag: - range: boolean - description: Whether the record is seasonal. - - slug_id: - range: integer - description: Slug ID. - - slug_name: - range: string - description: Slug name. - - report_series_title: - range: string - description: Title of the report series. - - frequency: - range: string - description: Frequency of the report. - - office_name: - range: string - description: Name of the office. - - office_city_id: - range: integer - description: Reference to LocationAddress. - - office_state_fips: - range: string - description: FIPS code of the office state. - - report_id: - range: integer - description: Reference to UsdaMarketReport. - - report_begin_date: - range: datetime - description: Begin date of the report. - - report_end_date: - range: datetime - description: End date of the report. - - report_date: - range: datetime - description: Date of the report. - - commodity_id: - range: integer - description: Reference to UsdaCommodity. - - market_type_id: - range: integer - description: ID of the market type. - - market_type_category: - range: string - description: Category of the market type. - - grp: - range: string - description: Group. - - market_category_id: - range: integer - description: ID of the market category. - - class_: - range: string - description: Class. - - grade: - range: string - description: Grade. - - variety: - range: string - description: Variety. - - protein_pct: - range: decimal - description: Protein percentage. - - application: - range: string - description: Application. - - pkg: - range: string - description: Package. - - sale_type: - range: string - description: Sale type. - - price_unit_id: - range: integer - description: Reference to Unit. - - freight: - range: string - description: Freight. - - trans_mode: - range: string - description: Transportation mode. - - polygon_id: - range: integer - description: Reference to Polygon. - - main_crop: - range: integer - description: Reference to PrimaryAgProduct. - - secondary_crop: - range: integer - description: Reference to PrimaryAgProduct. - - tertiary_crop: - range: integer - description: Reference to PrimaryAgProduct. - - quaternary_crop: - range: integer - description: Reference to PrimaryAgProduct. - - confidence: - range: integer - description: Confidence level. - - irrigated: - range: boolean - description: Whether the land is irrigated. - - acres: - range: float - description: Number of acres. - - version: - range: string - description: Version of the data source. - - subclass_id: - range: integer - description: Reference to ResourceSubclass. - - county_square_miles: - range: float - description: Square miles of the county. - - model_name: - range: string - description: Name of the model. - - scenario_name: - range: string - description: Name of the scenario. - - price_offered_usd: - range: decimal - description: Price offered in USD. - - production: - range: integer - description: Production amount. - - production_unit_id: - range: integer - description: Reference to Unit. - - btu_ton: - range: integer - description: BTU per ton. - - production_energy_content: - range: integer - description: Energy content of production. - - energy_content_unit_id: - range: integer - description: Reference to Unit. - - product_density_dtpersqmi: - range: decimal - description: Product density in dry tons per square mile. - - land_source: - range: string - description: Source of land data. - - geom: - range: string - description: Geometry (WKT or similar). - - test: - range: string - description: A test slot. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/billion_ton_2023_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/billion_ton_2023_record.yaml new file mode 100644 index 00000000..24e9e470 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/billion_ton_2023_record.yaml @@ -0,0 +1,89 @@ +id: https://w3id.org/ca_biositing/external_data/billion_ton_2023_record +name: billion_ton_2023_record +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../resource_information/resource + - ../resource_information/resource_subclass + - ../places/geography + - ../methods_parameters_units/unit +default_range: string + +classes: + BillionTon2023Record: + is_a: BaseEntity + description: Billion Ton 2023 record. + slots: + - subclass_id + - resource_id + - geoid + - county_square_miles + - model_name + - scenario_name + - price_offered_usd + - production + - production_unit_id + - btu_ton + - production_energy_content + - energy_content_unit_id + - product_density_dtpersqmi + - land_source + +slots: + subclass_id: + range: ResourceSubclass + description: Reference to ResourceSubclass. + + resource_id: + range: Resource + description: Reference to Resource. + + geoid: + range: Geography + description: Reference to Geography. + + county_square_miles: + range: float + description: Square miles of the county. + + model_name: + range: string + description: Name of the model. + + scenario_name: + range: string + description: Name of the scenario. + + price_offered_usd: + range: decimal + description: Price offered in USD. + + production: + range: integer + description: Production amount. + + production_unit_id: + range: Unit + description: Reference to Unit. + + btu_ton: + range: integer + description: BTU per ton. + + production_energy_content: + range: integer + description: Energy content of production. + + energy_content_unit_id: + range: Unit + description: Reference to Unit. + + product_density_dtpersqmi: + range: decimal + description: Product density in dry tons per square mile. + + land_source: + range: string + description: Source of land data. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/landiq_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/landiq_record.yaml new file mode 100644 index 00000000..1827575b --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/landiq_record.yaml @@ -0,0 +1,69 @@ +id: https://w3id.org/ca_biositing/external_data/landiq_record +name: landiq_record +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../data_sources_metadata/data_source + - polygon + - ../resource_information/primary_ag_product +default_range: string + +classes: + LandiqRecord: + is_a: BaseEntity + description: LandIQ record. + slots: + - dataset_id + - polygon_id + - main_crop + - secondary_crop + - tertiary_crop + - quaternary_crop + - confidence + - irrigated + - acres + - version + - note + +slots: + dataset_id: + range: DataSource + description: Reference to DataSource. + + polygon_id: + range: Polygon + description: Reference to Polygon. + + main_crop: + range: PrimaryAgProduct + description: Reference to PrimaryAgProduct. + + secondary_crop: + range: PrimaryAgProduct + description: Reference to PrimaryAgProduct. + + tertiary_crop: + range: PrimaryAgProduct + description: Reference to PrimaryAgProduct. + + quaternary_crop: + range: PrimaryAgProduct + description: Reference to PrimaryAgProduct. + + confidence: + range: integer + description: Confidence level. + + irrigated: + range: boolean + description: Whether the land is irrigated. + + acres: + range: float + description: Number of acres. + + version: + range: string + description: Version of the data source. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/polygon.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/polygon.yaml new file mode 100644 index 00000000..5af8c173 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/polygon.yaml @@ -0,0 +1,30 @@ +id: https://w3id.org/ca_biositing/external_data/polygon +name: polygon +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../places/geography +default_range: string + +classes: + Polygon: + description: Geospatial polygon. + slots: + - id + - geoid + - geom + slot_usage: + id: + identifier: true + range: integer + +slots: + geoid: + range: Geography + description: Reference to Geography. + + geom: + range: string + description: Geometry (WKT or similar). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/resource_usda_commodity_map.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/resource_usda_commodity_map.yaml new file mode 100644 index 00000000..68ed2726 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/resource_usda_commodity_map.yaml @@ -0,0 +1,39 @@ +id: https://w3id.org/ca_biositing/external_data/resource_usda_commodity_map +name: resource_usda_commodity_map +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../resource_information/resource + - ../resource_information/primary_ag_product + - usda_commodity +default_range: string + +classes: + ResourceUsdaCommodityMap: + is_a: BaseEntity + description: Mapping between resources/crops and USDA commodities. + slots: + - resource_id + - primary_ag_product_id + - usda_commodity_id + - match_tier + - note + +slots: + resource_id: + range: Resource + description: Reference to Resource. + + primary_ag_product_id: + range: PrimaryAgProduct + description: Reference to PrimaryAgProduct. + + usda_commodity_id: + range: UsdaCommodity + description: Reference to UsdaCommodity. + + match_tier: + range: string + description: Tier of the match. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_census_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_census_record.yaml new file mode 100644 index 00000000..0760d9cd --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_census_record.yaml @@ -0,0 +1,44 @@ +id: https://w3id.org/ca_biositing/external_data/usda_census_record +name: usda_census_record +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../data_sources_metadata/data_source + - ../places/geography + - usda_commodity +default_range: string + +classes: + UsdaCensusRecord: + is_a: BaseEntity + description: USDA census record. + slots: + - dataset_id + - geoid + - commodity_code + - year + - source_reference + - note + +slots: + dataset_id: + range: DataSource + description: Reference to DataSource. + + geoid: + range: Geography + description: Reference to Geography. + + commodity_code: + range: UsdaCommodity + description: Reference to UsdaCommodity. + + year: + range: integer + description: Year of the record. + + source_reference: + range: string + description: Reference to the source. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_commodity.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_commodity.yaml new file mode 100644 index 00000000..4bb95641 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_commodity.yaml @@ -0,0 +1,30 @@ +id: https://w3id.org/ca_biositing/external_data/usda_commodity +name: usda_commodity +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + UsdaCommodity: + is_a: LookupBase + description: USDA commodity. + slots: + - usda_source + - usda_code + - parent_commodity_id + +slots: + usda_source: + range: string + description: Source of the USDA definition (NASS, AMS). + + usda_code: + range: string + description: Official USDA code. + + parent_commodity_id: + range: UsdaCommodity + description: Reference to parent UsdaCommodity. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_domain.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_domain.yaml new file mode 100644 index 00000000..6e12bb15 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_domain.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/external_data/usda_domain +name: usda_domain +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + UsdaDomain: + is_a: LookupBase + description: USDA domain. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_market_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_market_record.yaml new file mode 100644 index 00000000..c128596a --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_market_record.yaml @@ -0,0 +1,119 @@ +id: https://w3id.org/ca_biositing/external_data/usda_market_record +name: usda_market_record +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - usda_market_report + - ../data_sources_metadata/data_source + - usda_commodity + - ../methods_parameters_units/unit +default_range: string + +classes: + UsdaMarketRecord: + is_a: BaseEntity + description: USDA market record. + slots: + - report_id + - dataset_id + - report_begin_date + - report_end_date + - report_date + - commodity_id + - market_type_id + - market_type_category + - grp + - market_category_id + - class_ + - grade + - variety + - protein_pct + - application + - pkg + - sale_type + - price_unit_id + - freight + - trans_mode + +slots: + report_id: + range: UsdaMarketReport + description: Reference to UsdaMarketReport. + + dataset_id: + range: DataSource + description: Reference to DataSource. + + report_begin_date: + range: datetime + description: Begin date of the report. + + report_end_date: + range: datetime + description: End date of the report. + + report_date: + range: datetime + description: Date of the report. + + commodity_id: + range: UsdaCommodity + description: Reference to UsdaCommodity. + + market_type_id: + range: integer + description: ID of the market type. + + market_type_category: + range: string + description: Category of the market type. + + grp: + range: string + description: Group. + + market_category_id: + range: integer + description: ID of the market category. + + class_: + range: string + description: Class. + + grade: + range: string + description: Grade. + + variety: + range: string + description: Variety. + + protein_pct: + range: decimal + description: Protein percentage. + + application: + range: string + description: Application. + + pkg: + range: string + description: Package. + + sale_type: + range: string + description: Sale type. + + price_unit_id: + range: Unit + description: Reference to Unit. + + freight: + range: string + description: Freight. + + trans_mode: + range: string + description: Transportation mode. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_market_report.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_market_report.yaml new file mode 100644 index 00000000..f5254218 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_market_report.yaml @@ -0,0 +1,57 @@ +id: https://w3id.org/ca_biositing/external_data/usda_market_report +name: usda_market_report +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../places/location_address + - ../data_sources_metadata/data_source +default_range: string + +classes: + UsdaMarketReport: + is_a: BaseEntity + description: USDA market report. + slots: + - slug_id + - slug_name + - report_series_title + - frequency + - office_name + - office_city_id + - office_state_fips + - source_id + +slots: + slug_id: + range: integer + description: Slug ID. + + slug_name: + range: string + description: Slug name. + + report_series_title: + range: string + description: Title of the report series. + + frequency: + range: string + description: Frequency of the report. + + office_name: + range: string + description: Name of the office. + + office_city_id: + range: LocationAddress + description: Reference to LocationAddress. + + office_state_fips: + range: string + description: FIPS code of the office state. + + source_id: + range: DataSource + description: Reference to DataSource. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_statistic_category.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_statistic_category.yaml new file mode 100644 index 00000000..5a410d79 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_statistic_category.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/external_data/usda_statistic_category +name: usda_statistic_category +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + UsdaStatisticCategory: + is_a: LookupBase + description: USDA statistic category. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_survey_program.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_survey_program.yaml new file mode 100644 index 00000000..1933375d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_survey_program.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/external_data/usda_survey_program +name: usda_survey_program +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + UsdaSurveyProgram: + is_a: LookupBase + description: USDA survey program. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_survey_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_survey_record.yaml new file mode 100644 index 00000000..653ea194 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_survey_record.yaml @@ -0,0 +1,60 @@ +id: https://w3id.org/ca_biositing/external_data/usda_survey_record +name: usda_survey_record +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../data_sources_metadata/data_source + - ../places/geography + - usda_commodity + - usda_survey_program +default_range: string + +classes: + UsdaSurveyRecord: + is_a: BaseEntity + description: USDA survey record. + slots: + - dataset_id + - geoid + - commodity_code + - year + - survey_program_id + - survey_period + - reference_month + - seasonal_flag + - note + +slots: + dataset_id: + range: DataSource + description: Reference to DataSource. + + geoid: + range: Geography + description: Reference to Geography. + + commodity_code: + range: UsdaCommodity + description: Reference to UsdaCommodity. + + year: + range: integer + description: Year of the record. + + survey_program_id: + range: UsdaSurveyProgram + description: Reference to UsdaSurveyProgram. + + survey_period: + range: string + description: Period of the survey. + + reference_month: + range: string + description: Reference month. + + seasonal_flag: + range: boolean + description: Whether the record is seasonal. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_term_map.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_term_map.yaml new file mode 100644 index 00000000..17711897 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/external_data/usda_term_map.yaml @@ -0,0 +1,42 @@ +id: https://w3id.org/ca_biositing/external_data/usda_term_map +name: usda_term_map +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - usda_commodity +default_range: string + +classes: + UsdaTermMap: + is_a: BaseEntity + description: Mapping of raw terms to USDA commodities. + slots: + - source_system + - source_context + - raw_term + - usda_commodity_id + - is_verified + - note + +slots: + source_system: + range: string + description: Source system (NASS, AMS). + + source_context: + range: string + description: Context of the source (Group, Slug ID). + + raw_term: + range: string + description: Raw term from the source. + + usda_commodity_id: + range: UsdaCommodity + description: Reference to UsdaCommodity. + + is_verified: + range: boolean + description: Whether the mapping is verified. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml deleted file mode 100644 index 74ab00d6..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling.yaml +++ /dev/null @@ -1,200 +0,0 @@ -id: https://w3id.org/ca_biositing/field_sampling -name: field_sampling -title: Field Sampling -description: Field sampling and preparation. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - places - - people - - resource_information - - methods_parameters_units - -classes: - FieldSample: - is_a: BaseEntity - description: Sample collected from the field. - slots: - - name - - resource_id - - provider_id - - collector_id - - sample_collection_source - - amount_collected - - amount_collected_unit_id - - sampling_location_id - - field_storage_method_id - - field_storage_duration_value - - field_storage_duration_unit_id - - field_storage_location_id - - collection_timestamp - - collection_method_id - - harvest_method_id - - harvest_date - - field_sample_storage_location_id - - note - - PhysicalCharacteristic: - is_a: BaseEntity - description: Physical characteristics of a sample. - slots: - - field_sample_id - - particle_length - - particle_width - - particle_height - - particle_unit_id - - FieldSampleCondition: - is_a: BaseEntity - description: Condition of the field sample. - slots: - - field_sample_id - - ag_treatment_id - - last_application_date - - treatment_amount_per_acre - - processing_method_id - - FieldStorageMethod: - is_a: LookupBase - description: Method of field storage. - - CollectionMethod: - is_a: LookupBase - description: Method of collection. - - HarvestMethod: - is_a: LookupBase - description: Method of harvest. - - ProcessingMethod: - is_a: LookupBase - description: Method of processing. - - SoilType: - is_a: LookupBase - description: Type of soil. - - AgTreatment: - is_a: LookupBase - description: Agricultural treatment. - - LocationSoilType: - is_a: BaseEntity - description: Soil type at a location. - slots: - - location_id - - soil_type_id - -slots: - provider_id: - range: integer - description: Reference to Provider. - - collector_id: - range: integer - description: Reference to Contact (collector). - - sample_collection_source: - range: string - description: Source of sample collection. - - amount_collected: - range: decimal - description: Amount collected. - - amount_collected_unit_id: - range: integer - description: Reference to Unit. - - sampling_location_id: - range: integer - description: Reference to LocationAddress. - - field_storage_method_id: - range: integer - description: Reference to FieldStorageMethod. - - field_storage_duration_value: - range: decimal - description: Duration of field storage. - - field_storage_duration_unit_id: - range: integer - description: Reference to Unit. - - field_storage_location_id: - range: integer - description: Reference to LocationAddress. - - collection_timestamp: - range: datetime - description: Timestamp of collection. - - collection_method_id: - range: integer - description: Reference to CollectionMethod. - - harvest_method_id: - range: integer - description: Reference to HarvestMethod. - - harvest_date: - range: date - description: Date of harvest. - - field_sample_storage_location_id: - range: integer - description: Reference to LocationAddress. - - field_sample_id: - range: integer - description: Reference to FieldSample. - - particle_length: - range: decimal - description: Length of particle. - - particle_width: - range: decimal - description: Width of particle. - - particle_height: - range: decimal - description: Height of particle. - - particle_unit_id: - range: integer - description: Reference to Unit. - - ag_treatment_id: - range: integer - description: Reference to AgTreatment. - - last_application_date: - range: date - description: Date of last application. - - treatment_amount_per_acre: - range: float - description: Amount of treatment per acre. - - processing_method_id: - range: integer - description: Reference to ProcessingMethod. - - location_id: - range: integer - description: Reference to LocationAddress. - - soil_type_id: - range: integer - description: Reference to SoilType. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/ag_treatment.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/ag_treatment.yaml new file mode 100644 index 00000000..1edf4f87 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/ag_treatment.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/field_sampling/ag_treatment +name: ag_treatment +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + AgTreatment: + is_a: LookupBase + description: Agricultural treatment. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/collection_method.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/collection_method.yaml new file mode 100644 index 00000000..3aa95cc5 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/collection_method.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/field_sampling/collection_method +name: collection_method +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + CollectionMethod: + is_a: LookupBase + description: Method of collection. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/field_sample.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/field_sample.yaml new file mode 100644 index 00000000..4f520bf6 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/field_sample.yaml @@ -0,0 +1,105 @@ +id: https://w3id.org/ca_biositing/field_sampling/field_sample +name: field_sample +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../places/location_address + - ../people/contact + - ../people/provider + - ../resource_information/resource + - ../methods_parameters_units/unit + - field_storage_method + - collection_method + - harvest_method +default_range: string + +classes: + FieldSample: + is_a: BaseEntity + description: Sample collected from the field. + slots: + - name + - resource_id + - provider_id + - collector_id + - sample_collection_source + - amount_collected + - amount_collected_unit_id + - sampling_location_id + - field_storage_method_id + - field_storage_duration_value + - field_storage_duration_unit_id + - field_storage_location_id + - collection_timestamp + - collection_method_id + - harvest_method_id + - harvest_date + - field_sample_storage_location_id + - note + +slots: + resource_id: + range: Resource + description: Reference to Resource. + + provider_id: + range: Provider + description: Reference to Provider. + + collector_id: + range: Contact + description: Reference to Contact (collector). + + sample_collection_source: + range: string + description: Source of sample collection. + + amount_collected: + range: decimal + description: Amount collected. + + amount_collected_unit_id: + range: Unit + description: Reference to Unit. + + sampling_location_id: + range: LocationAddress + description: Reference to LocationAddress. + + field_storage_method_id: + range: FieldStorageMethod + description: Reference to FieldStorageMethod. + + field_storage_duration_value: + range: decimal + description: Duration of field storage. + + field_storage_duration_unit_id: + range: Unit + description: Reference to Unit. + + field_storage_location_id: + range: LocationAddress + description: Reference to LocationAddress. + + collection_timestamp: + range: datetime + description: Timestamp of collection. + + collection_method_id: + range: CollectionMethod + description: Reference to CollectionMethod. + + harvest_method_id: + range: HarvestMethod + description: Reference to HarvestMethod. + + harvest_date: + range: date + description: Date of harvest. + + field_sample_storage_location_id: + range: LocationAddress + description: Reference to LocationAddress. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/field_sample_condition.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/field_sample_condition.yaml new file mode 100644 index 00000000..37ed41b0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/field_sample_condition.yaml @@ -0,0 +1,43 @@ +id: https://w3id.org/ca_biositing/field_sampling/field_sample_condition +name: field_sample_condition +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - field_sample + - ag_treatment + - processing_method +default_range: string + +classes: + FieldSampleCondition: + is_a: BaseEntity + description: Condition of the field sample. + slots: + - field_sample_id + - ag_treatment_id + - last_application_date + - treatment_amount_per_acre + - processing_method_id + +slots: + field_sample_id: + range: FieldSample + description: Reference to FieldSample. + + ag_treatment_id: + range: AgTreatment + description: Reference to AgTreatment. + + last_application_date: + range: date + description: Date of last application. + + treatment_amount_per_acre: + range: float + description: Amount of treatment per acre. + + processing_method_id: + range: ProcessingMethod + description: Reference to ProcessingMethod. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/field_storage_method.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/field_storage_method.yaml new file mode 100644 index 00000000..9eeebd9b --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/field_storage_method.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/field_sampling/field_storage_method +name: field_storage_method +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + FieldStorageMethod: + is_a: LookupBase + description: Method of field storage. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/harvest_method.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/harvest_method.yaml new file mode 100644 index 00000000..4ec880db --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/harvest_method.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/field_sampling/harvest_method +name: harvest_method +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + HarvestMethod: + is_a: LookupBase + description: Method of harvest. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/location_soil_type.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/location_soil_type.yaml new file mode 100644 index 00000000..584486c8 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/location_soil_type.yaml @@ -0,0 +1,27 @@ +id: https://w3id.org/ca_biositing/field_sampling/location_soil_type +name: location_soil_type +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../places/location_address + - soil_type +default_range: string + +classes: + LocationSoilType: + is_a: BaseEntity + description: Soil type at a location. + slots: + - location_id + - soil_type_id + +slots: + location_id: + range: LocationAddress + description: Reference to LocationAddress. + + soil_type_id: + range: SoilType + description: Reference to SoilType. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/physical_characteristic.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/physical_characteristic.yaml new file mode 100644 index 00000000..6644bbb9 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/physical_characteristic.yaml @@ -0,0 +1,42 @@ +id: https://w3id.org/ca_biositing/field_sampling/physical_characteristic +name: physical_characteristic +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - field_sample + - ../methods_parameters_units/unit +default_range: string + +classes: + PhysicalCharacteristic: + is_a: BaseEntity + description: Physical characteristics of a sample. + slots: + - field_sample_id + - particle_length + - particle_width + - particle_height + - particle_unit_id + +slots: + field_sample_id: + range: FieldSample + description: Reference to FieldSample. + + particle_length: + range: decimal + description: Length of particle. + + particle_width: + range: decimal + description: Width of particle. + + particle_height: + range: decimal + description: Height of particle. + + particle_unit_id: + range: Unit + description: Reference to Unit. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/processing_method.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/processing_method.yaml new file mode 100644 index 00000000..603c4842 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/processing_method.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/field_sampling/processing_method +name: processing_method +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + ProcessingMethod: + is_a: LookupBase + description: Method of processing. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/soil_type.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/soil_type.yaml new file mode 100644 index 00000000..b232bc63 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/field_sampling/soil_type.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/field_sampling/soil_type +name: soil_type +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + SoilType: + is_a: LookupBase + description: Type of soil. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml deleted file mode 100644 index 6f9db701..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis.yaml +++ /dev/null @@ -1,97 +0,0 @@ -id: https://w3id.org/ca_biositing/general_analysis -name: general_analysis -title: General Analysis -description: General analysis definitions. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - data_sources_metadata - - methods_parameters_units - -classes: - AnalysisType: - is_a: LookupBase - description: Type of analysis. - - Dataset: - is_a: BaseEntity - description: Dataset definition. - slots: - - name - - record_type - - source_id - - start_date - - end_date - - description - - DimensionType: - is_a: LookupBase - description: Type of dimension. - - Observation: - is_a: BaseEntity - description: Observation data. - slots: - - dataset_id - - record_type - - record_id - - parameter_id - - value - - unit_id - - dimension_type_id - - dimension_value - - dimension_unit_id - - note - -slots: - #Slots imported - #parameter_id: from methods.yaml - #note: from core.yaml - - record_type: - range: string - description: Type of record. - - start_date: - range: date - description: Start date of the dataset. - - end_date: - range: date - description: End date of the dataset. - - dataset_id: - range: integer - description: Reference to Dataset. - - record_id: - range: integer - description: ID of the record. - - value: - range: decimal - description: Value of the observation. - - unit_id: - range: integer - description: Reference to Unit. - - dimension_type_id: - range: integer - description: Reference to DimensionType. - - dimension_value: - range: decimal - description: Value of the dimension. - - dimension_unit_id: - range: integer diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/analysis_type.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/analysis_type.yaml new file mode 100644 index 00000000..6f84aff3 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/analysis_type.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/general_analysis/analysis_type +name: analysis_type +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + AnalysisType: + is_a: LookupBase + description: Type of analysis. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/dataset.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/dataset.yaml new file mode 100644 index 00000000..8d3d7550 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/dataset.yaml @@ -0,0 +1,38 @@ +id: https://w3id.org/ca_biositing/general_analysis/dataset +name: dataset +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../data_sources_metadata/data_source +default_range: string + +classes: + Dataset: + is_a: BaseEntity + description: Dataset definition. + slots: + - name + - record_type + - source_id + - start_date + - end_date + - description + +slots: + record_type: + range: string + description: Type of record. + + source_id: + range: DataSource + description: Reference to DataSource. + + start_date: + range: date + description: Start date of the dataset. + + end_date: + range: date + description: End date of the dataset. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/dimension_type.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/dimension_type.yaml new file mode 100644 index 00000000..f92b6838 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/dimension_type.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/general_analysis/dimension_type +name: dimension_type +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + DimensionType: + is_a: LookupBase + description: Type of dimension. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/observation.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/observation.yaml new file mode 100644 index 00000000..f990843c --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/general_analysis/observation.yaml @@ -0,0 +1,64 @@ +id: https://w3id.org/ca_biositing/general_analysis/observation +name: observation +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - dataset + - ../methods_parameters_units/unit + - dimension_type +default_range: string + +classes: + Observation: + is_a: BaseEntity + description: Observation data. + slots: + - dataset_id + - record_type + - record_id + - parameter_id + - value + - unit_id + - dimension_type_id + - dimension_value + - dimension_unit_id + - note + +slots: + dataset_id: + range: Dataset + description: Reference to Dataset. + + record_type: + range: string + description: Type of record. + + record_id: + range: integer + description: ID of the record. + + parameter_id: + range: Parameter + description: Reference to Parameter. + + value: + range: decimal + description: Value of the observation. + + unit_id: + range: Unit + description: Reference to Unit. + + dimension_type_id: + range: DimensionType + description: Reference to DimensionType. + + dimension_value: + range: decimal + description: Value of the dimension. + + dimension_unit_id: + range: Unit + description: Reference to Unit. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml deleted file mode 100644 index 0b6ec0eb..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/geography.yaml +++ /dev/null @@ -1,109 +0,0 @@ -id: https://w3id.org/ca_biositing/geography -name: geography -title: Geography Definitions -description: Geospatial entities and locations. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - -classes: - Geography: - description: Geographic region definition (e.g. county, state). - slots: - - geoid - - state_name - - state_fips - - county_name - - county_fips - - region_name - - agg_level_desc - slot_usage: - geoid: - identifier: true - - LocationAddress: - is_a: BaseEntity - description: Specific physical location. - slots: - - geography_id - - address_line1 - - address_line2 - - city - - zip - - lat - - lon - - is_anonymous - -slots: - geoid: - range: string - description: Geographic identifier. - - state_name: - range: string - description: Name of the state. - - state_fips: - range: string - description: FIPS code of the state. - - county_name: - range: string - description: Name of the county. - - county_fips: - range: string - description: FIPS code of the county. - - region_name: - range: string - description: Name of the region. - - agg_level_desc: - range: string - description: Description of the aggregation level. - - geography_id: - range: string - description: Reference to Geography geoid. - - address_line1: - range: string - description: Address line 1. - - address_line2: - range: string - description: Address line 2. - - city: - range: string - description: City name. - - zip: - range: string - description: ZIP code. - - lat: - range: float - description: Latitude. - - lon: - range: float - description: Longitude. - - is_anonymous: - range: boolean - description: Whether the location is anonymous. - - geom: - range: string # TODO: Define geometry type properly, maybe using a custom type or string for WKT - description: Geometry of the polygon. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure.yaml deleted file mode 100644 index 6ce9edf9..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure.yaml +++ /dev/null @@ -1,1069 +0,0 @@ -id: https://w3id.org/ca_biositing/infrastructure -name: infrastructure -title: Infrastructure -description: Infrastructure and facility data. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - general_analysis - - places - - resource_information - -classes: - FacilityRecord: - is_a: BaseEntity - description: Facility record. - slots: - - dataset_id - - facility_name - - location_id - - capacity_mw - - resource_id - - operator - - start_year - - note - - InfrastructureBiodieselPlants: - description: Biodiesel plants infrastructure. - slots: - - biodiesel_plant_id - - company - - bbi_index - - city - - state - - capacity_mmg_per_y - - feedstock - - status - - address - - coordinates - - latitude - - longitude - - source - slot_usage: - biodiesel_plant_id: - identifier: true - range: integer - - InfrastructureBiosolidsFacilities: - description: Biosolids facilities infrastructure. - slots: - - biosolid_facility_id - - report_submitted_date - - latitude - - longitude - - facility - - authority - - plant_type - - aqmd - - facility_address - - facility_city - - state - - facility_zip - - facility_county - - mailing_street_1 - - mailing_city - - mailing_state - - mailing_zip - - biosolids_number - - biosolids_contact - - biosolids_contact_phone - - biosolids_contact_email - - adwf - - potw_biosolids_generated - - twtds_biosolids_treated - - class_b_land_app - - class_b_applier - - class_a_compost - - class_a_heat_dried - - class_a_other - - class_a_other_applier - - twtds_transfer_to_second_preparer - - twtds_second_preparer_name - - adc_or_final_c - - landfill - - landfill_name - - surface_disposal - - deepwell_injection - - stored - - longterm_treatment - - other - - name_of_other - - incineration - slot_usage: - biosolid_facility_id: - identifier: true - range: integer - - InfrastructureCafoManureLocations: - description: CAFO manure locations infrastructure. - slots: - - cafo_manure_id - - latitude - - longitude - - owner_name - - facility_name - - address - - town - - state - - zip - - animal - - animal_feed_operation_type - - animal_units - - animal_count - - manure_total_solids - - source - - date_accessed - slot_usage: - cafo_manure_id: - identifier: true - range: integer - - InfrastructureEthanolBiorefineries: - description: Ethanol biorefineries infrastructure. - slots: - - ethanol_biorefinery_id - - name - - city - - state - - address - - type - - capacity_mgy - - production_mgy - - constr_exp - slot_usage: - ethanol_biorefinery_id: - identifier: true - range: integer - - InfrastructureLandfills: - description: Landfills infrastructure. - slots: - - project_id - - project_int_id - - ghgrp_id - - landfill_id - - landfill_name - - state - - physical_address - - city - - county - - zip_code - - latitude - - longitude - - ownership_type - - landfill_owner_orgs - - landfill_opened_year - - landfill_closure_year - - landfill_status - - waste_in_place - - waste_in_place_year - - lfg_system_in_place - - lfg_collected - - lfg_flared - - project_status - - project_name - - project_start_date - - project_shutdown_date - - project_type_category - - lfg_energy_project_type - - rng_delivery_method - - actual_mw_generation - - rated_mw_capacity - - lfg_flow_to_project - - direct_emission_reductions - - avoided_emission_reductions - slot_usage: - project_id: - identifier: true - range: string - - InfrastructureLivestockAnaerobicDigesters: - description: Livestock anaerobic digesters infrastructure. - slots: - - digester_id - - project_name - - project_type - - city - - state - - digester_type - - profile - - year_operational - - animal_type_class - - animal_types - - pop_feeding_digester - - total_pop_feeding_digester - - cattle - - dairy - - poultry - - swine - - codigestion - - biogas_generation_estimate - - electricity_generated - - biogas_end_uses - - methane_emission_reductions - - latitude - - longitude - slot_usage: - digester_id: - identifier: true - range: integer - - InfrastructureSafAndRenewableDieselPlants: - description: SAF and renewable diesel plants infrastructure. - slots: - - ibcc_index - - company - - city - - state - - country - - capacity - - feedstock - - products - - status - - address - - coordinates - - latitude - - longitude - slot_usage: - ibcc_index: - identifier: true - range: integer - - InfrastructureWastewaterTreatmentPlants: - description: Wastewater treatment plants infrastructure. - slots: - - plant_id - - name - - state - - codigestion - - flow_design_adjusted - - flow_average - - biosolids - - excess_flow - - biogas_utilized - - flaring - - excess_mass_loading_rate - - excess_mass_loading_rate_wet - - methane_production - - energy_content - - electric_kw - - thermal_mmbtu_d - - electric_kwh - - thermal_annual_mmbtu_y - - anaerobic_digestion_facility - - county - - dayload_bdt - - dayload - - equivalent_generation - - facility_type - - feedstock - - type - - city - - latitude - - longitude - - zipcode - slot_usage: - plant_id: - identifier: true - range: integer - - InfrastructureCombustionPlants: - description: Combustion plants infrastructure. - slots: - - combustion_fid - - objectid - - status - - city - - name - - county - - equivalent_generation - - np_mw - - cf - - yearload - - fuel - - notes - - type - - wkt_geom - - geom - - latitude - - longitude - slot_usage: - combustion_fid: - identifier: true - range: integer - - InfrastructureDistrictEnergySystems: - description: District energy systems infrastructure. - slots: - - des_fid - - cbg_id - - name - - system - - object_id - - city - - state - - primary_fuel - - secondary_fuel - - usetype - - cap_st - - cap_hw - - cap_cw - - chpcg_cap - - excess_c - - excess_h - - type - - wkt_geom - - geom - - latitude - - longitude - slot_usage: - des_fid: - identifier: true - range: integer - - InfrastructureFoodProcessingFacilities: - description: Food processing facilities infrastructure. - slots: - - processing_facility_id - - address - - county - - city - - company - - join_count - - master_type - - state - - subtype - - target_fid - - processing_type - - zip - - type - - wkt_geom - - geom - - latitude - - longitude - slot_usage: - processing_facility_id: - identifier: true - range: integer - - InfrastructureMswToEnergyAnaerobicDigesters: - description: MSW to energy anaerobic digesters infrastructure. - slots: - - wte_id - - city - - county - - equivalent_generation - - feedstock - - dayload - - dayload_bdt - - facility_type - - status - - notes - - source - - type - - wkt_geom - - geom - - latitude - - longitude - slot_usage: - wte_id: - identifier: true - range: integer - -slots: - facility_name: - range: string - description: Name of the facility. - - capacity_mw: - range: decimal - description: Capacity in MW. - - operator: - range: string - description: Operator of the facility. - - start_year: - range: integer - description: Start year of the facility. - - biodiesel_plant_id: - range: integer - description: ID of the biodiesel plant. - - company: - range: string - description: Company name. - - bbi_index: - range: integer - description: BBI index. - - city: - range: string - description: City. - - state: - range: string - description: State. - - capacity_mmg_per_y: - range: integer - description: Capacity in MMG per year. - - feedstock: - range: string - description: Feedstock. - - status: - range: string - description: Status. - - address: - range: string - description: Address. - - coordinates: - range: string - description: Coordinates. - - latitude: - range: decimal - description: Latitude. - - longitude: - range: decimal - description: Longitude. - - source: - range: string - description: Source. - - biosolid_facility_id: - range: integer - description: ID of the biosolids facility. - - report_submitted_date: - range: date - description: Date report submitted. - - facility: - range: string - description: Facility name. - - authority: - range: string - description: Authority. - - plant_type: - range: string - description: Plant type. - - aqmd: - range: string - description: AQMD. - - facility_address: - range: string - description: Facility address. - - facility_city: - range: string - description: Facility city. - - facility_zip: - range: string - description: Facility zip. - - facility_county: - range: string - description: Facility county. - - mailing_street_1: - range: string - description: Mailing street 1. - - mailing_city: - range: string - description: Mailing city. - - mailing_state: - range: string - description: Mailing state. - - mailing_zip: - range: string - description: Mailing zip. - - biosolids_number: - range: string - description: Biosolids number. - - biosolids_contact: - range: string - description: Biosolids contact. - - biosolids_contact_phone: - range: string - description: Biosolids contact phone. - - biosolids_contact_email: - range: string - description: Biosolids contact email. - - adwf: - range: decimal - description: ADWF. - - potw_biosolids_generated: - range: integer - description: POTW biosolids generated. - - twtds_biosolids_treated: - range: integer - description: TWTDS biosolids treated. - - class_b_land_app: - range: integer - description: Class B land application. - - class_b_applier: - range: string - description: Class B applier. - - class_a_compost: - range: integer - description: Class A compost. - - class_a_heat_dried: - range: integer - description: Class A heat dried. - - class_a_other: - range: integer - description: Class A other. - - class_a_other_applier: - range: string - description: Class A other applier. - - twtds_transfer_to_second_preparer: - range: integer - description: TWTDS transfer to second preparer. - - twtds_second_preparer_name: - range: string - description: TWTDS second preparer name. - - adc_or_final_c: - range: integer - description: ADC or final cover. - - landfill: - range: integer - description: Landfill. - - landfill_name: - range: string - description: Landfill name. - - surface_disposal: - range: integer - description: Surface disposal. - - deepwell_injection: - range: string - description: Deepwell injection. - - stored: - range: integer - description: Stored. - - longterm_treatment: - range: integer - description: Longterm treatment. - - other: - range: integer - description: Other. - - name_of_other: - range: string - description: Name of other. - - incineration: - range: integer - description: Incineration. - - cafo_manure_id: - range: integer - description: ID of the CAFO manure location. - - owner_name: - range: string - description: Owner name. - - town: - range: string - description: Town. - - zip: - range: string - description: Zip code. - - animal: - range: string - description: Animal. - - animal_feed_operation_type: - range: string - description: Animal feed operation type. - - animal_units: - range: integer - description: Animal units. - - animal_count: - range: integer - description: Animal count. - - manure_total_solids: - range: decimal - description: Manure total solids. - - date_accessed: - range: date - description: Date accessed. - - ethanol_biorefinery_id: - range: integer - description: ID of the ethanol biorefinery. - - type: - range: string - description: Type. - - capacity_mgy: - range: integer - description: Capacity in MGY. - - production_mgy: - range: integer - description: Production in MGY. - - constr_exp: - range: integer - description: Construction/expansion. - - project_id: - range: string - description: Project ID. - - project_int_id: - range: integer - description: Project integer ID. - - ghgrp_id: - range: string - description: GHGRP ID. - - landfill_id: - range: integer - description: Landfill ID. - - physical_address: - range: string - description: Physical address. - - county: - range: string - description: County. - - zip_code: - range: string - description: Zip code. - - ownership_type: - range: string - description: Ownership type. - - landfill_owner_orgs: - range: string - description: Landfill owner organizations. - - landfill_opened_year: - range: date - description: Landfill opened year. - - landfill_closure_year: - range: date - description: Landfill closure year. - - landfill_status: - range: string - description: Landfill status. - - waste_in_place: - range: integer - description: Waste in place. - - waste_in_place_year: - range: date - description: Waste in place year. - - lfg_system_in_place: - range: boolean - description: LFG system in place. - - lfg_collected: - range: decimal - description: LFG collected. - - lfg_flared: - range: decimal - description: LFG flared. - - project_status: - range: string - description: Project status. - - project_name: - range: string - description: Project name. - - project_start_date: - range: date - description: Project start date. - - project_shutdown_date: - range: date - description: Project shutdown date. - - project_type_category: - range: string - description: Project type category. - - lfg_energy_project_type: - range: string - description: LFG energy project type. - - rng_delivery_method: - range: string - description: RNG delivery method. - - actual_mw_generation: - range: decimal - description: Actual MW generation. - - rated_mw_capacity: - range: decimal - description: Rated MW capacity. - - lfg_flow_to_project: - range: decimal - description: LFG flow to project. - - direct_emission_reductions: - range: decimal - description: Direct emission reductions. - - avoided_emission_reductions: - range: decimal - description: Avoided emission reductions. - - digester_id: - range: integer - description: ID of the digester. - - project_type: - range: string - description: Project type. - - digester_type: - range: string - description: Digester type. - - profile: - range: string - description: Profile. - - year_operational: - range: date - description: Year operational. - - animal_type_class: - range: string - description: Animal type class. - - animal_types: - range: string - description: Animal types. - - pop_feeding_digester: - range: string - description: Population feeding digester. - - total_pop_feeding_digester: - range: integer - description: Total population feeding digester. - - cattle: - range: integer - description: Cattle. - - dairy: - range: integer - description: Dairy. - - poultry: - range: integer - description: Poultry. - - swine: - range: integer - description: Swine. - - codigestion: - range: string - description: Codigestion. - - biogas_generation_estimate: - range: integer - description: Biogas generation estimate. - - electricity_generated: - range: integer - description: Electricity generated. - - biogas_end_uses: - range: string - description: Biogas end uses. - - methane_emission_reductions: - range: integer - description: Methane emission reductions. - - ibcc_index: - range: integer - description: IBCC index. - - country: - range: string - description: Country. - - capacity: - range: string - description: Capacity. - - products: - range: string - description: Products. - - plant_id: - range: integer - description: ID of the plant. - - flow_design_adjusted: - range: decimal - description: Flow design adjusted. - - flow_average: - range: decimal - description: Flow average. - - biosolids: - range: decimal - description: Biosolids. - - excess_flow: - range: decimal - description: Excess flow. - - biogas_utilized: - range: boolean - description: Biogas utilized. - - flaring: - range: boolean - description: Flaring. - - excess_mass_loading_rate: - range: decimal - description: Excess mass loading rate. - - excess_mass_loading_rate_wet: - range: decimal - description: Excess mass loading rate wet. - - methane_production: - range: decimal - description: Methane production. - - energy_content: - range: decimal - description: Energy content. - - electric_kw: - range: decimal - description: Electric KW. - - thermal_mmbtu_d: - range: decimal - description: Thermal MMBTU/d. - - electric_kwh: - range: decimal - description: Electric KWh. - - thermal_annual_mmbtu_y: - range: decimal - description: Thermal annual MMBTU/y. - - anaerobic_digestion_facility: - range: string - description: Anaerobic digestion facility. - - dayload_bdt: - range: decimal - description: Dayload BDT. - - dayload: - range: decimal - description: Dayload. - - equivalent_generation: - range: decimal - description: Equivalent generation. - - facility_type: - range: string - description: Facility type. - - zipcode: - range: string - description: Zipcode. - - combustion_fid: - range: integer - description: Combustion FID. - - objectid: - range: integer - description: Object ID. - - np_mw: - range: decimal - description: NP MW. - - cf: - range: decimal - description: CF. - - yearload: - range: integer - description: Yearload. - - fuel: - range: string - description: Fuel. - - notes: - range: string - description: Notes. - - wkt_geom: - range: string - description: WKT geometry. - - geom: - range: string - description: Geometry. - - des_fid: - range: integer - description: DES FID. - - cbg_id: - range: integer - description: CBG ID. - - system: - range: string - description: System. - - object_id: - range: integer - description: Object ID. - - primary_fuel: - range: string - description: Primary fuel. - - secondary_fuel: - range: string - description: Secondary fuel. - - usetype: - range: string - description: Use type. - - cap_st: - range: decimal - description: Cap ST. - - cap_hw: - range: decimal - description: Cap HW. - - cap_cw: - range: decimal - description: Cap CW. - - chpcg_cap: - range: decimal - description: CHPCG Cap. - - excess_c: - range: decimal - description: Excess C. - - excess_h: - range: decimal - description: Excess H. - - processing_facility_id: - range: integer - description: Processing facility ID. - - join_count: - range: integer - description: Join count. - - master_type: - range: string - description: Master type. - - subtype: - range: string - description: Subtype. - - target_fid: - range: integer - description: Target FID. - - processing_type: - range: string - description: Processing type. - - wte_id: - range: integer - description: WTE ID. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/facility_record.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/facility_record.yaml new file mode 100644 index 00000000..f5aebba0 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/facility_record.yaml @@ -0,0 +1,54 @@ +id: https://w3id.org/ca_biositing/infrastructure/facility_record +name: facility_record +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../general_analysis/dataset + - ../places/location_address + - ../resource_information/resource +default_range: string + +classes: + FacilityRecord: + is_a: BaseEntity + description: Facility record. + slots: + - dataset_id + - facility_name + - location_id + - capacity_mw + - resource_id + - operator + - start_year + - note + +slots: + dataset_id: + range: Dataset + description: Reference to Dataset. + + facility_name: + range: string + description: Name of the facility. + + location_id: + range: LocationAddress + description: Reference to LocationAddress. + + capacity_mw: + range: decimal + description: Capacity in MW. + + resource_id: + range: Resource + description: Reference to Resource. + + operator: + range: string + description: Operator of the facility. + + start_year: + range: integer + description: Start year of the facility. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_biodiesel_plants.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_biodiesel_plants.yaml new file mode 100644 index 00000000..12e5137d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_biodiesel_plants.yaml @@ -0,0 +1,83 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_biodiesel_plants +name: infrastructure_biodiesel_plants +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureBiodieselPlants: + description: Biodiesel plants infrastructure. + slots: + - biodiesel_plant_id + - company + - bbi_index + - city + - state + - capacity_mmg_per_y + - feedstock + - status + - address + - coordinates + - latitude + - longitude + - source + slot_usage: + biodiesel_plant_id: + identifier: true + range: integer + +slots: + biodiesel_plant_id: + range: integer + description: ID of the biodiesel plant. + + company: + range: string + description: Company name. + + bbi_index: + range: integer + description: BBI index. + + city: + range: string + description: City. + + state: + range: string + description: State. + + capacity_mmg_per_y: + range: integer + description: Capacity in MMG per year. + + feedstock: + range: string + description: Feedstock. + + status: + range: string + description: Status. + + address: + range: string + description: Address. + + coordinates: + range: string + description: Coordinates. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. + + source: + range: string + description: Source. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_biosolids_facilities.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_biosolids_facilities.yaml new file mode 100644 index 00000000..4c74b6bf --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_biosolids_facilities.yaml @@ -0,0 +1,228 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_biosolids_facilities +name: infrastructure_biosolids_facilities +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureBiosolidsFacilities: + description: Biosolids facilities infrastructure. + slots: + - biosolid_facility_id + - report_submitted_date + - latitude + - longitude + - facility + - authority + - plant_type + - aqmd + - facility_address + - facility_city + - state + - facility_zip + - facility_county + - mailing_street_1 + - mailing_city + - mailing_state + - mailing_zip + - biosolids_number + - biosolids_contact + - biosolids_contact_phone + - biosolids_contact_email + - adwf + - potw_biosolids_generated + - twtds_biosolids_treated + - class_b_land_app + - class_b_applier + - class_a_compost + - class_a_heat_dried + - class_a_other + - class_a_other_applier + - twtds_transfer_to_second_preparer + - twtds_second_preparer_name + - adc_or_final_c + - landfill + - landfill_name + - surface_disposal + - deepwell_injection + - stored + - longterm_treatment + - other + - name_of_other + - incineration + slot_usage: + biosolid_facility_id: + identifier: true + range: integer + +slots: + biosolid_facility_id: + range: integer + description: ID of the biosolids facility. + + report_submitted_date: + range: date + description: Date report submitted. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. + + facility: + range: string + description: Facility name. + + authority: + range: string + description: Authority. + + plant_type: + range: string + description: Plant type. + + aqmd: + range: string + description: AQMD. + + facility_address: + range: string + description: Facility address. + + facility_city: + range: string + description: Facility city. + + state: + range: string + description: State. + + facility_zip: + range: string + description: Facility zip. + + facility_county: + range: string + description: Facility county. + + mailing_street_1: + range: string + description: Mailing street 1. + + mailing_city: + range: string + description: Mailing city. + + mailing_state: + range: string + description: Mailing state. + + mailing_zip: + range: string + description: Mailing zip. + + biosolids_number: + range: string + description: Biosolids number. + + biosolids_contact: + range: string + description: Biosolids contact. + + biosolids_contact_phone: + range: string + description: Biosolids contact phone. + + biosolids_contact_email: + range: string + description: Biosolids contact email. + + adwf: + range: decimal + description: ADWF. + + potw_biosolids_generated: + range: integer + description: POTW biosolids generated. + + twtds_biosolids_treated: + range: integer + description: TWTDS biosolids treated. + + class_b_land_app: + range: integer + description: Class B land application. + + class_b_applier: + range: string + description: Class B applier. + + class_a_compost: + range: integer + description: Class A compost. + + class_a_heat_dried: + range: integer + description: Class A heat dried. + + class_a_other: + range: integer + description: Class A other. + + class_a_other_applier: + range: string + description: Class A other applier. + + twtds_transfer_to_second_preparer: + range: integer + description: TWTDS transfer to second preparer. + + twtds_second_preparer_name: + range: string + description: TWTDS second preparer name. + + adc_or_final_c: + range: integer + description: ADC or final cover. + + landfill: + range: integer + description: Landfill. + + landfill_name: + range: string + description: Landfill name. + + surface_disposal: + range: integer + description: Surface disposal. + + deepwell_injection: + range: string + description: Deepwell injection. + + stored: + range: integer + description: Stored. + + longterm_treatment: + range: integer + description: Longterm treatment. + + other: + range: integer + description: Other. + + name_of_other: + range: string + description: Name of other. + + incineration: + range: integer + description: Incineration. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_cafo_manure_locations.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_cafo_manure_locations.yaml new file mode 100644 index 00000000..41222103 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_cafo_manure_locations.yaml @@ -0,0 +1,98 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_cafo_manure_locations +name: infrastructure_cafo_manure_locations +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureCafoManureLocations: + description: CAFO manure locations infrastructure. + slots: + - cafo_manure_id + - latitude + - longitude + - owner_name + - facility_name + - address + - town + - state + - zip + - animal + - animal_feed_operation_type + - animal_units + - animal_count + - manure_total_solids + - source + - date_accessed + slot_usage: + cafo_manure_id: + identifier: true + range: integer + +slots: + cafo_manure_id: + range: integer + description: ID of the CAFO manure location. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. + + owner_name: + range: string + description: Owner name. + + facility_name: + range: string + description: Facility name. + + address: + range: string + description: Address. + + town: + range: string + description: Town. + + state: + range: string + description: State. + + zip: + range: string + description: Zip code. + + animal: + range: string + description: Animal. + + animal_feed_operation_type: + range: string + description: Animal feed operation type. + + animal_units: + range: integer + description: Animal units. + + animal_count: + range: integer + description: Animal count. + + manure_total_solids: + range: decimal + description: Manure total solids. + + source: + range: string + description: Source. + + date_accessed: + range: date + description: Date accessed. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_combustion_plants.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_combustion_plants.yaml new file mode 100644 index 00000000..82ec57af --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_combustion_plants.yaml @@ -0,0 +1,103 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_combustion_plants +name: infrastructure_combustion_plants +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureCombustionPlants: + description: Combustion plants infrastructure. + slots: + - combustion_fid + - objectid + - status + - city + - name + - county + - equivalent_generation + - np_mw + - cf + - yearload + - fuel + - notes + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + combustion_fid: + identifier: true + range: integer + +slots: + combustion_fid: + range: integer + description: Combustion FID. + + objectid: + range: integer + description: Object ID. + + status: + range: string + description: Status. + + city: + range: string + description: City. + + name: + range: string + description: Name. + + county: + range: string + description: County. + + equivalent_generation: + range: decimal + description: Equivalent generation. + + np_mw: + range: decimal + description: NP MW. + + cf: + range: decimal + description: CF. + + yearload: + range: integer + description: Yearload. + + fuel: + range: string + description: Fuel. + + notes: + range: string + description: Notes. + + type: + range: string + description: Type. + + wkt_geom: + range: string + description: WKT geometry. + + geom: + range: string + description: Geometry. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_district_energy_systems.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_district_energy_systems.yaml new file mode 100644 index 00000000..bab9f9f3 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_district_energy_systems.yaml @@ -0,0 +1,123 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_district_energy_systems +name: infrastructure_district_energy_systems +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureDistrictEnergySystems: + description: District energy systems infrastructure. + slots: + - des_fid + - cbg_id + - name + - system + - object_id + - city + - state + - primary_fuel + - secondary_fuel + - usetype + - cap_st + - cap_hw + - cap_cw + - chpcg_cap + - excess_c + - excess_h + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + des_fid: + identifier: true + range: integer + +slots: + des_fid: + range: integer + description: DES FID. + + cbg_id: + range: integer + description: CBG ID. + + name: + range: string + description: Name. + + system: + range: string + description: System. + + object_id: + range: integer + description: Object ID. + + city: + range: string + description: City. + + state: + range: string + description: State. + + primary_fuel: + range: string + description: Primary fuel. + + secondary_fuel: + range: string + description: Secondary fuel. + + usetype: + range: string + description: Use type. + + cap_st: + range: decimal + description: Cap ST. + + cap_hw: + range: decimal + description: Cap HW. + + cap_cw: + range: decimal + description: Cap CW. + + chpcg_cap: + range: decimal + description: CHPCG Cap. + + excess_c: + range: decimal + description: Excess C. + + excess_h: + range: decimal + description: Excess H. + + type: + range: string + description: Type. + + wkt_geom: + range: string + description: WKT geometry. + + geom: + range: string + description: Geometry. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_ethanol_biorefineries.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_ethanol_biorefineries.yaml new file mode 100644 index 00000000..eb68fc54 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_ethanol_biorefineries.yaml @@ -0,0 +1,63 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_ethanol_biorefineries +name: infrastructure_ethanol_biorefineries +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureEthanolBiorefineries: + description: Ethanol biorefineries infrastructure. + slots: + - ethanol_biorefinery_id + - name + - city + - state + - address + - type + - capacity_mgy + - production_mgy + - constr_exp + slot_usage: + ethanol_biorefinery_id: + identifier: true + range: integer + +slots: + ethanol_biorefinery_id: + range: integer + description: ID of the ethanol biorefinery. + + name: + range: string + description: Name. + + city: + range: string + description: City. + + state: + range: string + description: State. + + address: + range: string + description: Address. + + type: + range: string + description: Type. + + capacity_mgy: + range: integer + description: Capacity in MGY. + + production_mgy: + range: integer + description: Production in MGY. + + constr_exp: + range: integer + description: Construction/expansion. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_food_processing_facilities.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_food_processing_facilities.yaml new file mode 100644 index 00000000..30835964 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_food_processing_facilities.yaml @@ -0,0 +1,103 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_food_processing_facilities +name: infrastructure_food_processing_facilities +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureFoodProcessingFacilities: + description: Food processing facilities infrastructure. + slots: + - processing_facility_id + - address + - county + - city + - company + - join_count + - master_type + - state + - subtype + - target_fid + - processing_type + - zip + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + processing_facility_id: + identifier: true + range: integer + +slots: + processing_facility_id: + range: integer + description: Processing facility ID. + + address: + range: string + description: Address. + + county: + range: string + description: County. + + city: + range: string + description: City. + + company: + range: string + description: Company. + + join_count: + range: integer + description: Join count. + + master_type: + range: string + description: Master type. + + state: + range: string + description: State. + + subtype: + range: string + description: Subtype. + + target_fid: + range: integer + description: Target FID. + + processing_type: + range: string + description: Processing type. + + zip: + range: string + description: Zip. + + type: + range: string + description: Type. + + wkt_geom: + range: string + description: WKT geometry. + + geom: + range: string + description: Geometry. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_landfills.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_landfills.yaml new file mode 100644 index 00000000..cee6d298 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_landfills.yaml @@ -0,0 +1,188 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_landfills +name: infrastructure_landfills +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureLandfills: + description: Landfills infrastructure. + slots: + - project_id + - project_int_id + - ghgrp_id + - landfill_id + - landfill_name + - state + - physical_address + - city + - county + - zip_code + - latitude + - longitude + - ownership_type + - landfill_owner_orgs + - landfill_opened_year + - landfill_closure_year + - landfill_status + - waste_in_place + - waste_in_place_year + - lfg_system_in_place + - lfg_collected + - lfg_flared + - project_status + - project_name + - project_start_date + - project_shutdown_date + - project_type_category + - lfg_energy_project_type + - rng_delivery_method + - actual_mw_generation + - rated_mw_capacity + - lfg_flow_to_project + - direct_emission_reductions + - avoided_emission_reductions + slot_usage: + project_id: + identifier: true + range: string + +slots: + project_id: + range: string + description: Project ID. + + project_int_id: + range: integer + description: Project integer ID. + + ghgrp_id: + range: string + description: GHGRP ID. + + landfill_id: + range: integer + description: Landfill ID. + + landfill_name: + range: string + description: Landfill name. + + state: + range: string + description: State. + + physical_address: + range: string + description: Physical address. + + city: + range: string + description: City. + + county: + range: string + description: County. + + zip_code: + range: string + description: Zip code. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. + + ownership_type: + range: string + description: Ownership type. + + landfill_owner_orgs: + range: string + description: Landfill owner organizations. + + landfill_opened_year: + range: date + description: Landfill opened year. + + landfill_closure_year: + range: date + description: Landfill closure year. + + landfill_status: + range: string + description: Landfill status. + + waste_in_place: + range: integer + description: Waste in place. + + waste_in_place_year: + range: date + description: Waste in place year. + + lfg_system_in_place: + range: boolean + description: LFG system in place. + + lfg_collected: + range: decimal + description: LFG collected. + + lfg_flared: + range: decimal + description: LFG flared. + + project_status: + range: string + description: Project status. + + project_name: + range: string + description: Project name. + + project_start_date: + range: date + description: Project start date. + + project_shutdown_date: + range: date + description: Project shutdown date. + + project_type_category: + range: string + description: Project type category. + + lfg_energy_project_type: + range: string + description: LFG energy project type. + + rng_delivery_method: + range: string + description: RNG delivery method. + + actual_mw_generation: + range: decimal + description: Actual MW generation. + + rated_mw_capacity: + range: decimal + description: Rated MW capacity. + + lfg_flow_to_project: + range: decimal + description: LFG flow to project. + + direct_emission_reductions: + range: decimal + description: Direct emission reductions. + + avoided_emission_reductions: + range: decimal + description: Avoided emission reductions. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_livestock_anaerobic_digesters.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_livestock_anaerobic_digesters.yaml new file mode 100644 index 00000000..d8781afa --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_livestock_anaerobic_digesters.yaml @@ -0,0 +1,133 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_livestock_anaerobic_digesters +name: infrastructure_livestock_anaerobic_digesters +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureLivestockAnaerobicDigesters: + description: Livestock anaerobic digesters infrastructure. + slots: + - digester_id + - project_name + - project_type + - city + - state + - digester_type + - profile + - year_operational + - animal_type_class + - animal_types + - pop_feeding_digester + - total_pop_feeding_digester + - cattle + - dairy + - poultry + - swine + - codigestion + - biogas_generation_estimate + - electricity_generated + - biogas_end_uses + - methane_emission_reductions + - latitude + - longitude + slot_usage: + digester_id: + identifier: true + range: integer + +slots: + digester_id: + range: integer + description: ID of the digester. + + project_name: + range: string + description: Project name. + + project_type: + range: string + description: Project type. + + city: + range: string + description: City. + + state: + range: string + description: State. + + digester_type: + range: string + description: Digester type. + + profile: + range: string + description: Profile. + + year_operational: + range: date + description: Year operational. + + animal_type_class: + range: string + description: Animal type class. + + animal_types: + range: string + description: Animal types. + + pop_feeding_digester: + range: string + description: Population feeding digester. + + total_pop_feeding_digester: + range: integer + description: Total population feeding digester. + + cattle: + range: integer + description: Cattle. + + dairy: + range: integer + description: Dairy. + + poultry: + range: integer + description: Poultry. + + swine: + range: integer + description: Swine. + + codigestion: + range: string + description: Codigestion. + + biogas_generation_estimate: + range: integer + description: Biogas generation estimate. + + electricity_generated: + range: integer + description: Electricity generated. + + biogas_end_uses: + range: string + description: Biogas end uses. + + methane_emission_reductions: + range: integer + description: Methane emission reductions. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_msw_to_energy_anaerobic_digesters.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_msw_to_energy_anaerobic_digesters.yaml new file mode 100644 index 00000000..f8f1cd29 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_msw_to_energy_anaerobic_digesters.yaml @@ -0,0 +1,98 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_msw_to_energy_anaerobic_digesters +name: infrastructure_msw_to_energy_anaerobic_digesters +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureMswToEnergyAnaerobicDigesters: + description: MSW to energy anaerobic digesters infrastructure. + slots: + - wte_id + - city + - county + - equivalent_generation + - feedstock + - dayload + - dayload_bdt + - facility_type + - status + - notes + - source + - type + - wkt_geom + - geom + - latitude + - longitude + slot_usage: + wte_id: + identifier: true + range: integer + +slots: + wte_id: + range: integer + description: WTE ID. + + city: + range: string + description: City. + + county: + range: string + description: County. + + equivalent_generation: + range: decimal + description: Equivalent generation. + + feedstock: + range: string + description: Feedstock. + + dayload: + range: decimal + description: Dayload. + + dayload_bdt: + range: decimal + description: Dayload BDT. + + facility_type: + range: string + description: Facility type. + + status: + range: string + description: Status. + + notes: + range: string + description: Notes. + + source: + range: string + description: Source. + + type: + range: string + description: Type. + + wkt_geom: + range: string + description: WKT geometry. + + geom: + range: string + description: Geometry. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_saf_and_renewable_diesel_plants.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_saf_and_renewable_diesel_plants.yaml new file mode 100644 index 00000000..3b32e504 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_saf_and_renewable_diesel_plants.yaml @@ -0,0 +1,83 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_saf_and_renewable_diesel_plants +name: infrastructure_saf_and_renewable_diesel_plants +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureSafAndRenewableDieselPlants: + description: SAF and renewable diesel plants infrastructure. + slots: + - ibcc_index + - company + - city + - state + - country + - capacity + - feedstock + - products + - status + - address + - coordinates + - latitude + - longitude + slot_usage: + ibcc_index: + identifier: true + range: integer + +slots: + ibcc_index: + range: integer + description: IBCC index. + + company: + range: string + description: Company name. + + city: + range: string + description: City. + + state: + range: string + description: State. + + country: + range: string + description: Country. + + capacity: + range: string + description: Capacity. + + feedstock: + range: string + description: Feedstock. + + products: + range: string + description: Products. + + status: + range: string + description: Status. + + address: + range: string + description: Address. + + coordinates: + range: string + description: Coordinates. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_wastewater_treatment_plants.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_wastewater_treatment_plants.yaml new file mode 100644 index 00000000..745ac52b --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/infrastructure/infrastructure_wastewater_treatment_plants.yaml @@ -0,0 +1,168 @@ +id: https://w3id.org/ca_biositing/infrastructure/infrastructure_wastewater_treatment_plants +name: infrastructure_wastewater_treatment_plants +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + InfrastructureWastewaterTreatmentPlants: + description: Wastewater treatment plants infrastructure. + slots: + - plant_id + - name + - state + - codigestion + - flow_design_adjusted + - flow_average + - biosolids + - excess_flow + - biogas_utilized + - flaring + - excess_mass_loading_rate + - excess_mass_loading_rate_wet + - methane_production + - energy_content + - electric_kw + - thermal_mmbtu_d + - electric_kwh + - thermal_annual_mmbtu_y + - anaerobic_digestion_facility + - county + - dayload_bdt + - dayload + - equivalent_generation + - facility_type + - feedstock + - type + - city + - latitude + - longitude + - zipcode + slot_usage: + plant_id: + identifier: true + range: integer + +slots: + plant_id: + range: integer + description: ID of the plant. + + name: + range: string + description: Name. + + state: + range: string + description: State. + + codigestion: + range: string + description: Codigestion. + + flow_design_adjusted: + range: decimal + description: Flow design adjusted. + + flow_average: + range: decimal + description: Flow average. + + biosolids: + range: decimal + description: Biosolids. + + excess_flow: + range: decimal + description: Excess flow. + + biogas_utilized: + range: boolean + description: Biogas utilized. + + flaring: + range: boolean + description: Flaring. + + excess_mass_loading_rate: + range: decimal + description: Excess mass loading rate. + + excess_mass_loading_rate_wet: + range: decimal + description: Excess mass loading rate wet. + + methane_production: + range: decimal + description: Methane production. + + energy_content: + range: decimal + description: Energy content. + + electric_kw: + range: decimal + description: Electric KW. + + thermal_mmbtu_d: + range: decimal + description: Thermal MMBTU/d. + + electric_kwh: + range: decimal + description: Electric KWh. + + thermal_annual_mmbtu_y: + range: decimal + description: Thermal annual MMBTU/y. + + anaerobic_digestion_facility: + range: string + description: Anaerobic digestion facility. + + county: + range: string + description: County. + + dayload_bdt: + range: decimal + description: Dayload BDT. + + dayload: + range: decimal + description: Dayload. + + equivalent_generation: + range: decimal + description: Equivalent generation. + + facility_type: + range: string + description: Facility type. + + feedstock: + range: string + description: Feedstock. + + type: + range: string + description: Type. + + city: + range: string + description: City. + + latitude: + range: decimal + description: Latitude. + + longitude: + range: decimal + description: Longitude. + + zipcode: + range: string + description: Zipcode. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml deleted file mode 100644 index ed0d6c99..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage.yaml +++ /dev/null @@ -1,88 +0,0 @@ -id: https://w3id.org/ca_biositing/lineage -name: lineage -title: Lineage Definitions -description: Data lineage and ETL tracking. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - -classes: - LineageGroup: - description: Grouping for lineage information. - slots: - - id - - etl_run_id - - note - slot_usage: - id: - identifier: true - range: integer - - EntityLineage: - description: Lineage information for a specific entity. - slots: - - id - - lineage_group_id - - source_table - - source_row_id - - note - slot_usage: - id: - identifier: true - range: integer - - EtlRun: - description: Information about an ETL run. - slots: - - id - - started_at - - completed_at - - pipeline_name - - status - - records_ingested - - note - slot_usage: - id: - identifier: true - -slots: - #Slots for EntityLineage class - - source_table: - range: string - description: Source table name. - - source_row_id: - range: string - description: Source row identifier. - - #Slots for EtlRun class - - started_at: - range: datetime - description: Start time of the ETL run. - - completed_at: - range: datetime - description: Completion time of the ETL run. - - pipeline_name: - range: string - description: Name of the pipeline. - - status: - range: string - description: Status of the ETL run. - - records_ingested: - range: integer - description: Number of records ingested. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage/entity_lineage.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage/entity_lineage.yaml new file mode 100644 index 00000000..70e0b1fc --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage/entity_lineage.yaml @@ -0,0 +1,36 @@ +id: https://w3id.org/ca_biositing/lineage/entity_lineage +name: entity_lineage +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - lineage_group +default_range: string + +classes: + EntityLineage: + description: Lineage information for a specific entity. + slots: + - id + - lineage_group_id + - source_table + - source_row_id + - note + slot_usage: + id: + identifier: true + range: integer + +slots: + lineage_group_id: + range: LineageGroup + description: Reference to the lineage group. + + source_table: + range: string + description: Source table name. + + source_row_id: + range: string + description: Source row identifier. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage/etl_run.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage/etl_run.yaml new file mode 100644 index 00000000..122bd183 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage/etl_run.yaml @@ -0,0 +1,44 @@ +id: https://w3id.org/ca_biositing/lineage/etl_run +name: etl_run +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + EtlRun: + description: Information about an ETL run. + slots: + - id + - started_at + - completed_at + - pipeline_name + - status + - records_ingested + - note + slot_usage: + id: + identifier: true + +slots: + started_at: + range: datetime + description: Start time of the ETL run. + + completed_at: + range: datetime + description: Completion time of the ETL run. + + pipeline_name: + range: string + description: Name of the pipeline. + + status: + range: string + description: Status of the ETL run. + + records_ingested: + range: integer + description: Number of records ingested. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage/lineage_group.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage/lineage_group.yaml new file mode 100644 index 00000000..3a996250 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/lineage/lineage_group.yaml @@ -0,0 +1,25 @@ +id: https://w3id.org/ca_biositing/lineage/lineage_group +name: lineage_group +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + LineageGroup: + description: Grouping for lineage information. + slots: + - id + - etl_run_id + - note + slot_usage: + id: + identifier: true + range: integer + +slots: + etl_run_id: + range: string + description: Identifier of the ETL run. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml deleted file mode 100644 index 579609c2..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units.yaml +++ /dev/null @@ -1,130 +0,0 @@ -id: https://w3id.org/ca_biositing/methods_parameters_units -name: methods_parameters_units -title: Methods, Parameters, and Units -description: Analytical methods, parameters, and units of measurement. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - data_sources_metadata - -classes: - Unit: - is_a: LookupBase - description: Unit of measurement. - - Method: - is_a: BaseEntity - description: Analytical method. - slots: - - name - - method_abbrev_id - - method_category_id - - method_standard_id - - description - - detection_limits - - source_id - - MethodAbbrev: - is_a: LookupBase - description: Abbreviation for method. - - MethodCategory: - is_a: LookupBase - description: Category of method. - - MethodStandard: - is_a: LookupBase - description: Standard associated with the method. - - Parameter: - is_a: BaseEntity - description: Parameter being measured. - slots: - - name - - standard_unit_id - - calculated - - description - - ParameterCategory: - is_a: LookupBase - description: Category of parameter. - - ParameterCategoryParameter: - description: Link between Parameter and ParameterCategory. - slots: - - id - - parameter_id - - parameter_category_id - slot_usage: - id: - identifier: true - range: integer - - ParameterUnit: - description: Link between Parameter and Unit (alternate units). - slots: - - id - - parameter_id - - alternate_unit_id - slot_usage: - id: - identifier: true - range: integer - -slots: - #Method slots - - method_abbrev_id: - range: integer - description: Reference to MethodAbbrev. - - method_category_id: - range: integer - description: Reference to MethodCategory. - - method_standard_id: - range: integer - description: Reference to MethodStandard. - - detection_limits: - range: string - description: Detection limits of the method. - - source_id: - range: integer - description: Reference to DataSource. - - #Parameter slots - - standard_unit_id: - range: integer - description: Reference to Unit. - - calculated: - range: boolean - description: Whether the parameter is calculated. - - #ParameterCategoryParameter slots - - parameter_id: - range: integer - description: Reference to Parameter. - - parameter_category_id: - range: integer - description: Reference to ParameterCategory. - - #ParameterUnit slots - - alternate_unit_id: - range: integer - description: Reference to Unit. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method.yaml new file mode 100644 index 00000000..613a296a --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method.yaml @@ -0,0 +1,46 @@ +id: https://w3id.org/ca_biositing/methods_parameters_units/method +name: method +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../data_sources_metadata/data_source + - method_abbrev + - method_category + - method_standard +default_range: string + +classes: + Method: + is_a: BaseEntity + description: method. + slots: + - name + - method_abbrev_id + - method_category_id + - method_standard_id + - description + - detection_limits + - source_id + +slots: + method_abbrev_id: + range: MethodAbbrev + description: Reference to MethodAbbrev. + + method_category_id: + range: MethodCategory + description: Reference to MethodCategory. + + method_standard_id: + range: MethodStandard + description: Reference to MethodStandard. + + detection_limits: + range: string + description: Detection limits of the method. + + source_id: + range: DataSource + description: Reference to DataSource. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method_abbrev.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method_abbrev.yaml new file mode 100644 index 00000000..a719e522 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method_abbrev.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/methods_parameters_units/method_abbrev +name: method_abbrev +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + MethodAbbrev: + is_a: LookupBase + description: Abbreviation for method. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method_category.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method_category.yaml new file mode 100644 index 00000000..ffbe07af --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method_category.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/methods_parameters_units/method_category +name: method_category +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + MethodCategory: + is_a: LookupBase + description: Category of method. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method_standard.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method_standard.yaml new file mode 100644 index 00000000..40bb316d --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/method_standard.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/methods_parameters_units/method_standard +name: method_standard +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + MethodStandard: + is_a: LookupBase + description: Standard associated with the method. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter.yaml new file mode 100644 index 00000000..d633260c --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter.yaml @@ -0,0 +1,28 @@ +id: https://w3id.org/ca_biositing/methods_parameters_units/parameter +name: parameter +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - unit +default_range: string + +classes: + Parameter: + is_a: BaseEntity + description: Parameter being measured. + slots: + - name + - standard_unit_id + - calculated + - description + +slots: + standard_unit_id: + range: Unit + description: Reference to Unit. + + calculated: + range: boolean + description: Whether the parameter is calculated. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter_category.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter_category.yaml new file mode 100644 index 00000000..1169b661 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter_category.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/methods_parameters_units/parameter_category +name: parameter_category +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + ParameterCategory: + is_a: LookupBase + description: Category of parameter. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter_category_parameter.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter_category_parameter.yaml new file mode 100644 index 00000000..79b08162 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter_category_parameter.yaml @@ -0,0 +1,31 @@ +id: https://w3id.org/ca_biositing/methods_parameters_units/parameter_category_parameter +name: parameter_category_parameter +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - parameter + - parameter_category +default_range: string + +classes: + ParameterCategoryParameter: + description: Link between Parameter and ParameterCategory. + slots: + - id + - parameter_id + - parameter_category_id + slot_usage: + id: + identifier: true + range: integer + +slots: + parameter_id: + range: Parameter + description: Reference to Parameter. + + parameter_category_id: + range: ParameterCategory + description: Reference to ParameterCategory. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter_unit.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter_unit.yaml new file mode 100644 index 00000000..0ed87eb3 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/parameter_unit.yaml @@ -0,0 +1,31 @@ +id: https://w3id.org/ca_biositing/methods_parameters_units/parameter_unit +name: parameter_unit +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - parameter + - unit +default_range: string + +classes: + ParameterUnit: + description: Link between Parameter and Unit (alternate units). + slots: + - id + - parameter_id + - alternate_unit_id + slot_usage: + id: + identifier: true + range: integer + +slots: + parameter_id: + range: Parameter + description: Reference to Parameter. + + alternate_unit_id: + range: Unit + description: Reference to Unit. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/unit.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/unit.yaml new file mode 100644 index 00000000..1fea7b71 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/methods_parameters_units/unit.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/methods_parameters_units/unit +name: unit +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + Unit: + is_a: LookupBase + description: Unit of measurement. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people/contact.yaml similarity index 53% rename from src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people/contact.yaml index 5f5c59f5..ec33e8de 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people/contact.yaml @@ -1,19 +1,11 @@ -id: https://w3id.org/ca_biositing/people -name: people -title: People Definitions -description: Contact and provider information. -license: https://creativecommons.org/publicdomain/zero/1.0/ - +id: https://w3id.org/ca_biositing/people/contact +name: contact prefixes: linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - imports: - linkml:types - - core + - ../core/base_entity +default_range: string classes: Contact: @@ -29,16 +21,6 @@ classes: identifier: true range: integer - Provider: - is_a: BaseEntity - description: Provider information. - slots: - - codename - slot_usage: - id: - identifier: true - range: integer - slots: first_name: range: string @@ -55,7 +37,3 @@ slots: affiliation: range: string description: Affiliation. - - codename: - range: string - description: Codename for the provider. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people/provider.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people/provider.yaml new file mode 100644 index 00000000..31a9c842 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/people/provider.yaml @@ -0,0 +1,24 @@ +id: https://w3id.org/ca_biositing/people/provider +name: provider +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + Provider: + is_a: BaseEntity + description: Provider information. + slots: + - codename + slot_usage: + id: + identifier: true + range: integer + +slots: + codename: + range: string + description: Codename for the provider. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml deleted file mode 100644 index 5a6342d3..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places.yaml +++ /dev/null @@ -1,105 +0,0 @@ -id: https://w3id.org/ca_biositing/places -name: places -title: Places Definitions -description: Geographic locations and addresses. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - -classes: - Geography: - description: Geographic location. - slots: - - geoid - - state_name - - state_fips - - county_name - - county_fips - - region_name - - agg_level_desc - slot_usage: - geoid: - identifier: true - - LocationAddress: - is_a: BaseEntity - description: Physical address. - slots: - - geography_id - - address_line1 - - address_line2 - - city - - zip - - lat - - lon - - is_anonymous - -slots: - geoid: - range: string - description: Unique identifier for geography. - - state_name: - range: string - description: State name. - - state_fips: - range: string - description: State FIPS code. - - county_name: - range: string - description: County name. - - county_fips: - range: string - description: County FIPS code. - - region_name: - range: string - description: Region name. - - agg_level_desc: - range: string - description: Aggregation level description. - - geography_id: - range: string - description: Reference to Geography. - - address_line1: - range: string - description: Address line 1. - - address_line2: - range: string - description: Address line 2. - - city: - range: string - description: City. - - zip: - range: string - description: ZIP code. - - lat: - range: float - description: Latitude. - - lon: - range: float - description: Longitude. - - is_anonymous: - range: boolean - description: Whether the location is anonymous. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places/geography.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places/geography.yaml new file mode 100644 index 00000000..98cc3fcc --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places/geography.yaml @@ -0,0 +1,52 @@ +id: https://w3id.org/ca_biositing/places/geography +name: geography +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity +default_range: string + +classes: + Geography: + description: Geographic location. + slots: + - geoid + - state_name + - state_fips + - county_name + - county_fips + - region_name + - agg_level_desc + slot_usage: + geoid: + identifier: true + +slots: + geoid: + range: string + description: Unique identifier for geography. + + state_name: + range: string + description: State name. + + state_fips: + range: string + description: State FIPS code. + + county_name: + range: string + description: County name. + + county_fips: + range: string + description: County FIPS code. + + region_name: + range: string + description: Region name. + + agg_level_desc: + range: string + description: Aggregation level description. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places/location_address.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places/location_address.yaml new file mode 100644 index 00000000..b967e799 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/places/location_address.yaml @@ -0,0 +1,56 @@ +id: https://w3id.org/ca_biositing/places/location_address +name: location_address +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - geography +default_range: string + +classes: + LocationAddress: + is_a: BaseEntity + description: Physical address. + slots: + - geography_id + - address_line1 + - address_line2 + - city + - zip + - lat + - lon + - is_anonymous + +slots: + geography_id: + range: Geography + description: Reference to Geography. + + address_line1: + range: string + description: Address line 1. + + address_line2: + range: string + description: Address line 2. + + city: + range: string + description: City. + + zip: + range: string + description: ZIP code. + + lat: + range: float + description: Latitude. + + lon: + range: float + description: Longitude. + + is_anonymous: + range: boolean + description: Whether the location is anonymous. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/primary_ag_product.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/primary_ag_product.yaml deleted file mode 100644 index 2c5c9b4c..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/primary_ag_product.yaml +++ /dev/null @@ -1,23 +0,0 @@ -id: https://w3id.org/ca_biositing/primary_ag_product -name: primary_ag_product -title: Primary Agricultural Product -description: Core definitions for primary agricultural products. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - -classes: - PrimaryAgProduct: - is_a: LookupBase - description: Primary agricultural product definition. - slots: - - note diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_availability.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_availability.yaml deleted file mode 100644 index 9bf95246..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_availability.yaml +++ /dev/null @@ -1,35 +0,0 @@ -id: https://w3id.org/ca_biositing/resource_availability -name: resource_availability -title: Resource Availability -description: Availability of a resource in a location. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - places - - resource_information - -classes: - ResourceAvailability: - is_a: BaseEntity - description: Availability of a resource in a location. - slots: - - resource_id - - geoid - - from_month - - to_month - - year_round - - note - -slots: - resource_id: - range: Resource - description: Reference to Resource. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_counterfactual.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_counterfactual.yaml deleted file mode 100644 index d346b197..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_counterfactual.yaml +++ /dev/null @@ -1,47 +0,0 @@ -id: https://w3id.org/ca_biositing/resource_counterfactual -name: resource_counterfactual -title: Resource Counterfactual -description: Counterfactual uses of a resource. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - places - - resource_information - - data_sources_metadata - -classes: - ResourceCounterfactual: - is_a: BaseEntity - description: Counterfactual uses of a resource. - slots: - - geoid - - resource_id - - counterfactual_description - - animal_bedding_percent - - animal_bedding_source_id - - animal_feed_percent - - animal_feed_source_id - - bioelectricty_percent - - bioelectricty_source_id - - burn_percent - - burn_source_id - - compost_percent - - compost_source_id - - landfill_percent - - landfill_source_id - - counterfactual_date - - note - -slots: - resource_id: - range: Resource - description: Reference to Resource. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml deleted file mode 100644 index 82237cae..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information.yaml +++ /dev/null @@ -1,189 +0,0 @@ -id: https://w3id.org/ca_biositing/resource_information -name: resource_information -title: Resource Information -description: Biomass resources and their classifications. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - places - -classes: - Resource: - is_a: BaseEntity - description: Biomass resource definition. - slots: - - name - - primary_ag_product_id - - resource_class_id - - resource_subclass_id - - note - - test - - ResourceClass: - is_a: LookupBase - description: Classification of resources. - - ResourceSubclass: - is_a: LookupBase - description: Sub-classification of resources. - - PrimaryAgProduct: - is_a: LookupBase - description: Primary agricultural product definition. - slots: - - note - - ResourceAvailability: - is_a: BaseEntity - description: Availability of a resource in a location. - slots: - - resource_id - - geoid - - from_month - - to_month - - year_round - - note - - ResourceCounterfactual: - is_a: BaseEntity - description: Counterfactual uses of a resource. - slots: - - geoid - - resource_id - - counterfactual_description - - animal_bedding_percent - - animal_bedding_source_id - - animal_feed_percent - - animal_feed_source_id - - bioelectricty_percent - - bioelectricty_source_id - - burn_percent - - burn_source_id - - compost_percent - - compost_source_id - - landfill_percent - - landfill_source_id - - counterfactual_date - - note - - ResourceMorphology: - description: Morphology of a resource. - slots: - - id - - resource_id - - morphology_uri - slot_usage: - id: - identifier: true - range: integer - -slots: - #Resource slots - - primary_ag_product_id: - range: integer - description: Reference to PrimaryAgProduct. - - resource_class_id: - range: integer - description: Reference to ResourceClass. - - resource_subclass_id: - range: integer - description: Reference to ResourceSubclass. - - test: - range: string - description: Test field. - - #ResourceAvailability slots - - resource_id: - range: integer - description: Reference to Resource. - - geoid: - range: string - description: Reference to Geography. - - from_month: - range: integer - description: Start month of availability. - - to_month: - range: integer - description: End month of availability. - - year_round: - range: boolean - description: Whether available year-round. - - #ResourceCounterfactual slots - - counterfactual_description: - range: string - description: Description of counterfactual scenario. - - animal_bedding_percent: - range: decimal - description: Percentage used for animal bedding. - - animal_bedding_source_id: - range: integer - description: Source for animal bedding data. - - animal_feed_percent: - range: decimal - description: Percentage used for animal feed. - - animal_feed_source_id: - range: integer - description: Source for animal feed data. - - bioelectricty_percent: - range: decimal - description: Percentage used for bioelectricity. - - bioelectricty_source_id: - range: integer - description: Source for bioelectricity data. - - burn_percent: - range: decimal - description: Percentage burned. - - burn_source_id: - range: integer - description: Source for burn data. - - compost_percent: - range: decimal - description: Percentage composted. - - compost_source_id: - range: integer - description: Source for compost data. - - landfill_percent: - range: decimal - description: Percentage landfilled. - - landfill_source_id: - range: integer - description: Source for landfill data. - - counterfactual_date: - range: date - description: Date of counterfactual data. - - morphology_uri: - range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/primary_ag_product.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/primary_ag_product.yaml new file mode 100644 index 00000000..94937588 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/primary_ag_product.yaml @@ -0,0 +1,14 @@ +id: https://w3id.org/ca_biositing/resource_information/primary_ag_product +name: primary_ag_product +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + PrimaryAgProduct: + is_a: LookupBase + description: Primary agricultural product definition. + slots: diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource.yaml new file mode 100644 index 00000000..87baf0e7 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource.yaml @@ -0,0 +1,44 @@ +id: https://w3id.org/ca_biositing/resource_information/resource +name: resource +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - primary_ag_product + - resource_class + - resource_subclass +default_range: string + +classes: + Resource: + is_a: BaseEntity + description: Biomass resource definition. + slots: + - name + - primary_ag_product_id + - resource_class_id + - resource_subclass_id + - note + - test + +slots: + primary_ag_product_id: + range: PrimaryAgProduct + description: Reference to PrimaryAgProduct. + + resource_class_id: + range: ResourceClass + description: Reference to ResourceClass. + + resource_subclass_id: + range: ResourceSubclass + description: Reference to ResourceSubclass. + + note: + range: string + description: Additional notes about the resource. + + test: + range: string + description: Test field. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_availability.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_availability.yaml new file mode 100644 index 00000000..761ecccb --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_availability.yaml @@ -0,0 +1,43 @@ +id: https://w3id.org/ca_biositing/resource_information/resource_availability +name: resource_availability +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - resource + - ../places/geography +default_range: string + +classes: + ResourceAvailability: + is_a: BaseEntity + description: Availability of a resource in a location. + slots: + - resource_id + - geoid + - from_month + - to_month + - year_round + - note + +slots: + resource_id: + range: Resource + description: Reference to Resource. + + geoid: + range: Geography + description: Reference to Geography. + + from_month: + range: integer + description: Start month of availability. + + to_month: + range: integer + description: End month of availability. + + year_round: + range: boolean + description: Whether available year-round. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_class.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_class.yaml new file mode 100644 index 00000000..0bace74e --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_class.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/resource_information/resource_class +name: resource_class +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + ResourceClass: + is_a: LookupBase + description: Classification of resources. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_counterfactual.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_counterfactual.yaml new file mode 100644 index 00000000..62c02afb --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_counterfactual.yaml @@ -0,0 +1,96 @@ +id: https://w3id.org/ca_biositing/resource_information/resource_counterfactual +name: resource_counterfactual +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - resource + - ../places/geography + #- ../data_sources_metadata/data_source +default_range: string + +classes: + ResourceCounterfactual: + description: Counterfactual uses of a resource. + slots: + - geoid + - resource_id + - counterfactual_description + - animal_bedding_percent + - animal_bedding_source_id + - animal_feed_percent + - animal_feed_source_id + - bioelectricty_percent + - bioelectricty_source_id + - burn_percent + - burn_source_id + - compost_percent + - compost_source_id + - landfill_percent + - landfill_source_id + - counterfactual_date + +slots: + geoid: + range: Geography + description: Reference to Geography. + + resource_id: + range: Resource + description: Reference to Resource. + + counterfactual_description: + range: string + description: Description of counterfactual scenario. + + animal_bedding_percent: + range: decimal + description: Percentage used for animal bedding. + + animal_bedding_source_id: + range: integer + description: Source for animal bedding data. + + animal_feed_percent: + range: decimal + description: Percentage used for animal feed. + + animal_feed_source_id: + range: integer + description: Source for animal feed data. + + bioelectricty_percent: + range: decimal + description: Percentage used for bioelectricity. + + bioelectricty_source_id: + range: integer + description: Source for bioelectricity data. + + burn_percent: + range: decimal + description: Percentage burned. + + burn_source_id: + range: integer + description: Source for burn data. + + compost_percent: + range: decimal + description: Percentage composted. + + compost_source_id: + range: integer + description: Source for compost data. + + landfill_percent: + range: decimal + description: Percentage landfilled. + + landfill_source_id: + range: integer + description: Source for landfill data. + + counterfactual_date: + range: date + description: Date of counterfactual data. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_morphology.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_morphology.yaml similarity index 58% rename from src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_morphology.yaml rename to src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_morphology.yaml index f9d93c67..11192995 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_morphology.yaml +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_morphology.yaml @@ -1,20 +1,12 @@ -id: https://w3id.org/ca_biositing/resource_morphology +id: https://w3id.org/ca_biositing/resource_information/resource_morphology name: resource_morphology -title: Resource Morphology -description: Morphology of a resource. -license: https://creativecommons.org/publicdomain/zero/1.0/ - prefixes: linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - imports: - linkml:types - - core - - resource_information + - ../core/base_entity + - resource +default_range: string classes: ResourceMorphology: @@ -32,3 +24,6 @@ slots: resource_id: range: Resource description: Reference to Resource. + + morphology_uri: + range: string diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_subclass.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_subclass.yaml new file mode 100644 index 00000000..bbde717b --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_information/resource_subclass.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/resource_information/resource_subclass +name: resource_subclass +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + ResourceSubclass: + is_a: LookupBase + description: Sub-classification of resources. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_subclass.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_subclass.yaml deleted file mode 100644 index 0236bca8..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/resource_subclass.yaml +++ /dev/null @@ -1,21 +0,0 @@ -id: https://w3id.org/ca_biositing/resource_subclass -name: resource_subclass -title: Resource Subclass -description: Sub-classification of resources. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - -classes: - ResourceSubclass: - is_a: LookupBase - description: Sub-classification of resources. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation.yaml deleted file mode 100644 index 758bb6c8..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation.yaml +++ /dev/null @@ -1,70 +0,0 @@ -id: https://w3id.org/ca_biositing/sample_preparation -name: sample_preparation -title: Sample Preparation -description: Sample preparation methods and records. -license: https://creativecommons.org/publicdomain/zero/1.0/ - -prefixes: - linkml: https://w3id.org/linkml/ - ca_biositing: https://w3id.org/ca_biositing/ - -default_prefix: ca_biositing -default_range: string - -imports: - - linkml:types - - core - - field_sampling - - people - -classes: - PreparationMethod: - is_a: BaseEntity - description: Method of sample preparation. - slots: - - name - - description - - prep_method_abbrev_id - - prep_temp_c - - uri - - drying_step - - PreparationMethodAbbreviation: - is_a: LookupBase - description: Abbreviation for preparation method. - - PreparedSample: - is_a: BaseEntity - description: Sample that has been prepared. - slots: - - name - - field_sample_id - - prep_method_id - - prep_date - - preparer_id - - note - -slots: - prep_method_abbrev_id: - range: integer - description: Reference to PreparationMethodAbbreviation. - - prep_temp_c: - range: decimal - description: Preparation temperature in Celsius. - - drying_step: - range: boolean - description: Whether drying step was involved. - - prep_method_id: - range: integer - description: Reference to PreparationMethod. - - prep_date: - range: date - description: Date of preparation. - - preparer_id: - range: integer - description: Reference to Contact (preparer). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation/preparation_method.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation/preparation_method.yaml new file mode 100644 index 00000000..8abf57c2 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation/preparation_method.yaml @@ -0,0 +1,34 @@ +id: https://w3id.org/ca_biositing/sample_preparation/preparation_method +name: preparation_method +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - preparation_method_abbreviation +default_range: string + +classes: + PreparationMethod: + is_a: BaseEntity + description: Method of sample preparation. + slots: + - name + - description + - prep_method_abbrev_id + - prep_temp_c + - uri + - drying_step + +slots: + prep_method_abbrev_id: + range: PreparationMethodAbbreviation + description: Reference to PreparationMethodAbbreviation. + + prep_temp_c: + range: decimal + description: Preparation temperature in Celsius. + + drying_step: + range: boolean + description: Whether drying step was involved. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation/preparation_method_abbreviation.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation/preparation_method_abbreviation.yaml new file mode 100644 index 00000000..9a6c3c01 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation/preparation_method_abbreviation.yaml @@ -0,0 +1,13 @@ +id: https://w3id.org/ca_biositing/sample_preparation/preparation_method_abbreviation +name: preparation_method_abbreviation +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/lookup_base +default_range: string + +classes: + PreparationMethodAbbreviation: + is_a: LookupBase + description: Abbreviation for preparation method. diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation/prepared_sample.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation/prepared_sample.yaml new file mode 100644 index 00000000..6afccf07 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/modules/sample_preparation/prepared_sample.yaml @@ -0,0 +1,40 @@ +id: https://w3id.org/ca_biositing/sample_preparation/prepared_sample +name: prepared_sample +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - ../core/base_entity + - ../field_sampling/field_sample + - preparation_method + - ../people/contact +default_range: string + +classes: + PreparedSample: + is_a: BaseEntity + description: Sample that has been prepared. + slots: + - name + - field_sample_id + - prep_method_id + - prep_date + - preparer_id + - note + +slots: + field_sample_id: + range: FieldSample + description: Reference to FieldSample. + + prep_method_id: + range: PreparationMethod + description: Reference to PreparationMethod. + + prep_date: + range: date + description: Date of preparation. + + preparer_id: + range: Contact + description: Reference to Contact (preparer). diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema1.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema1.yaml new file mode 100644 index 00000000..ad80703a --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema1.yaml @@ -0,0 +1,18 @@ +id: https://example.com/schema1 +name: schema1 +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types +default_range: string + +classes: + ClassA: + slots: + - id + id_prefixes: + - A + +slots: + id: + identifier: true diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema2.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema2.yaml new file mode 100644 index 00000000..0571c541 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema2.yaml @@ -0,0 +1,22 @@ +id: https://example.com/schema2 +name: schema2 +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - schema1 +default_range: string + +classes: + ClassB: + slots: + - id + - class_a_id + id_prefixes: + - B + +slots: + id: + identifier: true + class_a_id: + range: ClassA diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema3.yaml b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema3.yaml new file mode 100644 index 00000000..cbc18b87 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/linkml/test_schemas/schema3.yaml @@ -0,0 +1,26 @@ +id: https://example.com/schema3 +name: schema3 +prefixes: + linkml: https://w3id.org/linkml/ +imports: + - linkml:types + - schema1 + - schema2 +default_range: string + +classes: + ClassC: + slots: + - id + - class_a_id + - class_b_id + id_prefixes: + - C + +slots: + id: + identifier: true + class_a_id: + range: ClassA + class_b_id: + range: ClassB diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py deleted file mode 100644 index 85b02306..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim1_records.py +++ /dev/null @@ -1,1747 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class ExperimentMethod(Base): - """ - Link between Experiment and Method. - """ - __tablename__ = 'experiment_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - method_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" - - - - - - -class ExperimentEquipment(Base): - """ - Link between Experiment and Equipment. - """ - __tablename__ = 'experiment_equipment' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - equipment_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" - - - - - - -class ExperimentAnalysis(Base): - """ - Link between Experiment and AnalysisType. - """ - __tablename__ = 'experiment_analysis' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - analysis_type_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" - - - - - - -class ExperimentPreparedSample(Base): - """ - Link between Experiment and PreparedSample. - """ - __tablename__ = 'experiment_prepared_sample' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - prepared_sample_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class Aim1RecordBase(BaseEntity): - """ - - """ - __tablename__ = 'aim1_record_base' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Dataset(BaseEntity): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(Date()) - end_date = Column(Date()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension. - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Observation(BaseEntity): - """ - Observation data. - """ - __tablename__ = 'observation' - - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample that has been prepared. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source (e.g. database, literature). - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Experiment(BaseEntity): - """ - Experiment definition. - """ - __tablename__ = 'experiment' - - analyst_id = Column(Integer()) - exper_start_date = Column(Date()) - exper_duration = Column(Numeric()) - exper_duration_unit_id = Column(Integer()) - exper_location_id = Column(Integer()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Equipment(LookupBase): - """ - Equipment used in experiments. - """ - __tablename__ = 'equipment' - - equipment_location_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProximateRecord(Aim1RecordBase): - """ - Proximate analysis record. - """ - __tablename__ = 'proximate_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ProximateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UltimateRecord(Aim1RecordBase): - """ - Ultimate analysis record. - """ - __tablename__ = 'ultimate_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UltimateRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CompositionalRecord(Aim1RecordBase): - """ - Compositional analysis record. - """ - __tablename__ = 'compositional_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"CompositionalRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class IcpRecord(Aim1RecordBase): - """ - ICP analysis record. - """ - __tablename__ = 'icp_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"IcpRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class XrfRecord(Aim1RecordBase): - """ - XRF analysis record. - """ - __tablename__ = 'xrf_record' - - maybe_wavelength_nm = Column(Numeric()) - maybe_intensity = Column(Numeric()) - maybe_energy_slope = Column(Numeric()) - maybe_energy_offset = Column(Numeric()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class XrdRecord(Aim1RecordBase): - """ - XRD analysis record. - """ - __tablename__ = 'xrd_record' - - maybe_scan_low_nm = Column(Integer()) - maybe_scan_high_nm = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CalorimetryRecord(Aim1RecordBase): - """ - Calorimetry analysis record. - """ - __tablename__ = 'calorimetry_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"CalorimetryRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FtnirRecord(Aim1RecordBase): - """ - FT-NIR analysis record. - """ - __tablename__ = 'ftnir_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FtnirRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class RgbRecord(Aim1RecordBase): - """ - RGB analysis record. - """ - __tablename__ = 'rgb_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"RgbRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py deleted file mode 100644 index 374bbf8b..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/aim2_records.py +++ /dev/null @@ -1,1600 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class ExperimentMethod(Base): - """ - Link between Experiment and Method. - """ - __tablename__ = 'experiment_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - method_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" - - - - - - -class ExperimentEquipment(Base): - """ - Link between Experiment and Equipment. - """ - __tablename__ = 'experiment_equipment' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - equipment_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" - - - - - - -class ExperimentAnalysis(Base): - """ - Link between Experiment and AnalysisType. - """ - __tablename__ = 'experiment_analysis' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - analysis_type_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" - - - - - - -class ExperimentPreparedSample(Base): - """ - Link between Experiment and PreparedSample. - """ - __tablename__ = 'experiment_prepared_sample' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - prepared_sample_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class Aim2RecordBase(BaseEntity): - """ - - """ - __tablename__ = 'aim2_record_base' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - calc_method_id = Column(Integer()) - calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Strain(LookupBase): - """ - Strain used in fermentation. - """ - __tablename__ = 'strain' - - parent_strain_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Dataset(BaseEntity): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(Date()) - end_date = Column(Date()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension. - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Observation(BaseEntity): - """ - Observation data. - """ - __tablename__ = 'observation' - - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample that has been prepared. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source (e.g. database, literature). - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Experiment(BaseEntity): - """ - Experiment definition. - """ - __tablename__ = 'experiment' - - analyst_id = Column(Integer()) - exper_start_date = Column(Date()) - exper_duration = Column(Numeric()) - exper_duration_unit_id = Column(Integer()) - exper_location_id = Column(Integer()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Equipment(LookupBase): - """ - Equipment used in experiments. - """ - __tablename__ = 'equipment' - - equipment_location_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PretreatmentRecord(Aim2RecordBase): - """ - Pretreatment record. - """ - __tablename__ = 'pretreatment_record' - - pretreatment_method_id = Column(Integer()) - eh_method_id = Column(Integer()) - reaction_block_id = Column(Integer()) - block_position = Column(Text()) - temperature = Column(Numeric()) - replicate_no = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - calc_method_id = Column(Integer()) - calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PretreatmentRecord(pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},reaction_block_id={self.reaction_block_id},block_position={self.block_position},temperature={self.temperature},replicate_no={self.replicate_no},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FermentationRecord(Aim2RecordBase): - """ - Fermentation record. - """ - __tablename__ = 'fermentation_record' - - strain_id = Column(Integer()) - pretreatment_method_id = Column(Integer()) - eh_method_id = Column(Integer()) - replicate_no = Column(Integer()) - well_position = Column(Text()) - temperature = Column(Numeric()) - agitation_rpm = Column(Numeric()) - vessel_id = Column(Integer()) - analyte_detection_equipment_id = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - calc_method_id = Column(Integer()) - calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class GasificationRecord(Aim2RecordBase): - """ - Gasification record. - """ - __tablename__ = 'gasification_record' - - feedstock_mass = Column(Numeric()) - bed_temperature = Column(Numeric()) - gas_flow_rate = Column(Numeric()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - calc_method_id = Column(Integer()) - calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"GasificationRecord(feedstock_mass={self.feedstock_mass},bed_temperature={self.bed_temperature},gas_flow_rate={self.gas_flow_rate},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AutoclaveRecord(Aim2RecordBase): - """ - Autoclave record. - """ - __tablename__ = 'autoclave_record' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - calc_method_id = Column(Integer()) - calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"AutoclaveRecord(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py index 6fc7680f..0fcd6b01 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py @@ -50,143 +50,38 @@ def __repr__(self): -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class LineageGroup(Base): - """ - Grouping for lineage information. - """ - __tablename__ = 'lineage_group' - - id = Column(Integer(), primary_key=True, nullable=False ) - etl_run_id = Column(Text()) - note = Column(Text()) - - - def __repr__(self): - return f"LineageGroup(id={self.id},etl_run_id={self.etl_run_id},note={self.note},)" - - - - - - -class EntityLineage(Base): - """ - Lineage information for a specific entity. - """ - __tablename__ = 'entity_lineage' - - id = Column(Integer(), primary_key=True, nullable=False ) - lineage_group_id = Column(Integer()) - source_table = Column(Text()) - source_row_id = Column(Text()) - note = Column(Text()) - - - def __repr__(self): - return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" - - - - - - -class EtlRun(Base): - """ - Information about an ETL run. - """ - __tablename__ = 'etl_run' - - id = Column(Integer(), primary_key=True, nullable=False ) - started_at = Column(DateTime()) - completed_at = Column(DateTime()) - pipeline_name = Column(Text()) - status = Column(Text()) - records_ingested = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" - - - - - - -class ParameterCategoryParameter(Base): +class ExperimentAnalysis(Base): """ - Link between Parameter and ParameterCategory. + Link between Experiment and AnalysisType. """ - __tablename__ = 'parameter_category_parameter' + __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + analysis_type_id = Column(Integer(), ForeignKey('AnalysisType.id')) def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" + return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" -class ParameterUnit(Base): +class ExperimentEquipment(Base): """ - Link between Parameter and Unit (alternate units). + Link between Experiment and Equipment. """ - __tablename__ = 'parameter_unit' + __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + equipment_id = Column(Integer(), ForeignKey('Equipment.id')) def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" + return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" @@ -200,8 +95,8 @@ class ExperimentMethod(Base): __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - method_id = Column(Integer()) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + method_id = Column(Integer(), ForeignKey('Method.id')) def __repr__(self): @@ -212,57 +107,42 @@ def __repr__(self): -class ExperimentEquipment(Base): - """ - Link between Experiment and Equipment. - """ - __tablename__ = 'experiment_equipment' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - equipment_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" - - - - - - -class ExperimentAnalysis(Base): +class ExperimentPreparedSample(Base): """ - Link between Experiment and AnalysisType. + Link between Experiment and PreparedSample. """ - __tablename__ = 'experiment_analysis' + __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - analysis_type_id = Column(Integer()) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + prepared_sample_id = Column(Integer(), ForeignKey('PreparedSample.id')) def __repr__(self): - return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" + return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" -class ExperimentPreparedSample(Base): +class Geography(Base): """ - Link between Experiment and PreparedSample. + Geographic location. """ - __tablename__ = 'experiment_prepared_sample' + __tablename__ = 'geography' - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - prepared_sample_id = Column(Integer()) + geoid = Column(Text(), primary_key=True, nullable=False ) + state_name = Column(Text()) + state_fips = Column(Text()) + county_name = Column(Text()) + county_fips = Column(Text()) + region_name = Column(Text()) + agg_level_desc = Column(Text()) def __repr__(self): - return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" + return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" @@ -407,89 +287,192 @@ def __repr__(self): -class InfrastructureEthanolBiorefineries(Base): +class InfrastructureCombustionPlants(Base): """ - Ethanol biorefineries infrastructure. + Combustion plants infrastructure. """ - __tablename__ = 'infrastructure_ethanol_biorefineries' + __tablename__ = 'infrastructure_combustion_plants' - ethanol_biorefinery_id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) + combustion_fid = Column(Integer(), primary_key=True, nullable=False ) + objectid = Column(Integer()) + status = Column(Text()) city = Column(Text()) - state = Column(Text()) - address = Column(Text()) + name = Column(Text()) + county = Column(Text()) + equivalent_generation = Column(Numeric()) + np_mw = Column(Numeric()) + cf = Column(Numeric()) + yearload = Column(Integer()) + fuel = Column(Text()) + notes = Column(Text()) type = Column(Text()) - capacity_mgy = Column(Integer()) - production_mgy = Column(Integer()) - constr_exp = Column(Integer()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) def __repr__(self): - return f"InfrastructureEthanolBiorefineries(ethanol_biorefinery_id={self.ethanol_biorefinery_id},name={self.name},city={self.city},state={self.state},address={self.address},type={self.type},capacity_mgy={self.capacity_mgy},production_mgy={self.production_mgy},constr_exp={self.constr_exp},)" + return f"InfrastructureCombustionPlants(combustion_fid={self.combustion_fid},objectid={self.objectid},status={self.status},city={self.city},name={self.name},county={self.county},equivalent_generation={self.equivalent_generation},np_mw={self.np_mw},cf={self.cf},yearload={self.yearload},fuel={self.fuel},notes={self.notes},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" -class InfrastructureLandfills(Base): +class InfrastructureDistrictEnergySystems(Base): """ - Landfills infrastructure. + District energy systems infrastructure. """ - __tablename__ = 'infrastructure_landfills' + __tablename__ = 'infrastructure_district_energy_systems' - project_id = Column(Text(), primary_key=True, nullable=False ) - project_int_id = Column(Integer()) - ghgrp_id = Column(Text()) - landfill_id = Column(Integer()) - landfill_name = Column(Text()) - state = Column(Text()) - physical_address = Column(Text()) + des_fid = Column(Integer(), primary_key=True, nullable=False ) + cbg_id = Column(Integer()) + name = Column(Text()) + system = Column(Text()) + object_id = Column(Integer()) city = Column(Text()) - county = Column(Text()) - zip_code = Column(Text()) + state = Column(Text()) + primary_fuel = Column(Text()) + secondary_fuel = Column(Text()) + usetype = Column(Text()) + cap_st = Column(Numeric()) + cap_hw = Column(Numeric()) + cap_cw = Column(Numeric()) + chpcg_cap = Column(Numeric()) + excess_c = Column(Numeric()) + excess_h = Column(Numeric()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) latitude = Column(Numeric()) longitude = Column(Numeric()) - ownership_type = Column(Text()) - landfill_owner_orgs = Column(Text()) - landfill_opened_year = Column(Date()) - landfill_closure_year = Column(Date()) - landfill_status = Column(Text()) - waste_in_place = Column(Integer()) - waste_in_place_year = Column(Date()) - lfg_system_in_place = Column(Boolean()) - lfg_collected = Column(Numeric()) - lfg_flared = Column(Numeric()) - project_status = Column(Text()) - project_name = Column(Text()) - project_start_date = Column(Date()) - project_shutdown_date = Column(Date()) - project_type_category = Column(Text()) - lfg_energy_project_type = Column(Text()) - rng_delivery_method = Column(Text()) - actual_mw_generation = Column(Numeric()) - rated_mw_capacity = Column(Numeric()) - lfg_flow_to_project = Column(Numeric()) - direct_emission_reductions = Column(Numeric()) - avoided_emission_reductions = Column(Numeric()) def __repr__(self): - return f"InfrastructureLandfills(project_id={self.project_id},project_int_id={self.project_int_id},ghgrp_id={self.ghgrp_id},landfill_id={self.landfill_id},landfill_name={self.landfill_name},state={self.state},physical_address={self.physical_address},city={self.city},county={self.county},zip_code={self.zip_code},latitude={self.latitude},longitude={self.longitude},ownership_type={self.ownership_type},landfill_owner_orgs={self.landfill_owner_orgs},landfill_opened_year={self.landfill_opened_year},landfill_closure_year={self.landfill_closure_year},landfill_status={self.landfill_status},waste_in_place={self.waste_in_place},waste_in_place_year={self.waste_in_place_year},lfg_system_in_place={self.lfg_system_in_place},lfg_collected={self.lfg_collected},lfg_flared={self.lfg_flared},project_status={self.project_status},project_name={self.project_name},project_start_date={self.project_start_date},project_shutdown_date={self.project_shutdown_date},project_type_category={self.project_type_category},lfg_energy_project_type={self.lfg_energy_project_type},rng_delivery_method={self.rng_delivery_method},actual_mw_generation={self.actual_mw_generation},rated_mw_capacity={self.rated_mw_capacity},lfg_flow_to_project={self.lfg_flow_to_project},direct_emission_reductions={self.direct_emission_reductions},avoided_emission_reductions={self.avoided_emission_reductions},)" + return f"InfrastructureDistrictEnergySystems(des_fid={self.des_fid},cbg_id={self.cbg_id},name={self.name},system={self.system},object_id={self.object_id},city={self.city},state={self.state},primary_fuel={self.primary_fuel},secondary_fuel={self.secondary_fuel},usetype={self.usetype},cap_st={self.cap_st},cap_hw={self.cap_hw},cap_cw={self.cap_cw},chpcg_cap={self.chpcg_cap},excess_c={self.excess_c},excess_h={self.excess_h},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" -class InfrastructureLivestockAnaerobicDigesters(Base): +class InfrastructureEthanolBiorefineries(Base): """ - Livestock anaerobic digesters infrastructure. + Ethanol biorefineries infrastructure. """ - __tablename__ = 'infrastructure_livestock_anaerobic_digesters' + __tablename__ = 'infrastructure_ethanol_biorefineries' - digester_id = Column(Integer(), primary_key=True, nullable=False ) - project_name = Column(Text()) + ethanol_biorefinery_id = Column(Integer(), primary_key=True, nullable=False ) + name = Column(Text()) + city = Column(Text()) + state = Column(Text()) + address = Column(Text()) + type = Column(Text()) + capacity_mgy = Column(Integer()) + production_mgy = Column(Integer()) + constr_exp = Column(Integer()) + + + def __repr__(self): + return f"InfrastructureEthanolBiorefineries(ethanol_biorefinery_id={self.ethanol_biorefinery_id},name={self.name},city={self.city},state={self.state},address={self.address},type={self.type},capacity_mgy={self.capacity_mgy},production_mgy={self.production_mgy},constr_exp={self.constr_exp},)" + + + + + + +class InfrastructureFoodProcessingFacilities(Base): + """ + Food processing facilities infrastructure. + """ + __tablename__ = 'infrastructure_food_processing_facilities' + + processing_facility_id = Column(Integer(), primary_key=True, nullable=False ) + address = Column(Text()) + county = Column(Text()) + city = Column(Text()) + company = Column(Text()) + join_count = Column(Integer()) + master_type = Column(Text()) + state = Column(Text()) + subtype = Column(Text()) + target_fid = Column(Integer()) + processing_type = Column(Text()) + zip = Column(Text()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureFoodProcessingFacilities(processing_facility_id={self.processing_facility_id},address={self.address},county={self.county},city={self.city},company={self.company},join_count={self.join_count},master_type={self.master_type},state={self.state},subtype={self.subtype},target_fid={self.target_fid},processing_type={self.processing_type},zip={self.zip},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + +class InfrastructureLandfills(Base): + """ + Landfills infrastructure. + """ + __tablename__ = 'infrastructure_landfills' + + project_id = Column(Text(), primary_key=True, nullable=False ) + project_int_id = Column(Integer()) + ghgrp_id = Column(Text()) + landfill_id = Column(Integer()) + landfill_name = Column(Text()) + state = Column(Text()) + physical_address = Column(Text()) + city = Column(Text()) + county = Column(Text()) + zip_code = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + ownership_type = Column(Text()) + landfill_owner_orgs = Column(Text()) + landfill_opened_year = Column(Date()) + landfill_closure_year = Column(Date()) + landfill_status = Column(Text()) + waste_in_place = Column(Integer()) + waste_in_place_year = Column(Date()) + lfg_system_in_place = Column(Boolean()) + lfg_collected = Column(Numeric()) + lfg_flared = Column(Numeric()) + project_status = Column(Text()) + project_name = Column(Text()) + project_start_date = Column(Date()) + project_shutdown_date = Column(Date()) + project_type_category = Column(Text()) + lfg_energy_project_type = Column(Text()) + rng_delivery_method = Column(Text()) + actual_mw_generation = Column(Numeric()) + rated_mw_capacity = Column(Numeric()) + lfg_flow_to_project = Column(Numeric()) + direct_emission_reductions = Column(Numeric()) + avoided_emission_reductions = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureLandfills(project_id={self.project_id},project_int_id={self.project_int_id},ghgrp_id={self.ghgrp_id},landfill_id={self.landfill_id},landfill_name={self.landfill_name},state={self.state},physical_address={self.physical_address},city={self.city},county={self.county},zip_code={self.zip_code},latitude={self.latitude},longitude={self.longitude},ownership_type={self.ownership_type},landfill_owner_orgs={self.landfill_owner_orgs},landfill_opened_year={self.landfill_opened_year},landfill_closure_year={self.landfill_closure_year},landfill_status={self.landfill_status},waste_in_place={self.waste_in_place},waste_in_place_year={self.waste_in_place_year},lfg_system_in_place={self.lfg_system_in_place},lfg_collected={self.lfg_collected},lfg_flared={self.lfg_flared},project_status={self.project_status},project_name={self.project_name},project_start_date={self.project_start_date},project_shutdown_date={self.project_shutdown_date},project_type_category={self.project_type_category},lfg_energy_project_type={self.lfg_energy_project_type},rng_delivery_method={self.rng_delivery_method},actual_mw_generation={self.actual_mw_generation},rated_mw_capacity={self.rated_mw_capacity},lfg_flow_to_project={self.lfg_flow_to_project},direct_emission_reductions={self.direct_emission_reductions},avoided_emission_reductions={self.avoided_emission_reductions},)" + + + + + + +class InfrastructureLivestockAnaerobicDigesters(Base): + """ + Livestock anaerobic digesters infrastructure. + """ + __tablename__ = 'infrastructure_livestock_anaerobic_digesters' + + digester_id = Column(Integer(), primary_key=True, nullable=False ) + project_name = Column(Text()) project_type = Column(Text()) city = Column(Text()) state = Column(Text()) @@ -521,6 +504,38 @@ def __repr__(self): +class InfrastructureMswToEnergyAnaerobicDigesters(Base): + """ + MSW to energy anaerobic digesters infrastructure. + """ + __tablename__ = 'infrastructure_msw_to_energy_anaerobic_digesters' + + wte_id = Column(Integer(), primary_key=True, nullable=False ) + city = Column(Text()) + county = Column(Text()) + equivalent_generation = Column(Numeric()) + feedstock = Column(Text()) + dayload = Column(Numeric()) + dayload_bdt = Column(Numeric()) + facility_type = Column(Text()) + status = Column(Text()) + notes = Column(Text()) + source = Column(Text()) + type = Column(Text()) + wkt_geom = Column(Text()) + geom = Column(Text()) + latitude = Column(Numeric()) + longitude = Column(Numeric()) + + + def __repr__(self): + return f"InfrastructureMswToEnergyAnaerobicDigesters(wte_id={self.wte_id},city={self.city},county={self.county},equivalent_generation={self.equivalent_generation},feedstock={self.feedstock},dayload={self.dayload},dayload_bdt={self.dayload_bdt},facility_type={self.facility_type},status={self.status},notes={self.notes},source={self.source},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + + + + + + class InfrastructureSafAndRenewableDieselPlants(Base): """ SAF and renewable diesel plants infrastructure. @@ -596,153 +611,152 @@ def __repr__(self): -class InfrastructureCombustionPlants(Base): +class LineageGroup(Base): """ - Combustion plants infrastructure. + Grouping for lineage information. """ - __tablename__ = 'infrastructure_combustion_plants' + __tablename__ = 'lineage_group' - combustion_fid = Column(Integer(), primary_key=True, nullable=False ) - objectid = Column(Integer()) + id = Column(Integer(), primary_key=True, nullable=False ) + etl_run_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"LineageGroup(id={self.id},etl_run_id={self.etl_run_id},note={self.note},)" + + + + + + +class EntityLineage(Base): + """ + Lineage information for a specific entity. + """ + __tablename__ = 'entity_lineage' + + id = Column(Integer(), primary_key=True, nullable=False ) + lineage_group_id = Column(Integer()) + source_table = Column(Text()) + source_row_id = Column(Text()) + note = Column(Text()) + + + def __repr__(self): + return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" + + + + + + +class EtlRun(Base): + """ + Information about an ETL run. + """ + __tablename__ = 'etl_run' + + id = Column(Integer(), primary_key=True, nullable=False ) + started_at = Column(DateTime()) + completed_at = Column(DateTime()) + pipeline_name = Column(Text()) status = Column(Text()) - city = Column(Text()) - name = Column(Text()) - county = Column(Text()) - equivalent_generation = Column(Numeric()) - np_mw = Column(Numeric()) - cf = Column(Numeric()) - yearload = Column(Integer()) - fuel = Column(Text()) - notes = Column(Text()) - type = Column(Text()) - wkt_geom = Column(Text()) - geom = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) + records_ingested = Column(Integer()) + note = Column(Text()) def __repr__(self): - return f"InfrastructureCombustionPlants(combustion_fid={self.combustion_fid},objectid={self.objectid},status={self.status},city={self.city},name={self.name},county={self.county},equivalent_generation={self.equivalent_generation},np_mw={self.np_mw},cf={self.cf},yearload={self.yearload},fuel={self.fuel},notes={self.notes},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" -class InfrastructureDistrictEnergySystems(Base): +class ParameterCategoryParameter(Base): """ - District energy systems infrastructure. + Link between Parameter and ParameterCategory. """ - __tablename__ = 'infrastructure_district_energy_systems' + __tablename__ = 'parameter_category_parameter' - des_fid = Column(Integer(), primary_key=True, nullable=False ) - cbg_id = Column(Integer()) - name = Column(Text()) - system = Column(Text()) - object_id = Column(Integer()) - city = Column(Text()) - state = Column(Text()) - primary_fuel = Column(Text()) - secondary_fuel = Column(Text()) - usetype = Column(Text()) - cap_st = Column(Numeric()) - cap_hw = Column(Numeric()) - cap_cw = Column(Numeric()) - chpcg_cap = Column(Numeric()) - excess_c = Column(Numeric()) - excess_h = Column(Numeric()) - type = Column(Text()) - wkt_geom = Column(Text()) - geom = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer(), ForeignKey('Parameter.id')) + parameter_category_id = Column(Integer(), ForeignKey('ParameterCategory.id')) def __repr__(self): - return f"InfrastructureDistrictEnergySystems(des_fid={self.des_fid},cbg_id={self.cbg_id},name={self.name},system={self.system},object_id={self.object_id},city={self.city},state={self.state},primary_fuel={self.primary_fuel},secondary_fuel={self.secondary_fuel},usetype={self.usetype},cap_st={self.cap_st},cap_hw={self.cap_hw},cap_cw={self.cap_cw},chpcg_cap={self.chpcg_cap},excess_c={self.excess_c},excess_h={self.excess_h},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" -class InfrastructureFoodProcessingFacilities(Base): +class ParameterUnit(Base): """ - Food processing facilities infrastructure. + Link between Parameter and Unit (alternate units). """ - __tablename__ = 'infrastructure_food_processing_facilities' + __tablename__ = 'parameter_unit' - processing_facility_id = Column(Integer(), primary_key=True, nullable=False ) - address = Column(Text()) - county = Column(Text()) - city = Column(Text()) - company = Column(Text()) - join_count = Column(Integer()) - master_type = Column(Text()) - state = Column(Text()) - subtype = Column(Text()) - target_fid = Column(Integer()) - processing_type = Column(Text()) - zip = Column(Text()) - type = Column(Text()) - wkt_geom = Column(Text()) - geom = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) + id = Column(Integer(), primary_key=True, nullable=False ) + parameter_id = Column(Integer(), ForeignKey('Parameter.id')) + alternate_unit_id = Column(Integer(), ForeignKey('Unit.id')) def __repr__(self): - return f"InfrastructureFoodProcessingFacilities(processing_facility_id={self.processing_facility_id},address={self.address},county={self.county},city={self.city},company={self.company},join_count={self.join_count},master_type={self.master_type},state={self.state},subtype={self.subtype},target_fid={self.target_fid},processing_type={self.processing_type},zip={self.zip},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" -class InfrastructureMswToEnergyAnaerobicDigesters(Base): +class ResourceMorphology(Base): """ - MSW to energy anaerobic digesters infrastructure. + Morphology of a resource. """ - __tablename__ = 'infrastructure_msw_to_energy_anaerobic_digesters' + __tablename__ = 'resource_morphology' - wte_id = Column(Integer(), primary_key=True, nullable=False ) - city = Column(Text()) - county = Column(Text()) - equivalent_generation = Column(Numeric()) - feedstock = Column(Text()) - dayload = Column(Numeric()) - dayload_bdt = Column(Numeric()) - facility_type = Column(Text()) - status = Column(Text()) - notes = Column(Text()) - source = Column(Text()) - type = Column(Text()) - wkt_geom = Column(Text()) - geom = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) + id = Column(Integer(), primary_key=True, nullable=False ) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + morphology_uri = Column(Text()) def __repr__(self): - return f"InfrastructureMswToEnergyAnaerobicDigesters(wte_id={self.wte_id},city={self.city},county={self.county},equivalent_generation={self.equivalent_generation},feedstock={self.feedstock},dayload={self.dayload},dayload_bdt={self.dayload_bdt},facility_type={self.facility_type},status={self.status},notes={self.notes},source={self.source},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" + return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" -class Resource(BaseEntity): +class DataSource(BaseEntity): """ - Biomass resource definition. + Source of data. """ - __tablename__ = 'resource' + __tablename__ = 'data_source' name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) + description = Column(Text()) + data_source_type_id = Column(Integer(), ForeignKey('DataSourceType.id')) + full_title = Column(Text()) + creator = Column(Text()) + subject = Column(Text()) + publisher = Column(Text()) + contributor = Column(Text()) + date = Column(DateTime()) + type = Column(Text()) + biocirv = Column(Boolean()) + format = Column(Text()) + language = Column(Text()) + relation = Column(Text()) + temporal_coverage = Column(Text()) + location_coverage_id = Column(Integer(), ForeignKey('LocationResolution.id')) + rights = Column(Text()) + license = Column(Text()) + uri = Column(Text()) note = Column(Text()) - test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -751,7 +765,7 @@ class Resource(BaseEntity): def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -763,20 +777,22 @@ def __repr__(self): -class ResourceClass(LookupBase): +class DataSourceType(BaseEntity): """ - Classification of resources. + Type of data source (e.g. database, literature). """ - __tablename__ = 'resource_class' + __tablename__ = 'data_source_type' + source_type_id = Column(Integer(), ForeignKey('SourceType.id')) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -788,11 +804,43 @@ def __repr__(self): -class ResourceSubclass(LookupBase): +class FileObjectMetadata(BaseEntity): """ - Sub-classification of resources. + Metadata for a file object. """ - __tablename__ = 'resource_subclass' + __tablename__ = 'file_object_metadata' + + data_source_id = Column(Integer(), ForeignKey('DataSource.id')) + bucket_path = Column(Text()) + file_format = Column(Text()) + file_size = Column(Integer()) + checksum_md5 = Column(Text()) + checksum_sha256 = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) + + + def __repr__(self): + return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + + + + + # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html + __mapper_args__ = { + 'concrete': True + } + + + +class LocationResolution(LookupBase): + """ + Resolution of the location (e.g. nation, state, county). + """ + __tablename__ = 'location_resolution' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -801,7 +849,7 @@ class ResourceSubclass(LookupBase): def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -813,13 +861,12 @@ def __repr__(self): -class PrimaryAgProduct(LookupBase): +class SourceType(LookupBase): """ - Primary agricultural product definition. + Type of source (e.g. database, literature). """ - __tablename__ = 'primary_ag_product' + __tablename__ = 'source_type' - note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) description = Column(Text()) @@ -827,7 +874,7 @@ class PrimaryAgProduct(LookupBase): def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -839,27 +886,21 @@ def __repr__(self): -class ResourceAvailability(BaseEntity): +class Equipment(LookupBase): """ - Availability of a resource in a location. + Equipment used in experiments. """ - __tablename__ = 'resource_availability' + __tablename__ = 'equipment' - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) + equipment_location_id = Column(Integer(), ForeignKey('LocationAddress.id')) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -871,29 +912,18 @@ def __repr__(self): -class ResourceCounterfactual(BaseEntity): +class Experiment(BaseEntity): """ - Counterfactual uses of a resource. + Experiment definition. """ - __tablename__ = 'resource_counterfactual' + __tablename__ = 'experiment' - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) + analyst_id = Column(Integer(), ForeignKey('Contact.id')) + exper_start_date = Column(Date()) + exper_duration = Column(Numeric()) + exper_duration_unit_id = Column(Integer(), ForeignKey('Unit.id')) + exper_location_id = Column(Integer(), ForeignKey('LocationAddress.id')) + description = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -902,7 +932,7 @@ class ResourceCounterfactual(BaseEntity): def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -914,39 +944,20 @@ def __repr__(self): -class FieldSample(BaseEntity): +class AnalysisType(LookupBase): """ - Sample collected from the field. + Type of analysis. """ - __tablename__ = 'field_sample' + __tablename__ = 'analysis_type' - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -958,17 +969,19 @@ def __repr__(self): -class PhysicalCharacteristic(BaseEntity): +class Method(BaseEntity): """ - Physical characteristics of a sample. + method. """ - __tablename__ = 'physical_characteristic' + __tablename__ = 'method' - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) + name = Column(Text()) + method_abbrev_id = Column(Integer(), ForeignKey('MethodAbbrev.id')) + method_category_id = Column(Integer(), ForeignKey('MethodCategory.id')) + method_standard_id = Column(Integer(), ForeignKey('MethodStandard.id')) + description = Column(Text()) + detection_limits = Column(Text()) + source_id = Column(Integer(), ForeignKey('DataSource.id')) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -977,7 +990,7 @@ class PhysicalCharacteristic(BaseEntity): def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -989,17 +1002,18 @@ def __repr__(self): -class FieldSampleCondition(BaseEntity): +class PreparedSample(BaseEntity): """ - Condition of the field sample. + Sample that has been prepared. """ - __tablename__ = 'field_sample_condition' + __tablename__ = 'prepared_sample' - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) + name = Column(Text()) + field_sample_id = Column(Integer(), ForeignKey('FieldSample.id')) + prep_method_id = Column(Integer(), ForeignKey('PreparationMethod.id')) + prep_date = Column(Date()) + preparer_id = Column(Integer(), ForeignKey('Contact.id')) + note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1008,7 +1022,7 @@ class FieldSampleCondition(BaseEntity): def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1020,20 +1034,27 @@ def __repr__(self): -class FieldStorageMethod(LookupBase): +class Resource(BaseEntity): """ - Method of field storage. + Biomass resource definition. """ - __tablename__ = 'field_storage_method' + __tablename__ = 'resource' - id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + primary_ag_product_id = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) + resource_class_id = Column(Integer(), ForeignKey('ResourceClass.id')) + resource_subclass_id = Column(Integer(), ForeignKey('ResourceSubclass.id')) + note = Column(Text()) + test = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1045,11 +1066,11 @@ def __repr__(self): -class CollectionMethod(LookupBase): +class ResourceSubclass(LookupBase): """ - Method of collection. + Sub-classification of resources. """ - __tablename__ = 'collection_method' + __tablename__ = 'resource_subclass' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1058,7 +1079,7 @@ class CollectionMethod(LookupBase): def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1070,11 +1091,11 @@ def __repr__(self): -class HarvestMethod(LookupBase): +class Unit(LookupBase): """ - Method of harvest. + Unit of measurement. """ - __tablename__ = 'harvest_method' + __tablename__ = 'unit' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1083,7 +1104,7 @@ class HarvestMethod(LookupBase): def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1095,20 +1116,35 @@ def __repr__(self): -class ProcessingMethod(LookupBase): +class BillionTon2023Record(BaseEntity): """ - Method of processing. + Billion Ton 2023 record. """ - __tablename__ = 'processing_method' + __tablename__ = 'billion_ton2023_record' + subclass_id = Column(Integer(), ForeignKey('ResourceSubclass.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + geoid = Column(Text()) + county_square_miles = Column(Float()) + model_name = Column(Text()) + scenario_name = Column(Text()) + price_offered_usd = Column(Numeric()) + production = Column(Integer()) + production_unit_id = Column(Integer(), ForeignKey('Unit.id')) + btu_ton = Column(Integer()) + production_energy_content = Column(Integer()) + energy_content_unit_id = Column(Integer(), ForeignKey('Unit.id')) + product_density_dtpersqmi = Column(Numeric()) + land_source = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"BillionTon2023Record(subclass_id={self.subclass_id},resource_id={self.resource_id},geoid={self.geoid},county_square_miles={self.county_square_miles},model_name={self.model_name},scenario_name={self.scenario_name},price_offered_usd={self.price_offered_usd},production={self.production},production_unit_id={self.production_unit_id},btu_ton={self.btu_ton},production_energy_content={self.production_energy_content},energy_content_unit_id={self.energy_content_unit_id},product_density_dtpersqmi={self.product_density_dtpersqmi},land_source={self.land_source},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1120,11 +1156,11 @@ def __repr__(self): -class SoilType(LookupBase): +class PrimaryAgProduct(LookupBase): """ - Type of soil. + Primary agricultural product definition. """ - __tablename__ = 'soil_type' + __tablename__ = 'primary_ag_product' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1133,7 +1169,7 @@ class SoilType(LookupBase): def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PrimaryAgProduct(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1145,20 +1181,32 @@ def __repr__(self): -class AgTreatment(LookupBase): +class LandiqRecord(BaseEntity): """ - Agricultural treatment. + LandIQ record. """ - __tablename__ = 'ag_treatment' + __tablename__ = 'landiq_record' + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + polygon_id = Column(Integer(), ForeignKey('Polygon.id')) + main_crop = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) + secondary_crop = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) + tertiary_crop = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) + quaternary_crop = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) + confidence = Column(Integer()) + irrigated = Column(Boolean()) + acres = Column(Float()) + version = Column(Text()) + note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1170,23 +1218,23 @@ def __repr__(self): -class LocationSoilType(BaseEntity): +class UsdaCommodity(LookupBase): """ - Soil type at a location. + USDA commodity. """ - __tablename__ = 'location_soil_type' + __tablename__ = 'usda_commodity' - location_id = Column(Integer()) - soil_type_id = Column(Integer()) + usda_source = Column(Text()) + usda_code = Column(Text()) + parent_commodity_id = Column(Integer(), ForeignKey('UsdaCommodity.id')) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1198,20 +1246,17 @@ def __repr__(self): -class LocationAddress(BaseEntity): +class ResourceUsdaCommodityMap(BaseEntity): """ - Physical address. + Mapping between resources/crops and USDA commodities. """ - __tablename__ = 'location_address' + __tablename__ = 'resource_usda_commodity_map' - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + primary_ag_product_id = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) + usda_commodity_id = Column(Integer(), ForeignKey('UsdaCommodity.id')) + match_tier = Column(Text()) + note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1220,7 +1265,7 @@ class LocationAddress(BaseEntity): def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_ag_product_id={self.primary_ag_product_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1232,16 +1277,18 @@ def __repr__(self): -class Contact(BaseEntity): +class UsdaCensusRecord(BaseEntity): """ - Contact information for a person. + USDA census record. """ - __tablename__ = 'contact' + __tablename__ = 'usda_census_record' - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + geoid = Column(Text()) + commodity_code = Column(Integer(), ForeignKey('UsdaCommodity.id')) + year = Column(Integer()) + source_reference = Column(Text()) + note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1250,7 +1297,7 @@ class Contact(BaseEntity): def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1262,22 +1309,20 @@ def __repr__(self): -class Provider(BaseEntity): +class UsdaDomain(LookupBase): """ - Provider information. + USDA domain. """ - __tablename__ = 'provider' + __tablename__ = 'usda_domain' - codename = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaDomain(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1289,32 +1334,20 @@ def __repr__(self): -class DataSource(BaseEntity): +class UsdaMarketReport(BaseEntity): """ - Source of data. + USDA market report. """ - __tablename__ = 'data_source' + __tablename__ = 'usda_market_report' - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) + slug_id = Column(Integer()) + slug_name = Column(Text()) + report_series_title = Column(Text()) + frequency = Column(Text()) + office_name = Column(Text()) + office_city_id = Column(Integer(), ForeignKey('LocationAddress.id')) + office_state_fips = Column(Text()) + source_id = Column(Integer(), ForeignKey('DataSource.id')) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1323,7 +1356,7 @@ class DataSource(BaseEntity): def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaMarketReport(slug_id={self.slug_id},slug_name={self.slug_name},report_series_title={self.report_series_title},frequency={self.frequency},office_name={self.office_name},office_city_id={self.office_city_id},office_state_fips={self.office_state_fips},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1335,18 +1368,32 @@ def __repr__(self): -class FileObjectMetadata(BaseEntity): +class UsdaMarketRecord(BaseEntity): """ - Metadata for a file object. + USDA market record. """ - __tablename__ = 'file_object_metadata' + __tablename__ = 'usda_market_record' - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) + report_id = Column(Integer(), ForeignKey('UsdaMarketReport.id')) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + report_begin_date = Column(DateTime()) + report_end_date = Column(DateTime()) + report_date = Column(DateTime()) + commodity_id = Column(Integer(), ForeignKey('UsdaCommodity.id')) + market_type_id = Column(Integer()) + market_type_category = Column(Text()) + grp = Column(Text()) + market_category_id = Column(Integer()) + class_ = Column(Text()) + grade = Column(Text()) + variety = Column(Text()) + protein_pct = Column(Numeric()) + application = Column(Text()) + pkg = Column(Text()) + sale_type = Column(Text()) + price_unit_id = Column(Integer(), ForeignKey('Unit.id')) + freight = Column(Text()) + trans_mode = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1355,7 +1402,7 @@ class FileObjectMetadata(BaseEntity): def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_category={self.market_type_category},grp={self.grp},market_category_id={self.market_category_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1367,13 +1414,20 @@ def __repr__(self): -class DataSourceType(BaseEntity): +class LocationAddress(BaseEntity): """ - Type of data source (e.g. database, literature). + Physical address. """ - __tablename__ = 'data_source_type' + __tablename__ = 'location_address' - source_type_id = Column(Integer()) + geography_id = Column(Text(), ForeignKey('Geography.geoid')) + address_line1 = Column(Text()) + address_line2 = Column(Text()) + city = Column(Text()) + zip = Column(Text()) + lat = Column(Float()) + lon = Column(Float()) + is_anonymous = Column(Boolean()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1382,7 +1436,7 @@ class DataSourceType(BaseEntity): def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1394,11 +1448,11 @@ def __repr__(self): -class LocationResolution(LookupBase): +class UsdaStatisticCategory(LookupBase): """ - Resolution of the location (e.g. nation, state, county). + USDA statistic category. """ - __tablename__ = 'location_resolution' + __tablename__ = 'usda_statistic_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1407,7 +1461,7 @@ class LocationResolution(LookupBase): def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"UsdaStatisticCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1419,11 +1473,11 @@ def __repr__(self): -class SourceType(LookupBase): +class UsdaSurveyProgram(LookupBase): """ - Type of source (e.g. database, literature). + USDA survey program. """ - __tablename__ = 'source_type' + __tablename__ = 'usda_survey_program' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1432,7 +1486,7 @@ class SourceType(LookupBase): def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"UsdaSurveyProgram(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1444,18 +1498,21 @@ def __repr__(self): -class PreparationMethod(BaseEntity): +class UsdaSurveyRecord(BaseEntity): """ - Method of sample preparation. + USDA survey record. """ - __tablename__ = 'preparation_method' + __tablename__ = 'usda_survey_record' - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + geoid = Column(Text()) + commodity_code = Column(Integer(), ForeignKey('UsdaCommodity.id')) + year = Column(Integer()) + survey_program_id = Column(Integer(), ForeignKey('UsdaSurveyProgram.id')) + survey_period = Column(Text()) + reference_month = Column(Text()) + seasonal_flag = Column(Boolean()) + note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1464,7 +1521,7 @@ class PreparationMethod(BaseEntity): def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1476,20 +1533,27 @@ def __repr__(self): -class PreparationMethodAbbreviation(LookupBase): +class UsdaTermMap(BaseEntity): """ - Abbreviation for preparation method. + Mapping of raw terms to USDA commodities. """ - __tablename__ = 'preparation_method_abbreviation' + __tablename__ = 'usda_term_map' + source_system = Column(Text()) + source_context = Column(Text()) + raw_term = Column(Text()) + usda_commodity_id = Column(Integer(), ForeignKey('UsdaCommodity.id')) + is_verified = Column(Boolean()) + note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1501,27 +1565,20 @@ def __repr__(self): -class PreparedSample(BaseEntity): +class AgTreatment(LookupBase): """ - Sample that has been prepared. + Agricultural treatment. """ - __tablename__ = 'prepared_sample' + __tablename__ = 'ag_treatment' - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1533,11 +1590,11 @@ def __repr__(self): -class Unit(LookupBase): +class CollectionMethod(LookupBase): """ - Unit of measurement. + Method of collection. """ - __tablename__ = 'unit' + __tablename__ = 'collection_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1546,7 +1603,7 @@ class Unit(LookupBase): def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1558,19 +1615,30 @@ def __repr__(self): -class Method(BaseEntity): +class FieldSample(BaseEntity): """ - Analytical method. + Sample collected from the field. """ - __tablename__ = 'method' + __tablename__ = 'field_sample' name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + provider_id = Column(Integer(), ForeignKey('Provider.id')) + collector_id = Column(Integer(), ForeignKey('Contact.id')) + sample_collection_source = Column(Text()) + amount_collected = Column(Numeric()) + amount_collected_unit_id = Column(Integer(), ForeignKey('Unit.id')) + sampling_location_id = Column(Integer(), ForeignKey('LocationAddress.id')) + field_storage_method_id = Column(Integer(), ForeignKey('FieldStorageMethod.id')) + field_storage_duration_value = Column(Numeric()) + field_storage_duration_unit_id = Column(Integer(), ForeignKey('Unit.id')) + field_storage_location_id = Column(Integer(), ForeignKey('LocationAddress.id')) + collection_timestamp = Column(DateTime()) + collection_method_id = Column(Integer(), ForeignKey('CollectionMethod.id')) + harvest_method_id = Column(Integer(), ForeignKey('HarvestMethod.id')) + harvest_date = Column(Date()) + field_sample_storage_location_id = Column(Integer(), ForeignKey('LocationAddress.id')) + note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1579,7 +1647,7 @@ class Method(BaseEntity): def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1591,11 +1659,11 @@ def __repr__(self): -class MethodAbbrev(LookupBase): +class ProcessingMethod(LookupBase): """ - Abbreviation for method. + Method of processing. """ - __tablename__ = 'method_abbrev' + __tablename__ = 'processing_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1604,7 +1672,7 @@ class MethodAbbrev(LookupBase): def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1616,20 +1684,26 @@ def __repr__(self): -class MethodCategory(LookupBase): +class FieldSampleCondition(BaseEntity): """ - Category of method. + Condition of the field sample. """ - __tablename__ = 'method_category' + __tablename__ = 'field_sample_condition' + field_sample_id = Column(Integer(), ForeignKey('FieldSample.id')) + ag_treatment_id = Column(Integer(), ForeignKey('AgTreatment.id')) + last_application_date = Column(Date()) + treatment_amount_per_acre = Column(Float()) + processing_method_id = Column(Integer(), ForeignKey('ProcessingMethod.id')) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1641,11 +1715,11 @@ def __repr__(self): -class MethodStandard(LookupBase): +class FieldStorageMethod(LookupBase): """ - Standard associated with the method. + Method of field storage. """ - __tablename__ = 'method_standard' + __tablename__ = 'field_storage_method' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1654,7 +1728,7 @@ class MethodStandard(LookupBase): def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1666,25 +1740,20 @@ def __repr__(self): -class Parameter(BaseEntity): +class HarvestMethod(LookupBase): """ - Parameter being measured. + Method of harvest. """ - __tablename__ = 'parameter' + __tablename__ = 'harvest_method' + id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + uri = Column(Text()) def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1696,11 +1765,11 @@ def __repr__(self): -class ParameterCategory(LookupBase): +class SoilType(LookupBase): """ - Category of parameter. + Type of soil. """ - __tablename__ = 'parameter_category' + __tablename__ = 'soil_type' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -1709,7 +1778,7 @@ class ParameterCategory(LookupBase): def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1721,18 +1790,14 @@ def __repr__(self): -class Experiment(BaseEntity): +class LocationSoilType(BaseEntity): """ - Experiment definition. + Soil type at a location. """ - __tablename__ = 'experiment' + __tablename__ = 'location_soil_type' - analyst_id = Column(Integer()) - exper_start_date = Column(Date()) - exper_duration = Column(Numeric()) - exper_duration_unit_id = Column(Integer()) - exper_location_id = Column(Integer()) - description = Column(Text()) + location_id = Column(Integer(), ForeignKey('LocationAddress.id')) + soil_type_id = Column(Integer(), ForeignKey('SoilType.id')) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1741,33 +1806,7 @@ class Experiment(BaseEntity): def __repr__(self): - return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Equipment(LookupBase): - """ - Equipment used in experiments. - """ - __tablename__ = 'equipment' - - equipment_location_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1779,20 +1818,26 @@ def __repr__(self): -class AnalysisType(LookupBase): +class PhysicalCharacteristic(BaseEntity): """ - Type of analysis. + Physical characteristics of a sample. """ - __tablename__ = 'analysis_type' + __tablename__ = 'physical_characteristic' + field_sample_id = Column(Integer(), ForeignKey('FieldSample.id')) + particle_length = Column(Numeric()) + particle_width = Column(Numeric()) + particle_height = Column(Numeric()) + particle_unit_id = Column(Integer(), ForeignKey('Unit.id')) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1812,7 +1857,7 @@ class Dataset(BaseEntity): name = Column(Text()) record_type = Column(Text()) - source_id = Column(Integer()) + source_id = Column(Integer(), ForeignKey('DataSource.id')) start_date = Column(Date()) end_date = Column(Date()) description = Column(Text()) @@ -1867,15 +1912,15 @@ class Observation(BaseEntity): """ __tablename__ = 'observation' - dataset_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) record_type = Column(Text()) record_id = Column(Integer()) - parameter_id = Column(Integer()) + parameter_id = Column(Integer(), ForeignKey('Parameter.id')) value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) + unit_id = Column(Integer(), ForeignKey('Unit.id')) + dimension_type_id = Column(Integer(), ForeignKey('DimensionType.id')) dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) + dimension_unit_id = Column(Integer(), ForeignKey('Unit.id')) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -1897,59 +1942,19 @@ def __repr__(self): -class Aim1RecordBase(BaseEntity): - """ - - """ - __tablename__ = 'aim1_record_base' - - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_no = Column(Integer()) - technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Aim2RecordBase(BaseEntity): +class FacilityRecord(BaseEntity): """ - + Facility record. """ - __tablename__ = 'aim2_record_base' + __tablename__ = 'facility_record' - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) - sample_id = Column(Integer()) - technical_replicate_total = Column(Integer()) - technical_replicate_no = Column(Integer()) - calc_method_id = Column(Integer()) - calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) - qc_pass = Column(Boolean()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + facility_name = Column(Text()) + location_id = Column(Integer(), ForeignKey('LocationAddress.id')) + capacity_mw = Column(Numeric()) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + operator = Column(Text()) + start_year = Column(Integer()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -1959,7 +1964,7 @@ class Aim2RecordBase(BaseEntity): def __repr__(self): - return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"FacilityRecord(dataset_id={self.dataset_id},facility_name={self.facility_name},location_id={self.location_id},capacity_mw={self.capacity_mw},resource_id={self.resource_id},operator={self.operator},start_year={self.start_year},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -1971,13 +1976,12 @@ def __repr__(self): -class Strain(LookupBase): +class MethodAbbrev(LookupBase): """ - Strain used in fermentation. + Abbreviation for method. """ - __tablename__ = 'strain' + __tablename__ = 'method_abbrev' - parent_strain_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) description = Column(Text()) @@ -1985,7 +1989,7 @@ class Strain(LookupBase): def __repr__(self): - return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -1997,11 +2001,11 @@ def __repr__(self): -class UsdaDomain(LookupBase): +class MethodCategory(LookupBase): """ - USDA domain. + Category of method. """ - __tablename__ = 'usda_domain' + __tablename__ = 'method_category' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -2010,7 +2014,7 @@ class UsdaDomain(LookupBase): def __repr__(self): - return f"UsdaDomain(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -2022,11 +2026,11 @@ def __repr__(self): -class UsdaStatisticCategory(LookupBase): +class MethodStandard(LookupBase): """ - USDA statistic category. + Standard associated with the method. """ - __tablename__ = 'usda_statistic_category' + __tablename__ = 'method_standard' id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) @@ -2035,7 +2039,7 @@ class UsdaStatisticCategory(LookupBase): def __repr__(self): - return f"UsdaStatisticCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -2047,20 +2051,25 @@ def __repr__(self): -class UsdaSurveyProgram(LookupBase): +class Parameter(BaseEntity): """ - USDA survey program. + Parameter being measured. """ - __tablename__ = 'usda_survey_program' + __tablename__ = 'parameter' - id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) + standard_unit_id = Column(Integer(), ForeignKey('Unit.id')) + calculated = Column(Boolean()) description = Column(Text()) - uri = Column(Text()) + id = Column(Integer(), primary_key=True, nullable=False ) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"UsdaSurveyProgram(id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -2072,27 +2081,20 @@ def __repr__(self): -class UsdaCensusRecord(BaseEntity): +class ParameterCategory(LookupBase): """ - USDA census record. + Category of parameter. """ - __tablename__ = 'usda_census_record' + __tablename__ = 'parameter_category' - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - source_reference = Column(Text()) - note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -2104,21 +2106,16 @@ def __repr__(self): -class UsdaSurveyRecord(BaseEntity): +class Contact(BaseEntity): """ - USDA survey record. + Contact information for a person. """ - __tablename__ = 'usda_survey_record' + __tablename__ = 'contact' - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - survey_program_id = Column(Integer()) - survey_period = Column(Text()) - reference_month = Column(Text()) - seasonal_flag = Column(Boolean()) - note = Column(Text()) + first_name = Column(Text()) + last_name = Column(Text()) + email = Column(Text()) + affiliation = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -2127,7 +2124,7 @@ class UsdaSurveyRecord(BaseEntity): def __repr__(self): - return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -2139,23 +2136,22 @@ def __repr__(self): -class UsdaCommodity(LookupBase): +class Provider(BaseEntity): """ - USDA commodity. + Provider information. """ - __tablename__ = 'usda_commodity' + __tablename__ = 'provider' - usda_source = Column(Text()) - usda_code = Column(Text()) - parent_commodity_id = Column(Integer()) + codename = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) + created_at = Column(DateTime()) + updated_at = Column(DateTime()) + etl_run_id = Column(Text()) + lineage_group_id = Column(Integer()) def __repr__(self): - return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" + return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -2167,17 +2163,22 @@ def __repr__(self): -class UsdaTermMap(BaseEntity): +class Aim1RecordBase(BaseEntity): """ - Mapping of raw terms to USDA commodities. + """ - __tablename__ = 'usda_term_map' + __tablename__ = 'aim1_record_base' - source_system = Column(Text()) - source_context = Column(Text()) - raw_term = Column(Text()) - usda_commodity_id = Column(Integer()) - is_verified = Column(Boolean()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + sample_id = Column(Integer()) + technical_replicate_no = Column(Integer()) + technical_replicate_total = Column(Integer()) + method_id = Column(Integer(), ForeignKey('Method.id')) + analyst_id = Column(Integer(), ForeignKey('Contact.id')) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -2187,7 +2188,7 @@ class UsdaTermMap(BaseEntity): def __repr__(self): - return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Aim1RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -2199,16 +2200,22 @@ def __repr__(self): -class ResourceUsdaCommodityMap(BaseEntity): +class Aim2RecordBase(BaseEntity): """ - Mapping between resources/crops and USDA commodities. + """ - __tablename__ = 'resource_usda_commodity_map' + __tablename__ = 'aim2_record_base' - resource_id = Column(Integer()) - primary_ag_product_id = Column(Integer()) - usda_commodity_id = Column(Integer()) - match_tier = Column(Text()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + sample_id = Column(Integer()) + technical_replicate_total = Column(Integer()) + technical_replicate_no = Column(Integer()) + calc_method_id = Column(Integer()) + calc_analyst_id = Column(Integer()) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -2218,7 +2225,7 @@ class ResourceUsdaCommodityMap(BaseEntity): def __repr__(self): - return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_ag_product_id={self.primary_ag_product_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Aim2RecordBase(dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -2230,29 +2237,21 @@ def __repr__(self): -class UsdaMarketReport(BaseEntity): +class Strain(LookupBase): """ - USDA market report. + Strain used in fermentation. """ - __tablename__ = 'usda_market_report' + __tablename__ = 'strain' - slug_id = Column(Integer()) - slug_name = Column(Text()) - report_series_title = Column(Text()) - frequency = Column(Text()) - office_name = Column(Text()) - office_city_id = Column(Integer()) - office_state_fips = Column(Text()) - source_id = Column(Integer()) + parent_strain_id = Column(Integer()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"UsdaMarketReport(slug_id={self.slug_id},slug_name={self.slug_name},report_series_title={self.report_series_title},frequency={self.frequency},office_name={self.office_name},office_city_id={self.office_city_id},office_state_fips={self.office_state_fips},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"Strain(parent_strain_id={self.parent_strain_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -2264,32 +2263,18 @@ def __repr__(self): -class UsdaMarketRecord(BaseEntity): +class ResourceAvailability(BaseEntity): """ - USDA market record. + Availability of a resource in a location. """ - __tablename__ = 'usda_market_record' + __tablename__ = 'resource_availability' - report_id = Column(Integer()) - dataset_id = Column(Integer()) - report_begin_date = Column(DateTime()) - report_end_date = Column(DateTime()) - report_date = Column(DateTime()) - commodity_id = Column(Integer()) - market_type_id = Column(Integer()) - market_type_category = Column(Text()) - grp = Column(Text()) - market_category_id = Column(Integer()) - class_ = Column(Text()) - grade = Column(Text()) - variety = Column(Text()) - protein_pct = Column(Numeric()) - application = Column(Text()) - pkg = Column(Text()) - sale_type = Column(Text()) - price_unit_id = Column(Integer()) - freight = Column(Text()) - trans_mode = Column(Text()) + resource_id = Column(Integer(), ForeignKey('Resource.id')) + geoid = Column(Text()) + from_month = Column(Integer()) + to_month = Column(Integer()) + year_round = Column(Boolean()) + note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -2298,7 +2283,7 @@ class UsdaMarketRecord(BaseEntity): def __repr__(self): - return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_category={self.market_type_category},grp={self.grp},market_category_id={self.market_category_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -2310,32 +2295,20 @@ def __repr__(self): -class LandiqRecord(BaseEntity): +class ResourceClass(LookupBase): """ - LandIQ record. + Classification of resources. """ - __tablename__ = 'landiq_record' + __tablename__ = 'resource_class' - dataset_id = Column(Integer()) - polygon_id = Column(Integer()) - main_crop = Column(Integer()) - secondary_crop = Column(Integer()) - tertiary_crop = Column(Integer()) - quaternary_crop = Column(Integer()) - confidence = Column(Integer()) - irrigated = Column(Boolean()) - acres = Column(Float()) - version = Column(Text()) - note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -2347,26 +2320,18 @@ def __repr__(self): -class BillionTon2023Record(BaseEntity): +class PreparationMethod(BaseEntity): """ - Billion Ton 2023 record. + Method of sample preparation. """ - __tablename__ = 'billion_ton2023_record' + __tablename__ = 'preparation_method' - subclass_id = Column(Integer()) - resource_id = Column(Integer()) - geoid = Column(Text()) - county_square_miles = Column(Float()) - model_name = Column(Text()) - scenario_name = Column(Text()) - price_offered_usd = Column(Numeric()) - production = Column(Integer()) - production_unit_id = Column(Integer()) - btu_ton = Column(Integer()) - production_energy_content = Column(Integer()) - energy_content_unit_id = Column(Integer()) - product_density_dtpersqmi = Column(Numeric()) - land_source = Column(Text()) + name = Column(Text()) + description = Column(Text()) + prep_method_abbrev_id = Column(Integer(), ForeignKey('PreparationMethodAbbreviation.id')) + prep_temp_c = Column(Numeric()) + uri = Column(Text()) + drying_step = Column(Boolean()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -2375,7 +2340,7 @@ class BillionTon2023Record(BaseEntity): def __repr__(self): - return f"BillionTon2023Record(subclass_id={self.subclass_id},resource_id={self.resource_id},geoid={self.geoid},county_square_miles={self.county_square_miles},model_name={self.model_name},scenario_name={self.scenario_name},price_offered_usd={self.price_offered_usd},production={self.production},production_unit_id={self.production_unit_id},btu_ton={self.btu_ton},production_energy_content={self.production_energy_content},energy_content_unit_id={self.energy_content_unit_id},product_density_dtpersqmi={self.product_density_dtpersqmi},land_source={self.land_source},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -2387,29 +2352,20 @@ def __repr__(self): -class FacilityRecord(BaseEntity): +class PreparationMethodAbbreviation(LookupBase): """ - Facility record. + Abbreviation for preparation method. """ - __tablename__ = 'facility_record' + __tablename__ = 'preparation_method_abbreviation' - dataset_id = Column(Integer()) - facility_name = Column(Text()) - location_id = Column(Integer()) - capacity_mw = Column(Numeric()) - resource_id = Column(Integer()) - operator = Column(Text()) - start_year = Column(Integer()) - note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) + name = Column(Text()) + description = Column(Text()) + uri = Column(Text()) def __repr__(self): - return f"FacilityRecord(dataset_id={self.dataset_id},facility_name={self.facility_name},location_id={self.location_id},capacity_mw={self.capacity_mw},resource_id={self.resource_id},operator={self.operator},start_year={self.start_year},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" @@ -2427,15 +2383,15 @@ class ProximateRecord(Aim1RecordBase): """ __tablename__ = 'proximate_record' - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + method_id = Column(Integer(), ForeignKey('Method.id')) + analyst_id = Column(Integer(), ForeignKey('Contact.id')) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2464,15 +2420,15 @@ class UltimateRecord(Aim1RecordBase): """ __tablename__ = 'ultimate_record' - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + method_id = Column(Integer(), ForeignKey('Method.id')) + analyst_id = Column(Integer(), ForeignKey('Contact.id')) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2501,15 +2457,15 @@ class CompositionalRecord(Aim1RecordBase): """ __tablename__ = 'compositional_record' - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + method_id = Column(Integer(), ForeignKey('Method.id')) + analyst_id = Column(Integer(), ForeignKey('Contact.id')) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2538,15 +2494,15 @@ class IcpRecord(Aim1RecordBase): """ __tablename__ = 'icp_record' - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + method_id = Column(Integer(), ForeignKey('Method.id')) + analyst_id = Column(Integer(), ForeignKey('Contact.id')) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2575,19 +2531,19 @@ class XrfRecord(Aim1RecordBase): """ __tablename__ = 'xrf_record' - maybe_wavelength_nm = Column(Numeric()) - maybe_intensity = Column(Numeric()) - maybe_energy_slope = Column(Numeric()) - maybe_energy_offset = Column(Numeric()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + wavelength_nm = Column(Numeric()) + intensity = Column(Numeric()) + energy_slope = Column(Numeric()) + energy_offset = Column(Numeric()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + method_id = Column(Integer(), ForeignKey('Method.id')) + analyst_id = Column(Integer(), ForeignKey('Contact.id')) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2598,7 +2554,7 @@ class XrfRecord(Aim1RecordBase): def __repr__(self): - return f"XrfRecord(maybe_wavelength_nm={self.maybe_wavelength_nm},maybe_intensity={self.maybe_intensity},maybe_energy_slope={self.maybe_energy_slope},maybe_energy_offset={self.maybe_energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"XrfRecord(wavelength_nm={self.wavelength_nm},intensity={self.intensity},energy_slope={self.energy_slope},energy_offset={self.energy_offset},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -2616,17 +2572,17 @@ class XrdRecord(Aim1RecordBase): """ __tablename__ = 'xrd_record' - maybe_scan_low_nm = Column(Integer()) - maybe_scan_high_nm = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + scan_low_nm = Column(Integer()) + scan_high_nm = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + method_id = Column(Integer(), ForeignKey('Method.id')) + analyst_id = Column(Integer(), ForeignKey('Contact.id')) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2637,7 +2593,7 @@ class XrdRecord(Aim1RecordBase): def __repr__(self): - return f"XrdRecord(maybe_scan_low_nm={self.maybe_scan_low_nm},maybe_scan_high_nm={self.maybe_scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"XrdRecord(scan_low_nm={self.scan_low_nm},scan_high_nm={self.scan_high_nm},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_no={self.technical_replicate_no},technical_replicate_total={self.technical_replicate_total},method_id={self.method_id},analyst_id={self.analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -2655,15 +2611,15 @@ class CalorimetryRecord(Aim1RecordBase): """ __tablename__ = 'calorimetry_record' - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + method_id = Column(Integer(), ForeignKey('Method.id')) + analyst_id = Column(Integer(), ForeignKey('Contact.id')) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2692,15 +2648,15 @@ class FtnirRecord(Aim1RecordBase): """ __tablename__ = 'ftnir_record' - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + method_id = Column(Integer(), ForeignKey('Method.id')) + analyst_id = Column(Integer(), ForeignKey('Contact.id')) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2729,15 +2685,15 @@ class RgbRecord(Aim1RecordBase): """ __tablename__ = 'rgb_record' - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer()) - analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + method_id = Column(Integer(), ForeignKey('Method.id')) + analyst_id = Column(Integer(), ForeignKey('Contact.id')) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2772,15 +2728,15 @@ class PretreatmentRecord(Aim2RecordBase): block_position = Column(Text()) temperature = Column(Numeric()) replicate_no = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_total = Column(Integer()) technical_replicate_no = Column(Integer()) calc_method_id = Column(Integer()) calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2812,21 +2768,20 @@ class FermentationRecord(Aim2RecordBase): strain_id = Column(Integer()) pretreatment_method_id = Column(Integer()) eh_method_id = Column(Integer()) - replicate_no = Column(Integer()) well_position = Column(Text()) temperature = Column(Numeric()) agitation_rpm = Column(Numeric()) vessel_id = Column(Integer()) analyte_detection_equipment_id = Column(Integer()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_total = Column(Integer()) technical_replicate_no = Column(Integer()) calc_method_id = Column(Integer()) calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2837,7 +2792,7 @@ class FermentationRecord(Aim2RecordBase): def __repr__(self): - return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},replicate_no={self.replicate_no},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" + return f"FermentationRecord(strain_id={self.strain_id},pretreatment_method_id={self.pretreatment_method_id},eh_method_id={self.eh_method_id},well_position={self.well_position},temperature={self.temperature},agitation_rpm={self.agitation_rpm},vessel_id={self.vessel_id},analyte_detection_equipment_id={self.analyte_detection_equipment_id},dataset_id={self.dataset_id},experiment_id={self.experiment_id},resource_id={self.resource_id},sample_id={self.sample_id},technical_replicate_total={self.technical_replicate_total},technical_replicate_no={self.technical_replicate_no},calc_method_id={self.calc_method_id},calc_analyst_id={self.calc_analyst_id},raw_data_id={self.raw_data_id},qc_pass={self.qc_pass},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" @@ -2858,15 +2813,15 @@ class GasificationRecord(Aim2RecordBase): feedstock_mass = Column(Numeric()) bed_temperature = Column(Numeric()) gas_flow_rate = Column(Numeric()) - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_total = Column(Integer()) technical_replicate_no = Column(Integer()) calc_method_id = Column(Integer()) calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2895,15 +2850,15 @@ class AutoclaveRecord(Aim2RecordBase): """ __tablename__ = 'autoclave_record' - dataset_id = Column(Integer()) - experiment_id = Column(Integer()) - resource_id = Column(Integer()) + dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + experiment_id = Column(Integer(), ForeignKey('Experiment.id')) + resource_id = Column(Integer(), ForeignKey('Resource.id')) sample_id = Column(Integer()) technical_replicate_total = Column(Integer()) technical_replicate_no = Column(Integer()) calc_method_id = Column(Integer()) calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer()) + raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py deleted file mode 100644 index 20ba55a2..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/core.py +++ /dev/null @@ -1,46 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py deleted file mode 100644 index 10206eab..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/data_sources_metadata.py +++ /dev/null @@ -1,1030 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source (e.g. database, literature). - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py deleted file mode 100644 index d27ecc16..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/experiment_equipment.py +++ /dev/null @@ -1,1371 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ExperimentMethod(Base): - """ - Link between Experiment and Method. - """ - __tablename__ = 'experiment_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - method_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentMethod(id={self.id},experiment_id={self.experiment_id},method_id={self.method_id},)" - - - - - - -class ExperimentEquipment(Base): - """ - Link between Experiment and Equipment. - """ - __tablename__ = 'experiment_equipment' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - equipment_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentEquipment(id={self.id},experiment_id={self.experiment_id},equipment_id={self.equipment_id},)" - - - - - - -class ExperimentAnalysis(Base): - """ - Link between Experiment and AnalysisType. - """ - __tablename__ = 'experiment_analysis' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - analysis_type_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentAnalysis(id={self.id},experiment_id={self.experiment_id},analysis_type_id={self.analysis_type_id},)" - - - - - - -class ExperimentPreparedSample(Base): - """ - Link between Experiment and PreparedSample. - """ - __tablename__ = 'experiment_prepared_sample' - - id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer()) - prepared_sample_id = Column(Integer()) - - - def __repr__(self): - return f"ExperimentPreparedSample(id={self.id},experiment_id={self.experiment_id},prepared_sample_id={self.prepared_sample_id},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class Experiment(BaseEntity): - """ - Experiment definition. - """ - __tablename__ = 'experiment' - - analyst_id = Column(Integer()) - exper_start_date = Column(Date()) - exper_duration = Column(Numeric()) - exper_duration_unit_id = Column(Integer()) - exper_location_id = Column(Integer()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Experiment(analyst_id={self.analyst_id},exper_start_date={self.exper_start_date},exper_duration={self.exper_duration},exper_duration_unit_id={self.exper_duration_unit_id},exper_location_id={self.exper_location_id},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Equipment(LookupBase): - """ - Equipment used in experiments. - """ - __tablename__ = 'equipment' - - equipment_location_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Equipment(equipment_location_id={self.equipment_location_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample that has been prepared. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source (e.g. database, literature). - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Dataset(BaseEntity): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(Date()) - end_date = Column(Date()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension. - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Observation(BaseEntity): - """ - Observation data. - """ - __tablename__ = 'observation' - - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py deleted file mode 100644 index deaaf7e6..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/external_data.py +++ /dev/null @@ -1,1557 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class Polygon(Base): - """ - Geospatial polygon. - """ - __tablename__ = 'polygon' - - id = Column(Integer(), primary_key=True, nullable=False ) - geoid = Column(Text()) - geom = Column(Text()) - - - def __repr__(self): - return f"Polygon(id={self.id},geoid={self.geoid},geom={self.geom},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class UsdaDomain(LookupBase): - """ - USDA domain. - """ - __tablename__ = 'usda_domain' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaDomain(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaStatisticCategory(LookupBase): - """ - USDA statistic category. - """ - __tablename__ = 'usda_statistic_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaStatisticCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaSurveyProgram(LookupBase): - """ - USDA survey program. - """ - __tablename__ = 'usda_survey_program' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaSurveyProgram(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaCensusRecord(BaseEntity): - """ - USDA census record. - """ - __tablename__ = 'usda_census_record' - - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - source_reference = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaCensusRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},source_reference={self.source_reference},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaSurveyRecord(BaseEntity): - """ - USDA survey record. - """ - __tablename__ = 'usda_survey_record' - - dataset_id = Column(Integer()) - geoid = Column(Text()) - commodity_code = Column(Integer()) - year = Column(Integer()) - survey_program_id = Column(Integer()) - survey_period = Column(Text()) - reference_month = Column(Text()) - seasonal_flag = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaSurveyRecord(dataset_id={self.dataset_id},geoid={self.geoid},commodity_code={self.commodity_code},year={self.year},survey_program_id={self.survey_program_id},survey_period={self.survey_period},reference_month={self.reference_month},seasonal_flag={self.seasonal_flag},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaCommodity(LookupBase): - """ - USDA commodity. - """ - __tablename__ = 'usda_commodity' - - usda_source = Column(Text()) - usda_code = Column(Text()) - parent_commodity_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"UsdaCommodity(usda_source={self.usda_source},usda_code={self.usda_code},parent_commodity_id={self.parent_commodity_id},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaTermMap(BaseEntity): - """ - Mapping of raw terms to USDA commodities. - """ - __tablename__ = 'usda_term_map' - - source_system = Column(Text()) - source_context = Column(Text()) - raw_term = Column(Text()) - usda_commodity_id = Column(Integer()) - is_verified = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaTermMap(source_system={self.source_system},source_context={self.source_context},raw_term={self.raw_term},usda_commodity_id={self.usda_commodity_id},is_verified={self.is_verified},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceUsdaCommodityMap(BaseEntity): - """ - Mapping between resources/crops and USDA commodities. - """ - __tablename__ = 'resource_usda_commodity_map' - - resource_id = Column(Integer()) - primary_ag_product_id = Column(Integer()) - usda_commodity_id = Column(Integer()) - match_tier = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceUsdaCommodityMap(resource_id={self.resource_id},primary_ag_product_id={self.primary_ag_product_id},usda_commodity_id={self.usda_commodity_id},match_tier={self.match_tier},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaMarketReport(BaseEntity): - """ - USDA market report. - """ - __tablename__ = 'usda_market_report' - - slug_id = Column(Integer()) - slug_name = Column(Text()) - report_series_title = Column(Text()) - frequency = Column(Text()) - office_name = Column(Text()) - office_city_id = Column(Integer()) - office_state_fips = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaMarketReport(slug_id={self.slug_id},slug_name={self.slug_name},report_series_title={self.report_series_title},frequency={self.frequency},office_name={self.office_name},office_city_id={self.office_city_id},office_state_fips={self.office_state_fips},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class UsdaMarketRecord(BaseEntity): - """ - USDA market record. - """ - __tablename__ = 'usda_market_record' - - report_id = Column(Integer()) - dataset_id = Column(Integer()) - report_begin_date = Column(DateTime()) - report_end_date = Column(DateTime()) - report_date = Column(DateTime()) - commodity_id = Column(Integer()) - market_type_id = Column(Integer()) - market_type_category = Column(Text()) - grp = Column(Text()) - market_category_id = Column(Integer()) - class_ = Column(Text()) - grade = Column(Text()) - variety = Column(Text()) - protein_pct = Column(Numeric()) - application = Column(Text()) - pkg = Column(Text()) - sale_type = Column(Text()) - price_unit_id = Column(Integer()) - freight = Column(Text()) - trans_mode = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"UsdaMarketRecord(report_id={self.report_id},dataset_id={self.dataset_id},report_begin_date={self.report_begin_date},report_end_date={self.report_end_date},report_date={self.report_date},commodity_id={self.commodity_id},market_type_id={self.market_type_id},market_type_category={self.market_type_category},grp={self.grp},market_category_id={self.market_category_id},class_={self.class_},grade={self.grade},variety={self.variety},protein_pct={self.protein_pct},application={self.application},pkg={self.pkg},sale_type={self.sale_type},price_unit_id={self.price_unit_id},freight={self.freight},trans_mode={self.trans_mode},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LandiqRecord(BaseEntity): - """ - LandIQ record. - """ - __tablename__ = 'landiq_record' - - dataset_id = Column(Integer()) - polygon_id = Column(Integer()) - main_crop = Column(Integer()) - secondary_crop = Column(Integer()) - tertiary_crop = Column(Integer()) - quaternary_crop = Column(Integer()) - confidence = Column(Integer()) - irrigated = Column(Boolean()) - acres = Column(Float()) - version = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LandiqRecord(dataset_id={self.dataset_id},polygon_id={self.polygon_id},main_crop={self.main_crop},secondary_crop={self.secondary_crop},tertiary_crop={self.tertiary_crop},quaternary_crop={self.quaternary_crop},confidence={self.confidence},irrigated={self.irrigated},acres={self.acres},version={self.version},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class BillionTon2023Record(BaseEntity): - """ - Billion Ton 2023 record. - """ - __tablename__ = 'billion_ton2023_record' - - subclass_id = Column(Integer()) - resource_id = Column(Integer()) - geoid = Column(Text()) - county_square_miles = Column(Float()) - model_name = Column(Text()) - scenario_name = Column(Text()) - price_offered_usd = Column(Numeric()) - production = Column(Integer()) - production_unit_id = Column(Integer()) - btu_ton = Column(Integer()) - production_energy_content = Column(Integer()) - energy_content_unit_id = Column(Integer()) - product_density_dtpersqmi = Column(Numeric()) - land_source = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BillionTon2023Record(subclass_id={self.subclass_id},resource_id={self.resource_id},geoid={self.geoid},county_square_miles={self.county_square_miles},model_name={self.model_name},scenario_name={self.scenario_name},price_offered_usd={self.price_offered_usd},production={self.production},production_unit_id={self.production_unit_id},btu_ton={self.btu_ton},production_energy_content={self.production_energy_content},energy_content_unit_id={self.energy_content_unit_id},product_density_dtpersqmi={self.product_density_dtpersqmi},land_source={self.land_source},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source (e.g. database, literature). - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Dataset(BaseEntity): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(Date()) - end_date = Column(Date()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension. - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Observation(BaseEntity): - """ - Observation data. - """ - __tablename__ = 'observation' - - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py deleted file mode 100644 index 0e5c3b47..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/field_sampling.py +++ /dev/null @@ -1,1030 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source (e.g. database, literature). - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py deleted file mode 100644 index 5e8fd492..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/general_analysis.py +++ /dev/null @@ -1,1148 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Dataset(BaseEntity): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(Date()) - end_date = Column(Date()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension. - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Observation(BaseEntity): - """ - Observation data. - """ - __tablename__ = 'observation' - - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source (e.g. database, literature). - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py deleted file mode 100644 index 349885b9..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/geography.py +++ /dev/null @@ -1,106 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class Geography(Base): - """ - Geographic region definition (e.g. county, state). - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class LocationAddress(BaseEntity): - """ - Specific physical location. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py deleted file mode 100644 index 021a9423..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/infrastructure.py +++ /dev/null @@ -1,1625 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class InfrastructureBiodieselPlants(Base): - """ - Biodiesel plants infrastructure. - """ - __tablename__ = 'infrastructure_biodiesel_plants' - - biodiesel_plant_id = Column(Integer(), primary_key=True, nullable=False ) - company = Column(Text()) - bbi_index = Column(Integer()) - city = Column(Text()) - state = Column(Text()) - capacity_mmg_per_y = Column(Integer()) - feedstock = Column(Text()) - status = Column(Text()) - address = Column(Text()) - coordinates = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) - source = Column(Text()) - - - def __repr__(self): - return f"InfrastructureBiodieselPlants(biodiesel_plant_id={self.biodiesel_plant_id},company={self.company},bbi_index={self.bbi_index},city={self.city},state={self.state},capacity_mmg_per_y={self.capacity_mmg_per_y},feedstock={self.feedstock},status={self.status},address={self.address},coordinates={self.coordinates},latitude={self.latitude},longitude={self.longitude},source={self.source},)" - - - - - - -class InfrastructureBiosolidsFacilities(Base): - """ - Biosolids facilities infrastructure. - """ - __tablename__ = 'infrastructure_biosolids_facilities' - - biosolid_facility_id = Column(Integer(), primary_key=True, nullable=False ) - report_submitted_date = Column(Date()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) - facility = Column(Text()) - authority = Column(Text()) - plant_type = Column(Text()) - aqmd = Column(Text()) - facility_address = Column(Text()) - facility_city = Column(Text()) - state = Column(Text()) - facility_zip = Column(Text()) - facility_county = Column(Text()) - mailing_street_1 = Column(Text()) - mailing_city = Column(Text()) - mailing_state = Column(Text()) - mailing_zip = Column(Text()) - biosolids_number = Column(Text()) - biosolids_contact = Column(Text()) - biosolids_contact_phone = Column(Text()) - biosolids_contact_email = Column(Text()) - adwf = Column(Numeric()) - potw_biosolids_generated = Column(Integer()) - twtds_biosolids_treated = Column(Integer()) - class_b_land_app = Column(Integer()) - class_b_applier = Column(Text()) - class_a_compost = Column(Integer()) - class_a_heat_dried = Column(Integer()) - class_a_other = Column(Integer()) - class_a_other_applier = Column(Text()) - twtds_transfer_to_second_preparer = Column(Integer()) - twtds_second_preparer_name = Column(Text()) - adc_or_final_c = Column(Integer()) - landfill = Column(Integer()) - landfill_name = Column(Text()) - surface_disposal = Column(Integer()) - deepwell_injection = Column(Text()) - stored = Column(Integer()) - longterm_treatment = Column(Integer()) - other = Column(Integer()) - name_of_other = Column(Text()) - incineration = Column(Integer()) - - - def __repr__(self): - return f"InfrastructureBiosolidsFacilities(biosolid_facility_id={self.biosolid_facility_id},report_submitted_date={self.report_submitted_date},latitude={self.latitude},longitude={self.longitude},facility={self.facility},authority={self.authority},plant_type={self.plant_type},aqmd={self.aqmd},facility_address={self.facility_address},facility_city={self.facility_city},state={self.state},facility_zip={self.facility_zip},facility_county={self.facility_county},mailing_street_1={self.mailing_street_1},mailing_city={self.mailing_city},mailing_state={self.mailing_state},mailing_zip={self.mailing_zip},biosolids_number={self.biosolids_number},biosolids_contact={self.biosolids_contact},biosolids_contact_phone={self.biosolids_contact_phone},biosolids_contact_email={self.biosolids_contact_email},adwf={self.adwf},potw_biosolids_generated={self.potw_biosolids_generated},twtds_biosolids_treated={self.twtds_biosolids_treated},class_b_land_app={self.class_b_land_app},class_b_applier={self.class_b_applier},class_a_compost={self.class_a_compost},class_a_heat_dried={self.class_a_heat_dried},class_a_other={self.class_a_other},class_a_other_applier={self.class_a_other_applier},twtds_transfer_to_second_preparer={self.twtds_transfer_to_second_preparer},twtds_second_preparer_name={self.twtds_second_preparer_name},adc_or_final_c={self.adc_or_final_c},landfill={self.landfill},landfill_name={self.landfill_name},surface_disposal={self.surface_disposal},deepwell_injection={self.deepwell_injection},stored={self.stored},longterm_treatment={self.longterm_treatment},other={self.other},name_of_other={self.name_of_other},incineration={self.incineration},)" - - - - - - -class InfrastructureCafoManureLocations(Base): - """ - CAFO manure locations infrastructure. - """ - __tablename__ = 'infrastructure_cafo_manure_locations' - - cafo_manure_id = Column(Integer(), primary_key=True, nullable=False ) - latitude = Column(Numeric()) - longitude = Column(Numeric()) - owner_name = Column(Text()) - facility_name = Column(Text()) - address = Column(Text()) - town = Column(Text()) - state = Column(Text()) - zip = Column(Text()) - animal = Column(Text()) - animal_feed_operation_type = Column(Text()) - animal_units = Column(Integer()) - animal_count = Column(Integer()) - manure_total_solids = Column(Numeric()) - source = Column(Text()) - date_accessed = Column(Date()) - - - def __repr__(self): - return f"InfrastructureCafoManureLocations(cafo_manure_id={self.cafo_manure_id},latitude={self.latitude},longitude={self.longitude},owner_name={self.owner_name},facility_name={self.facility_name},address={self.address},town={self.town},state={self.state},zip={self.zip},animal={self.animal},animal_feed_operation_type={self.animal_feed_operation_type},animal_units={self.animal_units},animal_count={self.animal_count},manure_total_solids={self.manure_total_solids},source={self.source},date_accessed={self.date_accessed},)" - - - - - - -class InfrastructureEthanolBiorefineries(Base): - """ - Ethanol biorefineries infrastructure. - """ - __tablename__ = 'infrastructure_ethanol_biorefineries' - - ethanol_biorefinery_id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - city = Column(Text()) - state = Column(Text()) - address = Column(Text()) - type = Column(Text()) - capacity_mgy = Column(Integer()) - production_mgy = Column(Integer()) - constr_exp = Column(Integer()) - - - def __repr__(self): - return f"InfrastructureEthanolBiorefineries(ethanol_biorefinery_id={self.ethanol_biorefinery_id},name={self.name},city={self.city},state={self.state},address={self.address},type={self.type},capacity_mgy={self.capacity_mgy},production_mgy={self.production_mgy},constr_exp={self.constr_exp},)" - - - - - - -class InfrastructureLandfills(Base): - """ - Landfills infrastructure. - """ - __tablename__ = 'infrastructure_landfills' - - project_id = Column(Text(), primary_key=True, nullable=False ) - project_int_id = Column(Integer()) - ghgrp_id = Column(Text()) - landfill_id = Column(Integer()) - landfill_name = Column(Text()) - state = Column(Text()) - physical_address = Column(Text()) - city = Column(Text()) - county = Column(Text()) - zip_code = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) - ownership_type = Column(Text()) - landfill_owner_orgs = Column(Text()) - landfill_opened_year = Column(Date()) - landfill_closure_year = Column(Date()) - landfill_status = Column(Text()) - waste_in_place = Column(Integer()) - waste_in_place_year = Column(Date()) - lfg_system_in_place = Column(Boolean()) - lfg_collected = Column(Numeric()) - lfg_flared = Column(Numeric()) - project_status = Column(Text()) - project_name = Column(Text()) - project_start_date = Column(Date()) - project_shutdown_date = Column(Date()) - project_type_category = Column(Text()) - lfg_energy_project_type = Column(Text()) - rng_delivery_method = Column(Text()) - actual_mw_generation = Column(Numeric()) - rated_mw_capacity = Column(Numeric()) - lfg_flow_to_project = Column(Numeric()) - direct_emission_reductions = Column(Numeric()) - avoided_emission_reductions = Column(Numeric()) - - - def __repr__(self): - return f"InfrastructureLandfills(project_id={self.project_id},project_int_id={self.project_int_id},ghgrp_id={self.ghgrp_id},landfill_id={self.landfill_id},landfill_name={self.landfill_name},state={self.state},physical_address={self.physical_address},city={self.city},county={self.county},zip_code={self.zip_code},latitude={self.latitude},longitude={self.longitude},ownership_type={self.ownership_type},landfill_owner_orgs={self.landfill_owner_orgs},landfill_opened_year={self.landfill_opened_year},landfill_closure_year={self.landfill_closure_year},landfill_status={self.landfill_status},waste_in_place={self.waste_in_place},waste_in_place_year={self.waste_in_place_year},lfg_system_in_place={self.lfg_system_in_place},lfg_collected={self.lfg_collected},lfg_flared={self.lfg_flared},project_status={self.project_status},project_name={self.project_name},project_start_date={self.project_start_date},project_shutdown_date={self.project_shutdown_date},project_type_category={self.project_type_category},lfg_energy_project_type={self.lfg_energy_project_type},rng_delivery_method={self.rng_delivery_method},actual_mw_generation={self.actual_mw_generation},rated_mw_capacity={self.rated_mw_capacity},lfg_flow_to_project={self.lfg_flow_to_project},direct_emission_reductions={self.direct_emission_reductions},avoided_emission_reductions={self.avoided_emission_reductions},)" - - - - - - -class InfrastructureLivestockAnaerobicDigesters(Base): - """ - Livestock anaerobic digesters infrastructure. - """ - __tablename__ = 'infrastructure_livestock_anaerobic_digesters' - - digester_id = Column(Integer(), primary_key=True, nullable=False ) - project_name = Column(Text()) - project_type = Column(Text()) - city = Column(Text()) - state = Column(Text()) - digester_type = Column(Text()) - profile = Column(Text()) - year_operational = Column(Date()) - animal_type_class = Column(Text()) - animal_types = Column(Text()) - pop_feeding_digester = Column(Text()) - total_pop_feeding_digester = Column(Integer()) - cattle = Column(Integer()) - dairy = Column(Integer()) - poultry = Column(Integer()) - swine = Column(Integer()) - codigestion = Column(Text()) - biogas_generation_estimate = Column(Integer()) - electricity_generated = Column(Integer()) - biogas_end_uses = Column(Text()) - methane_emission_reductions = Column(Integer()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) - - - def __repr__(self): - return f"InfrastructureLivestockAnaerobicDigesters(digester_id={self.digester_id},project_name={self.project_name},project_type={self.project_type},city={self.city},state={self.state},digester_type={self.digester_type},profile={self.profile},year_operational={self.year_operational},animal_type_class={self.animal_type_class},animal_types={self.animal_types},pop_feeding_digester={self.pop_feeding_digester},total_pop_feeding_digester={self.total_pop_feeding_digester},cattle={self.cattle},dairy={self.dairy},poultry={self.poultry},swine={self.swine},codigestion={self.codigestion},biogas_generation_estimate={self.biogas_generation_estimate},electricity_generated={self.electricity_generated},biogas_end_uses={self.biogas_end_uses},methane_emission_reductions={self.methane_emission_reductions},latitude={self.latitude},longitude={self.longitude},)" - - - - - - -class InfrastructureSafAndRenewableDieselPlants(Base): - """ - SAF and renewable diesel plants infrastructure. - """ - __tablename__ = 'infrastructure_saf_and_renewable_diesel_plants' - - ibcc_index = Column(Integer(), primary_key=True, nullable=False ) - company = Column(Text()) - city = Column(Text()) - state = Column(Text()) - country = Column(Text()) - capacity = Column(Text()) - feedstock = Column(Text()) - products = Column(Text()) - status = Column(Text()) - address = Column(Text()) - coordinates = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) - - - def __repr__(self): - return f"InfrastructureSafAndRenewableDieselPlants(ibcc_index={self.ibcc_index},company={self.company},city={self.city},state={self.state},country={self.country},capacity={self.capacity},feedstock={self.feedstock},products={self.products},status={self.status},address={self.address},coordinates={self.coordinates},latitude={self.latitude},longitude={self.longitude},)" - - - - - - -class InfrastructureWastewaterTreatmentPlants(Base): - """ - Wastewater treatment plants infrastructure. - """ - __tablename__ = 'infrastructure_wastewater_treatment_plants' - - plant_id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - state = Column(Text()) - codigestion = Column(Text()) - flow_design_adjusted = Column(Numeric()) - flow_average = Column(Numeric()) - biosolids = Column(Numeric()) - excess_flow = Column(Numeric()) - biogas_utilized = Column(Boolean()) - flaring = Column(Boolean()) - excess_mass_loading_rate = Column(Numeric()) - excess_mass_loading_rate_wet = Column(Numeric()) - methane_production = Column(Numeric()) - energy_content = Column(Numeric()) - electric_kw = Column(Numeric()) - thermal_mmbtu_d = Column(Numeric()) - electric_kwh = Column(Numeric()) - thermal_annual_mmbtu_y = Column(Numeric()) - anaerobic_digestion_facility = Column(Text()) - county = Column(Text()) - dayload_bdt = Column(Numeric()) - dayload = Column(Numeric()) - equivalent_generation = Column(Numeric()) - facility_type = Column(Text()) - feedstock = Column(Text()) - type = Column(Text()) - city = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) - zipcode = Column(Text()) - - - def __repr__(self): - return f"InfrastructureWastewaterTreatmentPlants(plant_id={self.plant_id},name={self.name},state={self.state},codigestion={self.codigestion},flow_design_adjusted={self.flow_design_adjusted},flow_average={self.flow_average},biosolids={self.biosolids},excess_flow={self.excess_flow},biogas_utilized={self.biogas_utilized},flaring={self.flaring},excess_mass_loading_rate={self.excess_mass_loading_rate},excess_mass_loading_rate_wet={self.excess_mass_loading_rate_wet},methane_production={self.methane_production},energy_content={self.energy_content},electric_kw={self.electric_kw},thermal_mmbtu_d={self.thermal_mmbtu_d},electric_kwh={self.electric_kwh},thermal_annual_mmbtu_y={self.thermal_annual_mmbtu_y},anaerobic_digestion_facility={self.anaerobic_digestion_facility},county={self.county},dayload_bdt={self.dayload_bdt},dayload={self.dayload},equivalent_generation={self.equivalent_generation},facility_type={self.facility_type},feedstock={self.feedstock},type={self.type},city={self.city},latitude={self.latitude},longitude={self.longitude},zipcode={self.zipcode},)" - - - - - - -class InfrastructureCombustionPlants(Base): - """ - Combustion plants infrastructure. - """ - __tablename__ = 'infrastructure_combustion_plants' - - combustion_fid = Column(Integer(), primary_key=True, nullable=False ) - objectid = Column(Integer()) - status = Column(Text()) - city = Column(Text()) - name = Column(Text()) - county = Column(Text()) - equivalent_generation = Column(Numeric()) - np_mw = Column(Numeric()) - cf = Column(Numeric()) - yearload = Column(Integer()) - fuel = Column(Text()) - notes = Column(Text()) - type = Column(Text()) - wkt_geom = Column(Text()) - geom = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) - - - def __repr__(self): - return f"InfrastructureCombustionPlants(combustion_fid={self.combustion_fid},objectid={self.objectid},status={self.status},city={self.city},name={self.name},county={self.county},equivalent_generation={self.equivalent_generation},np_mw={self.np_mw},cf={self.cf},yearload={self.yearload},fuel={self.fuel},notes={self.notes},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" - - - - - - -class InfrastructureDistrictEnergySystems(Base): - """ - District energy systems infrastructure. - """ - __tablename__ = 'infrastructure_district_energy_systems' - - des_fid = Column(Integer(), primary_key=True, nullable=False ) - cbg_id = Column(Integer()) - name = Column(Text()) - system = Column(Text()) - object_id = Column(Integer()) - city = Column(Text()) - state = Column(Text()) - primary_fuel = Column(Text()) - secondary_fuel = Column(Text()) - usetype = Column(Text()) - cap_st = Column(Numeric()) - cap_hw = Column(Numeric()) - cap_cw = Column(Numeric()) - chpcg_cap = Column(Numeric()) - excess_c = Column(Numeric()) - excess_h = Column(Numeric()) - type = Column(Text()) - wkt_geom = Column(Text()) - geom = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) - - - def __repr__(self): - return f"InfrastructureDistrictEnergySystems(des_fid={self.des_fid},cbg_id={self.cbg_id},name={self.name},system={self.system},object_id={self.object_id},city={self.city},state={self.state},primary_fuel={self.primary_fuel},secondary_fuel={self.secondary_fuel},usetype={self.usetype},cap_st={self.cap_st},cap_hw={self.cap_hw},cap_cw={self.cap_cw},chpcg_cap={self.chpcg_cap},excess_c={self.excess_c},excess_h={self.excess_h},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" - - - - - - -class InfrastructureFoodProcessingFacilities(Base): - """ - Food processing facilities infrastructure. - """ - __tablename__ = 'infrastructure_food_processing_facilities' - - processing_facility_id = Column(Integer(), primary_key=True, nullable=False ) - address = Column(Text()) - county = Column(Text()) - city = Column(Text()) - company = Column(Text()) - join_count = Column(Integer()) - master_type = Column(Text()) - state = Column(Text()) - subtype = Column(Text()) - target_fid = Column(Integer()) - processing_type = Column(Text()) - zip = Column(Text()) - type = Column(Text()) - wkt_geom = Column(Text()) - geom = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) - - - def __repr__(self): - return f"InfrastructureFoodProcessingFacilities(processing_facility_id={self.processing_facility_id},address={self.address},county={self.county},city={self.city},company={self.company},join_count={self.join_count},master_type={self.master_type},state={self.state},subtype={self.subtype},target_fid={self.target_fid},processing_type={self.processing_type},zip={self.zip},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" - - - - - - -class InfrastructureMswToEnergyAnaerobicDigesters(Base): - """ - MSW to energy anaerobic digesters infrastructure. - """ - __tablename__ = 'infrastructure_msw_to_energy_anaerobic_digesters' - - wte_id = Column(Integer(), primary_key=True, nullable=False ) - city = Column(Text()) - county = Column(Text()) - equivalent_generation = Column(Numeric()) - feedstock = Column(Text()) - dayload = Column(Numeric()) - dayload_bdt = Column(Numeric()) - facility_type = Column(Text()) - status = Column(Text()) - notes = Column(Text()) - source = Column(Text()) - type = Column(Text()) - wkt_geom = Column(Text()) - geom = Column(Text()) - latitude = Column(Numeric()) - longitude = Column(Numeric()) - - - def __repr__(self): - return f"InfrastructureMswToEnergyAnaerobicDigesters(wte_id={self.wte_id},city={self.city},county={self.county},equivalent_generation={self.equivalent_generation},feedstock={self.feedstock},dayload={self.dayload},dayload_bdt={self.dayload_bdt},facility_type={self.facility_type},status={self.status},notes={self.notes},source={self.source},type={self.type},wkt_geom={self.wkt_geom},geom={self.geom},latitude={self.latitude},longitude={self.longitude},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class FacilityRecord(BaseEntity): - """ - Facility record. - """ - __tablename__ = 'facility_record' - - dataset_id = Column(Integer()) - facility_name = Column(Text()) - location_id = Column(Integer()) - capacity_mw = Column(Numeric()) - resource_id = Column(Integer()) - operator = Column(Text()) - start_year = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FacilityRecord(dataset_id={self.dataset_id},facility_name={self.facility_name},location_id={self.location_id},capacity_mw={self.capacity_mw},resource_id={self.resource_id},operator={self.operator},start_year={self.start_year},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source (e.g. database, literature). - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AnalysisType(LookupBase): - """ - Type of analysis. - """ - __tablename__ = 'analysis_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AnalysisType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Dataset(BaseEntity): - """ - Dataset definition. - """ - __tablename__ = 'dataset' - - name = Column(Text()) - record_type = Column(Text()) - source_id = Column(Integer()) - start_date = Column(Date()) - end_date = Column(Date()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Dataset(name={self.name},record_type={self.record_type},source_id={self.source_id},start_date={self.start_date},end_date={self.end_date},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DimensionType(LookupBase): - """ - Type of dimension. - """ - __tablename__ = 'dimension_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"DimensionType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Observation(BaseEntity): - """ - Observation data. - """ - __tablename__ = 'observation' - - dataset_id = Column(Integer()) - record_type = Column(Text()) - record_id = Column(Integer()) - parameter_id = Column(Integer()) - value = Column(Numeric()) - unit_id = Column(Integer()) - dimension_type_id = Column(Integer()) - dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Observation(dataset_id={self.dataset_id},record_type={self.record_type},record_id={self.record_id},parameter_id={self.parameter_id},value={self.value},unit_id={self.unit_id},dimension_type_id={self.dimension_type_id},dimension_value={self.dimension_value},dimension_unit_id={self.dimension_unit_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py deleted file mode 100644 index c1fb6e9a..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/lineage.py +++ /dev/null @@ -1,109 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class LineageGroup(Base): - """ - Grouping for lineage information. - """ - __tablename__ = 'lineage_group' - - id = Column(Integer(), primary_key=True, nullable=False ) - etl_run_id = Column(Text()) - note = Column(Text()) - - - def __repr__(self): - return f"LineageGroup(id={self.id},etl_run_id={self.etl_run_id},note={self.note},)" - - - - - - -class EntityLineage(Base): - """ - Lineage information for a specific entity. - """ - __tablename__ = 'entity_lineage' - - id = Column(Integer(), primary_key=True, nullable=False ) - lineage_group_id = Column(Integer()) - source_table = Column(Text()) - source_row_id = Column(Text()) - note = Column(Text()) - - - def __repr__(self): - return f"EntityLineage(id={self.id},lineage_group_id={self.lineage_group_id},source_table={self.source_table},source_row_id={self.source_row_id},note={self.note},)" - - - - - - -class EtlRun(Base): - """ - Information about an ETL run. - """ - __tablename__ = 'etl_run' - - id = Column(Integer(), primary_key=True, nullable=False ) - started_at = Column(DateTime()) - completed_at = Column(DateTime()) - pipeline_name = Column(Text()) - status = Column(Text()) - records_ingested = Column(Integer()) - note = Column(Text()) - - - def __repr__(self): - return f"EtlRun(id={self.id},started_at={self.started_at},completed_at={self.completed_at},pipeline_name={self.pipeline_name},status={self.status},records_ingested={self.records_ingested},note={self.note},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py deleted file mode 100644 index 85ddde97..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/methods_parameters_units.py +++ /dev/null @@ -1,1030 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source (e.g. database, literature). - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py deleted file mode 100644 index 8219be89..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/people.py +++ /dev/null @@ -1,106 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py deleted file mode 100644 index 4eccd8ac..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/places.py +++ /dev/null @@ -1,106 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/primary_ag_product.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/primary_ag_product.py deleted file mode 100644 index dfa0f14f..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/primary_ag_product.py +++ /dev/null @@ -1,75 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_availability.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_availability.py deleted file mode 100644 index c02c738f..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_availability.py +++ /dev/null @@ -1,308 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer(), ForeignKey('Resource.id')) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer(), ForeignKey('Resource.id')) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer(), ForeignKey('Resource.id')) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_class.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_class.py deleted file mode 100644 index b47201f8..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_class.py +++ /dev/null @@ -1,74 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_counterfactual.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_counterfactual.py deleted file mode 100644 index 4568cca1..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_counterfactual.py +++ /dev/null @@ -1,1030 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer(), ForeignKey('Resource.id')) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer(), ForeignKey('Resource.id')) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer(), ForeignKey('Resource.id')) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source (e.g. database, literature). - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer(), ForeignKey('Resource.id')) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py deleted file mode 100644 index 627f9124..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_information.py +++ /dev/null @@ -1,308 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_morphology.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_morphology.py deleted file mode 100644 index 0b9bcf94..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_morphology.py +++ /dev/null @@ -1,308 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer(), ForeignKey('Resource.id')) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer(), ForeignKey('Resource.id')) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer(), ForeignKey('Resource.id')) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_subclass.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_subclass.py deleted file mode 100644 index a3919852..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/resource_subclass.py +++ /dev/null @@ -1,74 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py deleted file mode 100644 index ae68592c..00000000 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/sample_preparation.py +++ /dev/null @@ -1,1119 +0,0 @@ - -from sqlalchemy import Column, Index, Table, ForeignKey -from sqlalchemy.orm import relationship -from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base -from sqlalchemy.ext.associationproxy import association_proxy - -Base = declarative_base() -metadata = Base.metadata - - -class BaseEntity(Base): - """ - Base entity included in all main entity tables. - """ - __tablename__ = 'base_entity' - - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"BaseEntity(id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - - -class LookupBase(Base): - """ - Base class for enum/ontology-like tables. - """ - __tablename__ = 'lookup_base' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LookupBase(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - - -class Geography(Base): - """ - Geographic location. - """ - __tablename__ = 'geography' - - geoid = Column(Text(), primary_key=True, nullable=False ) - state_name = Column(Text()) - state_fips = Column(Text()) - county_name = Column(Text()) - county_fips = Column(Text()) - region_name = Column(Text()) - agg_level_desc = Column(Text()) - - - def __repr__(self): - return f"Geography(geoid={self.geoid},state_name={self.state_name},state_fips={self.state_fips},county_name={self.county_name},county_fips={self.county_fips},region_name={self.region_name},agg_level_desc={self.agg_level_desc},)" - - - - - - -class ResourceMorphology(Base): - """ - Morphology of a resource. - """ - __tablename__ = 'resource_morphology' - - id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer()) - morphology_uri = Column(Text()) - - - def __repr__(self): - return f"ResourceMorphology(id={self.id},resource_id={self.resource_id},morphology_uri={self.morphology_uri},)" - - - - - - -class ParameterCategoryParameter(Base): - """ - Link between Parameter and ParameterCategory. - """ - __tablename__ = 'parameter_category_parameter' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - parameter_category_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterCategoryParameter(id={self.id},parameter_id={self.parameter_id},parameter_category_id={self.parameter_category_id},)" - - - - - - -class ParameterUnit(Base): - """ - Link between Parameter and Unit (alternate units). - """ - __tablename__ = 'parameter_unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer()) - alternate_unit_id = Column(Integer()) - - - def __repr__(self): - return f"ParameterUnit(id={self.id},parameter_id={self.parameter_id},alternate_unit_id={self.alternate_unit_id},)" - - - - - - -class PreparationMethod(BaseEntity): - """ - Method of sample preparation. - """ - __tablename__ = 'preparation_method' - - name = Column(Text()) - description = Column(Text()) - prep_method_abbrev_id = Column(Integer()) - prep_temp_c = Column(Numeric()) - uri = Column(Text()) - drying_step = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparationMethod(name={self.name},description={self.description},prep_method_abbrev_id={self.prep_method_abbrev_id},prep_temp_c={self.prep_temp_c},uri={self.uri},drying_step={self.drying_step},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparationMethodAbbreviation(LookupBase): - """ - Abbreviation for preparation method. - """ - __tablename__ = 'preparation_method_abbreviation' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PreparationMethodAbbreviation(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PreparedSample(BaseEntity): - """ - Sample that has been prepared. - """ - __tablename__ = 'prepared_sample' - - name = Column(Text()) - field_sample_id = Column(Integer()) - prep_method_id = Column(Integer()) - prep_date = Column(Date()) - preparer_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PreparedSample(name={self.name},field_sample_id={self.field_sample_id},prep_method_id={self.prep_method_id},prep_date={self.prep_date},preparer_id={self.preparer_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationAddress(BaseEntity): - """ - Physical address. - """ - __tablename__ = 'location_address' - - geography_id = Column(Text()) - address_line1 = Column(Text()) - address_line2 = Column(Text()) - city = Column(Text()) - zip = Column(Text()) - lat = Column(Float()) - lon = Column(Float()) - is_anonymous = Column(Boolean()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationAddress(geography_id={self.geography_id},address_line1={self.address_line1},address_line2={self.address_line2},city={self.city},zip={self.zip},lat={self.lat},lon={self.lon},is_anonymous={self.is_anonymous},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Contact(BaseEntity): - """ - Contact information for a person. - """ - __tablename__ = 'contact' - - first_name = Column(Text()) - last_name = Column(Text()) - email = Column(Text()) - affiliation = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Contact(first_name={self.first_name},last_name={self.last_name},email={self.email},affiliation={self.affiliation},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Provider(BaseEntity): - """ - Provider information. - """ - __tablename__ = 'provider' - - codename = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Provider(codename={self.codename},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Resource(BaseEntity): - """ - Biomass resource definition. - """ - __tablename__ = 'resource' - - name = Column(Text()) - primary_ag_product_id = Column(Integer()) - resource_class_id = Column(Integer()) - resource_subclass_id = Column(Integer()) - note = Column(Text()) - test = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Resource(name={self.name},primary_ag_product_id={self.primary_ag_product_id},resource_class_id={self.resource_class_id},resource_subclass_id={self.resource_subclass_id},note={self.note},test={self.test},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceClass(LookupBase): - """ - Classification of resources. - """ - __tablename__ = 'resource_class' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceClass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceSubclass(LookupBase): - """ - Sub-classification of resources. - """ - __tablename__ = 'resource_subclass' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ResourceSubclass(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PrimaryAgProduct(LookupBase): - """ - Primary agricultural product definition. - """ - __tablename__ = 'primary_ag_product' - - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"PrimaryAgProduct(note={self.note},id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceAvailability(BaseEntity): - """ - Availability of a resource in a location. - """ - __tablename__ = 'resource_availability' - - resource_id = Column(Integer()) - geoid = Column(Text()) - from_month = Column(Integer()) - to_month = Column(Integer()) - year_round = Column(Boolean()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceAvailability(resource_id={self.resource_id},geoid={self.geoid},from_month={self.from_month},to_month={self.to_month},year_round={self.year_round},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ResourceCounterfactual(BaseEntity): - """ - Counterfactual uses of a resource. - """ - __tablename__ = 'resource_counterfactual' - - geoid = Column(Text()) - resource_id = Column(Integer()) - counterfactual_description = Column(Text()) - animal_bedding_percent = Column(Numeric()) - animal_bedding_source_id = Column(Integer()) - animal_feed_percent = Column(Numeric()) - animal_feed_source_id = Column(Integer()) - bioelectricty_percent = Column(Numeric()) - bioelectricty_source_id = Column(Integer()) - burn_percent = Column(Numeric()) - burn_source_id = Column(Integer()) - compost_percent = Column(Numeric()) - compost_source_id = Column(Integer()) - landfill_percent = Column(Numeric()) - landfill_source_id = Column(Integer()) - counterfactual_date = Column(Date()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"ResourceCounterfactual(geoid={self.geoid},resource_id={self.resource_id},counterfactual_description={self.counterfactual_description},animal_bedding_percent={self.animal_bedding_percent},animal_bedding_source_id={self.animal_bedding_source_id},animal_feed_percent={self.animal_feed_percent},animal_feed_source_id={self.animal_feed_source_id},bioelectricty_percent={self.bioelectricty_percent},bioelectricty_source_id={self.bioelectricty_source_id},burn_percent={self.burn_percent},burn_source_id={self.burn_source_id},compost_percent={self.compost_percent},compost_source_id={self.compost_source_id},landfill_percent={self.landfill_percent},landfill_source_id={self.landfill_source_id},counterfactual_date={self.counterfactual_date},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSample(BaseEntity): - """ - Sample collected from the field. - """ - __tablename__ = 'field_sample' - - name = Column(Text()) - resource_id = Column(Integer()) - provider_id = Column(Integer()) - collector_id = Column(Integer()) - sample_collection_source = Column(Text()) - amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer()) - sampling_location_id = Column(Integer()) - field_storage_method_id = Column(Integer()) - field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer()) - field_storage_location_id = Column(Integer()) - collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer()) - harvest_method_id = Column(Integer()) - harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSample(name={self.name},resource_id={self.resource_id},provider_id={self.provider_id},collector_id={self.collector_id},sample_collection_source={self.sample_collection_source},amount_collected={self.amount_collected},amount_collected_unit_id={self.amount_collected_unit_id},sampling_location_id={self.sampling_location_id},field_storage_method_id={self.field_storage_method_id},field_storage_duration_value={self.field_storage_duration_value},field_storage_duration_unit_id={self.field_storage_duration_unit_id},field_storage_location_id={self.field_storage_location_id},collection_timestamp={self.collection_timestamp},collection_method_id={self.collection_method_id},harvest_method_id={self.harvest_method_id},harvest_date={self.harvest_date},field_sample_storage_location_id={self.field_sample_storage_location_id},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class PhysicalCharacteristic(BaseEntity): - """ - Physical characteristics of a sample. - """ - __tablename__ = 'physical_characteristic' - - field_sample_id = Column(Integer()) - particle_length = Column(Numeric()) - particle_width = Column(Numeric()) - particle_height = Column(Numeric()) - particle_unit_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"PhysicalCharacteristic(field_sample_id={self.field_sample_id},particle_length={self.particle_length},particle_width={self.particle_width},particle_height={self.particle_height},particle_unit_id={self.particle_unit_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldSampleCondition(BaseEntity): - """ - Condition of the field sample. - """ - __tablename__ = 'field_sample_condition' - - field_sample_id = Column(Integer()) - ag_treatment_id = Column(Integer()) - last_application_date = Column(Date()) - treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FieldSampleCondition(field_sample_id={self.field_sample_id},ag_treatment_id={self.ag_treatment_id},last_application_date={self.last_application_date},treatment_amount_per_acre={self.treatment_amount_per_acre},processing_method_id={self.processing_method_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FieldStorageMethod(LookupBase): - """ - Method of field storage. - """ - __tablename__ = 'field_storage_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"FieldStorageMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class CollectionMethod(LookupBase): - """ - Method of collection. - """ - __tablename__ = 'collection_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"CollectionMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class HarvestMethod(LookupBase): - """ - Method of harvest. - """ - __tablename__ = 'harvest_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"HarvestMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ProcessingMethod(LookupBase): - """ - Method of processing. - """ - __tablename__ = 'processing_method' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ProcessingMethod(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SoilType(LookupBase): - """ - Type of soil. - """ - __tablename__ = 'soil_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SoilType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class AgTreatment(LookupBase): - """ - Agricultural treatment. - """ - __tablename__ = 'ag_treatment' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"AgTreatment(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationSoilType(BaseEntity): - """ - Soil type at a location. - """ - __tablename__ = 'location_soil_type' - - location_id = Column(Integer()) - soil_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"LocationSoilType(location_id={self.location_id},soil_type_id={self.soil_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSource(BaseEntity): - """ - Source of data. - """ - __tablename__ = 'data_source' - - name = Column(Text()) - description = Column(Text()) - data_source_type_id = Column(Integer()) - full_title = Column(Text()) - creator = Column(Text()) - subject = Column(Text()) - publisher = Column(Text()) - contributor = Column(Text()) - date = Column(DateTime()) - type = Column(Text()) - biocirv = Column(Boolean()) - format = Column(Text()) - language = Column(Text()) - relation = Column(Text()) - temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer()) - rights = Column(Text()) - license = Column(Text()) - uri = Column(Text()) - note = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSource(name={self.name},description={self.description},data_source_type_id={self.data_source_type_id},full_title={self.full_title},creator={self.creator},subject={self.subject},publisher={self.publisher},contributor={self.contributor},date={self.date},type={self.type},biocirv={self.biocirv},format={self.format},language={self.language},relation={self.relation},temporal_coverage={self.temporal_coverage},location_coverage_id={self.location_coverage_id},rights={self.rights},license={self.license},uri={self.uri},note={self.note},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class FileObjectMetadata(BaseEntity): - """ - Metadata for a file object. - """ - __tablename__ = 'file_object_metadata' - - data_source_id = Column(Integer()) - bucket_path = Column(Text()) - file_format = Column(Text()) - file_size = Column(Integer()) - checksum_md5 = Column(Text()) - checksum_sha256 = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"FileObjectMetadata(data_source_id={self.data_source_id},bucket_path={self.bucket_path},file_format={self.file_format},file_size={self.file_size},checksum_md5={self.checksum_md5},checksum_sha256={self.checksum_sha256},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class DataSourceType(BaseEntity): - """ - Type of data source (e.g. database, literature). - """ - __tablename__ = 'data_source_type' - - source_type_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"DataSourceType(source_type_id={self.source_type_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class LocationResolution(LookupBase): - """ - Resolution of the location (e.g. nation, state, county). - """ - __tablename__ = 'location_resolution' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"LocationResolution(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class SourceType(LookupBase): - """ - Type of source (e.g. database, literature). - """ - __tablename__ = 'source_type' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"SourceType(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Unit(LookupBase): - """ - Unit of measurement. - """ - __tablename__ = 'unit' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"Unit(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Method(BaseEntity): - """ - Analytical method. - """ - __tablename__ = 'method' - - name = Column(Text()) - method_abbrev_id = Column(Integer()) - method_category_id = Column(Integer()) - method_standard_id = Column(Integer()) - description = Column(Text()) - detection_limits = Column(Text()) - source_id = Column(Integer()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Method(name={self.name},method_abbrev_id={self.method_abbrev_id},method_category_id={self.method_category_id},method_standard_id={self.method_standard_id},description={self.description},detection_limits={self.detection_limits},source_id={self.source_id},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodAbbrev(LookupBase): - """ - Abbreviation for method. - """ - __tablename__ = 'method_abbrev' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodAbbrev(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodCategory(LookupBase): - """ - Category of method. - """ - __tablename__ = 'method_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class MethodStandard(LookupBase): - """ - Standard associated with the method. - """ - __tablename__ = 'method_standard' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"MethodStandard(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class Parameter(BaseEntity): - """ - Parameter being measured. - """ - __tablename__ = 'parameter' - - name = Column(Text()) - standard_unit_id = Column(Integer()) - calculated = Column(Boolean()) - description = Column(Text()) - id = Column(Integer(), primary_key=True, nullable=False ) - created_at = Column(DateTime()) - updated_at = Column(DateTime()) - etl_run_id = Column(Text()) - lineage_group_id = Column(Integer()) - - - def __repr__(self): - return f"Parameter(name={self.name},standard_unit_id={self.standard_unit_id},calculated={self.calculated},description={self.description},id={self.id},created_at={self.created_at},updated_at={self.updated_at},etl_run_id={self.etl_run_id},lineage_group_id={self.lineage_group_id},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } - - - -class ParameterCategory(LookupBase): - """ - Category of parameter. - """ - __tablename__ = 'parameter_category' - - id = Column(Integer(), primary_key=True, nullable=False ) - name = Column(Text()) - description = Column(Text()) - uri = Column(Text()) - - - def __repr__(self): - return f"ParameterCategory(id={self.id},name={self.name},description={self.description},uri={self.uri},)" - - - - - # Using concrete inheritance: see https://docs.sqlalchemy.org/en/14/orm/inheritance.html - __mapper_args__ = { - 'concrete': True - } diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated_test/schema1.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated_test/schema1.py new file mode 100644 index 00000000..0fe4f136 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated_test/schema1.py @@ -0,0 +1,22 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ClassA(Base): + """ + + """ + __tablename__ = 'class_a' + + id = Column(Text(), primary_key=True, nullable=False ) + + + def __repr__(self): + return f"ClassA(id={self.id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated_test/schema2.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated_test/schema2.py new file mode 100644 index 00000000..a5013e54 --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated_test/schema2.py @@ -0,0 +1,40 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ClassB(Base): + """ + + """ + __tablename__ = 'class_b' + + id = Column(Text(), primary_key=True, nullable=False ) + class_a_id = Column(Text(), ForeignKey('ClassA.id')) + + + def __repr__(self): + return f"ClassB(id={self.id},class_a_id={self.class_a_id},)" + + + + + + +class ClassA(Base): + """ + + """ + __tablename__ = 'class_a' + + id = Column(Text(), primary_key=True, nullable=False ) + + + def __repr__(self): + return f"ClassA(id={self.id},)" diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated_test/schema3.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated_test/schema3.py new file mode 100644 index 00000000..876e3f8f --- /dev/null +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated_test/schema3.py @@ -0,0 +1,59 @@ + +from sqlalchemy import Column, Index, Table, ForeignKey +from sqlalchemy.orm import relationship +from sqlalchemy.sql.sqltypes import * +from sqlalchemy.orm import declarative_base +from sqlalchemy.ext.associationproxy import association_proxy + +Base = declarative_base() +metadata = Base.metadata + + +class ClassC(Base): + """ + + """ + __tablename__ = 'class_c' + + id = Column(Text(), primary_key=True, nullable=False ) + class_a_id = Column(Text(), ForeignKey('ClassA.id')) + class_b_id = Column(Text(), ForeignKey('ClassB.id')) + + + def __repr__(self): + return f"ClassC(id={self.id},class_a_id={self.class_a_id},class_b_id={self.class_b_id},)" + + + + + + +class ClassA(Base): + """ + + """ + __tablename__ = 'class_a' + + id = Column(Text(), primary_key=True, nullable=False ) + + + def __repr__(self): + return f"ClassA(id={self.id},)" + + + + + + +class ClassB(Base): + """ + + """ + __tablename__ = 'class_b' + + id = Column(Text(), primary_key=True, nullable=False ) + class_a_id = Column(Text(), ForeignKey('ClassA.id')) + + + def __repr__(self): + return f"ClassB(id={self.id},class_a_id={self.class_a_id},)" diff --git a/src/ca_biositing/datamodels/utils/generate_sqla.py b/src/ca_biositing/datamodels/utils/generate_sqla.py index 50c0825f..929d5298 100644 --- a/src/ca_biositing/datamodels/utils/generate_sqla.py +++ b/src/ca_biositing/datamodels/utils/generate_sqla.py @@ -41,28 +41,13 @@ def generate_sqla(): # Ensure output directory exists output_dir.mkdir(parents=True, exist_ok=True) - # Clean output directory + # Clean output directory recursively print(f"Cleaning output directory: {output_dir}") - for file in output_dir.glob("*.py"): - if file.name != "__init__.py": - file.unlink() + for f in output_dir.glob('**/*.py'): + if f.name != '__init__.py': + f.unlink() # Generate for modules - for yaml_file in modules_dir.glob("*.yaml"): - module_name = yaml_file.stem - output_file = output_dir / f"{module_name}.py" - print(f"Generating {output_file} from {yaml_file}...") - - cmd = [ - "python", "-m", "linkml.generators.sqlalchemygen", - "--no-mergeimports", - str(yaml_file) - ] - - with open(output_file, "w") as f: - subprocess.run(cmd, stdout=f, check=True) - - post_process_file(output_file) # Generate for main schema main_yaml = linkml_dir / "ca_biositing.yaml" @@ -71,7 +56,7 @@ def generate_sqla(): cmd = [ "python", "-m", "linkml.generators.sqlalchemygen", - "--no-mergeimports", + "--mergeimports", str(main_yaml) ] diff --git a/src/ca_biositing/datamodels/utils/generate_test_sqla.py b/src/ca_biositing/datamodels/utils/generate_test_sqla.py new file mode 100644 index 00000000..c98f3184 --- /dev/null +++ b/src/ca_biositing/datamodels/utils/generate_test_sqla.py @@ -0,0 +1,69 @@ +import os +import re +import subprocess +from pathlib import Path + +def to_snake_case(name): + """Converts PascalCase to snake_case.""" + s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name) + return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower() + +def post_process_file(file_path): + """ + Post-processes the generated file to convert table names to snake_case. + """ + with open(file_path, 'r') as f: + content = f.read() + + # Regex to find __tablename__ assignments + # Matches: __tablename__ = 'SomeName' + pattern = r"__tablename__ = '([A-Za-z0-9]+)'" + + def replace_tablename(match): + original_name = match.group(1) + snake_name = to_snake_case(original_name) + return f"__tablename__ = '{snake_name}'" + + new_content = re.sub(pattern, replace_tablename, content) + + with open(file_path, 'w') as f: + f.write(new_content) + +def generate_sqla(): + """ + Generates SQLAlchemy models from LinkML schema modules. + """ + base_dir = Path(__file__).parent.parent + linkml_dir = base_dir / "ca_biositing/datamodels/linkml/test_schemas" + output_dir = base_dir / "ca_biositing/datamodels/schemas/generated_test" + + # Ensure output directory exists + output_dir.mkdir(parents=True, exist_ok=True) + + # Clean output directory + print(f"Cleaning output directory: {output_dir}") + for file in output_dir.glob("*.py"): + if file.name != "__init__.py": + file.unlink() + + # Generate for modules + for yaml_file in linkml_dir.glob("*.yaml"): + module_name = yaml_file.stem + output_file = output_dir / f"{module_name}.py" + print(f"Generating {output_file} from {yaml_file}...") + + cmd = [ + "python", "-m", "linkml.generators.sqlalchemygen", + "--mergeimports", + str(yaml_file) + ] + + with open(output_file, "w") as f: + subprocess.run(cmd, stdout=f, check=True) + + post_process_file(output_file) + + print("Generation complete.") + +if __name__ == "__main__": + generate_sqla() diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb index 140d8709..beb63faf 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb @@ -20,15 +20,15 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 7, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2026-01-06 10:31:31,052 - INFO - Added project root '/Users/pjsmitty301/ca-biositing' to sys.path\n", - "2026-01-06 10:31:32,479 - INFO - Successfully imported all project modules.\n" + "2026-01-06 10:39:39,502 - INFO - Project root '/Users/pjsmitty301/ca-biositing' is already in sys.path\n", + "2026-01-06 10:39:39,503 - INFO - Successfully imported all project modules.\n" ] } ], @@ -89,7 +89,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 8, "metadata": {}, "outputs": [], "source": [ @@ -156,7 +156,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -193,6 +193,11 @@ " continue\n", " \n", " try:\n", + " # Skip normalization if the column is all NaN/None\n", + " if df_normalized[df_col].isnull().all():\n", + " logger.info(f\"Skipping normalization for column '{df_col}' as it contains only null values.\")\n", + " continue\n", + " \n", " logger.info(f\"Normalizing column '{df_col}' using model '{model.__name__}'.\")\n", " df_normalized, num_created = replace_name_with_id_df(\n", " db=db,\n", @@ -235,112 +240,109 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2026-01-06 10:31:40,834 - INFO - Starting data extraction...\n", - "2026-01-06 10:31:40,881 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-06 10:31:40,903 - INFO - Extracting raw data from '03.1-Proximate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", - "2026-01-06 10:31:42,948 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/csrf-token?client=ae9812ec-079b-4fe5-845c-493121391421 \"HTTP/1.1 422 Unprocessable Entity\"\n", - "2026-01-06 10:31:42,966 - INFO - HTTP Request: POST http://127.0.0.1:4200/api/logs/ \"HTTP/1.1 201 Created\"\n", - "2026-01-06 10:31:45,659 - INFO - Successfully extracted raw data.\n", - "2026-01-06 10:31:45,661 - INFO - Finished in state Completed()\n", - "2026-01-06 10:31:45,672 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-06 10:31:45,680 - INFO - Extracting raw data from '03.7-Ultimate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", - "2026-01-06 10:31:46,995 - INFO - HTTP Request: POST http://127.0.0.1:4200/api/logs/ \"HTTP/1.1 201 Created\"\n", - "2026-01-06 10:31:47,292 - INFO - Successfully extracted raw data.\n", - "2026-01-06 10:31:47,296 - INFO - Finished in state Completed()\n", - "2026-01-06 10:31:47,313 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-06 10:31:47,326 - INFO - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", - "2026-01-06 10:31:48,924 - INFO - Successfully extracted raw data.\n", - "2026-01-06 10:31:48,929 - INFO - Finished in state Completed()\n", - "2026-01-06 10:31:48,930 - INFO - Data extraction complete.\n", - "2026-01-06 10:31:48,931 - INFO - Starting data cleaning...\n", - "2026-01-06 10:31:48,933 - INFO - Starting DataFrame cleaning process.\n", - "2026-01-06 10:31:48,939 - INFO - Dropped 0 rows with missing values.\n", - "2026-01-06 10:31:48,950 - INFO - Successfully cleaned DataFrame.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + "2026-01-06 10:53:39,195 - INFO - Starting data extraction...\n", + "2026-01-06 10:53:39,212 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-06 10:53:39,266 - INFO - Extracting raw data from '03.1-Proximate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", + "2026-01-06 10:53:41,468 - INFO - Successfully extracted raw data.\n", + "2026-01-06 10:53:41,471 - INFO - Finished in state Completed()\n", + "2026-01-06 10:53:41,486 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-06 10:53:41,497 - INFO - Extracting raw data from '03.7-Ultimate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", + "2026-01-06 10:53:42,816 - INFO - Successfully extracted raw data.\n", + "2026-01-06 10:53:42,820 - INFO - Finished in state Completed()\n", + "2026-01-06 10:53:42,840 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-06 10:53:42,853 - INFO - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", + "2026-01-06 10:53:44,427 - INFO - Successfully extracted raw data.\n", + "2026-01-06 10:53:44,430 - INFO - Finished in state Completed()\n", + "2026-01-06 10:53:44,434 - INFO - Data extraction complete.\n", + "2026-01-06 10:53:44,434 - INFO - Starting data cleaning...\n", + "2026-01-06 10:53:44,435 - INFO - Starting DataFrame cleaning process.\n", + "2026-01-06 10:53:44,438 - INFO - Dropped 0 rows with missing values.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:40: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", + " df_cleaned = df_cleaned.replace(r'^\\s*$', np.nan, regex=True)\n", + "2026-01-06 10:53:44,450 - INFO - Successfully cleaned DataFrame.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:48: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", - "2026-01-06 10:31:48,958 - INFO - Converted all string data to lowercase.\n", - "2026-01-06 10:31:48,958 - INFO - Starting DataFrame cleaning process.\n", - "2026-01-06 10:31:48,959 - INFO - Dropped 0 rows with missing values.\n", - "2026-01-06 10:31:48,962 - INFO - Successfully cleaned DataFrame.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + "2026-01-06 10:53:44,455 - INFO - Converted all string data to lowercase.\n", + "2026-01-06 10:53:44,456 - INFO - Starting DataFrame cleaning process.\n", + "2026-01-06 10:53:44,457 - INFO - Dropped 0 rows with missing values.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:40: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", + " df_cleaned = df_cleaned.replace(r'^\\s*$', np.nan, regex=True)\n", + "2026-01-06 10:53:44,461 - INFO - Successfully cleaned DataFrame.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:48: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", - "2026-01-06 10:31:48,964 - INFO - Converted all string data to lowercase.\n", - "2026-01-06 10:31:48,964 - INFO - Starting DataFrame cleaning process.\n", - "2026-01-06 10:31:48,965 - INFO - Dropped 0 rows with missing values.\n", - "2026-01-06 10:31:48,969 - INFO - Successfully cleaned DataFrame.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/183192953.py:42: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + "2026-01-06 10:53:44,467 - INFO - Converted all string data to lowercase.\n", + "2026-01-06 10:53:44,468 - INFO - Starting DataFrame cleaning process.\n", + "2026-01-06 10:53:44,470 - INFO - Dropped 0 rows with missing values.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:40: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", + " df_cleaned = df_cleaned.replace(r'^\\s*$', np.nan, regex=True)\n", + "2026-01-06 10:53:44,480 - INFO - Successfully cleaned DataFrame.\n", + "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:48: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", - "2026-01-06 10:31:48,972 - INFO - Converted all string data to lowercase.\n", - "2026-01-06 10:31:48,973 - INFO - Data cleaning complete.\n", - "2026-01-06 10:31:48,973 - INFO - Starting data normalization...\n", - "2026-01-06 10:31:48,974 - INFO - Starting normalization process for 3 dataframes.\n", - "2026-01-06 10:31:48,974 - INFO - Processing DataFrame #1 with 1030 rows.\n", - "2026-01-06 10:31:48,974 - INFO - Normalizing column 'resource' using model 'Resource'.\n", - "2026-01-06 10:31:49,016 - INFO - HTTP Request: POST http://127.0.0.1:4200/api/logs/ \"HTTP/1.1 201 Created\"\n", - "2026-01-06 10:31:49,116 - INFO - Created 35 new records in 'Resource' table.\n", - "2026-01-06 10:31:49,116 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", - "2026-01-06 10:31:49,117 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", - "2026-01-06 10:31:49,120 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", - "2026-01-06 10:31:49,120 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", - "2026-01-06 10:31:49,123 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", - "2026-01-06 10:31:49,124 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", - "2026-01-06 10:31:49,144 - INFO - Created 1 new records in 'Parameter' table.\n", - "2026-01-06 10:31:49,145 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", - "2026-01-06 10:31:49,147 - INFO - Normalizing column 'unit' using model 'Unit'.\n", - "2026-01-06 10:31:49,167 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", - "2026-01-06 10:31:49,176 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", - "2026-01-06 10:31:49,182 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", - "2026-01-06 10:31:49,182 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", - "2026-01-06 10:31:49,189 - INFO - Created 1 new records in 'AnalysisType' table.\n", - "2026-01-06 10:31:49,189 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", - "2026-01-06 10:31:49,189 - WARNING - Column 'primary_ag_product' not in DataFrame #1. Skipping normalization for this column.\n", - "2026-01-06 10:31:49,190 - INFO - Finished processing DataFrame #1.\n", - "2026-01-06 10:31:49,190 - INFO - Processing DataFrame #2 with 64 rows.\n", - "2026-01-06 10:31:49,191 - INFO - Normalizing column 'resource' using model 'Resource'.\n", - "2026-01-06 10:31:49,197 - INFO - Created 1 new records in 'Resource' table.\n", - "2026-01-06 10:31:49,198 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", - "2026-01-06 10:31:49,198 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", - "2026-01-06 10:31:49,201 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", - "2026-01-06 10:31:49,202 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", - "2026-01-06 10:31:49,204 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", - "2026-01-06 10:31:49,204 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", - "2026-01-06 10:31:49,206 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", - "2026-01-06 10:31:49,206 - INFO - Normalizing column 'unit' using model 'Unit'.\n", - "2026-01-06 10:31:49,209 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", - "2026-01-06 10:31:49,209 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", - "2026-01-06 10:31:49,211 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", - "2026-01-06 10:31:49,212 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", - "2026-01-06 10:31:49,213 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", - "2026-01-06 10:31:49,213 - WARNING - Column 'primary_ag_product' not in DataFrame #2. Skipping normalization for this column.\n", - "2026-01-06 10:31:49,214 - INFO - Finished processing DataFrame #2.\n", - "2026-01-06 10:31:49,214 - INFO - Processing DataFrame #3 with 390 rows.\n", - "2026-01-06 10:31:49,215 - INFO - Normalizing column 'resource' using model 'Resource'.\n", - "2026-01-06 10:31:49,217 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", - "2026-01-06 10:31:49,217 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", - "2026-01-06 10:31:49,220 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", - "2026-01-06 10:31:49,220 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", - "2026-01-06 10:31:49,222 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", - "2026-01-06 10:31:49,222 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", - "2026-01-06 10:31:49,224 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", - "2026-01-06 10:31:49,224 - INFO - Normalizing column 'unit' using model 'Unit'.\n", - "2026-01-06 10:31:49,225 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", - "2026-01-06 10:31:49,225 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", - "2026-01-06 10:31:49,228 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", - "2026-01-06 10:31:49,228 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", - "2026-01-06 10:31:49,230 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", - "2026-01-06 10:31:49,230 - WARNING - Column 'primary_ag_product' not in DataFrame #3. Skipping normalization for this column.\n", - "2026-01-06 10:31:49,230 - INFO - Finished processing DataFrame #3.\n", - "2026-01-06 10:31:49,230 - INFO - Committing database session.\n", - "2026-01-06 10:31:49,232 - INFO - Database commit successful.\n", - "2026-01-06 10:31:49,241 - INFO - Data normalization complete.\n", - "2026-01-06 10:31:49,244 - INFO - Displaying results of normalization...\n" + "2026-01-06 10:53:44,487 - INFO - Converted all string data to lowercase.\n", + "2026-01-06 10:53:44,492 - INFO - Data cleaning complete.\n", + "2026-01-06 10:53:44,497 - INFO - Starting data normalization...\n", + "2026-01-06 10:53:44,498 - INFO - Starting normalization process for 3 dataframes.\n", + "2026-01-06 10:53:44,498 - INFO - Processing DataFrame #1 with 1030 rows.\n", + "2026-01-06 10:53:44,500 - INFO - Normalizing column 'resource' using model 'Resource'.\n", + "2026-01-06 10:53:44,526 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 46 null values.\n", + "2026-01-06 10:53:44,527 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", + "2026-01-06 10:53:44,531 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 22 null values.\n", + "2026-01-06 10:53:44,531 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", + "2026-01-06 10:53:44,533 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 22 null values.\n", + "2026-01-06 10:53:44,534 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", + "2026-01-06 10:53:44,536 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 22 null values.\n", + "2026-01-06 10:53:44,537 - INFO - Normalizing column 'unit' using model 'Unit'.\n", + "2026-01-06 10:53:44,539 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", + "2026-01-06 10:53:44,539 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", + "2026-01-06 10:53:44,542 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 550 null values.\n", + "2026-01-06 10:53:44,543 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", + "2026-01-06 10:53:44,546 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 550 null values.\n", + "2026-01-06 10:53:44,546 - WARNING - Column 'primary_ag_product' not in DataFrame #1. Skipping normalization for this column.\n", + "2026-01-06 10:53:44,546 - INFO - Finished processing DataFrame #1.\n", + "2026-01-06 10:53:44,546 - INFO - Processing DataFrame #2 with 64 rows.\n", + "2026-01-06 10:53:44,547 - INFO - Normalizing column 'resource' using model 'Resource'.\n", + "2026-01-06 10:53:44,550 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", + "2026-01-06 10:53:44,550 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", + "2026-01-06 10:53:44,552 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", + "2026-01-06 10:53:44,552 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", + "2026-01-06 10:53:44,554 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", + "2026-01-06 10:53:44,554 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", + "2026-01-06 10:53:44,556 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", + "2026-01-06 10:53:44,557 - INFO - Normalizing column 'unit' using model 'Unit'.\n", + "2026-01-06 10:53:44,558 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", + "2026-01-06 10:53:44,559 - INFO - Skipping normalization for column 'analyst_email' as it contains only null values.\n", + "2026-01-06 10:53:44,559 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", + "2026-01-06 10:53:44,561 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", + "2026-01-06 10:53:44,561 - WARNING - Column 'primary_ag_product' not in DataFrame #2. Skipping normalization for this column.\n", + "2026-01-06 10:53:44,561 - INFO - Finished processing DataFrame #2.\n", + "2026-01-06 10:53:44,562 - INFO - Processing DataFrame #3 with 390 rows.\n", + "2026-01-06 10:53:44,562 - INFO - Normalizing column 'resource' using model 'Resource'.\n", + "2026-01-06 10:53:44,567 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", + "2026-01-06 10:53:44,569 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", + "2026-01-06 10:53:44,580 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", + "2026-01-06 10:53:44,580 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", + "2026-01-06 10:53:44,592 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", + "2026-01-06 10:53:44,594 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", + "2026-01-06 10:53:44,597 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", + "2026-01-06 10:53:44,597 - INFO - Normalizing column 'unit' using model 'Unit'.\n", + "2026-01-06 10:53:44,598 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", + "2026-01-06 10:53:44,599 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", + "2026-01-06 10:53:44,606 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", + "2026-01-06 10:53:44,607 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", + "2026-01-06 10:53:44,610 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", + "2026-01-06 10:53:44,610 - WARNING - Column 'primary_ag_product' not in DataFrame #3. Skipping normalization for this column.\n", + "2026-01-06 10:53:44,610 - INFO - Finished processing DataFrame #3.\n", + "2026-01-06 10:53:44,611 - INFO - Committing database session.\n", + "2026-01-06 10:53:44,612 - INFO - Database commit successful.\n", + "2026-01-06 10:53:44,612 - INFO - Data normalization complete.\n", + "2026-01-06 10:53:44,613 - INFO - Displaying results of normalization...\n" ] }, { @@ -417,32 +419,32 @@ { "name": "upload_status", "rawType": "object", - "type": "string" + "type": "unknown" }, { "name": "note", - "rawType": "object", - "type": "string" + "rawType": "float64", + "type": "float" }, { "name": "resource_id", - "rawType": "int64", - "type": "integer" + "rawType": "float64", + "type": "float" }, { "name": "prepared_sample_id", - "rawType": "int64", - "type": "integer" + "rawType": "float64", + "type": "float" }, { "name": "preparation_method_id", - "rawType": "int64", - "type": "integer" + "rawType": "float64", + "type": "float" }, { "name": "parameter_id", - "rawType": "int64", - "type": "integer" + "rawType": "float64", + "type": "float" }, { "name": "unit_id", @@ -451,16 +453,16 @@ }, { "name": "analyst_email_id", - "rawType": "int64", - "type": "integer" + "rawType": "float64", + "type": "float" }, { "name": "analysis_type_id", - "rawType": "int64", - "type": "integer" + "rawType": "float64", + "type": "float" } ], - "ref": "b0e10f3c-2f75-4628-acc4-1c383e10ca93", + "ref": "bcafe3ce-a742-48cc-9fb2-da62f6c91695", "rows": [ [ "0", @@ -476,14 +478,14 @@ null, "pass", "not ready", - "", - "6", - "109", - "7", - "3", - "1", + null, + "5.0", + "109.0", + "7.0", + "3.0", "1", - "1" + "1.0", + "1.0" ], [ "1", @@ -499,14 +501,14 @@ null, "pass", "ready", - "", - "6", - "109", - "7", - "3", - "1", + null, + "5.0", + "109.0", + "7.0", + "3.0", "1", - "1" + "1.0", + "1.0" ], [ "2", @@ -522,14 +524,14 @@ null, "pass", "imported", - "", - "6", - "109", - "7", - "3", - "1", + null, + "5.0", + "109.0", + "7.0", + "3.0", "1", - "1" + "1.0", + "1.0" ], [ "3", @@ -545,14 +547,14 @@ null, "pass", "import failed", - "", - "6", - "109", - "7", - "4", - "1", + null, + "5.0", + "109.0", + "7.0", + "4.0", "1", - "1" + "1.0", + "1.0" ], [ "4", @@ -567,15 +569,15 @@ "2024-10-03 10:31:31", null, "pass", - "", - "", - "6", - "109", - "7", - "4", - "1", + null, + null, + "5.0", + "109.0", + "7.0", + "4.0", "1", - "1" + "1.0", + "1.0" ] ], "shape": { @@ -639,14 +641,14 @@ " NaT\n", " pass\n", " not ready\n", - " \n", - " 6\n", - " 109\n", - " 7\n", - " 3\n", - " 1\n", - " 1\n", + " NaN\n", + " 5.0\n", + " 109.0\n", + " 7.0\n", + " 3.0\n", " 1\n", + " 1.0\n", + " 1.0\n", " \n", " \n", " 1\n", @@ -662,14 +664,14 @@ " NaT\n", " pass\n", " ready\n", - " \n", - " 6\n", - " 109\n", - " 7\n", - " 3\n", - " 1\n", - " 1\n", + " NaN\n", + " 5.0\n", + " 109.0\n", + " 7.0\n", + " 3.0\n", " 1\n", + " 1.0\n", + " 1.0\n", " \n", " \n", " 2\n", @@ -685,14 +687,14 @@ " NaT\n", " pass\n", " imported\n", - " \n", - " 6\n", - " 109\n", - " 7\n", - " 3\n", - " 1\n", - " 1\n", + " NaN\n", + " 5.0\n", + " 109.0\n", + " 7.0\n", + " 3.0\n", " 1\n", + " 1.0\n", + " 1.0\n", " \n", " \n", " 3\n", @@ -708,14 +710,14 @@ " NaT\n", " pass\n", " import failed\n", - " \n", - " 6\n", - " 109\n", - " 7\n", - " 4\n", - " 1\n", - " 1\n", + " NaN\n", + " 5.0\n", + " 109.0\n", + " 7.0\n", + " 4.0\n", " 1\n", + " 1.0\n", + " 1.0\n", " \n", " \n", " 4\n", @@ -730,15 +732,15 @@ " 2024-10-03 10:31:31\n", " NaT\n", " pass\n", - " \n", - " \n", - " 6\n", - " 109\n", - " 7\n", - " 4\n", - " 1\n", - " 1\n", + " <NA>\n", + " NaN\n", + " 5.0\n", + " 109.0\n", + " 7.0\n", + " 4.0\n", " 1\n", + " 1.0\n", + " 1.0\n", " \n", " \n", "\n", @@ -759,26 +761,26 @@ "3 prox01xk 1.0 prox01xk(73)1 0.690000 2024-10-03 10:31:01 \n", "4 prox01xk 2.0 prox01xk(73)2 0.890000 2024-10-03 10:31:31 \n", "\n", - " updated_at qc_result upload_status note resource_id prepared_sample_id \\\n", - "0 NaT pass not ready 6 109 \n", - "1 NaT pass ready 6 109 \n", - "2 NaT pass imported 6 109 \n", - "3 NaT pass import failed 6 109 \n", - "4 NaT pass 6 109 \n", + " updated_at qc_result upload_status note resource_id prepared_sample_id \\\n", + "0 NaT pass not ready NaN 5.0 109.0 \n", + "1 NaT pass ready NaN 5.0 109.0 \n", + "2 NaT pass imported NaN 5.0 109.0 \n", + "3 NaT pass import failed NaN 5.0 109.0 \n", + "4 NaT pass NaN 5.0 109.0 \n", "\n", " preparation_method_id parameter_id unit_id analyst_email_id \\\n", - "0 7 3 1 1 \n", - "1 7 3 1 1 \n", - "2 7 3 1 1 \n", - "3 7 4 1 1 \n", - "4 7 4 1 1 \n", + "0 7.0 3.0 1 1.0 \n", + "1 7.0 3.0 1 1.0 \n", + "2 7.0 3.0 1 1.0 \n", + "3 7.0 4.0 1 1.0 \n", + "4 7.0 4.0 1 1.0 \n", "\n", " analysis_type_id \n", - "0 1 \n", - "1 1 \n", - "2 1 \n", - "3 1 \n", - "4 1 " + "0 1.0 \n", + "1 1.0 \n", + "2 1.0 \n", + "3 1.0 \n", + "4 1.0 " ] }, "metadata": {}, @@ -862,18 +864,23 @@ }, { "name": "equipment", - "rawType": "object", - "type": "string" + "rawType": "float64", + "type": "float" }, { "name": "raw_data_url", - "rawType": "object", - "type": "string" + "rawType": "float64", + "type": "float" + }, + { + "name": "analyst_email", + "rawType": "float64", + "type": "float" }, { "name": "upload_status", - "rawType": "object", - "type": "string" + "rawType": "float64", + "type": "float" }, { "name": "resource_id", @@ -900,18 +907,13 @@ "rawType": "int64", "type": "integer" }, - { - "name": "analyst_email_id", - "rawType": "int64", - "type": "integer" - }, { "name": "analysis_type_id", "rawType": "int64", "type": "integer" } ], - "ref": "0f732e49-22cb-4b72-a52a-9fade9af05ef", + "ref": "d0538baa-0f16-4d3e-992f-e11d99faffd6", "rows": [ [ "0", @@ -927,15 +929,15 @@ null, "pass", "1", - "", - "", - "", - "27", + null, + null, + null, + null, + "26", "80", "6", "8", "3", - "2", "2" ], [ @@ -952,15 +954,15 @@ null, "fail", " 1 dup", - "", - "", - "", - "27", + null, + null, + null, + null, + "26", "80", "6", "8", "3", - "2", "2" ], [ @@ -977,15 +979,15 @@ null, "pass", "2", - "", - "", - "", - "11", + null, + null, + null, + null, + "10", "96", "6", "8", "3", - "2", "2" ], [ @@ -1002,15 +1004,15 @@ null, "pass", "3", - "", - "", - "", - "12", + null, + null, + null, + null, + "11", "91", "9", "8", "3", - "2", "2" ], [ @@ -1027,15 +1029,15 @@ null, "pass", "4", - "", - "", - "", - "21", + null, + null, + null, + null, + "20", "153", "9", "8", "3", - "2", "2" ] ], @@ -1076,13 +1078,13 @@ " ...\n", " equipment\n", " raw_data_url\n", + " analyst_email\n", " upload_status\n", " resource_id\n", " prepared_sample_id\n", " preparation_method_id\n", " parameter_id\n", " unit_id\n", - " analyst_email_id\n", " analysis_type_id\n", " \n", " \n", @@ -1100,16 +1102,16 @@ " NaT\n", " NaT\n", " ...\n", - " \n", - " \n", - " \n", - " 27\n", + " NaN\n", + " NaN\n", + " NaN\n", + " NaN\n", + " 26\n", " 80\n", " 6\n", " 8\n", " 3\n", " 2\n", - " 2\n", " \n", " \n", " 1\n", @@ -1124,16 +1126,16 @@ " NaT\n", " NaT\n", " ...\n", - " \n", - " \n", - " \n", - " 27\n", + " NaN\n", + " NaN\n", + " NaN\n", + " NaN\n", + " 26\n", " 80\n", " 6\n", " 8\n", " 3\n", " 2\n", - " 2\n", " \n", " \n", " 2\n", @@ -1148,16 +1150,16 @@ " NaT\n", " NaT\n", " ...\n", - " \n", - " \n", - " \n", - " 11\n", + " NaN\n", + " NaN\n", + " NaN\n", + " NaN\n", + " 10\n", " 96\n", " 6\n", " 8\n", " 3\n", " 2\n", - " 2\n", " \n", " \n", " 3\n", @@ -1172,16 +1174,16 @@ " NaT\n", " NaT\n", " ...\n", - " \n", - " \n", - " \n", - " 12\n", + " NaN\n", + " NaN\n", + " NaN\n", + " NaN\n", + " 11\n", " 91\n", " 9\n", " 8\n", " 3\n", " 2\n", - " 2\n", " \n", " \n", " 4\n", @@ -1196,16 +1198,16 @@ " NaT\n", " NaT\n", " ...\n", - " \n", - " \n", - " \n", - " 21\n", + " NaN\n", + " NaN\n", + " NaN\n", + " NaN\n", + " 20\n", " 153\n", " 9\n", " 8\n", " 3\n", " 2\n", - " 2\n", " \n", " \n", "\n", @@ -1227,26 +1229,26 @@ "3 rt vacuum sealed ult26kh 1 ult26kh(82)1 92.199997 NaT \n", "4 rt vacuum sealed ult26kh 1 ult26kh(1b)1 93.800003 NaT \n", "\n", - " updated_at ... equipment raw_data_url upload_status resource_id \\\n", - "0 NaT ... 27 \n", - "1 NaT ... 27 \n", - "2 NaT ... 11 \n", - "3 NaT ... 12 \n", - "4 NaT ... 21 \n", + " updated_at ... equipment raw_data_url analyst_email upload_status \\\n", + "0 NaT ... NaN NaN NaN NaN \n", + "1 NaT ... NaN NaN NaN NaN \n", + "2 NaT ... NaN NaN NaN NaN \n", + "3 NaT ... NaN NaN NaN NaN \n", + "4 NaT ... NaN NaN NaN NaN \n", "\n", - " prepared_sample_id preparation_method_id parameter_id unit_id \\\n", - "0 80 6 8 3 \n", - "1 80 6 8 3 \n", - "2 96 6 8 3 \n", - "3 91 9 8 3 \n", - "4 153 9 8 3 \n", + " resource_id prepared_sample_id preparation_method_id parameter_id \\\n", + "0 26 80 6 8 \n", + "1 26 80 6 8 \n", + "2 10 96 6 8 \n", + "3 11 91 9 8 \n", + "4 20 153 9 8 \n", "\n", - " analyst_email_id analysis_type_id \n", - "0 2 2 \n", - "1 2 2 \n", - "2 2 2 \n", - "3 2 2 \n", - "4 2 2 \n", + " unit_id analysis_type_id \n", + "0 3 2 \n", + "1 3 2 \n", + "2 3 2 \n", + "3 3 2 \n", + "4 3 2 \n", "\n", "[5 rows x 22 columns]" ] @@ -1322,18 +1324,18 @@ }, { "name": "note", - "rawType": "object", - "type": "string" + "rawType": "float64", + "type": "float" }, { "name": "equipment", - "rawType": "object", - "type": "string" + "rawType": "float64", + "type": "float" }, { "name": "raw_data_url", - "rawType": "object", - "type": "string" + "rawType": "float64", + "type": "float" }, { "name": "upload_status", @@ -1376,7 +1378,7 @@ "type": "integer" } ], - "ref": "95361c64-4a65-4fd6-bde6-2efae692d84c", + "ref": "1f353831-a3bd-4f43-a253-769adc8b66eb", "rows": [ [ "0", @@ -1390,11 +1392,11 @@ "2025-01-23 09:00:01", null, "pass", - "", - "", - "", + null, + null, + null, "ready", - "6", + "5", "92", "8", "13", @@ -1414,11 +1416,11 @@ "2025-01-23 09:00:16", null, "pass", - "", - "", - "", + null, + null, + null, "ready", - "6", + "5", "92", "8", "13", @@ -1438,11 +1440,11 @@ "2025-01-23 09:00:31", null, "pass", - "", - "", - "", + null, + null, + null, "ready", - "6", + "5", "92", "8", "13", @@ -1462,11 +1464,11 @@ "2025-01-23 09:00:46", null, "pass", - "", - "", - "", + null, + null, + null, "ready", - "6", + "5", "92", "8", "11", @@ -1486,11 +1488,11 @@ "2025-01-23 09:01:01", null, "pass", - "", - "", - "", + null, + null, + null, "ready", - "6", + "5", "92", "8", "11", @@ -1560,10 +1562,10 @@ " NaT\n", " pass\n", " ...\n", - " \n", - " \n", + " NaN\n", + " NaN\n", " ready\n", - " 6\n", + " 5\n", " 92\n", " 8\n", " 13\n", @@ -1584,10 +1586,10 @@ " NaT\n", " pass\n", " ...\n", - " \n", - " \n", + " NaN\n", + " NaN\n", " ready\n", - " 6\n", + " 5\n", " 92\n", " 8\n", " 13\n", @@ -1608,10 +1610,10 @@ " NaT\n", " pass\n", " ...\n", - " \n", - " \n", + " NaN\n", + " NaN\n", " ready\n", - " 6\n", + " 5\n", " 92\n", " 8\n", " 13\n", @@ -1632,10 +1634,10 @@ " NaT\n", " pass\n", " ...\n", - " \n", - " \n", + " NaN\n", + " NaN\n", " ready\n", - " 6\n", + " 5\n", " 92\n", " 8\n", " 11\n", @@ -1656,10 +1658,10 @@ " NaT\n", " pass\n", " ...\n", - " \n", - " \n", + " NaN\n", + " NaN\n", " ready\n", - " 6\n", + " 5\n", " 92\n", " 8\n", " 11\n", @@ -1687,12 +1689,12 @@ "3 cmp04xk 1 cmp04xk(85)1 15.74 2025-01-23 09:00:46 NaT \n", "4 cmp04xk 2 cmp04xk(85)2 15.75 2025-01-23 09:01:01 NaT \n", "\n", - " qc_result ... equipment raw_data_url upload_status resource_id \\\n", - "0 pass ... ready 6 \n", - "1 pass ... ready 6 \n", - "2 pass ... ready 6 \n", - "3 pass ... ready 6 \n", - "4 pass ... ready 6 \n", + " qc_result ... equipment raw_data_url upload_status resource_id \\\n", + "0 pass ... NaN NaN ready 5 \n", + "1 pass ... NaN NaN ready 5 \n", + "2 pass ... NaN NaN ready 5 \n", + "3 pass ... NaN NaN ready 5 \n", + "4 pass ... NaN NaN ready 5 \n", "\n", " prepared_sample_id preparation_method_id parameter_id unit_id \\\n", "0 92 8 13 2 \n", From 234a235b182d454648fb9f5b4d64e29d44402b2f Mon Sep 17 00:00:00 2001 From: petercarbsmith Date: Wed, 7 Jan 2026 14:14:07 -0700 Subject: [PATCH 74/81] fixed the alembic import problems. models now have fk --- alembic/env.py | 25 +- .../04f37f9dbb48_test_test_test_test_test.py | 1602 +++++++++++++++++ .../1ace3fc9c593_initial_migration.py | 32 + ...b18e6e5e72d_trying_with_fixing_the_base.py | 32 + ...5d_fixed_alembic_environment_to_import_.py | 32 + ..._fixed_alembic_gen_sqla_so_all_inherit_.py | 32 + ...9be24ffa7bb9_refactor_and_update_env_py.py | 1462 +++++++++++++++ ...88_fixed_alembic_environment_to_import_.py | 32 + .../ca_biositing/datamodels/database.py | 20 +- .../schemas/generated/ca_biositing.py | 342 ++-- .../datamodels/utils/generate_sqla.py | 31 + 11 files changed, 3448 insertions(+), 194 deletions(-) create mode 100644 alembic/versions/04f37f9dbb48_test_test_test_test_test.py create mode 100644 alembic/versions/1ace3fc9c593_initial_migration.py create mode 100644 alembic/versions/2b18e6e5e72d_trying_with_fixing_the_base.py create mode 100644 alembic/versions/2b41e390fc5d_fixed_alembic_environment_to_import_.py create mode 100644 alembic/versions/62ef89b0050a_fixed_alembic_gen_sqla_so_all_inherit_.py create mode 100644 alembic/versions/9be24ffa7bb9_refactor_and_update_env_py.py create mode 100644 alembic/versions/a8a3ea954e88_fixed_alembic_environment_to_import_.py diff --git a/alembic/env.py b/alembic/env.py index 068e73bb..ad465742 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -24,16 +24,12 @@ # from ca_biositing.datamodels.sample_preprocessing import * # from ca_biositing.datamodels.specific_aalysis_results import * # from ca_biositing.datamodels.user import * +from ca_biositing.datamodels.schemas.generated import ca_biositing from ca_biositing.datamodels.schemas.generated.ca_biositing import * -from sqlmodel import SQLModel -import importlib.util -from pathlib import Path - -# --- Import generated models and their metadata --- -# from ca_biositing.datamodels.schemas.generated.census_survey import metadata as census_metadata -# from ca_biositing.datamodels.schemas.generated.geography import metadata as geography_metadata +from ca_biositing.datamodels.database import Base -# --- Alembic Config object, provides access to alembic.ini values --- +# this is the Alembic Config object, which provides +# access to the values within the .ini file in use. config = context.config # Override sqlalchemy.url in alembic.ini with value from .env @@ -43,16 +39,15 @@ else: raise RuntimeError("DATABASE_URL not found in .env file. Alembic cannot run migrations.") -# --- Configure logging (from alembic.ini logging section) --- +# Interpret the config file for Python logging. +# This line sets up loggers basically. if config.config_file_name is not None: fileConfig(config.config_file_name) -# --- Metadata from your models for autogenerate --- -# Combine metadata from all models -# See: https://alembic.sqlalchemy.org/en/latest/autogenerate.html#affecting-the-autogenerate-process - -# Start with the default SQLModel metadata -# target_metadata = SQLModel.metadata +# add your model's MetaData object here +# for 'autogenerate' support +# from myapp import mymodel +# target_metadata = mymodel.Base.metadata target_metadata = Base.metadata # Manually merge metadata from generated modules diff --git a/alembic/versions/04f37f9dbb48_test_test_test_test_test.py b/alembic/versions/04f37f9dbb48_test_test_test_test_test.py new file mode 100644 index 00000000..2ccc998f --- /dev/null +++ b/alembic/versions/04f37f9dbb48_test_test_test_test_test.py @@ -0,0 +1,1602 @@ +"""test test test test test + +Revision ID: 04f37f9dbb48 +Revises: 2b18e6e5e72d +Create Date: 2026-01-07 21:06:50.957245 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '04f37f9dbb48' +down_revision: Union[str, Sequence[str], None] = '2b18e6e5e72d' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('ag_treatment', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('analysis_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('base_entity', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('collection_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('contact', + sa.Column('first_name', sa.Text(), nullable=True), + sa.Column('last_name', sa.Text(), nullable=True), + sa.Column('email', sa.Text(), nullable=True), + sa.Column('affiliation', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('dimension_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('entity_lineage', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.Column('source_table', sa.Text(), nullable=True), + sa.Column('source_row_id', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('etl_run', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('started_at', sa.DateTime(), nullable=True), + sa.Column('completed_at', sa.DateTime(), nullable=True), + sa.Column('pipeline_name', sa.Text(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('records_ingested', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('field_storage_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('geography', + sa.Column('geoid', sa.Text(), nullable=False), + sa.Column('state_name', sa.Text(), nullable=True), + sa.Column('state_fips', sa.Text(), nullable=True), + sa.Column('county_name', sa.Text(), nullable=True), + sa.Column('county_fips', sa.Text(), nullable=True), + sa.Column('region_name', sa.Text(), nullable=True), + sa.Column('agg_level_desc', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('geoid') + ) + op.create_table('harvest_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('infrastructure_biodiesel_plants', + sa.Column('biodiesel_plant_id', sa.Integer(), nullable=False), + sa.Column('company', sa.Text(), nullable=True), + sa.Column('bbi_index', sa.Integer(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('capacity_mmg_per_y', sa.Integer(), nullable=True), + sa.Column('feedstock', sa.Text(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('address', sa.Text(), nullable=True), + sa.Column('coordinates', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('biodiesel_plant_id') + ) + op.create_table('infrastructure_biosolids_facilities', + sa.Column('biosolid_facility_id', sa.Integer(), nullable=False), + sa.Column('report_submitted_date', sa.Date(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('facility', sa.Text(), nullable=True), + sa.Column('authority', sa.Text(), nullable=True), + sa.Column('plant_type', sa.Text(), nullable=True), + sa.Column('aqmd', sa.Text(), nullable=True), + sa.Column('facility_address', sa.Text(), nullable=True), + sa.Column('facility_city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('facility_zip', sa.Text(), nullable=True), + sa.Column('facility_county', sa.Text(), nullable=True), + sa.Column('mailing_street_1', sa.Text(), nullable=True), + sa.Column('mailing_city', sa.Text(), nullable=True), + sa.Column('mailing_state', sa.Text(), nullable=True), + sa.Column('mailing_zip', sa.Text(), nullable=True), + sa.Column('biosolids_number', sa.Text(), nullable=True), + sa.Column('biosolids_contact', sa.Text(), nullable=True), + sa.Column('biosolids_contact_phone', sa.Text(), nullable=True), + sa.Column('biosolids_contact_email', sa.Text(), nullable=True), + sa.Column('adwf', sa.Numeric(), nullable=True), + sa.Column('potw_biosolids_generated', sa.Integer(), nullable=True), + sa.Column('twtds_biosolids_treated', sa.Integer(), nullable=True), + sa.Column('class_b_land_app', sa.Integer(), nullable=True), + sa.Column('class_b_applier', sa.Text(), nullable=True), + sa.Column('class_a_compost', sa.Integer(), nullable=True), + sa.Column('class_a_heat_dried', sa.Integer(), nullable=True), + sa.Column('class_a_other', sa.Integer(), nullable=True), + sa.Column('class_a_other_applier', sa.Text(), nullable=True), + sa.Column('twtds_transfer_to_second_preparer', sa.Integer(), nullable=True), + sa.Column('twtds_second_preparer_name', sa.Text(), nullable=True), + sa.Column('adc_or_final_c', sa.Integer(), nullable=True), + sa.Column('landfill', sa.Integer(), nullable=True), + sa.Column('landfill_name', sa.Text(), nullable=True), + sa.Column('surface_disposal', sa.Integer(), nullable=True), + sa.Column('deepwell_injection', sa.Text(), nullable=True), + sa.Column('stored', sa.Integer(), nullable=True), + sa.Column('longterm_treatment', sa.Integer(), nullable=True), + sa.Column('other', sa.Integer(), nullable=True), + sa.Column('name_of_other', sa.Text(), nullable=True), + sa.Column('incineration', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('biosolid_facility_id') + ) + op.create_table('infrastructure_cafo_manure_locations', + sa.Column('cafo_manure_id', sa.Integer(), nullable=False), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('owner_name', sa.Text(), nullable=True), + sa.Column('facility_name', sa.Text(), nullable=True), + sa.Column('address', sa.Text(), nullable=True), + sa.Column('town', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('zip', sa.Text(), nullable=True), + sa.Column('animal', sa.Text(), nullable=True), + sa.Column('animal_feed_operation_type', sa.Text(), nullable=True), + sa.Column('animal_units', sa.Integer(), nullable=True), + sa.Column('animal_count', sa.Integer(), nullable=True), + sa.Column('manure_total_solids', sa.Numeric(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('date_accessed', sa.Date(), nullable=True), + sa.PrimaryKeyConstraint('cafo_manure_id') + ) + op.create_table('infrastructure_combustion_plants', + sa.Column('combustion_fid', sa.Integer(), nullable=False), + sa.Column('objectid', sa.Integer(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('county', sa.Text(), nullable=True), + sa.Column('equivalent_generation', sa.Numeric(), nullable=True), + sa.Column('np_mw', sa.Numeric(), nullable=True), + sa.Column('cf', sa.Numeric(), nullable=True), + sa.Column('yearload', sa.Integer(), nullable=True), + sa.Column('fuel', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('wkt_geom', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('combustion_fid') + ) + op.create_table('infrastructure_district_energy_systems', + sa.Column('des_fid', sa.Integer(), nullable=False), + sa.Column('cbg_id', sa.Integer(), nullable=True), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('system', sa.Text(), nullable=True), + sa.Column('object_id', sa.Integer(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('primary_fuel', sa.Text(), nullable=True), + sa.Column('secondary_fuel', sa.Text(), nullable=True), + sa.Column('usetype', sa.Text(), nullable=True), + sa.Column('cap_st', sa.Numeric(), nullable=True), + sa.Column('cap_hw', sa.Numeric(), nullable=True), + sa.Column('cap_cw', sa.Numeric(), nullable=True), + sa.Column('chpcg_cap', sa.Numeric(), nullable=True), + sa.Column('excess_c', sa.Numeric(), nullable=True), + sa.Column('excess_h', sa.Numeric(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('wkt_geom', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('des_fid') + ) + op.create_table('infrastructure_ethanol_biorefineries', + sa.Column('ethanol_biorefinery_id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('address', sa.Text(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('capacity_mgy', sa.Integer(), nullable=True), + sa.Column('production_mgy', sa.Integer(), nullable=True), + sa.Column('constr_exp', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('ethanol_biorefinery_id') + ) + op.create_table('infrastructure_food_processing_facilities', + sa.Column('processing_facility_id', sa.Integer(), nullable=False), + sa.Column('address', sa.Text(), nullable=True), + sa.Column('county', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('company', sa.Text(), nullable=True), + sa.Column('join_count', sa.Integer(), nullable=True), + sa.Column('master_type', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('subtype', sa.Text(), nullable=True), + sa.Column('target_fid', sa.Integer(), nullable=True), + sa.Column('processing_type', sa.Text(), nullable=True), + sa.Column('zip', sa.Text(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('wkt_geom', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('processing_facility_id') + ) + op.create_table('infrastructure_landfills', + sa.Column('project_id', sa.Text(), nullable=False), + sa.Column('project_int_id', sa.Integer(), nullable=True), + sa.Column('ghgrp_id', sa.Text(), nullable=True), + sa.Column('landfill_id', sa.Integer(), nullable=True), + sa.Column('landfill_name', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('physical_address', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('county', sa.Text(), nullable=True), + sa.Column('zip_code', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('ownership_type', sa.Text(), nullable=True), + sa.Column('landfill_owner_orgs', sa.Text(), nullable=True), + sa.Column('landfill_opened_year', sa.Date(), nullable=True), + sa.Column('landfill_closure_year', sa.Date(), nullable=True), + sa.Column('landfill_status', sa.Text(), nullable=True), + sa.Column('waste_in_place', sa.Integer(), nullable=True), + sa.Column('waste_in_place_year', sa.Date(), nullable=True), + sa.Column('lfg_system_in_place', sa.Boolean(), nullable=True), + sa.Column('lfg_collected', sa.Numeric(), nullable=True), + sa.Column('lfg_flared', sa.Numeric(), nullable=True), + sa.Column('project_status', sa.Text(), nullable=True), + sa.Column('project_name', sa.Text(), nullable=True), + sa.Column('project_start_date', sa.Date(), nullable=True), + sa.Column('project_shutdown_date', sa.Date(), nullable=True), + sa.Column('project_type_category', sa.Text(), nullable=True), + sa.Column('lfg_energy_project_type', sa.Text(), nullable=True), + sa.Column('rng_delivery_method', sa.Text(), nullable=True), + sa.Column('actual_mw_generation', sa.Numeric(), nullable=True), + sa.Column('rated_mw_capacity', sa.Numeric(), nullable=True), + sa.Column('lfg_flow_to_project', sa.Numeric(), nullable=True), + sa.Column('direct_emission_reductions', sa.Numeric(), nullable=True), + sa.Column('avoided_emission_reductions', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('project_id') + ) + op.create_table('infrastructure_livestock_anaerobic_digesters', + sa.Column('digester_id', sa.Integer(), nullable=False), + sa.Column('project_name', sa.Text(), nullable=True), + sa.Column('project_type', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('digester_type', sa.Text(), nullable=True), + sa.Column('profile', sa.Text(), nullable=True), + sa.Column('year_operational', sa.Date(), nullable=True), + sa.Column('animal_type_class', sa.Text(), nullable=True), + sa.Column('animal_types', sa.Text(), nullable=True), + sa.Column('pop_feeding_digester', sa.Text(), nullable=True), + sa.Column('total_pop_feeding_digester', sa.Integer(), nullable=True), + sa.Column('cattle', sa.Integer(), nullable=True), + sa.Column('dairy', sa.Integer(), nullable=True), + sa.Column('poultry', sa.Integer(), nullable=True), + sa.Column('swine', sa.Integer(), nullable=True), + sa.Column('codigestion', sa.Text(), nullable=True), + sa.Column('biogas_generation_estimate', sa.Integer(), nullable=True), + sa.Column('electricity_generated', sa.Integer(), nullable=True), + sa.Column('biogas_end_uses', sa.Text(), nullable=True), + sa.Column('methane_emission_reductions', sa.Integer(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('digester_id') + ) + op.create_table('infrastructure_msw_to_energy_anaerobic_digesters', + sa.Column('wte_id', sa.Integer(), nullable=False), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('county', sa.Text(), nullable=True), + sa.Column('equivalent_generation', sa.Numeric(), nullable=True), + sa.Column('feedstock', sa.Text(), nullable=True), + sa.Column('dayload', sa.Numeric(), nullable=True), + sa.Column('dayload_bdt', sa.Numeric(), nullable=True), + sa.Column('facility_type', sa.Text(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('notes', sa.Text(), nullable=True), + sa.Column('source', sa.Text(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('wkt_geom', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('wte_id') + ) + op.create_table('infrastructure_saf_and_renewable_diesel_plants', + sa.Column('ibcc_index', sa.Integer(), nullable=False), + sa.Column('company', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('country', sa.Text(), nullable=True), + sa.Column('capacity', sa.Text(), nullable=True), + sa.Column('feedstock', sa.Text(), nullable=True), + sa.Column('products', sa.Text(), nullable=True), + sa.Column('status', sa.Text(), nullable=True), + sa.Column('address', sa.Text(), nullable=True), + sa.Column('coordinates', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.PrimaryKeyConstraint('ibcc_index') + ) + op.create_table('infrastructure_wastewater_treatment_plants', + sa.Column('plant_id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('state', sa.Text(), nullable=True), + sa.Column('codigestion', sa.Text(), nullable=True), + sa.Column('flow_design_adjusted', sa.Numeric(), nullable=True), + sa.Column('flow_average', sa.Numeric(), nullable=True), + sa.Column('biosolids', sa.Numeric(), nullable=True), + sa.Column('excess_flow', sa.Numeric(), nullable=True), + sa.Column('biogas_utilized', sa.Boolean(), nullable=True), + sa.Column('flaring', sa.Boolean(), nullable=True), + sa.Column('excess_mass_loading_rate', sa.Numeric(), nullable=True), + sa.Column('excess_mass_loading_rate_wet', sa.Numeric(), nullable=True), + sa.Column('methane_production', sa.Numeric(), nullable=True), + sa.Column('energy_content', sa.Numeric(), nullable=True), + sa.Column('electric_kw', sa.Numeric(), nullable=True), + sa.Column('thermal_mmbtu_d', sa.Numeric(), nullable=True), + sa.Column('electric_kwh', sa.Numeric(), nullable=True), + sa.Column('thermal_annual_mmbtu_y', sa.Numeric(), nullable=True), + sa.Column('anaerobic_digestion_facility', sa.Text(), nullable=True), + sa.Column('county', sa.Text(), nullable=True), + sa.Column('dayload_bdt', sa.Numeric(), nullable=True), + sa.Column('dayload', sa.Numeric(), nullable=True), + sa.Column('equivalent_generation', sa.Numeric(), nullable=True), + sa.Column('facility_type', sa.Text(), nullable=True), + sa.Column('feedstock', sa.Text(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('latitude', sa.Numeric(), nullable=True), + sa.Column('longitude', sa.Numeric(), nullable=True), + sa.Column('zipcode', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('plant_id') + ) + op.create_table('lineage_group', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('location_resolution', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('lookup_base', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method_abbrev', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method_category', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method_standard', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter_category', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('polygon', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('geom', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('preparation_method_abbreviation', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('primary_ag_product', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('processing_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('provider', + sa.Column('codename', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_class', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_subclass', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('soil_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('source_type', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('strain', + sa.Column('parent_strain_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('unit', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_commodity', + sa.Column('usda_source', sa.Text(), nullable=True), + sa.Column('usda_code', sa.Text(), nullable=True), + sa.Column('parent_commodity_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.ForeignKeyConstraint(['parent_commodity_id'], ['usda_commodity.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_domain', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_statistic_category', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_survey_program', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('data_source_type', + sa.Column('source_type_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['source_type_id'], ['source_type.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('location_address', + sa.Column('geography_id', sa.Text(), nullable=True), + sa.Column('address_line1', sa.Text(), nullable=True), + sa.Column('address_line2', sa.Text(), nullable=True), + sa.Column('city', sa.Text(), nullable=True), + sa.Column('zip', sa.Text(), nullable=True), + sa.Column('lat', sa.Float(), nullable=True), + sa.Column('lon', sa.Float(), nullable=True), + sa.Column('is_anonymous', sa.Boolean(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['geography_id'], ['geography.geoid'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('standard_unit_id', sa.Integer(), nullable=True), + sa.Column('calculated', sa.Boolean(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['standard_unit_id'], ['unit.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('preparation_method', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('prep_method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('prep_temp_c', sa.Numeric(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.Column('drying_step', sa.Boolean(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['prep_method_abbrev_id'], ['preparation_method_abbreviation.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('primary_ag_product_id', sa.Integer(), nullable=True), + sa.Column('resource_class_id', sa.Integer(), nullable=True), + sa.Column('resource_subclass_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('test', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['primary_ag_product_id'], ['primary_ag_product.id'], ), + sa.ForeignKeyConstraint(['resource_class_id'], ['resource_class.id'], ), + sa.ForeignKeyConstraint(['resource_subclass_id'], ['resource_subclass.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_term_map', + sa.Column('source_system', sa.Text(), nullable=True), + sa.Column('source_context', sa.Text(), nullable=True), + sa.Column('raw_term', sa.Text(), nullable=True), + sa.Column('usda_commodity_id', sa.Integer(), nullable=True), + sa.Column('is_verified', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['usda_commodity_id'], ['usda_commodity.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('billion_ton2023_record', + sa.Column('subclass_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('county_square_miles', sa.Float(), nullable=True), + sa.Column('model_name', sa.Text(), nullable=True), + sa.Column('scenario_name', sa.Text(), nullable=True), + sa.Column('price_offered_usd', sa.Numeric(), nullable=True), + sa.Column('production', sa.Integer(), nullable=True), + sa.Column('production_unit_id', sa.Integer(), nullable=True), + sa.Column('btu_ton', sa.Integer(), nullable=True), + sa.Column('production_energy_content', sa.Integer(), nullable=True), + sa.Column('energy_content_unit_id', sa.Integer(), nullable=True), + sa.Column('product_density_dtpersqmi', sa.Numeric(), nullable=True), + sa.Column('land_source', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['energy_content_unit_id'], ['unit.id'], ), + sa.ForeignKeyConstraint(['production_unit_id'], ['unit.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.ForeignKeyConstraint(['subclass_id'], ['resource_subclass.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('data_source', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('data_source_type_id', sa.Integer(), nullable=True), + sa.Column('full_title', sa.Text(), nullable=True), + sa.Column('creator', sa.Text(), nullable=True), + sa.Column('subject', sa.Text(), nullable=True), + sa.Column('publisher', sa.Text(), nullable=True), + sa.Column('contributor', sa.Text(), nullable=True), + sa.Column('date', sa.DateTime(), nullable=True), + sa.Column('type', sa.Text(), nullable=True), + sa.Column('biocirv', sa.Boolean(), nullable=True), + sa.Column('format', sa.Text(), nullable=True), + sa.Column('language', sa.Text(), nullable=True), + sa.Column('relation', sa.Text(), nullable=True), + sa.Column('temporal_coverage', sa.Text(), nullable=True), + sa.Column('location_coverage_id', sa.Integer(), nullable=True), + sa.Column('rights', sa.Text(), nullable=True), + sa.Column('license', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['data_source_type_id'], ['data_source_type.id'], ), + sa.ForeignKeyConstraint(['location_coverage_id'], ['location_resolution.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('equipment', + sa.Column('equipment_location_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('name', sa.Text(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('uri', sa.Text(), nullable=True), + sa.ForeignKeyConstraint(['equipment_location_id'], ['location_address.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment', + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('exper_start_date', sa.Date(), nullable=True), + sa.Column('exper_duration', sa.Numeric(), nullable=True), + sa.Column('exper_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('exper_location_id', sa.Integer(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analyst_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['exper_duration_unit_id'], ['unit.id'], ), + sa.ForeignKeyConstraint(['exper_location_id'], ['location_address.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('field_sample', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('provider_id', sa.Integer(), nullable=True), + sa.Column('collector_id', sa.Integer(), nullable=True), + sa.Column('sample_collection_source', sa.Text(), nullable=True), + sa.Column('amount_collected', sa.Numeric(), nullable=True), + sa.Column('amount_collected_unit_id', sa.Integer(), nullable=True), + sa.Column('sampling_location_id', sa.Integer(), nullable=True), + sa.Column('field_storage_method_id', sa.Integer(), nullable=True), + sa.Column('field_storage_duration_value', sa.Numeric(), nullable=True), + sa.Column('field_storage_duration_unit_id', sa.Integer(), nullable=True), + sa.Column('field_storage_location_id', sa.Integer(), nullable=True), + sa.Column('collection_timestamp', sa.DateTime(), nullable=True), + sa.Column('collection_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_method_id', sa.Integer(), nullable=True), + sa.Column('harvest_date', sa.Date(), nullable=True), + sa.Column('field_sample_storage_location_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['amount_collected_unit_id'], ['unit.id'], ), + sa.ForeignKeyConstraint(['collection_method_id'], ['collection_method.id'], ), + sa.ForeignKeyConstraint(['collector_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['field_sample_storage_location_id'], ['location_address.id'], ), + sa.ForeignKeyConstraint(['field_storage_duration_unit_id'], ['unit.id'], ), + sa.ForeignKeyConstraint(['field_storage_location_id'], ['location_address.id'], ), + sa.ForeignKeyConstraint(['field_storage_method_id'], ['field_storage_method.id'], ), + sa.ForeignKeyConstraint(['harvest_method_id'], ['harvest_method.id'], ), + sa.ForeignKeyConstraint(['provider_id'], ['provider.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.ForeignKeyConstraint(['sampling_location_id'], ['location_address.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('location_soil_type', + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('soil_type_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['location_id'], ['location_address.id'], ), + sa.ForeignKeyConstraint(['soil_type_id'], ['soil_type.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter_category_parameter', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('parameter_category_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['parameter_category_id'], ['parameter_category.id'], ), + sa.ForeignKeyConstraint(['parameter_id'], ['parameter.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('parameter_unit', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('alternate_unit_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['alternate_unit_id'], ['unit.id'], ), + sa.ForeignKeyConstraint(['parameter_id'], ['parameter.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_availability', + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('from_month', sa.Integer(), nullable=True), + sa.Column('to_month', sa.Integer(), nullable=True), + sa.Column('year_round', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_morphology', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('morphology_uri', sa.Text(), nullable=True), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('resource_usda_commodity_map', + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('primary_ag_product_id', sa.Integer(), nullable=True), + sa.Column('usda_commodity_id', sa.Integer(), nullable=True), + sa.Column('match_tier', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['primary_ag_product_id'], ['primary_ag_product.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.ForeignKeyConstraint(['usda_commodity_id'], ['usda_commodity.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('dataset', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('record_type', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('start_date', sa.Date(), nullable=True), + sa.Column('end_date', sa.Date(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['source_id'], ['data_source.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_analysis', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('analysis_type_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analysis_type_id'], ['analysis_type.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_equipment', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('equipment_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['equipment_id'], ['equipment.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('facility_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('facility_name', sa.Text(), nullable=True), + sa.Column('location_id', sa.Integer(), nullable=True), + sa.Column('capacity_mw', sa.Numeric(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('operator', sa.Text(), nullable=True), + sa.Column('start_year', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['location_id'], ['location_address.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('field_sample_condition', + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('ag_treatment_id', sa.Integer(), nullable=True), + sa.Column('last_application_date', sa.Date(), nullable=True), + sa.Column('treatment_amount_per_acre', sa.Float(), nullable=True), + sa.Column('processing_method_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['ag_treatment_id'], ['ag_treatment.id'], ), + sa.ForeignKeyConstraint(['field_sample_id'], ['field_sample.id'], ), + sa.ForeignKeyConstraint(['processing_method_id'], ['processing_method.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('file_object_metadata', + sa.Column('data_source_id', sa.Integer(), nullable=True), + sa.Column('bucket_path', sa.Text(), nullable=True), + sa.Column('file_format', sa.Text(), nullable=True), + sa.Column('file_size', sa.Integer(), nullable=True), + sa.Column('checksum_md5', sa.Text(), nullable=True), + sa.Column('checksum_sha256', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['data_source_id'], ['data_source.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('landiq_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('polygon_id', sa.Integer(), nullable=True), + sa.Column('main_crop', sa.Integer(), nullable=True), + sa.Column('secondary_crop', sa.Integer(), nullable=True), + sa.Column('tertiary_crop', sa.Integer(), nullable=True), + sa.Column('quaternary_crop', sa.Integer(), nullable=True), + sa.Column('confidence', sa.Integer(), nullable=True), + sa.Column('irrigated', sa.Boolean(), nullable=True), + sa.Column('acres', sa.Float(), nullable=True), + sa.Column('version', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['main_crop'], ['primary_ag_product.id'], ), + sa.ForeignKeyConstraint(['polygon_id'], ['polygon.id'], ), + sa.ForeignKeyConstraint(['quaternary_crop'], ['primary_ag_product.id'], ), + sa.ForeignKeyConstraint(['secondary_crop'], ['primary_ag_product.id'], ), + sa.ForeignKeyConstraint(['tertiary_crop'], ['primary_ag_product.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('method', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('method_abbrev_id', sa.Integer(), nullable=True), + sa.Column('method_category_id', sa.Integer(), nullable=True), + sa.Column('method_standard_id', sa.Integer(), nullable=True), + sa.Column('description', sa.Text(), nullable=True), + sa.Column('detection_limits', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['method_abbrev_id'], ['method_abbrev.id'], ), + sa.ForeignKeyConstraint(['method_category_id'], ['method_category.id'], ), + sa.ForeignKeyConstraint(['method_standard_id'], ['method_standard.id'], ), + sa.ForeignKeyConstraint(['source_id'], ['data_source.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('observation', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('record_type', sa.Text(), nullable=True), + sa.Column('record_id', sa.Integer(), nullable=True), + sa.Column('parameter_id', sa.Integer(), nullable=True), + sa.Column('value', sa.Numeric(), nullable=True), + sa.Column('unit_id', sa.Integer(), nullable=True), + sa.Column('dimension_type_id', sa.Integer(), nullable=True), + sa.Column('dimension_value', sa.Numeric(), nullable=True), + sa.Column('dimension_unit_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['dimension_type_id'], ['dimension_type.id'], ), + sa.ForeignKeyConstraint(['dimension_unit_id'], ['unit.id'], ), + sa.ForeignKeyConstraint(['parameter_id'], ['parameter.id'], ), + sa.ForeignKeyConstraint(['unit_id'], ['unit.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('physical_characteristic', + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('particle_length', sa.Numeric(), nullable=True), + sa.Column('particle_width', sa.Numeric(), nullable=True), + sa.Column('particle_height', sa.Numeric(), nullable=True), + sa.Column('particle_unit_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['field_sample_id'], ['field_sample.id'], ), + sa.ForeignKeyConstraint(['particle_unit_id'], ['unit.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('prepared_sample', + sa.Column('name', sa.Text(), nullable=True), + sa.Column('field_sample_id', sa.Integer(), nullable=True), + sa.Column('prep_method_id', sa.Integer(), nullable=True), + sa.Column('prep_date', sa.Date(), nullable=True), + sa.Column('preparer_id', sa.Integer(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['field_sample_id'], ['field_sample.id'], ), + sa.ForeignKeyConstraint(['prep_method_id'], ['preparation_method.id'], ), + sa.ForeignKeyConstraint(['preparer_id'], ['contact.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_census_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('commodity_code', sa.Integer(), nullable=True), + sa.Column('year', sa.Integer(), nullable=True), + sa.Column('source_reference', sa.Text(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['commodity_code'], ['usda_commodity.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_market_report', + sa.Column('slug_id', sa.Integer(), nullable=True), + sa.Column('slug_name', sa.Text(), nullable=True), + sa.Column('report_series_title', sa.Text(), nullable=True), + sa.Column('frequency', sa.Text(), nullable=True), + sa.Column('office_name', sa.Text(), nullable=True), + sa.Column('office_city_id', sa.Integer(), nullable=True), + sa.Column('office_state_fips', sa.Text(), nullable=True), + sa.Column('source_id', sa.Integer(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['office_city_id'], ['location_address.id'], ), + sa.ForeignKeyConstraint(['source_id'], ['data_source.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_survey_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('geoid', sa.Text(), nullable=True), + sa.Column('commodity_code', sa.Integer(), nullable=True), + sa.Column('year', sa.Integer(), nullable=True), + sa.Column('survey_program_id', sa.Integer(), nullable=True), + sa.Column('survey_period', sa.Text(), nullable=True), + sa.Column('reference_month', sa.Text(), nullable=True), + sa.Column('seasonal_flag', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['commodity_code'], ['usda_commodity.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['survey_program_id'], ['usda_survey_program.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('aim1_record_base', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analyst_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['method_id'], ['method.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('aim2_record_base', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('calc_method_id', sa.Integer(), nullable=True), + sa.Column('calc_analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('autoclave_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('calc_method_id', sa.Integer(), nullable=True), + sa.Column('calc_analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('calorimetry_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analyst_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['method_id'], ['method.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('compositional_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analyst_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['method_id'], ['method.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_method', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['method_id'], ['method.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('experiment_prepared_sample', + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('prepared_sample_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['prepared_sample_id'], ['prepared_sample.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('fermentation_record', + sa.Column('strain_id', sa.Integer(), nullable=True), + sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), + sa.Column('eh_method_id', sa.Integer(), nullable=True), + sa.Column('well_position', sa.Text(), nullable=True), + sa.Column('temperature', sa.Numeric(), nullable=True), + sa.Column('agitation_rpm', sa.Numeric(), nullable=True), + sa.Column('vessel_id', sa.Integer(), nullable=True), + sa.Column('analyte_detection_equipment_id', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('calc_method_id', sa.Integer(), nullable=True), + sa.Column('calc_analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ftnir_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analyst_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['method_id'], ['method.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('gasification_record', + sa.Column('feedstock_mass', sa.Numeric(), nullable=True), + sa.Column('bed_temperature', sa.Numeric(), nullable=True), + sa.Column('gas_flow_rate', sa.Numeric(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('calc_method_id', sa.Integer(), nullable=True), + sa.Column('calc_analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('icp_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analyst_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['method_id'], ['method.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('pretreatment_record', + sa.Column('pretreatment_method_id', sa.Integer(), nullable=True), + sa.Column('eh_method_id', sa.Integer(), nullable=True), + sa.Column('reaction_block_id', sa.Integer(), nullable=True), + sa.Column('block_position', sa.Text(), nullable=True), + sa.Column('temperature', sa.Numeric(), nullable=True), + sa.Column('replicate_no', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('calc_method_id', sa.Integer(), nullable=True), + sa.Column('calc_analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('proximate_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analyst_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['method_id'], ['method.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('rgb_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analyst_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['method_id'], ['method.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('ultimate_record', + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analyst_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['method_id'], ['method.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('usda_market_record', + sa.Column('report_id', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('report_begin_date', sa.DateTime(), nullable=True), + sa.Column('report_end_date', sa.DateTime(), nullable=True), + sa.Column('report_date', sa.DateTime(), nullable=True), + sa.Column('commodity_id', sa.Integer(), nullable=True), + sa.Column('market_type_id', sa.Integer(), nullable=True), + sa.Column('market_type_category', sa.Text(), nullable=True), + sa.Column('grp', sa.Text(), nullable=True), + sa.Column('market_category_id', sa.Integer(), nullable=True), + sa.Column('class_', sa.Text(), nullable=True), + sa.Column('grade', sa.Text(), nullable=True), + sa.Column('variety', sa.Text(), nullable=True), + sa.Column('protein_pct', sa.Numeric(), nullable=True), + sa.Column('application', sa.Text(), nullable=True), + sa.Column('pkg', sa.Text(), nullable=True), + sa.Column('sale_type', sa.Text(), nullable=True), + sa.Column('price_unit_id', sa.Integer(), nullable=True), + sa.Column('freight', sa.Text(), nullable=True), + sa.Column('trans_mode', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['commodity_id'], ['usda_commodity.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['price_unit_id'], ['unit.id'], ), + sa.ForeignKeyConstraint(['report_id'], ['usda_market_report.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('xrd_record', + sa.Column('scan_low_nm', sa.Integer(), nullable=True), + sa.Column('scan_high_nm', sa.Integer(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analyst_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['method_id'], ['method.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + op.create_table('xrf_record', + sa.Column('wavelength_nm', sa.Numeric(), nullable=True), + sa.Column('intensity', sa.Numeric(), nullable=True), + sa.Column('energy_slope', sa.Numeric(), nullable=True), + sa.Column('energy_offset', sa.Numeric(), nullable=True), + sa.Column('dataset_id', sa.Integer(), nullable=True), + sa.Column('experiment_id', sa.Integer(), nullable=True), + sa.Column('resource_id', sa.Integer(), nullable=True), + sa.Column('sample_id', sa.Integer(), nullable=True), + sa.Column('technical_replicate_no', sa.Integer(), nullable=True), + sa.Column('technical_replicate_total', sa.Integer(), nullable=True), + sa.Column('method_id', sa.Integer(), nullable=True), + sa.Column('analyst_id', sa.Integer(), nullable=True), + sa.Column('raw_data_id', sa.Integer(), nullable=True), + sa.Column('qc_pass', sa.Boolean(), nullable=True), + sa.Column('note', sa.Text(), nullable=True), + sa.Column('id', sa.Integer(), nullable=False), + sa.Column('created_at', sa.DateTime(), nullable=True), + sa.Column('updated_at', sa.DateTime(), nullable=True), + sa.Column('etl_run_id', sa.Text(), nullable=True), + sa.Column('lineage_group_id', sa.Integer(), nullable=True), + sa.ForeignKeyConstraint(['analyst_id'], ['contact.id'], ), + sa.ForeignKeyConstraint(['dataset_id'], ['data_source.id'], ), + sa.ForeignKeyConstraint(['experiment_id'], ['experiment.id'], ), + sa.ForeignKeyConstraint(['method_id'], ['method.id'], ), + sa.ForeignKeyConstraint(['raw_data_id'], ['file_object_metadata.id'], ), + sa.ForeignKeyConstraint(['resource_id'], ['resource.id'], ), + sa.PrimaryKeyConstraint('id') + ) + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('xrf_record') + op.drop_table('xrd_record') + op.drop_table('usda_market_record') + op.drop_table('ultimate_record') + op.drop_table('rgb_record') + op.drop_table('proximate_record') + op.drop_table('pretreatment_record') + op.drop_table('icp_record') + op.drop_table('gasification_record') + op.drop_table('ftnir_record') + op.drop_table('fermentation_record') + op.drop_table('experiment_prepared_sample') + op.drop_table('experiment_method') + op.drop_table('compositional_record') + op.drop_table('calorimetry_record') + op.drop_table('autoclave_record') + op.drop_table('aim2_record_base') + op.drop_table('aim1_record_base') + op.drop_table('usda_survey_record') + op.drop_table('usda_market_report') + op.drop_table('usda_census_record') + op.drop_table('prepared_sample') + op.drop_table('physical_characteristic') + op.drop_table('observation') + op.drop_table('method') + op.drop_table('landiq_record') + op.drop_table('file_object_metadata') + op.drop_table('field_sample_condition') + op.drop_table('facility_record') + op.drop_table('experiment_equipment') + op.drop_table('experiment_analysis') + op.drop_table('dataset') + op.drop_table('resource_usda_commodity_map') + op.drop_table('resource_morphology') + op.drop_table('resource_availability') + op.drop_table('parameter_unit') + op.drop_table('parameter_category_parameter') + op.drop_table('location_soil_type') + op.drop_table('field_sample') + op.drop_table('experiment') + op.drop_table('equipment') + op.drop_table('data_source') + op.drop_table('billion_ton2023_record') + op.drop_table('usda_term_map') + op.drop_table('resource') + op.drop_table('preparation_method') + op.drop_table('parameter') + op.drop_table('location_address') + op.drop_table('data_source_type') + op.drop_table('usda_survey_program') + op.drop_table('usda_statistic_category') + op.drop_table('usda_domain') + op.drop_table('usda_commodity') + op.drop_table('unit') + op.drop_table('strain') + op.drop_table('source_type') + op.drop_table('soil_type') + op.drop_table('resource_subclass') + op.drop_table('resource_class') + op.drop_table('provider') + op.drop_table('processing_method') + op.drop_table('primary_ag_product') + op.drop_table('preparation_method_abbreviation') + op.drop_table('polygon') + op.drop_table('parameter_category') + op.drop_table('method_standard') + op.drop_table('method_category') + op.drop_table('method_abbrev') + op.drop_table('lookup_base') + op.drop_table('location_resolution') + op.drop_table('lineage_group') + op.drop_table('infrastructure_wastewater_treatment_plants') + op.drop_table('infrastructure_saf_and_renewable_diesel_plants') + op.drop_table('infrastructure_msw_to_energy_anaerobic_digesters') + op.drop_table('infrastructure_livestock_anaerobic_digesters') + op.drop_table('infrastructure_landfills') + op.drop_table('infrastructure_food_processing_facilities') + op.drop_table('infrastructure_ethanol_biorefineries') + op.drop_table('infrastructure_district_energy_systems') + op.drop_table('infrastructure_combustion_plants') + op.drop_table('infrastructure_cafo_manure_locations') + op.drop_table('infrastructure_biosolids_facilities') + op.drop_table('infrastructure_biodiesel_plants') + op.drop_table('harvest_method') + op.drop_table('geography') + op.drop_table('field_storage_method') + op.drop_table('etl_run') + op.drop_table('entity_lineage') + op.drop_table('dimension_type') + op.drop_table('contact') + op.drop_table('collection_method') + op.drop_table('base_entity') + op.drop_table('analysis_type') + op.drop_table('ag_treatment') + # ### end Alembic commands ### diff --git a/alembic/versions/1ace3fc9c593_initial_migration.py b/alembic/versions/1ace3fc9c593_initial_migration.py new file mode 100644 index 00000000..de2d3da7 --- /dev/null +++ b/alembic/versions/1ace3fc9c593_initial_migration.py @@ -0,0 +1,32 @@ +"""Initial migration + +Revision ID: 1ace3fc9c593 +Revises: 62ef89b0050a +Create Date: 2026-01-07 18:39:13.836533 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '1ace3fc9c593' +down_revision: Union[str, Sequence[str], None] = '62ef89b0050a' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/alembic/versions/2b18e6e5e72d_trying_with_fixing_the_base.py b/alembic/versions/2b18e6e5e72d_trying_with_fixing_the_base.py new file mode 100644 index 00000000..bf17d4ad --- /dev/null +++ b/alembic/versions/2b18e6e5e72d_trying_with_fixing_the_base.py @@ -0,0 +1,32 @@ +"""trying with fixing the base + +Revision ID: 2b18e6e5e72d +Revises: 1ace3fc9c593 +Create Date: 2026-01-07 20:55:34.214689 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '2b18e6e5e72d' +down_revision: Union[str, Sequence[str], None] = '1ace3fc9c593' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/alembic/versions/2b41e390fc5d_fixed_alembic_environment_to_import_.py b/alembic/versions/2b41e390fc5d_fixed_alembic_environment_to_import_.py new file mode 100644 index 00000000..ca65e62d --- /dev/null +++ b/alembic/versions/2b41e390fc5d_fixed_alembic_environment_to_import_.py @@ -0,0 +1,32 @@ +"""Fixed alembic environment to import generated schemas again + +Revision ID: 2b41e390fc5d +Revises: a8a3ea954e88 +Create Date: 2026-01-07 18:18:18.527886 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '2b41e390fc5d' +down_revision: Union[str, Sequence[str], None] = 'a8a3ea954e88' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/alembic/versions/62ef89b0050a_fixed_alembic_gen_sqla_so_all_inherit_.py b/alembic/versions/62ef89b0050a_fixed_alembic_gen_sqla_so_all_inherit_.py new file mode 100644 index 00000000..80ad61d8 --- /dev/null +++ b/alembic/versions/62ef89b0050a_fixed_alembic_gen_sqla_so_all_inherit_.py @@ -0,0 +1,32 @@ +"""Fixed alembic gen_sqla so all inherit from same base + +Revision ID: 62ef89b0050a +Revises: 2b41e390fc5d +Create Date: 2026-01-07 18:33:17.030868 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = '62ef89b0050a' +down_revision: Union[str, Sequence[str], None] = '2b41e390fc5d' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/alembic/versions/9be24ffa7bb9_refactor_and_update_env_py.py b/alembic/versions/9be24ffa7bb9_refactor_and_update_env_py.py new file mode 100644 index 00000000..114405dc --- /dev/null +++ b/alembic/versions/9be24ffa7bb9_refactor_and_update_env_py.py @@ -0,0 +1,1462 @@ +"""refactor and update env.py + +Revision ID: 9be24ffa7bb9 +Revises: 15467b7f2f3d +Create Date: 2026-01-07 16:50:27.201523 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa +from sqlalchemy.dialects import postgresql + +# revision identifiers, used by Alembic. +revision: str = '9be24ffa7bb9' +down_revision: Union[str, Sequence[str], None] = '15467b7f2f3d' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.drop_table('resource_subclass') + op.drop_table('usda_market_report') + op.drop_table('infrastructure_cafo_manure_locations') + op.drop_table('experiment_equipment') + op.drop_table('lookup_base') + op.drop_table('infrastructure_ethanol_biorefineries') + op.drop_table('etl_run') + op.drop_table('polygon') + op.drop_table('calorimetry_record') + op.drop_table('base_entity') + op.drop_table('method') + op.drop_table('infrastructure_landfills') + op.drop_table('observation') + op.drop_table('equipment') + op.drop_table('pretreatment_record') + op.drop_table('infrastructure_biosolids_facilities') + op.drop_table('prepared_sample') + op.drop_table('infrastructure_district_energy_systems') + op.drop_table('parameter_category') + op.drop_table('xrd_record') + op.drop_table('resource_class') + op.drop_table('preparation_method') + op.drop_table('strain') + op.drop_table('infrastructure_food_processing_facilities') + op.drop_table('file_object_metadata') + op.drop_table('ftnir_record') + op.drop_table('collection_method') + op.drop_table('harvest_method') + op.drop_table('physical_characteristic') + op.drop_table('experiment') + op.drop_table('parameter') + op.drop_table('infrastructure_livestock_anaerobic_digesters') + op.drop_table('experiment_analysis') + op.drop_table('preparation_method_abbreviation') + op.drop_table('usda_term_map') + op.drop_table('xrf_record') + op.drop_table('source_type') + op.drop_table('lineage_group') + op.drop_table('icp_record') + op.drop_table('infrastructure_wastewater_treatment_plants') + op.drop_table('usda_commodity') + op.drop_table('infrastructure_combustion_plants') + op.drop_table('aim1_record_base') + op.drop_table('ultimate_record') + op.drop_table('soil_type') + op.drop_table('usda_survey_record') + op.drop_table('facility_record') + op.drop_table('autoclave_record') + op.drop_table('usda_domain') + op.drop_table('gasification_record') + op.drop_table('infrastructure_msw_to_energy_anaerobic_digesters') + op.drop_table('ag_treatment') + op.drop_table('location_resolution') + op.drop_table('analysis_type') + op.drop_table('method_category') + op.drop_table('resource_morphology') + op.drop_table('rgb_record') + op.drop_table('primary_ag_product') + op.drop_table('dimension_type') + op.drop_table('provider') + op.drop_table('location_address') + op.drop_table('parameter_category_parameter') + op.drop_table('resource_availability') + op.drop_table('billion_ton2023_record') + op.drop_table('processing_method') + op.drop_table('parameter_unit') + op.drop_table('infrastructure_saf_and_renewable_diesel_plants') + op.drop_table('usda_survey_program') + op.drop_table('method_abbrev') + op.drop_table('infrastructure_biodiesel_plants') + op.drop_table('compositional_record') + op.drop_table('resource_usda_commodity_map') + op.drop_table('dataset') + op.drop_table('field_sample') + op.drop_table('field_sample_condition') + op.drop_table('data_source') + op.drop_table('landiq_record') + op.drop_table('field_storage_method') + op.drop_table('method_standard') + op.drop_table('experiment_method') + op.drop_table('usda_census_record') + op.drop_table('location_soil_type') + op.drop_table('experiment_prepared_sample') + op.drop_table('fermentation_record') + op.drop_table('entity_lineage') + op.drop_table('data_source_type') + op.drop_table('resource_counterfactual') + op.drop_table('contact') + op.drop_table('proximate_record') + op.drop_table('usda_statistic_category') + op.drop_table('unit') + op.drop_table('aim2_record_base') + op.drop_table('geography') + op.drop_table('resource') + op.drop_table('usda_market_record') + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + op.create_table('usda_market_record', + sa.Column('report_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('report_begin_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('report_end_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('report_date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('market_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('grp', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('class_', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('grade', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('variety', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('protein_pct', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('application', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('pkg', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('sale_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('price_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('freight', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('trans_mode', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('market_type_category', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('market_category_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('usda_market_record_pkey')) + ) + op.create_table('resource', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('resource_class_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_subclass_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('test', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('primary_ag_product_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('resource_pkey')) + ) + op.create_table('geography', + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=False), + sa.Column('state_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state_fips', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county_fips', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('region_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('agg_level_desc', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('geoid', name=op.f('geography_pkey')) + ) + op.create_table('aim2_record_base', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calc_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calc_analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('aim2_record_base_pkey')) + ) + op.create_table('unit', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('unit_pkey')) + ) + op.create_table('usda_statistic_category', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('usda_statistic_category_pkey')) + ) + op.create_table('proximate_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('proximate_record_pkey')) + ) + op.create_table('contact', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('first_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('last_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('email', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('affiliation', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('contact_pkey')) + ) + op.create_table('resource_counterfactual', + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('counterfactual_description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('animal_bedding_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('animal_bedding_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('animal_feed_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('animal_feed_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('bioelectricty_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('bioelectricty_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('burn_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('burn_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('compost_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('compost_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('landfill_percent', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('landfill_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('counterfactual_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('resource_counterfactual_pkey')) + ) + op.create_table('data_source_type', + sa.Column('source_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('data_source_type_pkey')) + ) + op.create_table('entity_lineage', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('source_table', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_row_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('entity_lineage_pkey')) + ) + op.create_table('fermentation_record', + sa.Column('strain_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('pretreatment_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('eh_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('well_position', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('temperature', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('agitation_rpm', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('vessel_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyte_detection_equipment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calc_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calc_analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('fermentation_record_pkey')) + ) + op.create_table('experiment_prepared_sample', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prepared_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('experiment_prepared_sample_pkey')) + ) + op.create_table('location_soil_type', + sa.Column('location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('soil_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('location_soil_type_pkey')) + ) + op.create_table('usda_census_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('commodity_code', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('year', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('source_reference', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('usda_census_record_pkey')) + ) + op.create_table('experiment_method', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('experiment_method_pkey')) + ) + op.create_table('method_standard', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('method_standard_pkey')) + ) + op.create_table('field_storage_method', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('field_storage_method_pkey')) + ) + op.create_table('landiq_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('polygon_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('main_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('secondary_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('tertiary_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('quaternary_crop', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('confidence', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('irrigated', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('acres', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('version', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('landiq_record_pkey')) + ) + op.create_table('data_source', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('publisher', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('license', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('data_source_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('full_title', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('creator', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('subject', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('contributor', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('date', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('biocirv', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('format', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('language', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('relation', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('temporal_coverage', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('location_coverage_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('rights', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('data_source_pkey')) + ) + op.create_table('field_sample_condition', + sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('ag_treatment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('last_application_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('treatment_amount_per_acre', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('processing_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('field_sample_condition_pkey')) + ) + op.create_table('field_sample', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('provider_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('collector_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_collection_source', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('amount_collected', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('amount_collected_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sampling_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('field_storage_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('field_storage_duration_value', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('field_storage_duration_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('field_storage_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('collection_timestamp', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('collection_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('harvest_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('harvest_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('field_sample_storage_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('field_sample_pkey')) + ) + op.create_table('dataset', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('record_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('start_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('end_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('dataset_pkey')) + ) + op.create_table('resource_usda_commodity_map', + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('usda_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('match_tier', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('primary_ag_product_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('resource_usda_commodity_map_pkey')) + ) + op.create_table('compositional_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('compositional_record_pkey')) + ) + op.create_table('infrastructure_biodiesel_plants', + sa.Column('biodiesel_plant_id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('company', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('bbi_index', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('capacity_mmg_per_y', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('feedstock', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('address', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('coordinates', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('latitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('longitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('source', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('biodiesel_plant_id', name=op.f('infrastructure_biodiesel_plants_pkey')) + ) + op.create_table('method_abbrev', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('method_abbrev_pkey')) + ) + op.create_table('usda_survey_program', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('usda_survey_program_pkey')) + ) + op.create_table('infrastructure_saf_and_renewable_diesel_plants', + sa.Column('ibcc_index', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('company', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('country', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('capacity', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('feedstock', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('products', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('address', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('coordinates', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('latitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('longitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('ibcc_index', name=op.f('infrastructure_saf_and_renewable_diesel_plants_pkey')) + ) + op.create_table('parameter_unit', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('alternate_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('parameter_unit_pkey')) + ) + op.create_table('processing_method', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('processing_method_pkey')) + ) + op.create_table('billion_ton2023_record', + sa.Column('subclass_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county_square_miles', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('model_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('scenario_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('price_offered_usd', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('production', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('production_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('btu_ton', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('production_energy_content', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('energy_content_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('product_density_dtpersqmi', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('land_source', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('billion_ton2023_record_pkey')) + ) + op.create_table('resource_availability', + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('from_month', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('to_month', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('year_round', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('resource_availability_pkey')) + ) + op.create_table('parameter_category_parameter', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('parameter_category_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('parameter_category_parameter_pkey')) + ) + op.create_table('location_address', + sa.Column('geography_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('address_line1', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('address_line2', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('zip', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lat', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('lon', sa.DOUBLE_PRECISION(precision=53), autoincrement=False, nullable=True), + sa.Column('is_anonymous', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('location_address_pkey')) + ) + op.create_table('provider', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('codename', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('provider_pkey')) + ) + op.create_table('dimension_type', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('dimension_type_pkey')) + ) + op.create_table('primary_ag_product', + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('primary_ag_product_pkey')) + ) + op.create_table('rgb_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('rgb_record_pkey')) + ) + op.create_table('resource_morphology', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('morphology_uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('resource_morphology_pkey')) + ) + op.create_table('method_category', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('method_category_pkey')) + ) + op.create_table('analysis_type', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('analysis_type_pkey')) + ) + op.create_table('location_resolution', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('location_resolution_pkey')) + ) + op.create_table('ag_treatment', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ag_treatment_pkey')) + ) + op.create_table('infrastructure_msw_to_energy_anaerobic_digesters', + sa.Column('wte_id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('equivalent_generation', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('feedstock', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('dayload', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('dayload_bdt', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('facility_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('notes', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('wkt_geom', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('geom', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('latitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('longitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('wte_id', name=op.f('infrastructure_msw_to_energy_anaerobic_digesters_pkey')) + ) + op.create_table('gasification_record', + sa.Column('feedstock_mass', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('bed_temperature', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('gas_flow_rate', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calc_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calc_analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('gasification_record_pkey')) + ) + op.create_table('usda_domain', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('usda_domain_pkey')) + ) + op.create_table('autoclave_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calc_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calc_analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('autoclave_record_pkey')) + ) + op.create_table('facility_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('facility_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('capacity_mw', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('operator', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('start_year', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('facility_record_pkey')) + ) + op.create_table('usda_survey_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('commodity_code', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('year', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('survey_program_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('survey_period', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('reference_month', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('seasonal_flag', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('usda_survey_record_pkey')) + ) + op.create_table('soil_type', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('soil_type_pkey')) + ) + op.create_table('ultimate_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ultimate_record_pkey')) + ) + op.create_table('aim1_record_base', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('aim1_record_base_pkey')) + ) + op.create_table('infrastructure_combustion_plants', + sa.Column('combustion_fid', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('objectid', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('equivalent_generation', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('np_mw', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('cf', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('yearload', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('fuel', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('notes', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('wkt_geom', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('geom', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('latitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('longitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('combustion_fid', name=op.f('infrastructure_combustion_plants_pkey')) + ) + op.create_table('usda_commodity', + sa.Column('usda_source', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('usda_code', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('parent_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('usda_commodity_pkey')) + ) + op.create_table('infrastructure_wastewater_treatment_plants', + sa.Column('plant_id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('codigestion', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('flow_design_adjusted', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('flow_average', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('biosolids', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('excess_flow', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('biogas_utilized', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('flaring', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('excess_mass_loading_rate', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('excess_mass_loading_rate_wet', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('methane_production', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('energy_content', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('electric_kw', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('thermal_mmbtu_d', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('electric_kwh', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('thermal_annual_mmbtu_y', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('anaerobic_digestion_facility', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('dayload_bdt', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('dayload', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('equivalent_generation', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('facility_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('feedstock', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('latitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('longitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('zipcode', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('plant_id', name=op.f('infrastructure_wastewater_treatment_plants_pkey')) + ) + op.create_table('icp_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('icp_record_pkey')) + ) + op.create_table('lineage_group', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('lineage_group_pkey')) + ) + op.create_table('source_type', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('source_type_pkey')) + ) + op.create_table('xrf_record', + sa.Column('maybe_wavelength_nm', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('maybe_intensity', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('maybe_energy_slope', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('maybe_energy_offset', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('xrf_record_pkey')) + ) + op.create_table('usda_term_map', + sa.Column('source_system', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_context', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('raw_term', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('usda_commodity_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('is_verified', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('usda_term_map_pkey')) + ) + op.create_table('preparation_method_abbreviation', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('preparation_method_abbreviation_pkey')) + ) + op.create_table('experiment_analysis', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analysis_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('experiment_analysis_pkey')) + ) + op.create_table('infrastructure_livestock_anaerobic_digesters', + sa.Column('digester_id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('project_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('project_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('digester_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('profile', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('year_operational', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('animal_type_class', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('animal_types', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('pop_feeding_digester', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('total_pop_feeding_digester', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('cattle', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dairy', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('poultry', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('swine', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('codigestion', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('biogas_generation_estimate', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('electricity_generated', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('biogas_end_uses', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('methane_emission_reductions', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('latitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('longitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('digester_id', name=op.f('infrastructure_livestock_anaerobic_digesters_pkey')) + ) + op.create_table('parameter', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('standard_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calculated', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('parameter_pkey')) + ) + op.create_table('experiment', + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('exper_start_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('exper_duration', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('exper_duration_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('exper_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('experiment_pkey')) + ) + op.create_table('physical_characteristic', + sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('particle_length', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('particle_width', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('particle_height', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('particle_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('physical_characteristic_pkey')) + ) + op.create_table('harvest_method', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('harvest_method_pkey')) + ) + op.create_table('collection_method', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('collection_method_pkey')) + ) + op.create_table('ftnir_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('ftnir_record_pkey')) + ) + op.create_table('file_object_metadata', + sa.Column('data_source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('bucket_path', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('file_format', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('file_size', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('checksum_md5', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('checksum_sha256', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('file_object_metadata_pkey')) + ) + op.create_table('infrastructure_food_processing_facilities', + sa.Column('processing_facility_id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('address', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('company', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('join_count', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('master_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('subtype', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('target_fid', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('processing_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('zip', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('wkt_geom', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('geom', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('latitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('longitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('processing_facility_id', name=op.f('infrastructure_food_processing_facilities_pkey')) + ) + op.create_table('strain', + sa.Column('parent_strain_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('strain_pkey')) + ) + op.create_table('preparation_method', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('prep_method_abbrev_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prep_temp_c', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('drying_step', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('preparation_method_pkey')) + ) + op.create_table('resource_class', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('resource_class_pkey')) + ) + op.create_table('xrd_record', + sa.Column('maybe_scan_low_nm', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('maybe_scan_high_nm', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('xrd_record_pkey')) + ) + op.create_table('parameter_category', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('parameter_category_pkey')) + ) + op.create_table('infrastructure_district_energy_systems', + sa.Column('des_fid', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('cbg_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('system', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('object_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('primary_fuel', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('secondary_fuel', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('usetype', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('cap_st', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('cap_hw', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('cap_cw', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('chpcg_cap', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('excess_c', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('excess_h', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('wkt_geom', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('geom', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('latitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('longitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('des_fid', name=op.f('infrastructure_district_energy_systems_pkey')) + ) + op.create_table('prepared_sample', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('field_sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prep_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('prep_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('preparer_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('prepared_sample_pkey')) + ) + op.create_table('infrastructure_biosolids_facilities', + sa.Column('biosolid_facility_id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('report_submitted_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('latitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('longitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('facility', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('authority', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('plant_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('aqmd', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('facility_address', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('facility_city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('facility_zip', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('facility_county', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('mailing_street_1', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('mailing_city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('mailing_state', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('mailing_zip', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('biosolids_number', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('biosolids_contact', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('biosolids_contact_phone', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('biosolids_contact_email', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('adwf', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('potw_biosolids_generated', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('twtds_biosolids_treated', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('class_b_land_app', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('class_b_applier', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('class_a_compost', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('class_a_heat_dried', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('class_a_other', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('class_a_other_applier', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('twtds_transfer_to_second_preparer', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('twtds_second_preparer_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('adc_or_final_c', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('landfill', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('landfill_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('surface_disposal', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('deepwell_injection', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('stored', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('longterm_treatment', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('other', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('name_of_other', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('incineration', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('biosolid_facility_id', name=op.f('infrastructure_biosolids_facilities_pkey')) + ) + op.create_table('pretreatment_record', + sa.Column('pretreatment_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('eh_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('reaction_block_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('block_position', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('temperature', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calc_method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('calc_analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('pretreatment_record_pkey')) + ) + op.create_table('equipment', + sa.Column('equipment_location_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('equipment_pkey')) + ) + op.create_table('observation', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('record_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('record_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('parameter_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('value', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dimension_type_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('dimension_value', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('dimension_unit_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('observation_pkey')) + ) + op.create_table('infrastructure_landfills', + sa.Column('project_id', sa.TEXT(), autoincrement=False, nullable=False), + sa.Column('project_int_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('ghgrp_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('landfill_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('landfill_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('physical_address', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('county', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('zip_code', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('latitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('longitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('ownership_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('landfill_owner_orgs', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('landfill_opened_year', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('landfill_closure_year', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('landfill_status', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('waste_in_place', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('waste_in_place_year', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('lfg_system_in_place', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('lfg_collected', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('lfg_flared', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('project_status', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('project_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('project_start_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('project_shutdown_date', sa.DATE(), autoincrement=False, nullable=True), + sa.Column('project_type_category', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lfg_energy_project_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('rng_delivery_method', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('actual_mw_generation', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('rated_mw_capacity', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('lfg_flow_to_project', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('direct_emission_reductions', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('avoided_emission_reductions', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('project_id', name=op.f('infrastructure_landfills_pkey')) + ) + op.create_table('method', + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('method_abbrev_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_category_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_standard_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('detection_limits', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('method_pkey')) + ) + op.create_table('base_entity', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('base_entity_pkey')) + ) + op.create_table('calorimetry_record', + sa.Column('dataset_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('resource_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('sample_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_no', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('technical_replicate_total', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('method_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('raw_data_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('qc_pass', sa.BOOLEAN(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('analyst_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('calorimetry_record_pkey')) + ) + op.create_table('polygon', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('geoid', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('geom', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('polygon_pkey')) + ) + op.create_table('etl_run', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('started_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('completed_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('pipeline_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('records_ingested', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('note', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('etl_run_pkey')) + ) + op.create_table('infrastructure_ethanol_biorefineries', + sa.Column('ethanol_biorefinery_id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('city', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('address', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('capacity_mgy', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('production_mgy', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('constr_exp', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('ethanol_biorefinery_id', name=op.f('infrastructure_ethanol_biorefineries_pkey')) + ) + op.create_table('lookup_base', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('lookup_base_pkey')) + ) + op.create_table('experiment_equipment', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('experiment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('equipment_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('experiment_equipment_pkey')) + ) + op.create_table('infrastructure_cafo_manure_locations', + sa.Column('cafo_manure_id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('latitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('longitude', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('owner_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('facility_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('address', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('town', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('state', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('zip', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('animal', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('animal_feed_operation_type', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('animal_units', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('animal_count', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('manure_total_solids', sa.NUMERIC(), autoincrement=False, nullable=True), + sa.Column('source', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('date_accessed', sa.DATE(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('cafo_manure_id', name=op.f('infrastructure_cafo_manure_locations_pkey')) + ) + op.create_table('usda_market_report', + sa.Column('slug_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('slug_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('report_series_title', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('frequency', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('office_name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('office_city_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('office_state_fips', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('source_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('created_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('updated_at', postgresql.TIMESTAMP(), autoincrement=False, nullable=True), + sa.Column('etl_run_id', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('lineage_group_id', sa.INTEGER(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('usda_market_report_pkey')) + ) + op.create_table('resource_subclass', + sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False), + sa.Column('name', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True), + sa.Column('uri', sa.TEXT(), autoincrement=False, nullable=True), + sa.PrimaryKeyConstraint('id', name=op.f('resource_subclass_pkey')) + ) + # ### end Alembic commands ### diff --git a/alembic/versions/a8a3ea954e88_fixed_alembic_environment_to_import_.py b/alembic/versions/a8a3ea954e88_fixed_alembic_environment_to_import_.py new file mode 100644 index 00000000..dbf56278 --- /dev/null +++ b/alembic/versions/a8a3ea954e88_fixed_alembic_environment_to_import_.py @@ -0,0 +1,32 @@ +"""Fixed alembic environment to import generated schemas + +Revision ID: a8a3ea954e88 +Revises: 9be24ffa7bb9 +Create Date: 2026-01-07 17:03:49.308268 + +""" +from typing import Sequence, Union + +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision: str = 'a8a3ea954e88' +down_revision: Union[str, Sequence[str], None] = '9be24ffa7bb9' +branch_labels: Union[str, Sequence[str], None] = None +depends_on: Union[str, Sequence[str], None] = None + + +def upgrade() -> None: + """Upgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### + + +def downgrade() -> None: + """Downgrade schema.""" + # ### commands auto generated by Alembic - please adjust! ### + pass + # ### end Alembic commands ### diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py index 00dc9b3c..058d1c98 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/database.py @@ -1,23 +1,25 @@ -from sqlmodel import SQLModel, create_engine, Session +from sqlalchemy import create_engine +from sqlalchemy.orm import declarative_base, sessionmaker from .config import settings # Create engine using the database URL from settings # echo=False by default to avoid verbose SQL logging engine = create_engine(settings.database_url, echo=False) +SessionLocal = sessionmaker(autocommit=False, autoflush=False, bind=engine) + +Base = declarative_base() + def get_session(): """ Dependency that yields a database session. Useful for FastAPI dependencies. """ - with Session(engine) as session: - yield session - -def create_db_and_tables(): - """ - Create all tables defined in SQLModel metadata. - """ - SQLModel.metadata.create_all(engine) + db = SessionLocal() + try: + yield db + finally: + db.close() def get_engine(): """ diff --git a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py index 0fcd6b01..9d5955cd 100644 --- a/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py +++ b/src/ca_biositing/datamodels/ca_biositing/datamodels/schemas/generated/ca_biositing.py @@ -1,11 +1,13 @@ +from ...database import Base + +from ...database import Base + from sqlalchemy import Column, Index, Table, ForeignKey from sqlalchemy.orm import relationship from sqlalchemy.sql.sqltypes import * -from sqlalchemy.orm import declarative_base from sqlalchemy.ext.associationproxy import association_proxy -Base = declarative_base() metadata = Base.metadata @@ -57,8 +59,8 @@ class ExperimentAnalysis(Base): __tablename__ = 'experiment_analysis' id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - analysis_type_id = Column(Integer(), ForeignKey('AnalysisType.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + analysis_type_id = Column(Integer(), ForeignKey('analysis_type.id')) def __repr__(self): @@ -76,8 +78,8 @@ class ExperimentEquipment(Base): __tablename__ = 'experiment_equipment' id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - equipment_id = Column(Integer(), ForeignKey('Equipment.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + equipment_id = Column(Integer(), ForeignKey('equipment.id')) def __repr__(self): @@ -95,8 +97,8 @@ class ExperimentMethod(Base): __tablename__ = 'experiment_method' id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - method_id = Column(Integer(), ForeignKey('Method.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + method_id = Column(Integer(), ForeignKey('method.id')) def __repr__(self): @@ -114,8 +116,8 @@ class ExperimentPreparedSample(Base): __tablename__ = 'experiment_prepared_sample' id = Column(Integer(), primary_key=True, nullable=False ) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - prepared_sample_id = Column(Integer(), ForeignKey('PreparedSample.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + prepared_sample_id = Column(Integer(), ForeignKey('prepared_sample.id')) def __repr__(self): @@ -681,8 +683,8 @@ class ParameterCategoryParameter(Base): __tablename__ = 'parameter_category_parameter' id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer(), ForeignKey('Parameter.id')) - parameter_category_id = Column(Integer(), ForeignKey('ParameterCategory.id')) + parameter_id = Column(Integer(), ForeignKey('parameter.id')) + parameter_category_id = Column(Integer(), ForeignKey('parameter_category.id')) def __repr__(self): @@ -700,8 +702,8 @@ class ParameterUnit(Base): __tablename__ = 'parameter_unit' id = Column(Integer(), primary_key=True, nullable=False ) - parameter_id = Column(Integer(), ForeignKey('Parameter.id')) - alternate_unit_id = Column(Integer(), ForeignKey('Unit.id')) + parameter_id = Column(Integer(), ForeignKey('parameter.id')) + alternate_unit_id = Column(Integer(), ForeignKey('unit.id')) def __repr__(self): @@ -719,7 +721,7 @@ class ResourceMorphology(Base): __tablename__ = 'resource_morphology' id = Column(Integer(), primary_key=True, nullable=False ) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) morphology_uri = Column(Text()) @@ -739,7 +741,7 @@ class DataSource(BaseEntity): name = Column(Text()) description = Column(Text()) - data_source_type_id = Column(Integer(), ForeignKey('DataSourceType.id')) + data_source_type_id = Column(Integer(), ForeignKey('data_source_type.id')) full_title = Column(Text()) creator = Column(Text()) subject = Column(Text()) @@ -752,7 +754,7 @@ class DataSource(BaseEntity): language = Column(Text()) relation = Column(Text()) temporal_coverage = Column(Text()) - location_coverage_id = Column(Integer(), ForeignKey('LocationResolution.id')) + location_coverage_id = Column(Integer(), ForeignKey('location_resolution.id')) rights = Column(Text()) license = Column(Text()) uri = Column(Text()) @@ -783,7 +785,7 @@ class DataSourceType(BaseEntity): """ __tablename__ = 'data_source_type' - source_type_id = Column(Integer(), ForeignKey('SourceType.id')) + source_type_id = Column(Integer(), ForeignKey('source_type.id')) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -810,7 +812,7 @@ class FileObjectMetadata(BaseEntity): """ __tablename__ = 'file_object_metadata' - data_source_id = Column(Integer(), ForeignKey('DataSource.id')) + data_source_id = Column(Integer(), ForeignKey('data_source.id')) bucket_path = Column(Text()) file_format = Column(Text()) file_size = Column(Integer()) @@ -892,7 +894,7 @@ class Equipment(LookupBase): """ __tablename__ = 'equipment' - equipment_location_id = Column(Integer(), ForeignKey('LocationAddress.id')) + equipment_location_id = Column(Integer(), ForeignKey('location_address.id')) id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) description = Column(Text()) @@ -918,11 +920,11 @@ class Experiment(BaseEntity): """ __tablename__ = 'experiment' - analyst_id = Column(Integer(), ForeignKey('Contact.id')) + analyst_id = Column(Integer(), ForeignKey('contact.id')) exper_start_date = Column(Date()) exper_duration = Column(Numeric()) - exper_duration_unit_id = Column(Integer(), ForeignKey('Unit.id')) - exper_location_id = Column(Integer(), ForeignKey('LocationAddress.id')) + exper_duration_unit_id = Column(Integer(), ForeignKey('unit.id')) + exper_location_id = Column(Integer(), ForeignKey('location_address.id')) description = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -976,12 +978,12 @@ class Method(BaseEntity): __tablename__ = 'method' name = Column(Text()) - method_abbrev_id = Column(Integer(), ForeignKey('MethodAbbrev.id')) - method_category_id = Column(Integer(), ForeignKey('MethodCategory.id')) - method_standard_id = Column(Integer(), ForeignKey('MethodStandard.id')) + method_abbrev_id = Column(Integer(), ForeignKey('method_abbrev.id')) + method_category_id = Column(Integer(), ForeignKey('method_category.id')) + method_standard_id = Column(Integer(), ForeignKey('method_standard.id')) description = Column(Text()) detection_limits = Column(Text()) - source_id = Column(Integer(), ForeignKey('DataSource.id')) + source_id = Column(Integer(), ForeignKey('data_source.id')) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1009,10 +1011,10 @@ class PreparedSample(BaseEntity): __tablename__ = 'prepared_sample' name = Column(Text()) - field_sample_id = Column(Integer(), ForeignKey('FieldSample.id')) - prep_method_id = Column(Integer(), ForeignKey('PreparationMethod.id')) + field_sample_id = Column(Integer(), ForeignKey('field_sample.id')) + prep_method_id = Column(Integer(), ForeignKey('preparation_method.id')) prep_date = Column(Date()) - preparer_id = Column(Integer(), ForeignKey('Contact.id')) + preparer_id = Column(Integer(), ForeignKey('contact.id')) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -1041,9 +1043,9 @@ class Resource(BaseEntity): __tablename__ = 'resource' name = Column(Text()) - primary_ag_product_id = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) - resource_class_id = Column(Integer(), ForeignKey('ResourceClass.id')) - resource_subclass_id = Column(Integer(), ForeignKey('ResourceSubclass.id')) + primary_ag_product_id = Column(Integer(), ForeignKey('primary_ag_product.id')) + resource_class_id = Column(Integer(), ForeignKey('resource_class.id')) + resource_subclass_id = Column(Integer(), ForeignKey('resource_subclass.id')) note = Column(Text()) test = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1122,18 +1124,18 @@ class BillionTon2023Record(BaseEntity): """ __tablename__ = 'billion_ton2023_record' - subclass_id = Column(Integer(), ForeignKey('ResourceSubclass.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + subclass_id = Column(Integer(), ForeignKey('resource_subclass.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) geoid = Column(Text()) county_square_miles = Column(Float()) model_name = Column(Text()) scenario_name = Column(Text()) price_offered_usd = Column(Numeric()) production = Column(Integer()) - production_unit_id = Column(Integer(), ForeignKey('Unit.id')) + production_unit_id = Column(Integer(), ForeignKey('unit.id')) btu_ton = Column(Integer()) production_energy_content = Column(Integer()) - energy_content_unit_id = Column(Integer(), ForeignKey('Unit.id')) + energy_content_unit_id = Column(Integer(), ForeignKey('unit.id')) product_density_dtpersqmi = Column(Numeric()) land_source = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1187,12 +1189,12 @@ class LandiqRecord(BaseEntity): """ __tablename__ = 'landiq_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - polygon_id = Column(Integer(), ForeignKey('Polygon.id')) - main_crop = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) - secondary_crop = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) - tertiary_crop = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) - quaternary_crop = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + polygon_id = Column(Integer(), ForeignKey('polygon.id')) + main_crop = Column(Integer(), ForeignKey('primary_ag_product.id')) + secondary_crop = Column(Integer(), ForeignKey('primary_ag_product.id')) + tertiary_crop = Column(Integer(), ForeignKey('primary_ag_product.id')) + quaternary_crop = Column(Integer(), ForeignKey('primary_ag_product.id')) confidence = Column(Integer()) irrigated = Column(Boolean()) acres = Column(Float()) @@ -1226,7 +1228,7 @@ class UsdaCommodity(LookupBase): usda_source = Column(Text()) usda_code = Column(Text()) - parent_commodity_id = Column(Integer(), ForeignKey('UsdaCommodity.id')) + parent_commodity_id = Column(Integer(), ForeignKey('usda_commodity.id')) id = Column(Integer(), primary_key=True, nullable=False ) name = Column(Text()) description = Column(Text()) @@ -1252,9 +1254,9 @@ class ResourceUsdaCommodityMap(BaseEntity): """ __tablename__ = 'resource_usda_commodity_map' - resource_id = Column(Integer(), ForeignKey('Resource.id')) - primary_ag_product_id = Column(Integer(), ForeignKey('PrimaryAgProduct.id')) - usda_commodity_id = Column(Integer(), ForeignKey('UsdaCommodity.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) + primary_ag_product_id = Column(Integer(), ForeignKey('primary_ag_product.id')) + usda_commodity_id = Column(Integer(), ForeignKey('usda_commodity.id')) match_tier = Column(Text()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1283,9 +1285,9 @@ class UsdaCensusRecord(BaseEntity): """ __tablename__ = 'usda_census_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) geoid = Column(Text()) - commodity_code = Column(Integer(), ForeignKey('UsdaCommodity.id')) + commodity_code = Column(Integer(), ForeignKey('usda_commodity.id')) year = Column(Integer()) source_reference = Column(Text()) note = Column(Text()) @@ -1345,9 +1347,9 @@ class UsdaMarketReport(BaseEntity): report_series_title = Column(Text()) frequency = Column(Text()) office_name = Column(Text()) - office_city_id = Column(Integer(), ForeignKey('LocationAddress.id')) + office_city_id = Column(Integer(), ForeignKey('location_address.id')) office_state_fips = Column(Text()) - source_id = Column(Integer(), ForeignKey('DataSource.id')) + source_id = Column(Integer(), ForeignKey('data_source.id')) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1374,12 +1376,12 @@ class UsdaMarketRecord(BaseEntity): """ __tablename__ = 'usda_market_record' - report_id = Column(Integer(), ForeignKey('UsdaMarketReport.id')) - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + report_id = Column(Integer(), ForeignKey('usda_market_report.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) report_begin_date = Column(DateTime()) report_end_date = Column(DateTime()) report_date = Column(DateTime()) - commodity_id = Column(Integer(), ForeignKey('UsdaCommodity.id')) + commodity_id = Column(Integer(), ForeignKey('usda_commodity.id')) market_type_id = Column(Integer()) market_type_category = Column(Text()) grp = Column(Text()) @@ -1391,7 +1393,7 @@ class UsdaMarketRecord(BaseEntity): application = Column(Text()) pkg = Column(Text()) sale_type = Column(Text()) - price_unit_id = Column(Integer(), ForeignKey('Unit.id')) + price_unit_id = Column(Integer(), ForeignKey('unit.id')) freight = Column(Text()) trans_mode = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1420,7 +1422,7 @@ class LocationAddress(BaseEntity): """ __tablename__ = 'location_address' - geography_id = Column(Text(), ForeignKey('Geography.geoid')) + geography_id = Column(Text(), ForeignKey('geography.geoid')) address_line1 = Column(Text()) address_line2 = Column(Text()) city = Column(Text()) @@ -1504,11 +1506,11 @@ class UsdaSurveyRecord(BaseEntity): """ __tablename__ = 'usda_survey_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) geoid = Column(Text()) - commodity_code = Column(Integer(), ForeignKey('UsdaCommodity.id')) + commodity_code = Column(Integer(), ForeignKey('usda_commodity.id')) year = Column(Integer()) - survey_program_id = Column(Integer(), ForeignKey('UsdaSurveyProgram.id')) + survey_program_id = Column(Integer(), ForeignKey('usda_survey_program.id')) survey_period = Column(Text()) reference_month = Column(Text()) seasonal_flag = Column(Boolean()) @@ -1542,7 +1544,7 @@ class UsdaTermMap(BaseEntity): source_system = Column(Text()) source_context = Column(Text()) raw_term = Column(Text()) - usda_commodity_id = Column(Integer(), ForeignKey('UsdaCommodity.id')) + usda_commodity_id = Column(Integer(), ForeignKey('usda_commodity.id')) is_verified = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -1622,22 +1624,22 @@ class FieldSample(BaseEntity): __tablename__ = 'field_sample' name = Column(Text()) - resource_id = Column(Integer(), ForeignKey('Resource.id')) - provider_id = Column(Integer(), ForeignKey('Provider.id')) - collector_id = Column(Integer(), ForeignKey('Contact.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) + provider_id = Column(Integer(), ForeignKey('provider.id')) + collector_id = Column(Integer(), ForeignKey('contact.id')) sample_collection_source = Column(Text()) amount_collected = Column(Numeric()) - amount_collected_unit_id = Column(Integer(), ForeignKey('Unit.id')) - sampling_location_id = Column(Integer(), ForeignKey('LocationAddress.id')) - field_storage_method_id = Column(Integer(), ForeignKey('FieldStorageMethod.id')) + amount_collected_unit_id = Column(Integer(), ForeignKey('unit.id')) + sampling_location_id = Column(Integer(), ForeignKey('location_address.id')) + field_storage_method_id = Column(Integer(), ForeignKey('field_storage_method.id')) field_storage_duration_value = Column(Numeric()) - field_storage_duration_unit_id = Column(Integer(), ForeignKey('Unit.id')) - field_storage_location_id = Column(Integer(), ForeignKey('LocationAddress.id')) + field_storage_duration_unit_id = Column(Integer(), ForeignKey('unit.id')) + field_storage_location_id = Column(Integer(), ForeignKey('location_address.id')) collection_timestamp = Column(DateTime()) - collection_method_id = Column(Integer(), ForeignKey('CollectionMethod.id')) - harvest_method_id = Column(Integer(), ForeignKey('HarvestMethod.id')) + collection_method_id = Column(Integer(), ForeignKey('collection_method.id')) + harvest_method_id = Column(Integer(), ForeignKey('harvest_method.id')) harvest_date = Column(Date()) - field_sample_storage_location_id = Column(Integer(), ForeignKey('LocationAddress.id')) + field_sample_storage_location_id = Column(Integer(), ForeignKey('location_address.id')) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -1690,11 +1692,11 @@ class FieldSampleCondition(BaseEntity): """ __tablename__ = 'field_sample_condition' - field_sample_id = Column(Integer(), ForeignKey('FieldSample.id')) - ag_treatment_id = Column(Integer(), ForeignKey('AgTreatment.id')) + field_sample_id = Column(Integer(), ForeignKey('field_sample.id')) + ag_treatment_id = Column(Integer(), ForeignKey('ag_treatment.id')) last_application_date = Column(Date()) treatment_amount_per_acre = Column(Float()) - processing_method_id = Column(Integer(), ForeignKey('ProcessingMethod.id')) + processing_method_id = Column(Integer(), ForeignKey('processing_method.id')) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1796,8 +1798,8 @@ class LocationSoilType(BaseEntity): """ __tablename__ = 'location_soil_type' - location_id = Column(Integer(), ForeignKey('LocationAddress.id')) - soil_type_id = Column(Integer(), ForeignKey('SoilType.id')) + location_id = Column(Integer(), ForeignKey('location_address.id')) + soil_type_id = Column(Integer(), ForeignKey('soil_type.id')) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1824,11 +1826,11 @@ class PhysicalCharacteristic(BaseEntity): """ __tablename__ = 'physical_characteristic' - field_sample_id = Column(Integer(), ForeignKey('FieldSample.id')) + field_sample_id = Column(Integer(), ForeignKey('field_sample.id')) particle_length = Column(Numeric()) particle_width = Column(Numeric()) particle_height = Column(Numeric()) - particle_unit_id = Column(Integer(), ForeignKey('Unit.id')) + particle_unit_id = Column(Integer(), ForeignKey('unit.id')) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) updated_at = Column(DateTime()) @@ -1857,7 +1859,7 @@ class Dataset(BaseEntity): name = Column(Text()) record_type = Column(Text()) - source_id = Column(Integer(), ForeignKey('DataSource.id')) + source_id = Column(Integer(), ForeignKey('data_source.id')) start_date = Column(Date()) end_date = Column(Date()) description = Column(Text()) @@ -1912,15 +1914,15 @@ class Observation(BaseEntity): """ __tablename__ = 'observation' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) record_type = Column(Text()) record_id = Column(Integer()) - parameter_id = Column(Integer(), ForeignKey('Parameter.id')) + parameter_id = Column(Integer(), ForeignKey('parameter.id')) value = Column(Numeric()) - unit_id = Column(Integer(), ForeignKey('Unit.id')) - dimension_type_id = Column(Integer(), ForeignKey('DimensionType.id')) + unit_id = Column(Integer(), ForeignKey('unit.id')) + dimension_type_id = Column(Integer(), ForeignKey('dimension_type.id')) dimension_value = Column(Numeric()) - dimension_unit_id = Column(Integer(), ForeignKey('Unit.id')) + dimension_unit_id = Column(Integer(), ForeignKey('unit.id')) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) created_at = Column(DateTime()) @@ -1948,11 +1950,11 @@ class FacilityRecord(BaseEntity): """ __tablename__ = 'facility_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) facility_name = Column(Text()) - location_id = Column(Integer(), ForeignKey('LocationAddress.id')) + location_id = Column(Integer(), ForeignKey('location_address.id')) capacity_mw = Column(Numeric()) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) operator = Column(Text()) start_year = Column(Integer()) note = Column(Text()) @@ -2058,7 +2060,7 @@ class Parameter(BaseEntity): __tablename__ = 'parameter' name = Column(Text()) - standard_unit_id = Column(Integer(), ForeignKey('Unit.id')) + standard_unit_id = Column(Integer(), ForeignKey('unit.id')) calculated = Column(Boolean()) description = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2169,15 +2171,15 @@ class Aim1RecordBase(BaseEntity): """ __tablename__ = 'aim1_record_base' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer(), ForeignKey('Method.id')) - analyst_id = Column(Integer(), ForeignKey('Contact.id')) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + method_id = Column(Integer(), ForeignKey('method.id')) + analyst_id = Column(Integer(), ForeignKey('contact.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2206,15 +2208,15 @@ class Aim2RecordBase(BaseEntity): """ __tablename__ = 'aim2_record_base' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_total = Column(Integer()) technical_replicate_no = Column(Integer()) calc_method_id = Column(Integer()) calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2269,7 +2271,7 @@ class ResourceAvailability(BaseEntity): """ __tablename__ = 'resource_availability' - resource_id = Column(Integer(), ForeignKey('Resource.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) geoid = Column(Text()) from_month = Column(Integer()) to_month = Column(Integer()) @@ -2328,7 +2330,7 @@ class PreparationMethod(BaseEntity): name = Column(Text()) description = Column(Text()) - prep_method_abbrev_id = Column(Integer(), ForeignKey('PreparationMethodAbbreviation.id')) + prep_method_abbrev_id = Column(Integer(), ForeignKey('preparation_method_abbreviation.id')) prep_temp_c = Column(Numeric()) uri = Column(Text()) drying_step = Column(Boolean()) @@ -2383,15 +2385,15 @@ class ProximateRecord(Aim1RecordBase): """ __tablename__ = 'proximate_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer(), ForeignKey('Method.id')) - analyst_id = Column(Integer(), ForeignKey('Contact.id')) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + method_id = Column(Integer(), ForeignKey('method.id')) + analyst_id = Column(Integer(), ForeignKey('contact.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2420,15 +2422,15 @@ class UltimateRecord(Aim1RecordBase): """ __tablename__ = 'ultimate_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer(), ForeignKey('Method.id')) - analyst_id = Column(Integer(), ForeignKey('Contact.id')) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + method_id = Column(Integer(), ForeignKey('method.id')) + analyst_id = Column(Integer(), ForeignKey('contact.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2457,15 +2459,15 @@ class CompositionalRecord(Aim1RecordBase): """ __tablename__ = 'compositional_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer(), ForeignKey('Method.id')) - analyst_id = Column(Integer(), ForeignKey('Contact.id')) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + method_id = Column(Integer(), ForeignKey('method.id')) + analyst_id = Column(Integer(), ForeignKey('contact.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2494,15 +2496,15 @@ class IcpRecord(Aim1RecordBase): """ __tablename__ = 'icp_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer(), ForeignKey('Method.id')) - analyst_id = Column(Integer(), ForeignKey('Contact.id')) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + method_id = Column(Integer(), ForeignKey('method.id')) + analyst_id = Column(Integer(), ForeignKey('contact.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2535,15 +2537,15 @@ class XrfRecord(Aim1RecordBase): intensity = Column(Numeric()) energy_slope = Column(Numeric()) energy_offset = Column(Numeric()) - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer(), ForeignKey('Method.id')) - analyst_id = Column(Integer(), ForeignKey('Contact.id')) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + method_id = Column(Integer(), ForeignKey('method.id')) + analyst_id = Column(Integer(), ForeignKey('contact.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2574,15 +2576,15 @@ class XrdRecord(Aim1RecordBase): scan_low_nm = Column(Integer()) scan_high_nm = Column(Integer()) - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer(), ForeignKey('Method.id')) - analyst_id = Column(Integer(), ForeignKey('Contact.id')) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + method_id = Column(Integer(), ForeignKey('method.id')) + analyst_id = Column(Integer(), ForeignKey('contact.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2611,15 +2613,15 @@ class CalorimetryRecord(Aim1RecordBase): """ __tablename__ = 'calorimetry_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer(), ForeignKey('Method.id')) - analyst_id = Column(Integer(), ForeignKey('Contact.id')) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + method_id = Column(Integer(), ForeignKey('method.id')) + analyst_id = Column(Integer(), ForeignKey('contact.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2648,15 +2650,15 @@ class FtnirRecord(Aim1RecordBase): """ __tablename__ = 'ftnir_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer(), ForeignKey('Method.id')) - analyst_id = Column(Integer(), ForeignKey('Contact.id')) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + method_id = Column(Integer(), ForeignKey('method.id')) + analyst_id = Column(Integer(), ForeignKey('contact.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2685,15 +2687,15 @@ class RgbRecord(Aim1RecordBase): """ __tablename__ = 'rgb_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_no = Column(Integer()) technical_replicate_total = Column(Integer()) - method_id = Column(Integer(), ForeignKey('Method.id')) - analyst_id = Column(Integer(), ForeignKey('Contact.id')) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + method_id = Column(Integer(), ForeignKey('method.id')) + analyst_id = Column(Integer(), ForeignKey('contact.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2728,15 +2730,15 @@ class PretreatmentRecord(Aim2RecordBase): block_position = Column(Text()) temperature = Column(Numeric()) replicate_no = Column(Integer()) - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_total = Column(Integer()) technical_replicate_no = Column(Integer()) calc_method_id = Column(Integer()) calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2773,15 +2775,15 @@ class FermentationRecord(Aim2RecordBase): agitation_rpm = Column(Numeric()) vessel_id = Column(Integer()) analyte_detection_equipment_id = Column(Integer()) - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_total = Column(Integer()) technical_replicate_no = Column(Integer()) calc_method_id = Column(Integer()) calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2813,15 +2815,15 @@ class GasificationRecord(Aim2RecordBase): feedstock_mass = Column(Numeric()) bed_temperature = Column(Numeric()) gas_flow_rate = Column(Numeric()) - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_total = Column(Integer()) technical_replicate_no = Column(Integer()) calc_method_id = Column(Integer()) calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) @@ -2850,15 +2852,15 @@ class AutoclaveRecord(Aim2RecordBase): """ __tablename__ = 'autoclave_record' - dataset_id = Column(Integer(), ForeignKey('DataSource.id')) - experiment_id = Column(Integer(), ForeignKey('Experiment.id')) - resource_id = Column(Integer(), ForeignKey('Resource.id')) + dataset_id = Column(Integer(), ForeignKey('data_source.id')) + experiment_id = Column(Integer(), ForeignKey('experiment.id')) + resource_id = Column(Integer(), ForeignKey('resource.id')) sample_id = Column(Integer()) technical_replicate_total = Column(Integer()) technical_replicate_no = Column(Integer()) calc_method_id = Column(Integer()) calc_analyst_id = Column(Integer()) - raw_data_id = Column(Integer(), ForeignKey('FileObjectMetadata.id')) + raw_data_id = Column(Integer(), ForeignKey('file_object_metadata.id')) qc_pass = Column(Boolean()) note = Column(Text()) id = Column(Integer(), primary_key=True, nullable=False ) diff --git a/src/ca_biositing/datamodels/utils/generate_sqla.py b/src/ca_biositing/datamodels/utils/generate_sqla.py index 929d5298..ef48e08a 100644 --- a/src/ca_biositing/datamodels/utils/generate_sqla.py +++ b/src/ca_biositing/datamodels/utils/generate_sqla.py @@ -26,9 +26,40 @@ def replace_tablename(match): new_content = re.sub(pattern, replace_tablename, content) + # Convert ForeignKey references from class names to table names + # Matches: ForeignKey('SomeClass.id') -> ForeignKey('some_class.id') + # Convert ForeignKey references from class names to table names + # Matches: ForeignKey('SomeClass.column') -> ForeignKey('some_class.column') + def replace_foreign_key(match): + fk_content = match.group(0) + # Extract the table/class name and column name from inside the quotes + inner_match = re.search(r"ForeignKey\('([A-Za-z0-9]+)\.([A-Za-z0-9]+)'\)", fk_content) + if inner_match: + class_name = inner_match.group(1) + column_name = inner_match.group(2) + table_name = to_snake_case(class_name) + return fk_content.replace(f"'{class_name}.{column_name}'", f"'{table_name}.{column_name}'") + return fk_content + + # Apply to all ForeignKey occurrences + new_content = re.sub(r"ForeignKey\('[^']+\.[^']+'\)", replace_foreign_key, new_content) + + # Inject the Base import + new_content = "from ...database import Base\n\n" + new_content + + # Inject the Base import + new_content = "from ...database import Base\n\n" + new_content + + # Remove the line that redefines Base + new_content = re.sub(r"Base = declarative_base\(\)\n", "", new_content) + + # Remove the unused import if present + new_content = re.sub(r"from sqlalchemy\.orm import declarative_base\n", "", new_content) + with open(file_path, 'w') as f: f.write(new_content) + def generate_sqla(): """ Generates SQLAlchemy models from LinkML schema modules. From b08f15ec6d86be05c868d576b712dca99cf740f8 Mon Sep 17 00:00:00 2001 From: Avi <32148378+avi9664@users.noreply.github.com> Date: Sat, 10 Jan 2026 20:35:47 -0800 Subject: [PATCH 75/81] modified engine.py to get correct database url from env --- alembic/env.py | 2 +- docs/README.md | 2 +- docs/datamodels/README.md | 2 +- docs/deployment/README.md | 2 +- docs/pipeline/README.md | 2 +- docs/resources/README.md | 2 +- docs/webservice/README.md | 2 +- .../.ipynb_checkpoints/engine-checkpoint.py | 32 + .../etl_notebook-checkpoint.ipynb | 318 ++++ ...sheet_extraction_notebook-checkpoint.ipynb | 899 ++++++++++ .../ca_biositing/pipeline/utils/engine.py | 28 +- .../pipeline/utils/etl_notebook.ipynb | 1497 +---------------- .../utils/gsheet_extraction_notebook.ipynb | 1083 +++--------- 13 files changed, 1509 insertions(+), 2362 deletions(-) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/engine-checkpoint.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/etl_notebook-checkpoint.ipynb create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gsheet_extraction_notebook-checkpoint.ipynb diff --git a/alembic/env.py b/alembic/env.py index ad465742..8df293e1 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -26,7 +26,7 @@ # from ca_biositing.datamodels.user import * from ca_biositing.datamodels.schemas.generated import ca_biositing from ca_biositing.datamodels.schemas.generated.ca_biositing import * -from ca_biositing.datamodels.database import Base +# from ca_biositing.datamodels.database import Base # this is the Alembic Config object, which provides # access to the values within the .ini file in use. diff --git a/docs/README.md b/docs/README.md index 32d46ee8..94389aee 120000 --- a/docs/README.md +++ b/docs/README.md @@ -1 +1 @@ -../README.md \ No newline at end of file +../README.md diff --git a/docs/datamodels/README.md b/docs/datamodels/README.md index b62101ad..f3c7aa23 120000 --- a/docs/datamodels/README.md +++ b/docs/datamodels/README.md @@ -1 +1 @@ -../../src/ca_biositing/datamodels/README.md \ No newline at end of file +../../src/ca_biositing/datamodels/README.md diff --git a/docs/deployment/README.md b/docs/deployment/README.md index d5c46ad4..5159bcfe 120000 --- a/docs/deployment/README.md +++ b/docs/deployment/README.md @@ -1 +1 @@ -../../deployment/README.md \ No newline at end of file +../../deployment/README.md diff --git a/docs/pipeline/README.md b/docs/pipeline/README.md index 82a8c831..544d50b1 120000 --- a/docs/pipeline/README.md +++ b/docs/pipeline/README.md @@ -1 +1 @@ -../../src/ca_biositing/pipeline/README.md \ No newline at end of file +../../src/ca_biositing/pipeline/README.md diff --git a/docs/resources/README.md b/docs/resources/README.md index 9f21ec35..ea34ca59 120000 --- a/docs/resources/README.md +++ b/docs/resources/README.md @@ -1 +1 @@ -../../resources/README.md \ No newline at end of file +../../resources/README.md diff --git a/docs/webservice/README.md b/docs/webservice/README.md index 749a635e..24ea2883 120000 --- a/docs/webservice/README.md +++ b/docs/webservice/README.md @@ -1 +1 @@ -../../src/ca_biositing/webservice/README.md \ No newline at end of file +../../src/ca_biositing/webservice/README.md diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/engine-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/engine-checkpoint.py new file mode 100644 index 00000000..c5349511 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/engine-checkpoint.py @@ -0,0 +1,32 @@ +from sqlmodel import create_engine, Session +import os +from dotenv import load_dotenv + +#This module queries the db via the ORM + +# Get the root +path = os.getcwd() +project_root = None +while path != os.path.dirname(path): # Stop at the filesystem root + if 'pixi.toml' in os.listdir(path): + project_root = path + break + path = os.path.dirname(path) + +load_dotenv(dotenv_path=project_root + "\\resources\\docker\\.env") + +# Database Connection +POSTGRES_USER = os.getenv("POSTGRES_USER") +POSTGRES_PASSWORD= os.getenv("POSTGRES_PASSWORD") + +# 2. Host Port Mapping +# This is the port on your local machine that will connect to the container's port 5432. +POSTGRES_PORT= os.getenv("POSTGRES_PORT") + +DATABASE_URL = f"postgresql+psycopg2://{POSTGRES_USER}:{POSTGRES_PASSWORD}@localhost:{POSTGRES_PORT}/biocirv_db" + +# old: +# DATABASE_URL = "postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db" +engine = create_engine(DATABASE_URL) + +db_session = Session(engine) diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/etl_notebook-checkpoint.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/etl_notebook-checkpoint.ipynb new file mode 100644 index 00000000..3c8228d6 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/etl_notebook-checkpoint.ipynb @@ -0,0 +1,318 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## ETL Notebook for CA Biositing Project\n", + "\n", + "This notebook provides a documented walkthrough of the ETL (Extract, Transform, Load) process for the CA Biositing project. It is designed for interactive development and exploration before migrating logic into the production pipeline.\n", + "\n", + "It covers:\n", + "\n", + "1. **Setup**: Importing necessary libraries and establishing a connection to the database.\n", + "2. **Extraction**: Pulling raw data from Google Sheets.\n", + "3. **Cleaning**: Standardizing data types, handling missing values, and cleaning column names.\n", + "4. **Normalization**: Replacing human-readable names (e.g., \"Corn\") with database foreign key IDs (e.g., `resource_id: 1`).\n", + "5. **Utilities**: Common functions for data manipulation and analysis.\n", + "6. **Deployment Plan**: A step-by-step guide for moving the code from this notebook into the production ETL modules." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "import sys\n", + "import pandas as pd\n", + "import numpy as np\n", + "import janitor as jn\n", + "import logging\n", + "from IPython.display import display\n", + "from sqlalchemy.orm import Session\n", + "from sqlalchemy import select\n", + "\n", + "# --- Basic Logging Configuration for Notebook ---\n", + "# When running in a notebook, we use Python's standard logging.\n", + "# In the production pipeline, this will be replaced by Prefect's `get_run_logger()`\n", + "logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')\n", + "logger = logging.getLogger()\n", + "\n", + "# --- Robustly find the project root ---\n", + "# This ensures that the notebook can be run from any directory within the project.\n", + "path = os.getcwd()\n", + "project_root = None\n", + "while path != os.path.dirname(path):\n", + " if 'pixi.toml' in os.listdir(path):\n", + " project_root = path\n", + " break\n", + " path = os.path.dirname(path)\n", + "\n", + "if not project_root:\n", + " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", + "\n", + "# Add the project root to the Python path to allow for module imports\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + " logger.info(f\"Added project root '{project_root}' to sys.path\")\n", + "else:\n", + " logger.info(f\"Project root '{project_root}' is already in sys.path\")\n", + "\n", + "# --- Import project modules ---\n", + "try:\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", + " from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import replace_name_with_id_df\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate, ultimate, cmpana\n", + " logger.info('Successfully imported all project modules.')\n", + "except ImportError as e:\n", + " logger.error(f'Failed to import project modules: {e}', exc_info=True)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Data Cleaning Function" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "def clean_the_gsheets(df):\n", + " \"\"\"Cleans and standardizes a DataFrame extracted from Google Sheets.\n", + "\n", + " This function performs several key operations:\n", + " 1. Cleans column names to a standard format (snake_case).\n", + " 2. Drops rows where essential columns ('repl_no', 'value') are empty.\n", + " 3. Coerces data types for numeric and datetime columns, handling errors gracefully.\n", + " 4. Converts remaining columns to the best possible data types.\n", + "\n", + " Args:\n", + " df (pd.DataFrame): The raw DataFrame.\n", + "\n", + " Returns:\n", + " pd.DataFrame: The cleaned DataFrame.\n", + " \"\"\"\n", + " logger.info('Starting DataFrame cleaning process.')\n", + " if not isinstance(df, pd.DataFrame):\n", + " logger.error('Input is not a pandas DataFrame.')\n", + " return None\n", + " \n", + " try:\n", + " # 1. Clean names and drop rows with missing essential data\n", + " df_cleaned = df.clean_names().dropna(subset=['repl_no', 'value'])\n", + " logger.info(f'Dropped {len(df) - len(df_cleaned)} rows with missing values.')\n", + "\n", + " # 2. Coerce numeric types\n", + " df_cleaned['repl_no'] = pd.to_numeric(df_cleaned['repl_no'], errors='coerce').astype('Int32')\n", + " df_cleaned['value'] = pd.to_numeric(df_cleaned['value'], errors='coerce').astype(np.float32)\n", + "\n", + " # 3. Coerce datetime types\n", + " if 'created_at' in df_cleaned.columns:\n", + " df_cleaned['created_at'] = pd.to_datetime(df_cleaned['created_at'], errors='coerce')\n", + " if 'updated_at' in df_cleaned.columns:\n", + " df_cleaned['updated_at'] = pd.to_datetime(df_cleaned['updated_at'], errors='coerce')\n", + "\n", + " # 4. Replace empty strings with NaN so they are properly ignored\n", + " df_cleaned = df_cleaned.replace(r'^\\s*$', np.nan, regex=True)\n", + "\n", + " # 5. Convert other dtypes to best possible\n", + " df_cleaned = df_cleaned.convert_dtypes()\n", + " logger.info('Successfully cleaned DataFrame.')\n", + "\n", + " # 6. Convert all string data to lowercase\n", + " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + " logger.info('Converted all string data to lowercase.')\n", + " return df_cleaned\n", + "\n", + " except Exception as e:\n", + " logger.error(f'An error occurred during DataFrame cleaning: {e}', exc_info=True)\n", + " return None\n", + "\n", + " " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Data Normalization Function" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "def normalize_dataframes(dataframes, normalize_columns):\n", + " \"\"\"Normalizes a list of DataFrames by replacing name columns with foreign key IDs.\n", + "\n", + " This function iterates through a list of dataframes and, for each one, iterates\n", + " through a dictionary of columns that need to be normalized. It uses the \n", + " `replace_name_with_id_df` utility to look up or create the corresponding ID\n", + " in the database.\n", + "\n", + " Args:\n", + " dataframes (list[pd.DataFrame]): A list of DataFrames to normalize.\n", + " normalize_columns (dict): A dictionary mapping column names to SQLModel classes and attributes.\n", + "\n", + " Returns:\n", + " list[pd.DataFrame]: The list of normalized DataFrames.\n", + " \"\"\"\n", + " logger.info(f'Starting normalization process for {len(dataframes)} dataframes.')\n", + " normalized_dfs = []\n", + " try:\n", + " with Session(engine) as db:\n", + " for i, df in enumerate(dataframes):\n", + " if not isinstance(df, pd.DataFrame):\n", + " logger.warning(f'Item {i+1} is not a DataFrame, skipping.')\n", + " continue\n", + " \n", + " logger.info(f'Processing DataFrame #{i+1} with {len(df)} rows.')\n", + " df_normalized = df.copy()\n", + "\n", + " for df_col, (model, model_name_attr) in normalize_columns.items():\n", + " if df_col not in df_normalized.columns:\n", + " logger.warning(f\"Column '{df_col}' not in DataFrame #{i+1}. Skipping normalization for this column.\")\n", + " continue\n", + " \n", + " try:\n", + " # Skip normalization if the column is all NaN/None\n", + " if df_normalized[df_col].isnull().all():\n", + " logger.info(f\"Skipping normalization for column '{df_col}' as it contains only null values.\")\n", + " continue\n", + " \n", + " logger.info(f\"Normalizing column '{df_col}' using model '{model.__name__}'.\")\n", + " df_normalized, num_created = replace_name_with_id_df(\n", + " db=db,\n", + " df=df_normalized,\n", + " ref_model=model,\n", + " df_name_column=df_col,\n", + " model_name_attr=model_name_attr,\n", + " id_column_name='id',\n", + " final_column_name=f'{df_col}_id'\n", + " )\n", + " if num_created > 0:\n", + " logger.info(f\"Created {num_created} new records in '{model.__name__}' table.\")\n", + " new_col_name = f'{df_col}_id'\n", + " num_nulls = df_normalized[new_col_name].isnull().sum()\n", + " logger.info(f\"Successfully normalized '{df_col}'. New column '{new_col_name}' contains {num_nulls} null values.\")\n", + " except Exception as e:\n", + " logger.error(f\"Error normalizing column '{df_col}' in DataFrame #{i+1}: {e}\", exc_info=True)\n", + " continue # Continue to the next column\n", + " \n", + " normalized_dfs.append(df_normalized)\n", + " logger.info(f'Finished processing DataFrame #{i+1}.')\n", + " \n", + " logger.info('Committing database session.')\n", + " db.commit()\n", + " logger.info('Database commit successful.')\n", + " except Exception as e:\n", + " logger.error(f'A critical error occurred during the database session: {e}', exc_info=True)\n", + " db.rollback()\n", + " logger.info('Database session rolled back.')\n", + " \n", + " return normalized_dfs\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### ETL Execution Example" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# --- 1. Extraction ---\n", + "# In a real Prefect flow, each extraction would be a separate task.\n", + "logger.info('Starting data extraction...')\n", + "prox_df = proximate.extract(project_root=project_root)\n", + "ult_df = ultimate.extract(project_root=project_root)\n", + "cmp_df = cmpana.extract(project_root=project_root)\n", + "dataframes = [prox_df, ult_df, cmp_df]\n", + "logger.info('Data extraction complete.')\n", + "\n", + "# --- 2. Cleaning ---\n", + "# This list comprehension applies the cleaning function to each extracted dataframe.\n", + "logger.info('Starting data cleaning...')\n", + "clean_dataframes = [clean_the_gsheets(df) for df in dataframes if df is not None]\n", + "logger.info('Data cleaning complete.')\n", + "\n", + "# --- 3. Normalization ---\n", + "# This dictionary defines the columns to be normalized. \n", + "# The key is the column name in the DataFrame.\n", + "# The value is a tuple containing the corresponding SQLAlchemy model and the name of the attribute on the model to match against.\n", + "NORMALIZE_COLUMNS = {\n", + " 'resource': (Resource, 'name'),\n", + " 'prepared_sample': (PreparedSample, 'name'),\n", + " 'preparation_method': (PreparationMethod, 'name'),\n", + " 'parameter': (Parameter, 'name'),\n", + " 'unit': (Unit, 'name'),\n", + " 'analyst_email': (Contact, 'email'),\n", + " 'analysis_type': (AnalysisType, 'name'),\n", + " 'primary_ag_product': (PrimaryAgProduct, 'name')\n", + "}\n", + "\n", + "logger.info('Starting data normalization...')\n", + "normalized_dataframes = normalize_dataframes(clean_dataframes, NORMALIZE_COLUMNS)\n", + "logger.info('Data normalization complete.')\n", + "\n", + "# --- 4. Display Results ---\n", + "logger.info('Displaying results of normalization...')\n", + "for i, df in enumerate(normalized_dataframes):\n", + " print(f'--- Normalized DataFrame {i+1} ---')\n", + " display(df.head())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Deployment Plan\n", + "\n", + "The code in this notebook will be transitioned to the main ETL pipeline by following these steps:\n", + "\n", + "1. **Function Migration**: The `clean_the_gsheets` and `normalize_dataframes` functions will be moved to a new utility module, for example, `src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_utils.py`. Each function will be decorated with `@task` from Prefect to turn it into a reusable pipeline component.\n", + "2. **Flow Creation**: A new Prefect flow will be created in the `src/ca_biositing/pipeline/ca_biositing/pipeline/flows/` directory (e.g., `master_extraction_flow.py`). This flow will orchestrate the entire ETL process for a given data source.\n", + "3. **Task Integration**: The new flow will be composed of individual tasks. It will call the existing extraction tasks (`proximate.extract`, etc.), and then pass the results to the new cleaning and normalization tasks from `etl_utils.py`.\n", + "4. **Logging**: The `logging` module will be replaced with `get_run_logger()` from Prefect within the tasks to ensure logs are captured by the Prefect UI.\n", + "5. **Configuration**: The `NORMALIZE_COLUMNS` dictionary will be moved to a configuration file or defined within the relevant flow to make it easier to manage and modify without changing the code.\n", + "6. **Testing**: Unit tests will be written for the new utility functions in `etl_utils.py`. An integration test will be created for the new Prefect flow to ensure all the tasks work together correctly.\n", + "7. **Deployment**: Once the flow is complete and tested, it will be deployed to the Prefect server using the `pixi run deploy` command, making it available to be run on a schedule or manually via the UI." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.13.11" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gsheet_extraction_notebook-checkpoint.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gsheet_extraction_notebook-checkpoint.ipynb new file mode 100644 index 00000000..b9feba10 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gsheet_extraction_notebook-checkpoint.ipynb @@ -0,0 +1,899 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "import sys\n", + "import pandas as pd\n", + "import numpy as np\n", + "import janitor as jn\n", + "from IPython.display import display\n", + "\n", + "# --- Robustly find the project root ---\n", + "# The project root is the directory containing the 'pixi.toml' file.\n", + "path = os.getcwd()\n", + "project_root = None\n", + "while path != os.path.dirname(path): # Stop at the filesystem root\n", + " if 'pixi.toml' in os.listdir(path):\n", + " project_root = path\n", + " break\n", + " path = os.path.dirname(path)\n", + "\n", + "if not project_root:\n", + " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", + "\n", + "# --- Add project root to sys.path ---\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + " print(f\"Added project root '{project_root}' to sys.path\")\n", + "else:\n", + " print(f\"Project root '{project_root}' is already in sys.path\")\n", + "\n", + "# --- Import the module ---\n", + "try:\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate, ultimate, cmpana\n", + " print(\"Successfully imported all module.\")\n", + "except ImportError as e:\n", + " print(f\"Failed to import modules: {e}\")\n", + " print(f\"\\nFull sys.path: {sys.path}\")\n", + "\n", + "# --- Run the extraction ---\n", + "if 'proximate' in locals():\n", + " try:\n", + " # Pass the project_root to the extract function\n", + " df = proximate.extract(project_root=project_root)\n", + " if df is not None:\n", + " print(\"\\nSuccessfully extracted proximate data.\")\n", + " display(df.head())\n", + " else:\n", + " print(\"\\n Prox extraction returned no data. Check the logs above for errors.\")\n", + " except Exception as e:\n", + " print(f\"\\nAn error occurred during prox extraction: {e}\")\n", + "\n", + "if 'ultimate' in locals():\n", + " try:\n", + " df2 = ultimate.extract(project_root=project_root)\n", + " if df is not None:\n", + " print(\"\\nSuccessfully extracted Ultimate data.\")\n", + " display(df2.head())\n", + " else:\n", + " print(\"\\n Ultimate extraction returned no data. Check the logs above for errors.\")\n", + " except Exception as e:\n", + " print(f\"\\nAn error occurred during extraction: {e}\")\n", + "\n", + "if 'cmpana' in locals():\n", + " try:\n", + " df3 = cmpana.extract(project_root=project_root)\n", + " if df is not None:\n", + " print(\"\\nSuccessfully extracted CmpAna data.\")\n", + " display(df3.head())\n", + " else:\n", + " print(\"\\nCmpAna extraction returned no data. Check the logs above for errors.\")\n", + " except Exception as e:\n", + " print(f\"\\nAn error occurred during cmp ana extraction: {e}\")\n", + " finally:\n", + " print(\"\\nCmp Ana extraction process completed.\")" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "#### This function seeks to clean the incoming gsheet dataframes and coerce the types" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "def clean_the_gsheets(df):\n", + " # 1. Clean names and drop rows\n", + " df = df.clean_names().dropna(subset=['repl_no', 'value'])\n", + "\n", + " # 2. Coerce types (using errors='coerce' handles messy string data)\n", + " df['repl_no'] = pd.to_numeric(df['repl_no'], errors='coerce').astype('Int32') # Capital 'I' handles NaNs\n", + " df['value'] = pd.to_numeric(df['value'], errors='coerce').astype(np.float32)\n", + "\n", + " # 3. Dates\n", + " df['created_at'] = pd.to_datetime(df['created_at'], errors='coerce')\n", + " df['updated_at'] = pd.to_datetime(df['updated_at'], errors='coerce')\n", + "\n", + " # 4. Convert remaining objects to best possible types (like strings)\n", + " df = df.convert_dtypes()\n", + "\n", + " # 5. Convert all string data to lowercase\n", + " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "\n", + " # 6. Convert empty strings to NaN\n", + " df.replace(\"\", np.nan, inplace=True)\n", + "\n", + " return df # Return the FULL dataframe, not just .head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from sqlmodel import Session, select, create_engine\n", + "import pandas as pd\n", + "import os\n", + "import sys\n", + "from dotenv import load_dotenv\n", + "\n", + "#This module queries the db via the ORM\n", + "\n", + "load_dotenv(dotenv_path=project_root + \"\\\\resources\\\\docker\\\\.env\")\n", + "\n", + "# Database Connection\n", + "\n", + "POSTGRES_USER = os.getenv(\"POSTGRES_USER\")\n", + "POSTGRES_PASSWORD= os.getenv(\"POSTGRES_PASSWORD\")\n", + "\n", + "# 2. Host Port Mapping\n", + "# This is the port on your local machine that will connect to the container's port 5432.\n", + "POSTGRES_PORT= os.getenv(\"POSTGRES_PORT\")\n", + "\n", + "DATABASE_URL = f\"postgresql+psycopg2://{POSTGRES_USER}:{POSTGRES_PASSWORD}@localhost:{POSTGRES_PORT}/biocirv_db\"\n", + "engine = create_engine(DATABASE_URL)\n", + "print(f\"Connected to database.\")\n", + "\n", + "primary_ag_product = pd.read_sql(\"SELECT * FROM primary_ag_product;\", con=engine)\n", + "\n", + "#reorders columns so id and name are first\n", + "cols = ['id', 'name'] + [c for c in primary_ag_product.columns if c not in ['id', 'name']]\n", + "\n", + "primary_ag_product = primary_ag_product[[*cols]]\n", + "\n", + "primary_ag_product\n" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
20:08:34.613 | INFO    | Task run 'extract' - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n",
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To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", + " df.replace(\"\", np.nan, inplace=True)\n" + ] + }, + { + "ename": "NameError", + "evalue": "name 'Resource' is not defined", + "output_type": "error", + "traceback": [ + "\u001b[31m---------------------------------------------------------------------------\u001b[39m", + "\u001b[31mNameError\u001b[39m Traceback (most recent call last)", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[9]\u001b[39m\u001b[32m, line 20\u001b[39m\n\u001b[32m 10\u001b[39m df.replace(\u001b[33mr\u001b[39m\u001b[33m'\u001b[39m\u001b[33m^\u001b[39m\u001b[33m\\\u001b[39m\u001b[33ms*$\u001b[39m\u001b[33m'\u001b[39m, np.nan, regex=\u001b[38;5;28;01mTrue\u001b[39;00m, inplace=\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[32m 13\u001b[39m \u001b[38;5;66;03m# These are columns that need to be normalized, AKA replaced with IDs.\u001b[39;00m\n\u001b[32m 14\u001b[39m \u001b[38;5;66;03m# This is a mapping that has first, what it is called in pandas \"resource\"\u001b[39;00m\n\u001b[32m 15\u001b[39m \u001b[38;5;66;03m# then, the SQLAlchemy model \"Resource\", and then what it is called in the\u001b[39;00m\n\u001b[32m 16\u001b[39m \u001b[38;5;66;03m# database \"name\"\u001b[39;00m\n\u001b[32m 19\u001b[39m NORMALIZE_COLUMNS = {\n\u001b[32m---> \u001b[39m\u001b[32m20\u001b[39m \u001b[33m\"\u001b[39m\u001b[33mresource\u001b[39m\u001b[33m\"\u001b[39m: (\u001b[43mResource\u001b[49m, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 21\u001b[39m \u001b[33m\"\u001b[39m\u001b[33mprepared_sample\u001b[39m\u001b[33m\"\u001b[39m: (PreparedSample, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 22\u001b[39m \u001b[33m\"\u001b[39m\u001b[33mpreparation_method\u001b[39m\u001b[33m\"\u001b[39m: (PreparationMethod, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 23\u001b[39m \u001b[33m\"\u001b[39m\u001b[33mparameter\u001b[39m\u001b[33m\"\u001b[39m: (Parameter, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 24\u001b[39m \u001b[33m\"\u001b[39m\u001b[33munit\u001b[39m\u001b[33m\"\u001b[39m: (Unit, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 25\u001b[39m \u001b[33m\"\u001b[39m\u001b[33manalyst_email\u001b[39m\u001b[33m\"\u001b[39m: (Contact, \u001b[33m\"\u001b[39m\u001b[33memail\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 26\u001b[39m \u001b[33m\"\u001b[39m\u001b[33manalysis_type\u001b[39m\u001b[33m\"\u001b[39m: (AnalysisType, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 27\u001b[39m \u001b[33m\"\u001b[39m\u001b[33mprimary_ag_product\u001b[39m\u001b[33m\"\u001b[39m: (PrimaryAgProduct, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m)\n\u001b[32m 28\u001b[39m }\n\u001b[32m 30\u001b[39m df_normalized = df.copy()\n\u001b[32m 32\u001b[39m \u001b[38;5;28;01mwith\u001b[39;00m Session(engine) \u001b[38;5;28;01mas\u001b[39;00m db:\n", + "\u001b[31mNameError\u001b[39m: name 'Resource' is not defined" + ] + } + ], + "source": [ + "#This is a get_or_create type module for data normalization.\n", + "\n", + "# Extract a df from a gsheet\n", + "df = cmpana.extract(project_root=project_root)\n", + "\n", + "# Cleans the df names and coerces data types\n", + "df = clean_the_gsheets(df)\n", + "\n", + "# Replace empty strings with NaN\n", + "df.replace(r'^\\s*$', np.nan, regex=True, inplace=True)\n", + "\n", + "\n", + "# These are columns that need to be normalized, AKA replaced with IDs.\n", + "# This is a mapping that has first, what it is called in pandas \"resource\"\n", + "# then, the SQLAlchemy model \"Resource\", and then what it is called in the\n", + "# database \"name\"\n", + "\n", + "\n", + "NORMALIZE_COLUMNS = {\n", + " \"resource\": (Resource, \"name\"),\n", + " \"prepared_sample\": (PreparedSample, \"name\"),\n", + " \"preparation_method\": (PreparationMethod, \"name\"),\n", + " \"parameter\": (Parameter, \"name\"),\n", + " \"unit\": (Unit, \"name\"),\n", + " \"analyst_email\": (Contact, \"email\"),\n", + " \"analysis_type\": (AnalysisType, \"name\"),\n", + " \"primary_ag_product\": (PrimaryAgProduct, \"name\")\n", + "}\n", + "\n", + "df_normalized = df.copy()\n", + "\n", + "with Session(engine) as db:\n", + " for df_col, (model, model_name_attr) in NORMALIZE_COLUMNS.items():\n", + " if df_col not in df_normalized.columns:\n", + " continue\n", + "\n", + " df_normalized = replace_name_with_id_df(\n", + " db=db,\n", + " df=df_normalized,\n", + " ref_model=model,\n", + " df_name_column=df_col,\n", + " model_name_attr=model_name_attr,\n", + " id_column_name=\"id\",\n", + " final_column_name=f\"{df_col}_id\",\n", + " )\n", + "\n", + " db.commit()\n", + "\n", + "df_normalized.head()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:20: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", + " df.replace(\"\", np.nan, inplace=True)\n", + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:20: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", + " df.replace(\"\", np.nan, inplace=True)\n" + ] + }, + { + "data": { + "text/html": [ + "
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cmp_uuid_033record_idprepared_sampleresourcepreparation_methodstorage_condexper_abbrevrepl_norepl_idparameter...unitcreated_atupdated_atqc_resultnoteanalysis_typeequipmentraw_data_urlanalyst_emailupload_status
03ee2993d-86e3-1f16-c7ea-f8d555e114(85)e114oak-tmpm01o(85)tomato pomaceoven dryrt vacuum sealedcmp04xk1.0cmp04xk(85)1glucan...% dry weight2025-01-23 09:00:01NaTpassNaNcompositional analysisNaNNaNxkang2@lbl.govready
146878ef9-1226-22a0-d5d8-cf65e241cb(85)41cboak-tmpm01o(85)tomato pomaceoven dryrt vacuum sealedcmp04xk2.0cmp04xk(85)2glucan...% dry weight2025-01-23 09:00:16NaTpassNaNcompositional analysisNaNNaNxkang2@lbl.govready
276a7a2f4-c4e4-e60f-1187-dec6e02246(85)2246oak-tmpm01o(85)tomato pomaceoven dryrt vacuum sealedcmp04xk3.0cmp04xk(85)3glucan...% dry weight2025-01-23 09:00:31NaTpassNaNcompositional analysisNaNNaNxkang2@lbl.govready
37a136832-286b-07cb-62de-acf52f9311(85)9311oak-tmpm01o(85)tomato pomaceoven dryrt vacuum sealedcmp04xk1.0cmp04xk(85)1glucose...% dry weight2025-01-23 09:00:46NaTpassNaNcompositional analysisNaNNaNxkang2@lbl.govready
4b709ecee-f9a6-a55d-a59e-93b7b863d7(85)63d7oak-tmpm01o(85)tomato pomaceoven dryrt vacuum sealedcmp04xk2.0cmp04xk(85)2glucose...% dry weight2025-01-23 09:01:01NaTpassNaNcompositional analysisNaNNaNxkang2@lbl.govready
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" + ], + "text/plain": [ + " cmp_uuid_033 record_id prepared_sample \\\n", + "0 3ee2993d-86e3-1f16-c7ea-f8d555e114 (85)e114 oak-tmpm01o(85) \n", + "1 46878ef9-1226-22a0-d5d8-cf65e241cb (85)41cb oak-tmpm01o(85) \n", + "2 76a7a2f4-c4e4-e60f-1187-dec6e02246 (85)2246 oak-tmpm01o(85) \n", + "3 7a136832-286b-07cb-62de-acf52f9311 (85)9311 oak-tmpm01o(85) \n", + "4 b709ecee-f9a6-a55d-a59e-93b7b863d7 (85)63d7 oak-tmpm01o(85) \n", + "\n", + " resource preparation_method storage_cond exper_abbrev repl_no \\\n", + "0 tomato pomace oven dry rt vacuum sealed cmp04xk 1.0 \n", + "1 tomato pomace oven dry rt vacuum sealed cmp04xk 2.0 \n", + "2 tomato pomace oven dry rt vacuum sealed cmp04xk 3.0 \n", + "3 tomato pomace oven dry rt vacuum sealed cmp04xk 1.0 \n", + "4 tomato pomace oven dry rt vacuum sealed cmp04xk 2.0 \n", + "\n", + " repl_id parameter ... unit created_at updated_at \\\n", + "0 cmp04xk(85)1 glucan ... % dry weight 2025-01-23 09:00:01 NaT \n", + "1 cmp04xk(85)2 glucan ... % dry weight 2025-01-23 09:00:16 NaT \n", + "2 cmp04xk(85)3 glucan ... % dry weight 2025-01-23 09:00:31 NaT \n", + "3 cmp04xk(85)1 glucose ... % dry weight 2025-01-23 09:00:46 NaT \n", + "4 cmp04xk(85)2 glucose ... % dry weight 2025-01-23 09:01:01 NaT \n", + "\n", + " qc_result note analysis_type equipment raw_data_url \\\n", + "0 pass NaN compositional analysis NaN NaN \n", + "1 pass NaN compositional analysis NaN NaN \n", + "2 pass NaN compositional analysis NaN NaN \n", + "3 pass NaN compositional analysis NaN NaN \n", + "4 pass NaN compositional analysis NaN NaN \n", + "\n", + " analyst_email upload_status \n", + "0 xkang2@lbl.gov ready \n", + "1 xkang2@lbl.gov ready \n", + "2 xkang2@lbl.gov ready \n", + "3 xkang2@lbl.gov ready \n", + "4 xkang2@lbl.gov ready \n", + "\n", + "[5 rows x 21 columns]" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "dataframes = [df, df2, df3]\n", + "\n", + "clean_dataframes = [clean_the_gsheets(df) for df in dataframes]\n", + "\n", + "clean_dataframes[2].head()\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "from sqlalchemy.orm import Session\n", + "from sqlalchemy import select\n", + "import pandas as pd\n", + "import os\n", + "import sys\n", + "\n", + "# --- project root discovery (unchanged) ---\n", + "path = os.getcwd()\n", + "project_root = None\n", + "while path != os.path.dirname(path):\n", + " if 'pixi.toml' in os.listdir(path):\n", + " project_root = path\n", + " break\n", + " path = os.path.dirname(path)\n", + "\n", + "if not project_root:\n", + " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", + "\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + "\n", + "# --- imports ---\n", + "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", + "from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import PrimaryAgProduct\n", + "\n", + "# --- query + dataframe ---\n", + "with Session(engine) as db:\n", + " stmt = select(*PrimaryAgProduct.__table__.columns)\n", + " rows = db.execute(stmt).mappings().all()\n", + "\n", + "df = pd.DataFrame(rows)\n", + "\n", + "df.head()\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "summary_stats = clean_dataframes[0].\\\n", + " groupby(['resource', 'parameter'])['value'].\\\n", + " agg(['mean', 'median', 'min', 'max', 'std', 'count'])\n", + "\n", + "summary_stats" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "clean_dataframes[0][['resource', 'parameter', 'value', 'unit']].\\\n", + " groupby(['resource', 'parameter', 'unit'], as_index=False).\\\n", + " agg({'value': 'mean'}).\\\n", + " query('value > 30').\\\n", + " sort_values(by='value', ascending=False).\\\n", + " round({'value': 1})\n" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "ename": "KeyError", + "evalue": "'parameter'", + "output_type": "error", + "traceback": [ + "\u001b[31m---------------------------------------------------------------------------\u001b[39m", + "\u001b[31mKeyError\u001b[39m Traceback (most recent call last)", + "\u001b[36mFile \u001b[39m\u001b[32m~\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\pandas\\core\\indexes\\base.py:3812\u001b[39m, in \u001b[36mIndex.get_loc\u001b[39m\u001b[34m(self, key)\u001b[39m\n\u001b[32m 3811\u001b[39m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[32m-> \u001b[39m\u001b[32m3812\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m_engine\u001b[49m\u001b[43m.\u001b[49m\u001b[43mget_loc\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcasted_key\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 3813\u001b[39m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m err:\n", + "\u001b[36mFile \u001b[39m\u001b[32mpandas/_libs/index.pyx:167\u001b[39m, in \u001b[36mpandas._libs.index.IndexEngine.get_loc\u001b[39m\u001b[34m()\u001b[39m\n", + "\u001b[36mFile \u001b[39m\u001b[32mpandas/_libs/index.pyx:196\u001b[39m, in \u001b[36mpandas._libs.index.IndexEngine.get_loc\u001b[39m\u001b[34m()\u001b[39m\n", + "\u001b[36mFile \u001b[39m\u001b[32mpandas/_libs/hashtable_class_helper.pxi:7088\u001b[39m, in \u001b[36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[39m\u001b[34m()\u001b[39m\n", + "\u001b[36mFile \u001b[39m\u001b[32mpandas/_libs/hashtable_class_helper.pxi:7096\u001b[39m, in \u001b[36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[39m\u001b[34m()\u001b[39m\n", + "\u001b[31mKeyError\u001b[39m: 'parameter'", + "\nThe above exception was the direct cause of the following exception:\n", + "\u001b[31mKeyError\u001b[39m Traceback (most recent call last)", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[17]\u001b[39m\u001b[32m, line 9\u001b[39m\n\u001b[32m 6\u001b[39m df.loc[df[\u001b[33m'\u001b[39m\u001b[33mparameter\u001b[39m\u001b[33m'\u001b[39m].isin(list_of_param), \u001b[33m'\u001b[39m\u001b[33mcheck\u001b[39m\u001b[33m'\u001b[39m] = \u001b[33m\"\u001b[39m\u001b[33mIn list\u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m 7\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m df\n\u001b[32m----> \u001b[39m\u001b[32m9\u001b[39m \u001b[43mis_it_volatile_solids\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdf\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 11\u001b[39m df[[\u001b[33m'\u001b[39m\u001b[33mcheck\u001b[39m\u001b[33m'\u001b[39m, \u001b[33m'\u001b[39m\u001b[33mparameter\u001b[39m\u001b[33m'\u001b[39m]]\n", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[17]\u001b[39m\u001b[32m, line 6\u001b[39m, in \u001b[36mis_it_volatile_solids\u001b[39m\u001b[34m(df)\u001b[39m\n\u001b[32m 3\u001b[39m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34mis_it_volatile_solids\u001b[39m(df):\n\u001b[32m 4\u001b[39m df[\u001b[33m'\u001b[39m\u001b[33mcheck\u001b[39m\u001b[33m'\u001b[39m] = \u001b[33m\"\u001b[39m\u001b[33mVS\u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m6\u001b[39m df.loc[\u001b[43mdf\u001b[49m\u001b[43m[\u001b[49m\u001b[33;43m'\u001b[39;49m\u001b[33;43mparameter\u001b[39;49m\u001b[33;43m'\u001b[39;49m\u001b[43m]\u001b[49m.isin(list_of_param), \u001b[33m'\u001b[39m\u001b[33mcheck\u001b[39m\u001b[33m'\u001b[39m] = \u001b[33m\"\u001b[39m\u001b[33mIn list\u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m 7\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m df\n", + "\u001b[36mFile \u001b[39m\u001b[32m~\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\pandas\\core\\frame.py:4113\u001b[39m, in \u001b[36mDataFrame.__getitem__\u001b[39m\u001b[34m(self, key)\u001b[39m\n\u001b[32m 4111\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m.columns.nlevels > \u001b[32m1\u001b[39m:\n\u001b[32m 4112\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m._getitem_multilevel(key)\n\u001b[32m-> \u001b[39m\u001b[32m4113\u001b[39m indexer = \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mcolumns\u001b[49m\u001b[43m.\u001b[49m\u001b[43mget_loc\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 4114\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m is_integer(indexer):\n\u001b[32m 4115\u001b[39m indexer = [indexer]\n", + "\u001b[36mFile \u001b[39m\u001b[32m~\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\pandas\\core\\indexes\\base.py:3819\u001b[39m, in \u001b[36mIndex.get_loc\u001b[39m\u001b[34m(self, key)\u001b[39m\n\u001b[32m 3814\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(casted_key, \u001b[38;5;28mslice\u001b[39m) \u001b[38;5;129;01mor\u001b[39;00m (\n\u001b[32m 3815\u001b[39m \u001b[38;5;28misinstance\u001b[39m(casted_key, abc.Iterable)\n\u001b[32m 3816\u001b[39m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;28many\u001b[39m(\u001b[38;5;28misinstance\u001b[39m(x, \u001b[38;5;28mslice\u001b[39m) \u001b[38;5;28;01mfor\u001b[39;00m x \u001b[38;5;129;01min\u001b[39;00m casted_key)\n\u001b[32m 3817\u001b[39m ):\n\u001b[32m 3818\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m InvalidIndexError(key)\n\u001b[32m-> \u001b[39m\u001b[32m3819\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(key) \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01merr\u001b[39;00m\n\u001b[32m 3820\u001b[39m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m:\n\u001b[32m 3821\u001b[39m \u001b[38;5;66;03m# If we have a listlike key, _check_indexing_error will raise\u001b[39;00m\n\u001b[32m 3822\u001b[39m \u001b[38;5;66;03m# InvalidIndexError. Otherwise we fall through and re-raise\u001b[39;00m\n\u001b[32m 3823\u001b[39m \u001b[38;5;66;03m# the TypeError.\u001b[39;00m\n\u001b[32m 3824\u001b[39m \u001b[38;5;28mself\u001b[39m._check_indexing_error(key)\n", + "\u001b[31mKeyError\u001b[39m: 'parameter'" + ] + } + ], + "source": [ + "list_of_param = (\"Moisture\", \"Total solids\", \"Ash\")\n", + "\n", + "def is_it_volatile_solids(df):\n", + " df['check'] = \"VS\"\n", + "\n", + " df.loc[df['parameter'].isin(list_of_param), 'check'] = \"In list\"\n", + " return df\n", + "\n", + "is_it_volatile_solids(df)\n", + "\n", + "df[['check', 'parameter']]\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "#This defines a function to calculate the square root of the 'value' column in a DataFrame\n", + "def sqrtvalue(df):\n", + " df = df.assign(sqrtvalue = df['value'] ** 0.5)\n", + " return df\n", + "\n", + "#List comprehension to apply sqrtvalue to each DataFrame\n", + "clean_rooted_df = [sqrtvalue(df) for df in clean_dataframes]\n", + "\n", + "# Display the head of the third DataFrame\n", + "clean_rooted_df[2].head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "cmpana_raw = cmpana.extract(project_root=project_root)\n", + "\n", + "cmpana_raw.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", + " df.replace(\"\", np.nan, inplace=True)\n" + ] + }, + { + "ename": "TypeError", + "evalue": "replace_name_with_id_df() got an unexpected keyword argument 'name_column_name'. Did you mean 'id_column_name'?", + "output_type": "error", + "traceback": [ + "\u001b[31m---------------------------------------------------------------------------\u001b[39m", + "\u001b[31mTypeError\u001b[39m Traceback (most recent call last)", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[20]\u001b[39m\u001b[32m, line 16\u001b[39m\n\u001b[32m 14\u001b[39m \u001b[38;5;66;03m#this replaces the names with IDs\u001b[39;00m\n\u001b[32m 15\u001b[39m \u001b[38;5;28;01mwith\u001b[39;00m Session(engine) \u001b[38;5;28;01mas\u001b[39;00m db:\n\u001b[32m---> \u001b[39m\u001b[32m16\u001b[39m parameter_ids = \u001b[43mreplace_name_with_id_df\u001b[49m\u001b[43m(\u001b[49m\n\u001b[32m 17\u001b[39m \u001b[43m \u001b[49m\u001b[43mdb\u001b[49m\u001b[43m=\u001b[49m\u001b[43mdb\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m 18\u001b[39m \u001b[43m \u001b[49m\u001b[43mdf\u001b[49m\u001b[43m=\u001b[49m\u001b[43mtest_df\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m 19\u001b[39m \u001b[43m \u001b[49m\u001b[43mref_model\u001b[49m\u001b[43m=\u001b[49m\u001b[43mParameter\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m 20\u001b[39m \u001b[43m \u001b[49m\u001b[43mname_column_name\u001b[49m\u001b[43m=\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mname\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;66;43;03m# column in df + table\u001b[39;49;00m\n\u001b[32m 21\u001b[39m \u001b[43m \u001b[49m\u001b[43mid_column_name\u001b[49m\u001b[43m=\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mid\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;66;43;03m# PK column in table\u001b[39;49;00m\n\u001b[32m 22\u001b[39m \u001b[43m \u001b[49m\u001b[43mfinal_column_name\u001b[49m\u001b[43m=\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mparameter_id\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\n\u001b[32m 23\u001b[39m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 25\u001b[39m \u001b[38;5;66;03m##I EVENTUALLY WANT SOME LOGS ABOUT HOW MANY WERE ADDED, HOW MANY RETRIEVED, ETC. MAYBE PUT THAT IN THE \u001b[39;00m\n\u001b[32m 26\u001b[39m \u001b[38;5;66;03m#resource_id_mapping = df_with_ids.rename(columns={\"id\": \"resource_id\"})\u001b[39;00m\n\u001b[32m 27\u001b[39m \n\u001b[32m 28\u001b[39m \u001b[38;5;66;03m#resource_id_mapping\u001b[39;00m\n", + "\u001b[31mTypeError\u001b[39m: replace_name_with_id_df() got an unexpected keyword argument 'name_column_name'. Did you mean 'id_column_name'?" + ] + } + ], + "source": [ + "from sqlalchemy.orm import Session\n", + "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", + "from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", + "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import (\n", + " replace_name_with_id_df,\n", + ") \n", + "\n", + "#This extractst the raw proximate data\n", + "df = cmpana.extract(project_root=project_root)\n", + "\n", + "#this cleans the names to lowercase and parses data into a standard format. Also renames the column to match with what will be in the database\n", + "test_df = clean_the_gsheets(df).rename(columns={'parameter': 'name'})\n", + "\n", + "#this replaces the names with IDs\n", + "with Session(engine) as db:\n", + " parameter_ids = replace_name_with_id_df(\n", + " db=db,\n", + " df=test_df,\n", + " ref_model=Parameter,\n", + " name_column_name=\"name\", # column in df + table\n", + " id_column_name=\"id\", # PK column in table\n", + " final_column_name=\"parameter_id\"\n", + " )\n", + "\n", + "##I EVENTUALLY WANT SOME LOGS ABOUT HOW MANY WERE ADDED, HOW MANY RETRIEVED, ETC. MAYBE PUT THAT IN THE \n", + "#resource_id_mapping = df_with_ids.rename(columns={\"id\": \"resource_id\"})\n", + "\n", + "#resource_id_mapping\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "parameter_ids\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np\n", + "from prefect import get_run_logger\n", + "\n", + "resource = pd.read_sql(\"SELECT id, name FROM resource\", con=engine)\n", + "\n", + "resource['name'] = resource['name'].str.lower()\n", + "\n", + "resource['name'] = resource['name'].replace('', np.nan)\n", + "resource.dropna(subset=['name'], inplace=True)\n", + "\n", + "\n", + "resource\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "resource = pd.read_sql(\"SELECT id, name FROM resource\", con=engine)\n", + "\n", + "#this converts the entire dataframe to lowercase\n", + "df = df.map(lambda x: x.lower() if isinstance(x, str) else x)\n", + "\n", + "print(df)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "field_sample = pd.read_sql_query(\"SELECT * FROM field_sample\", con=engine)\n", + "\n", + "field_sample = field_sample[['id', 'name', 'resource_id']]\n", + "\n", + "field_sample" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "#This is a get_or_create type module for data normalization.\n", + "\n", + "# Extract a df from a gsheet\n", + "df = cmpana.extract(project_root=project_root)\n", + "\n", + "# Cleans the df names and coerces data types\n", + "df = clean_the_gsheets(df)\n", + "\n", + "# Replace empty strings with NaN\n", + "df.replace(r'^\\s*$', np.nan, regex=True, inplace=True)\n", + "\n", + "\n", + "# These are columns that need to be normalized, AKA replaced with IDs.\n", + "# This is a mapping that has first, what it is called in pandas \"resource\"\n", + "# then, the SQLAlchemy model \"Resource\", and then what it is called in the\n", + "# database \"name\"\n", + "\n", + "\n", + "NORMALIZE_COLUMNS = {\n", + " \"resource\": (Resource, \"name\"),\n", + " \"prepared_sample\": (PreparedSample, \"name\"),\n", + " \"preparation_method\": (PreparationMethod, \"name\"),\n", + " \"parameter\": (Parameter, \"name\"),\n", + " \"unit\": (Unit, \"name\"),\n", + " \"analyst_email\": (Contact, \"email\"),\n", + " \"analysis_type\": (AnalysisType, \"name\"),\n", + " \"primary_ag_product\": (PrimaryAgProduct, \"name\")\n", + "}\n", + "\n", + "df_normalized = df.copy()\n", + "\n", + "with Session(engine) as db:\n", + " for df_col, (model, model_name_attr) in NORMALIZE_COLUMNS.items():\n", + " if df_col not in df_normalized.columns:\n", + " continue\n", + "\n", + " df_normalized = replace_name_with_id_df(\n", + " db=db,\n", + " df=df_normalized,\n", + " ref_model=model,\n", + " df_name_column=df_col,\n", + " model_name_attr=model_name_attr,\n", + " id_column_name=\"id\",\n", + " final_column_name=f\"{df_col}_id\",\n", + " )\n", + "\n", + " db.commit()\n", + "\n", + "df_normalized.head()\n" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.13.11" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/engine.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/engine.py index a24e92a0..c5349511 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/engine.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/engine.py @@ -1,6 +1,32 @@ from sqlmodel import create_engine, Session +import os +from dotenv import load_dotenv -DATABASE_URL = "postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db" +#This module queries the db via the ORM + +# Get the root +path = os.getcwd() +project_root = None +while path != os.path.dirname(path): # Stop at the filesystem root + if 'pixi.toml' in os.listdir(path): + project_root = path + break + path = os.path.dirname(path) + +load_dotenv(dotenv_path=project_root + "\\resources\\docker\\.env") + +# Database Connection +POSTGRES_USER = os.getenv("POSTGRES_USER") +POSTGRES_PASSWORD= os.getenv("POSTGRES_PASSWORD") + +# 2. Host Port Mapping +# This is the port on your local machine that will connect to the container's port 5432. +POSTGRES_PORT= os.getenv("POSTGRES_PORT") + +DATABASE_URL = f"postgresql+psycopg2://{POSTGRES_USER}:{POSTGRES_PASSWORD}@localhost:{POSTGRES_PORT}/biocirv_db" + +# old: +# DATABASE_URL = "postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db" engine = create_engine(DATABASE_URL) db_session = Session(engine) diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb index beb63faf..3c8228d6 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_notebook.ipynb @@ -20,18 +20,9 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2026-01-06 10:39:39,502 - INFO - Project root '/Users/pjsmitty301/ca-biositing' is already in sys.path\n", - "2026-01-06 10:39:39,503 - INFO - Successfully imported all project modules.\n" - ] - } - ], + "outputs": [], "source": [ "import os\n", "import sys\n", @@ -89,7 +80,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -156,7 +147,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 4, "metadata": {}, "outputs": [], "source": [ @@ -240,1483 +231,9 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2026-01-06 10:53:39,195 - INFO - Starting data extraction...\n", - "2026-01-06 10:53:39,212 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-06 10:53:39,266 - INFO - Extracting raw data from '03.1-Proximate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", - "2026-01-06 10:53:41,468 - INFO - Successfully extracted raw data.\n", - "2026-01-06 10:53:41,471 - INFO - Finished in state Completed()\n", - "2026-01-06 10:53:41,486 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-06 10:53:41,497 - INFO - Extracting raw data from '03.7-Ultimate' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", - "2026-01-06 10:53:42,816 - INFO - Successfully extracted raw data.\n", - "2026-01-06 10:53:42,820 - INFO - Finished in state Completed()\n", - "2026-01-06 10:53:42,840 - INFO - HTTP Request: GET http://127.0.0.1:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-06 10:53:42,853 - INFO - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n", - "2026-01-06 10:53:44,427 - INFO - Successfully extracted raw data.\n", - "2026-01-06 10:53:44,430 - INFO - Finished in state Completed()\n", - "2026-01-06 10:53:44,434 - INFO - Data extraction complete.\n", - "2026-01-06 10:53:44,434 - INFO - Starting data cleaning...\n", - "2026-01-06 10:53:44,435 - INFO - Starting DataFrame cleaning process.\n", - "2026-01-06 10:53:44,438 - INFO - Dropped 0 rows with missing values.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:40: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", - " df_cleaned = df_cleaned.replace(r'^\\s*$', np.nan, regex=True)\n", - "2026-01-06 10:53:44,450 - INFO - Successfully cleaned DataFrame.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:48: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", - " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", - "2026-01-06 10:53:44,455 - INFO - Converted all string data to lowercase.\n", - "2026-01-06 10:53:44,456 - INFO - Starting DataFrame cleaning process.\n", - "2026-01-06 10:53:44,457 - INFO - Dropped 0 rows with missing values.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:40: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", - " df_cleaned = df_cleaned.replace(r'^\\s*$', np.nan, regex=True)\n", - "2026-01-06 10:53:44,461 - INFO - Successfully cleaned DataFrame.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:48: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", - " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", - "2026-01-06 10:53:44,467 - INFO - Converted all string data to lowercase.\n", - "2026-01-06 10:53:44,468 - INFO - Starting DataFrame cleaning process.\n", - "2026-01-06 10:53:44,470 - INFO - Dropped 0 rows with missing values.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:40: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", - " df_cleaned = df_cleaned.replace(r'^\\s*$', np.nan, regex=True)\n", - "2026-01-06 10:53:44,480 - INFO - Successfully cleaned DataFrame.\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_82269/2660420268.py:48: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", - " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", - "2026-01-06 10:53:44,487 - INFO - Converted all string data to lowercase.\n", - "2026-01-06 10:53:44,492 - INFO - Data cleaning complete.\n", - "2026-01-06 10:53:44,497 - INFO - Starting data normalization...\n", - "2026-01-06 10:53:44,498 - INFO - Starting normalization process for 3 dataframes.\n", - "2026-01-06 10:53:44,498 - INFO - Processing DataFrame #1 with 1030 rows.\n", - "2026-01-06 10:53:44,500 - INFO - Normalizing column 'resource' using model 'Resource'.\n", - "2026-01-06 10:53:44,526 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 46 null values.\n", - "2026-01-06 10:53:44,527 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", - "2026-01-06 10:53:44,531 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 22 null values.\n", - "2026-01-06 10:53:44,531 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", - "2026-01-06 10:53:44,533 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 22 null values.\n", - "2026-01-06 10:53:44,534 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", - "2026-01-06 10:53:44,536 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 22 null values.\n", - "2026-01-06 10:53:44,537 - INFO - Normalizing column 'unit' using model 'Unit'.\n", - "2026-01-06 10:53:44,539 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", - "2026-01-06 10:53:44,539 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", - "2026-01-06 10:53:44,542 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 550 null values.\n", - "2026-01-06 10:53:44,543 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", - "2026-01-06 10:53:44,546 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 550 null values.\n", - "2026-01-06 10:53:44,546 - WARNING - Column 'primary_ag_product' not in DataFrame #1. Skipping normalization for this column.\n", - "2026-01-06 10:53:44,546 - INFO - Finished processing DataFrame #1.\n", - "2026-01-06 10:53:44,546 - INFO - Processing DataFrame #2 with 64 rows.\n", - "2026-01-06 10:53:44,547 - INFO - Normalizing column 'resource' using model 'Resource'.\n", - "2026-01-06 10:53:44,550 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", - "2026-01-06 10:53:44,550 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", - "2026-01-06 10:53:44,552 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", - "2026-01-06 10:53:44,552 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", - "2026-01-06 10:53:44,554 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", - "2026-01-06 10:53:44,554 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", - "2026-01-06 10:53:44,556 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", - "2026-01-06 10:53:44,557 - INFO - Normalizing column 'unit' using model 'Unit'.\n", - "2026-01-06 10:53:44,558 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", - "2026-01-06 10:53:44,559 - INFO - Skipping normalization for column 'analyst_email' as it contains only null values.\n", - "2026-01-06 10:53:44,559 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", - "2026-01-06 10:53:44,561 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", - "2026-01-06 10:53:44,561 - WARNING - Column 'primary_ag_product' not in DataFrame #2. Skipping normalization for this column.\n", - "2026-01-06 10:53:44,561 - INFO - Finished processing DataFrame #2.\n", - "2026-01-06 10:53:44,562 - INFO - Processing DataFrame #3 with 390 rows.\n", - "2026-01-06 10:53:44,562 - INFO - Normalizing column 'resource' using model 'Resource'.\n", - "2026-01-06 10:53:44,567 - INFO - Successfully normalized 'resource'. New column 'resource_id' contains 0 null values.\n", - "2026-01-06 10:53:44,569 - INFO - Normalizing column 'prepared_sample' using model 'PreparedSample'.\n", - "2026-01-06 10:53:44,580 - INFO - Successfully normalized 'prepared_sample'. New column 'prepared_sample_id' contains 0 null values.\n", - "2026-01-06 10:53:44,580 - INFO - Normalizing column 'preparation_method' using model 'PreparationMethod'.\n", - "2026-01-06 10:53:44,592 - INFO - Successfully normalized 'preparation_method'. New column 'preparation_method_id' contains 0 null values.\n", - "2026-01-06 10:53:44,594 - INFO - Normalizing column 'parameter' using model 'Parameter'.\n", - "2026-01-06 10:53:44,597 - INFO - Successfully normalized 'parameter'. New column 'parameter_id' contains 0 null values.\n", - "2026-01-06 10:53:44,597 - INFO - Normalizing column 'unit' using model 'Unit'.\n", - "2026-01-06 10:53:44,598 - INFO - Successfully normalized 'unit'. New column 'unit_id' contains 0 null values.\n", - "2026-01-06 10:53:44,599 - INFO - Normalizing column 'analyst_email' using model 'Contact'.\n", - "2026-01-06 10:53:44,606 - INFO - Successfully normalized 'analyst_email'. New column 'analyst_email_id' contains 0 null values.\n", - "2026-01-06 10:53:44,607 - INFO - Normalizing column 'analysis_type' using model 'AnalysisType'.\n", - "2026-01-06 10:53:44,610 - INFO - Successfully normalized 'analysis_type'. New column 'analysis_type_id' contains 0 null values.\n", - "2026-01-06 10:53:44,610 - WARNING - Column 'primary_ag_product' not in DataFrame #3. Skipping normalization for this column.\n", - "2026-01-06 10:53:44,610 - INFO - Finished processing DataFrame #3.\n", - "2026-01-06 10:53:44,611 - INFO - Committing database session.\n", - "2026-01-06 10:53:44,612 - INFO - Database commit successful.\n", - "2026-01-06 10:53:44,612 - INFO - Data normalization complete.\n", - "2026-01-06 10:53:44,613 - INFO - Displaying results of normalization...\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "--- Normalized DataFrame 1 ---\n" - ] - }, - { - "data": { - "application/vnd.microsoft.datawrangler.viewer.v0+json": { - "columns": [ - { - "name": "index", - "rawType": "int64", - "type": "integer" - }, - { - "name": "prox_uuid_031", - "rawType": "object", - "type": "string" - }, - { - "name": "record_id", - "rawType": "object", - "type": "string" - }, - { - "name": "source_codename", - "rawType": "object", - "type": "string" - }, - { - "name": "storage_cond", - "rawType": "object", - "type": "string" - }, - { - "name": "exper_abbrev", - "rawType": "object", - "type": "string" - }, - { - "name": "repl_no", - "rawType": "float64", - "type": "float" - }, - { - "name": "repl_id", - "rawType": "object", - "type": "string" - }, - { - "name": "value", - "rawType": "float64", - "type": "float" - }, - { - "name": "created_at", - "rawType": "datetime64[ns]", - "type": "datetime" - }, - { - "name": "updated_at", - "rawType": "datetime64[ns]", - "type": "datetime" - }, - { - "name": "qc_result", - "rawType": "object", - "type": "string" - }, - { - "name": "upload_status", - "rawType": "object", - "type": "unknown" - }, - { - "name": "note", - "rawType": "float64", - "type": "float" - }, - { - "name": "resource_id", - "rawType": "float64", - "type": "float" - }, - { - "name": "prepared_sample_id", - "rawType": "float64", - "type": "float" - }, - { - "name": "preparation_method_id", - "rawType": "float64", - "type": "float" - }, - { - "name": "parameter_id", - "rawType": "float64", - "type": "float" - }, - { - "name": "unit_id", - "rawType": "int64", - "type": "integer" - }, - { - "name": "analyst_email_id", - "rawType": "float64", - "type": "float" - }, - { - "name": "analysis_type_id", - "rawType": "float64", - "type": "float" - } - ], - "ref": "bcafe3ce-a742-48cc-9fb2-da62f6c91695", - "rows": [ - [ - "0", - "d7965110-407f-e356-d41d-b3b9a2b7b7", - "(73)b7b7", - "oakleaf", - "4c", - "prox01xk", - "1.0", - "prox01xk(73)1", - "61.849998474121094", - "2024-10-02 10:31:01", - null, - "pass", - "not ready", - null, - "5.0", - "109.0", - "7.0", - "3.0", - "1", - "1.0", - "1.0" - ], - [ - "1", - "c8fea984-2e9a-8def-55fb-1a9d7d9ba8", - "(73)9ba8", - "oakleaf", - "4c", - "prox01xk", - "2.0", - "prox01xk(73)2", - "63.209999084472656", - "2024-10-02 10:31:31", - null, - "pass", - "ready", - null, - "5.0", - "109.0", - "7.0", - "3.0", - "1", - "1.0", - "1.0" - ], - [ - "2", - "df304d5d-3a85-4881-7142-6d4e5f957d", - "(73)957d", - "oakleaf", - "4c", - "prox01xk", - "3.0", - "prox01xk(73)3", - "63.27000045776367", - "2024-10-02 10:32:01", - null, - "pass", - "imported", - null, - "5.0", - "109.0", - "7.0", - "3.0", - "1", - "1.0", - "1.0" - ], - [ - "3", - "01c6c5be-cea6-54af-3924-b0bad69335", - "(73)9335", - "oakleaf", - "4c", - "prox01xk", - "1.0", - "prox01xk(73)1", - "0.6899999976158142", - "2024-10-03 10:31:01", - null, - "pass", - "import failed", - null, - "5.0", - "109.0", - "7.0", - "4.0", - "1", - "1.0", - "1.0" - ], - [ - "4", - "126745c7-dd41-2f6d-0dc5-28dbca415f", - "(73)415f", - "oakleaf", - "4c", - "prox01xk", - "2.0", - "prox01xk(73)2", - "0.8899999856948853", - "2024-10-03 10:31:31", - null, - "pass", - null, - null, - "5.0", - "109.0", - "7.0", - "4.0", - "1", - "1.0", - "1.0" - ] - ], - "shape": { - "columns": 20, - "rows": 5 - } - }, - "text/html": [ - "
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276a7a2f4-c4e4-e60f-1187-dec6e02246(85)2246rt vacuum sealedcmp04xk3cmp04xk(85)314.122025-01-23 09:00:31NaTpass...NaNNaNready592813213
37a136832-286b-07cb-62de-acf52f9311(85)9311rt vacuum sealedcmp04xk1cmp04xk(85)115.742025-01-23 09:00:46NaTpass...NaNNaNready592811213
4b709ecee-f9a6-a55d-a59e-93b7b863d7(85)63d7rt vacuum sealedcmp04xk2cmp04xk(85)215.752025-01-23 09:01:01NaTpass...NaNNaNready592811213
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idnamenotedescriptionuri
01Tomatoes for processingNoneNoneNone
12GrapesNoneNoneNone
23AlmondsNoneNoneNone
34WalnutsNoneNoneNone
45Sweet potatoesNoneNoneNone
56AlgaeNoneNoneNone
67Olives - processingNoneNoneNone
78Corn - allNoneNoneNone
89Hay - alfalfaNoneNoneNone
910Silage - wheatNoneNoneNone
1011RiceNoneNoneNone
1112PeachesNoneNoneNone
1213PotatoesNoneNoneNone
1314Cucumbers and picklesNoneNoneNone
1415PistachiosNoneNoneNone
1516CottonNoneNoneNone
1617Olives - marketNoneNoneNone
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" - ], - "text/plain": [ - " id name note description uri\n", - "0 1 Tomatoes for processing None None None\n", - "1 2 Grapes None None None\n", - "2 3 Almonds None None None\n", - "3 4 Walnuts None None None\n", - "4 5 Sweet potatoes None None None\n", - "5 6 Algae None None None\n", - "6 7 Olives - processing None None None\n", - "7 8 Corn - all None None None\n", - "8 9 Hay - alfalfa None None None\n", - "9 10 Silage - wheat None None None\n", - "10 11 Rice None None None\n", - "11 12 Peaches None None None\n", - "12 13 Potatoes None None None\n", - "13 14 Cucumbers and pickles None None None\n", - "14 15 Pistachios None None None\n", - "15 16 Cotton None None None\n", - "16 17 Olives - market None None None\n", - "17 18 None None None" - ] - }, - "execution_count": 11, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "from sqlmodel import Session, select, create_engine\n", "import pandas as pd\n", "import os\n", "import sys\n", + "from dotenv import load_dotenv\n", "\n", "#This module queries the db via the ORM\n", "\n", + "load_dotenv(dotenv_path=project_root + \"\\\\resources\\\\docker\\\\.env\")\n", + "\n", "# Database Connection\n", - "DATABASE_URL = \"postgresql+psycopg2://biocirv_user:biocirv_dev_password@localhost:5432/biocirv_db\"\n", + "\n", + "POSTGRES_USER = os.getenv(\"POSTGRES_USER\")\n", + "POSTGRES_PASSWORD= os.getenv(\"POSTGRES_PASSWORD\")\n", + "\n", + "# 2. Host Port Mapping\n", + "# This is the port on your local machine that will connect to the container's port 5432.\n", + "POSTGRES_PORT= os.getenv(\"POSTGRES_PORT\")\n", + "\n", + "DATABASE_URL = f\"postgresql+psycopg2://{POSTGRES_USER}:{POSTGRES_PASSWORD}@localhost:{POSTGRES_PORT}/biocirv_db\"\n", "engine = create_engine(DATABASE_URL)\n", "print(f\"Connected to database.\")\n", "\n", @@ -542,9 +157,70 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
20:08:34.613 | INFO    | Task run 'extract' - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n",
+       "
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20:08:36.203 | INFO    | Task run 'extract' - Successfully extracted raw data.\n",
+       "
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20:08:36.211 | INFO    | Task run 'extract' - Finished in state Completed()\n",
+       "
\n" + ], + "text/plain": [ + "20:08:36.211 | \u001b[36mINFO\u001b[0m | Task run 'extract' - Finished in state \u001b[32mCompleted\u001b[0m()\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:20: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", + " df.replace(\"\", np.nan, inplace=True)\n" + ] + }, + { + "ename": "NameError", + "evalue": "name 'Resource' is not defined", + "output_type": "error", + "traceback": [ + "\u001b[31m---------------------------------------------------------------------------\u001b[39m", + "\u001b[31mNameError\u001b[39m Traceback (most recent call last)", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[9]\u001b[39m\u001b[32m, line 20\u001b[39m\n\u001b[32m 10\u001b[39m df.replace(\u001b[33mr\u001b[39m\u001b[33m'\u001b[39m\u001b[33m^\u001b[39m\u001b[33m\\\u001b[39m\u001b[33ms*$\u001b[39m\u001b[33m'\u001b[39m, np.nan, regex=\u001b[38;5;28;01mTrue\u001b[39;00m, inplace=\u001b[38;5;28;01mTrue\u001b[39;00m)\n\u001b[32m 13\u001b[39m \u001b[38;5;66;03m# These are columns that need to be normalized, AKA replaced with IDs.\u001b[39;00m\n\u001b[32m 14\u001b[39m \u001b[38;5;66;03m# This is a mapping that has first, what it is called in pandas \"resource\"\u001b[39;00m\n\u001b[32m 15\u001b[39m \u001b[38;5;66;03m# then, the SQLAlchemy model \"Resource\", and then what it is called in the\u001b[39;00m\n\u001b[32m 16\u001b[39m \u001b[38;5;66;03m# database \"name\"\u001b[39;00m\n\u001b[32m 19\u001b[39m NORMALIZE_COLUMNS = {\n\u001b[32m---> \u001b[39m\u001b[32m20\u001b[39m \u001b[33m\"\u001b[39m\u001b[33mresource\u001b[39m\u001b[33m\"\u001b[39m: (\u001b[43mResource\u001b[49m, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 21\u001b[39m \u001b[33m\"\u001b[39m\u001b[33mprepared_sample\u001b[39m\u001b[33m\"\u001b[39m: (PreparedSample, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 22\u001b[39m \u001b[33m\"\u001b[39m\u001b[33mpreparation_method\u001b[39m\u001b[33m\"\u001b[39m: (PreparationMethod, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 23\u001b[39m \u001b[33m\"\u001b[39m\u001b[33mparameter\u001b[39m\u001b[33m\"\u001b[39m: (Parameter, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 24\u001b[39m \u001b[33m\"\u001b[39m\u001b[33munit\u001b[39m\u001b[33m\"\u001b[39m: (Unit, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 25\u001b[39m \u001b[33m\"\u001b[39m\u001b[33manalyst_email\u001b[39m\u001b[33m\"\u001b[39m: (Contact, \u001b[33m\"\u001b[39m\u001b[33memail\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 26\u001b[39m \u001b[33m\"\u001b[39m\u001b[33manalysis_type\u001b[39m\u001b[33m\"\u001b[39m: (AnalysisType, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m),\n\u001b[32m 27\u001b[39m \u001b[33m\"\u001b[39m\u001b[33mprimary_ag_product\u001b[39m\u001b[33m\"\u001b[39m: (PrimaryAgProduct, \u001b[33m\"\u001b[39m\u001b[33mname\u001b[39m\u001b[33m\"\u001b[39m)\n\u001b[32m 28\u001b[39m }\n\u001b[32m 30\u001b[39m df_normalized = df.copy()\n\u001b[32m 32\u001b[39m \u001b[38;5;28;01mwith\u001b[39;00m Session(engine) \u001b[38;5;28;01mas\u001b[39;00m db:\n", + "\u001b[31mNameError\u001b[39m: name 'Resource' is not defined" + ] + } + ], "source": [ "#This is a get_or_create type module for data normalization.\n", "\n", @@ -606,257 +282,20 @@ "name": "stderr", "output_type": "stream", "text": [ - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_9286/3648773749.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_9286/3648773749.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:20: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", + " df.replace(\"\", np.nan, inplace=True)\n", + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", - "/var/folders/2l/qpqn5_6578z142wxn32lbtw00000gn/T/ipykernel_9286/3648773749.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", - " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n" + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:20: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", + " df.replace(\"\", np.nan, inplace=True)\n" ] }, { "data": { - "application/vnd.microsoft.datawrangler.viewer.v0+json": { - "columns": [ - { - "name": "index", - "rawType": "int64", - "type": "integer" - }, - { - "name": "cmp_uuid_033", - "rawType": "object", - "type": "string" - }, - { - "name": "record_id", - "rawType": "object", - "type": "string" - }, - { - "name": "prepared_sample", - "rawType": "object", - "type": "string" - }, - { - "name": "resource", - "rawType": "object", - "type": "string" - }, - { - "name": "preparation_method", - "rawType": "object", - "type": "string" - }, - { - "name": "storage_cond", - "rawType": "object", - "type": "string" - }, - { - "name": "exper_abbrev", - "rawType": "object", - "type": "string" - }, - { - "name": "repl_no", - "rawType": "int64", - "type": "integer" - }, - { - "name": "repl_id", - "rawType": "object", - "type": "string" - }, - { - "name": "parameter", - "rawType": "object", - "type": "string" - }, - { - "name": "value", - "rawType": "float64", - "type": "float" - }, - { - "name": "unit", - "rawType": "object", - "type": "string" - }, - { - "name": "created_at", - "rawType": "datetime64[ns]", - "type": "datetime" - }, - { - "name": "updated_at", - "rawType": "datetime64[ns]", - "type": "datetime" - }, - { - "name": "qc_result", - "rawType": "object", - "type": "string" - }, - { - "name": "note", - "rawType": "object", - "type": "string" - }, - { - "name": "analysis_type", - "rawType": "object", - "type": "string" - }, - { - "name": "equipment", - "rawType": "object", - "type": "string" - }, - { - "name": "raw_data_url", - "rawType": "object", - "type": "string" - }, - { - "name": "analyst_email", - "rawType": "object", - "type": "string" - }, - { - "name": "upload_status", - "rawType": "object", - "type": "string" - } - ], - "ref": "b4e5431c-6847-48e5-894f-3a2387854a2b", - "rows": [ - [ - "0", - "3ee2993d-86e3-1f16-c7ea-f8d555e114", - "(85)e114", - "oak-tmpm01o(85)", - "tomato pomace", - "oven dry", - "rt vacuum sealed", - "cmp04xk", - "1", - "cmp04xk(85)1", - "glucan", - "14.15999984741211", - "% dry weight", - "2025-01-23 09:00:01", - null, - "pass", - "", - "chemical composition", - "", - "", - "xkang2@lbl.gov", - "ready" - ], - [ - "1", - "46878ef9-1226-22a0-d5d8-cf65e241cb", - "(85)41cb", - "oak-tmpm01o(85)", - "tomato pomace", - "oven dry", - "rt vacuum sealed", - "cmp04xk", - "2", - "cmp04xk(85)2", - "glucan", - "14.180000305175781", - "% dry weight", - "2025-01-23 09:00:16", - null, - "pass", - "", - "chemical composition", - "", - "", - "xkang2@lbl.gov", - "ready" - ], - [ - "2", - "76a7a2f4-c4e4-e60f-1187-dec6e02246", - "(85)2246", - "oak-tmpm01o(85)", - "tomato pomace", - "oven dry", - "rt vacuum sealed", - "cmp04xk", - "3", - "cmp04xk(85)3", - "glucan", - "14.119999885559082", - "% dry weight", - "2025-01-23 09:00:31", - null, - "pass", - "", - "chemical composition", - "", - "", - "xkang2@lbl.gov", - "ready" - ], - [ - "3", - "7a136832-286b-07cb-62de-acf52f9311", - "(85)9311", - "oak-tmpm01o(85)", - "tomato pomace", - "oven dry", - "rt vacuum sealed", - "cmp04xk", - "1", - "cmp04xk(85)1", - "glucose", - "15.739999771118164", - "% dry weight", - "2025-01-23 09:00:46", - null, - "pass", - "", - "chemical composition", - "", - "", - "xkang2@lbl.gov", - "ready" - ], - [ - "4", - "b709ecee-f9a6-a55d-a59e-93b7b863d7", - "(85)63d7", - "oak-tmpm01o(85)", - "tomato pomace", - "oven dry", - "rt vacuum sealed", - "cmp04xk", - "2", - "cmp04xk(85)2", - "glucose", - "15.75", - "% dry weight", - "2025-01-23 09:01:01", - null, - "pass", - "", - "chemical composition", - "", - "", - "xkang2@lbl.gov", - "ready" - ] - ], - "shape": { - "columns": 21, - "rows": 5 - } - }, "text/html": [ "
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" - ], - "text/plain": [ - " description id name note uri\n", - "0 None 1 Tomatoes for processing None None\n", - "1 None 2 Grapes None None\n", - "2 None 3 Almonds None None\n", - "3 None 4 Walnuts None None\n", - "4 None 5 Sweet potatoes None None" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "from sqlalchemy.orm import Session\n", "from sqlalchemy import select\n", @@ -1315,9 +586,32 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 17, "metadata": {}, - "outputs": [], + "outputs": [ + { + "ename": "KeyError", + "evalue": "'parameter'", + "output_type": "error", + "traceback": [ + "\u001b[31m---------------------------------------------------------------------------\u001b[39m", + "\u001b[31mKeyError\u001b[39m Traceback (most recent call last)", + "\u001b[36mFile \u001b[39m\u001b[32m~\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\pandas\\core\\indexes\\base.py:3812\u001b[39m, in \u001b[36mIndex.get_loc\u001b[39m\u001b[34m(self, key)\u001b[39m\n\u001b[32m 3811\u001b[39m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[32m-> \u001b[39m\u001b[32m3812\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m_engine\u001b[49m\u001b[43m.\u001b[49m\u001b[43mget_loc\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcasted_key\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 3813\u001b[39m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m err:\n", + "\u001b[36mFile \u001b[39m\u001b[32mpandas/_libs/index.pyx:167\u001b[39m, in \u001b[36mpandas._libs.index.IndexEngine.get_loc\u001b[39m\u001b[34m()\u001b[39m\n", + "\u001b[36mFile \u001b[39m\u001b[32mpandas/_libs/index.pyx:196\u001b[39m, in \u001b[36mpandas._libs.index.IndexEngine.get_loc\u001b[39m\u001b[34m()\u001b[39m\n", + "\u001b[36mFile \u001b[39m\u001b[32mpandas/_libs/hashtable_class_helper.pxi:7088\u001b[39m, in \u001b[36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[39m\u001b[34m()\u001b[39m\n", + "\u001b[36mFile \u001b[39m\u001b[32mpandas/_libs/hashtable_class_helper.pxi:7096\u001b[39m, in \u001b[36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[39m\u001b[34m()\u001b[39m\n", + "\u001b[31mKeyError\u001b[39m: 'parameter'", + "\nThe above exception was the direct cause of the following exception:\n", + "\u001b[31mKeyError\u001b[39m Traceback (most recent call last)", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[17]\u001b[39m\u001b[32m, line 9\u001b[39m\n\u001b[32m 6\u001b[39m df.loc[df[\u001b[33m'\u001b[39m\u001b[33mparameter\u001b[39m\u001b[33m'\u001b[39m].isin(list_of_param), \u001b[33m'\u001b[39m\u001b[33mcheck\u001b[39m\u001b[33m'\u001b[39m] = \u001b[33m\"\u001b[39m\u001b[33mIn list\u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m 7\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m df\n\u001b[32m----> \u001b[39m\u001b[32m9\u001b[39m \u001b[43mis_it_volatile_solids\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdf\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 11\u001b[39m df[[\u001b[33m'\u001b[39m\u001b[33mcheck\u001b[39m\u001b[33m'\u001b[39m, \u001b[33m'\u001b[39m\u001b[33mparameter\u001b[39m\u001b[33m'\u001b[39m]]\n", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[17]\u001b[39m\u001b[32m, line 6\u001b[39m, in \u001b[36mis_it_volatile_solids\u001b[39m\u001b[34m(df)\u001b[39m\n\u001b[32m 3\u001b[39m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34mis_it_volatile_solids\u001b[39m(df):\n\u001b[32m 4\u001b[39m df[\u001b[33m'\u001b[39m\u001b[33mcheck\u001b[39m\u001b[33m'\u001b[39m] = \u001b[33m\"\u001b[39m\u001b[33mVS\u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m6\u001b[39m df.loc[\u001b[43mdf\u001b[49m\u001b[43m[\u001b[49m\u001b[33;43m'\u001b[39;49m\u001b[33;43mparameter\u001b[39;49m\u001b[33;43m'\u001b[39;49m\u001b[43m]\u001b[49m.isin(list_of_param), \u001b[33m'\u001b[39m\u001b[33mcheck\u001b[39m\u001b[33m'\u001b[39m] = \u001b[33m\"\u001b[39m\u001b[33mIn list\u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m 7\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m df\n", + "\u001b[36mFile \u001b[39m\u001b[32m~\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\pandas\\core\\frame.py:4113\u001b[39m, in \u001b[36mDataFrame.__getitem__\u001b[39m\u001b[34m(self, key)\u001b[39m\n\u001b[32m 4111\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m.columns.nlevels > \u001b[32m1\u001b[39m:\n\u001b[32m 4112\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m._getitem_multilevel(key)\n\u001b[32m-> \u001b[39m\u001b[32m4113\u001b[39m indexer = \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mcolumns\u001b[49m\u001b[43m.\u001b[49m\u001b[43mget_loc\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 4114\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m is_integer(indexer):\n\u001b[32m 4115\u001b[39m indexer = [indexer]\n", + "\u001b[36mFile \u001b[39m\u001b[32m~\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\pandas\\core\\indexes\\base.py:3819\u001b[39m, in \u001b[36mIndex.get_loc\u001b[39m\u001b[34m(self, key)\u001b[39m\n\u001b[32m 3814\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(casted_key, \u001b[38;5;28mslice\u001b[39m) \u001b[38;5;129;01mor\u001b[39;00m (\n\u001b[32m 3815\u001b[39m \u001b[38;5;28misinstance\u001b[39m(casted_key, abc.Iterable)\n\u001b[32m 3816\u001b[39m \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;28many\u001b[39m(\u001b[38;5;28misinstance\u001b[39m(x, \u001b[38;5;28mslice\u001b[39m) \u001b[38;5;28;01mfor\u001b[39;00m x \u001b[38;5;129;01min\u001b[39;00m casted_key)\n\u001b[32m 3817\u001b[39m ):\n\u001b[32m 3818\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m InvalidIndexError(key)\n\u001b[32m-> \u001b[39m\u001b[32m3819\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(key) \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01merr\u001b[39;00m\n\u001b[32m 3820\u001b[39m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m:\n\u001b[32m 3821\u001b[39m \u001b[38;5;66;03m# If we have a listlike key, _check_indexing_error will raise\u001b[39;00m\n\u001b[32m 3822\u001b[39m \u001b[38;5;66;03m# InvalidIndexError. Otherwise we fall through and re-raise\u001b[39;00m\n\u001b[32m 3823\u001b[39m \u001b[38;5;66;03m# the TypeError.\u001b[39;00m\n\u001b[32m 3824\u001b[39m \u001b[38;5;28mself\u001b[39m._check_indexing_error(key)\n", + "\u001b[31mKeyError\u001b[39m: 'parameter'" + ] + } + ], "source": [ "list_of_param = (\"Moisture\", \"Total solids\", \"Ash\")\n", "\n", @@ -1365,9 +659,70 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 20, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
20:10:08.640 | INFO    | Task run 'extract' - Extracting raw data from '03.3-CmpAna' in 'Aim 1-Feedstock Collection and Processing Data-BioCirV'...\n",
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20:10:10.346 | INFO    | Task run 'extract' - Successfully extracted raw data.\n",
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20:10:10.356 | INFO    | Task run 'extract' - Finished in state Completed()\n",
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\n" + ], + "text/plain": [ + "20:10:10.356 | \u001b[36mINFO\u001b[0m | Task run 'extract' - Finished in state \u001b[32mCompleted\u001b[0m()\n" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:17: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.\n", + " df = df.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + "C:\\Users\\Abigail\\AppData\\Local\\Temp\\ipykernel_36096\\4080610521.py:20: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)`\n", + " df.replace(\"\", np.nan, inplace=True)\n" + ] + }, + { + "ename": "TypeError", + "evalue": "replace_name_with_id_df() got an unexpected keyword argument 'name_column_name'. Did you mean 'id_column_name'?", + "output_type": "error", + "traceback": [ + "\u001b[31m---------------------------------------------------------------------------\u001b[39m", + "\u001b[31mTypeError\u001b[39m Traceback (most recent call last)", + "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[20]\u001b[39m\u001b[32m, line 16\u001b[39m\n\u001b[32m 14\u001b[39m \u001b[38;5;66;03m#this replaces the names with IDs\u001b[39;00m\n\u001b[32m 15\u001b[39m \u001b[38;5;28;01mwith\u001b[39;00m Session(engine) \u001b[38;5;28;01mas\u001b[39;00m db:\n\u001b[32m---> \u001b[39m\u001b[32m16\u001b[39m parameter_ids = \u001b[43mreplace_name_with_id_df\u001b[49m\u001b[43m(\u001b[49m\n\u001b[32m 17\u001b[39m \u001b[43m \u001b[49m\u001b[43mdb\u001b[49m\u001b[43m=\u001b[49m\u001b[43mdb\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m 18\u001b[39m \u001b[43m \u001b[49m\u001b[43mdf\u001b[49m\u001b[43m=\u001b[49m\u001b[43mtest_df\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m 19\u001b[39m \u001b[43m \u001b[49m\u001b[43mref_model\u001b[49m\u001b[43m=\u001b[49m\u001b[43mParameter\u001b[49m\u001b[43m,\u001b[49m\n\u001b[32m 20\u001b[39m \u001b[43m \u001b[49m\u001b[43mname_column_name\u001b[49m\u001b[43m=\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mname\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;66;43;03m# column in df + table\u001b[39;49;00m\n\u001b[32m 21\u001b[39m \u001b[43m \u001b[49m\u001b[43mid_column_name\u001b[49m\u001b[43m=\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mid\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;66;43;03m# PK column in table\u001b[39;49;00m\n\u001b[32m 22\u001b[39m \u001b[43m \u001b[49m\u001b[43mfinal_column_name\u001b[49m\u001b[43m=\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mparameter_id\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\n\u001b[32m 23\u001b[39m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 25\u001b[39m \u001b[38;5;66;03m##I EVENTUALLY WANT SOME LOGS ABOUT HOW MANY WERE ADDED, HOW MANY RETRIEVED, ETC. MAYBE PUT THAT IN THE \u001b[39;00m\n\u001b[32m 26\u001b[39m \u001b[38;5;66;03m#resource_id_mapping = df_with_ids.rename(columns={\"id\": \"resource_id\"})\u001b[39;00m\n\u001b[32m 27\u001b[39m \n\u001b[32m 28\u001b[39m \u001b[38;5;66;03m#resource_id_mapping\u001b[39;00m\n", + "\u001b[31mTypeError\u001b[39m: replace_name_with_id_df() got an unexpected keyword argument 'name_column_name'. Did you mean 'id_column_name'?" + ] + } + ], "source": [ "from sqlalchemy.orm import Session\n", "from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", @@ -1522,7 +877,7 @@ ], "metadata": { "kernelspec": { - "display_name": "default", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, From 1c0d6816781cfd1cf7459dd0bbee9652913a3cee Mon Sep 17 00:00:00 2001 From: Avi <32148378+avi9664@users.noreply.github.com> Date: Tue, 13 Jan 2026 18:44:19 -0800 Subject: [PATCH 76/81] feat (pipeline): extract data from infrastructure gdrive folder --- .../.ipynb_checkpoints/cmpana-checkpoint.py | 59 ++++ .../experiments-checkpoint.py | 31 ++ .../.ipynb_checkpoints/ultimate-checkpoint.py | 59 ++++ .../external_etl_notebook-checkpoint.ipynb | 318 ++++++++++++++++++ .../utils/external_etl_notebook.ipynb | 318 ++++++++++++++++++ 5 files changed, 785 insertions(+) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/cmpana-checkpoint.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/experiments-checkpoint.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ultimate-checkpoint.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/cmpana-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/cmpana-checkpoint.py new file mode 100644 index 00000000..b34a39ca --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/cmpana-checkpoint.py @@ -0,0 +1,59 @@ +""" +ETL Extract Template +--- + +This module provides a template for extracting data from a Google Sheet. + +To use this template: +1. Copy this file to the appropriate subdirectory in `src/etl/extract/`. + For example: `src/etl/extract/new_module/new_data.py` +2. Update the configuration constants (`GSHEET_NAME`, `WORKSHEET_NAME`). +3. Ensure the `CREDENTIALS_PATH` is correct. +""" + +from typing import Optional +import os +import pandas as pd +from prefect import task, get_run_logger +from ...utils.gsheet_to_pandas import gsheet_to_df + +# --- CONFIGURATION --- +# TODO: Replace with the name of the Google Sheet file. +GSHEET_NAME = "Aim 1-Feedstock Collection and Processing Data-BioCirV" + +# TODO: Replace with the exact name of the worksheet/tab to extract data from. +WORKSHEET_NAME = "03.3-CmpAna" + +# The path to the credentials file. This is typically kept in the project root. +CREDENTIALS_PATH = "credentials.json" + + +@task +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: + """ + Extracts raw data from the specified Google Sheet worksheet. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + logger.info(f"Extracting raw data from '{WORKSHEET_NAME}' in '{GSHEET_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + + # The gsheet_to_df function handles authentication, data fetching, and error handling. + raw_df = gsheet_to_df(GSHEET_NAME, WORKSHEET_NAME, credentials_path) + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/experiments-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/experiments-checkpoint.py new file mode 100644 index 00000000..9a74e350 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/experiments-checkpoint.py @@ -0,0 +1,31 @@ +from typing import Optional +import pandas as pd +from prefect import task, get_run_logger +from ...utils.gsheet_to_pandas import gsheet_to_df + +@task +def extract_experiments() -> Optional[pd.DataFrame]: + """ + Extracts the raw data from the '03-Experiment' worksheet in the Google Sheet. + + This function is purely for extraction (the 'E' in ETL). It connects to the + data source and returns the data as is, without any transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + logger.info("Extracting raw data from '03-Experiments' worksheet...") + + GSHEET_NAME = "Aim 1-Feedstock Collection and Processing Data-BioCirV" + WORKSHEET_NAME = "03.0-Experiments" + CREDENTIALS_PATH = "credentials.json" + + raw_experiments_df = gsheet_to_df(GSHEET_NAME, WORKSHEET_NAME, CREDENTIALS_PATH) + + if raw_experiments_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_experiments_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ultimate-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ultimate-checkpoint.py new file mode 100644 index 00000000..c7495876 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ultimate-checkpoint.py @@ -0,0 +1,59 @@ +""" +ETL Extract Template +--- + +This module provides a template for extracting data from a Google Sheet. + +To use this template: +1. Copy this file to the appropriate subdirectory in `src/etl/extract/`. + For example: `src/etl/extract/new_module/new_data.py` +2. Update the configuration constants (`GSHEET_NAME`, `WORKSHEET_NAME`). +3. Ensure the `CREDENTIALS_PATH` is correct. +""" + +from typing import Optional +import os +import pandas as pd +from prefect import task, get_run_logger +from ...utils.gsheet_to_pandas import gsheet_to_df + +# --- CONFIGURATION --- +# TODO: Replace with the name of the Google Sheet file. +GSHEET_NAME = "Aim 1-Feedstock Collection and Processing Data-BioCirV" + +# TODO: Replace with the exact name of the worksheet/tab to extract data from. +WORKSHEET_NAME = "03.7-Ultimate" + +# The path to the credentials file. This is typically kept in the project root. +CREDENTIALS_PATH = "credentials.json" + + +@task +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: + """ + Extracts raw data from the specified Google Sheet worksheet. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + logger.info(f"Extracting raw data from '{WORKSHEET_NAME}' in '{GSHEET_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + + # The gsheet_to_df function handles authentication, data fetching, and error handling. + raw_df = gsheet_to_df(GSHEET_NAME, WORKSHEET_NAME, credentials_path) + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb new file mode 100644 index 00000000..3c8228d6 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb @@ -0,0 +1,318 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## ETL Notebook for CA Biositing Project\n", + "\n", + "This notebook provides a documented walkthrough of the ETL (Extract, Transform, Load) process for the CA Biositing project. It is designed for interactive development and exploration before migrating logic into the production pipeline.\n", + "\n", + "It covers:\n", + "\n", + "1. **Setup**: Importing necessary libraries and establishing a connection to the database.\n", + "2. **Extraction**: Pulling raw data from Google Sheets.\n", + "3. **Cleaning**: Standardizing data types, handling missing values, and cleaning column names.\n", + "4. **Normalization**: Replacing human-readable names (e.g., \"Corn\") with database foreign key IDs (e.g., `resource_id: 1`).\n", + "5. **Utilities**: Common functions for data manipulation and analysis.\n", + "6. **Deployment Plan**: A step-by-step guide for moving the code from this notebook into the production ETL modules." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "import sys\n", + "import pandas as pd\n", + "import numpy as np\n", + "import janitor as jn\n", + "import logging\n", + "from IPython.display import display\n", + "from sqlalchemy.orm import Session\n", + "from sqlalchemy import select\n", + "\n", + "# --- Basic Logging Configuration for Notebook ---\n", + "# When running in a notebook, we use Python's standard logging.\n", + "# In the production pipeline, this will be replaced by Prefect's `get_run_logger()`\n", + "logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')\n", + "logger = logging.getLogger()\n", + "\n", + "# --- Robustly find the project root ---\n", + "# This ensures that the notebook can be run from any directory within the project.\n", + "path = os.getcwd()\n", + "project_root = None\n", + "while path != os.path.dirname(path):\n", + " if 'pixi.toml' in os.listdir(path):\n", + " project_root = path\n", + " break\n", + " path = os.path.dirname(path)\n", + "\n", + "if not project_root:\n", + " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", + "\n", + "# Add the project root to the Python path to allow for module imports\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + " logger.info(f\"Added project root '{project_root}' to sys.path\")\n", + "else:\n", + " logger.info(f\"Project root '{project_root}' is already in sys.path\")\n", + "\n", + "# --- Import project modules ---\n", + "try:\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", + " from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import replace_name_with_id_df\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate, ultimate, cmpana\n", + " logger.info('Successfully imported all project modules.')\n", + "except ImportError as e:\n", + " logger.error(f'Failed to import project modules: {e}', exc_info=True)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Data Cleaning Function" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "def clean_the_gsheets(df):\n", + " \"\"\"Cleans and standardizes a DataFrame extracted from Google Sheets.\n", + "\n", + " This function performs several key operations:\n", + " 1. Cleans column names to a standard format (snake_case).\n", + " 2. Drops rows where essential columns ('repl_no', 'value') are empty.\n", + " 3. Coerces data types for numeric and datetime columns, handling errors gracefully.\n", + " 4. Converts remaining columns to the best possible data types.\n", + "\n", + " Args:\n", + " df (pd.DataFrame): The raw DataFrame.\n", + "\n", + " Returns:\n", + " pd.DataFrame: The cleaned DataFrame.\n", + " \"\"\"\n", + " logger.info('Starting DataFrame cleaning process.')\n", + " if not isinstance(df, pd.DataFrame):\n", + " logger.error('Input is not a pandas DataFrame.')\n", + " return None\n", + " \n", + " try:\n", + " # 1. Clean names and drop rows with missing essential data\n", + " df_cleaned = df.clean_names().dropna(subset=['repl_no', 'value'])\n", + " logger.info(f'Dropped {len(df) - len(df_cleaned)} rows with missing values.')\n", + "\n", + " # 2. Coerce numeric types\n", + " df_cleaned['repl_no'] = pd.to_numeric(df_cleaned['repl_no'], errors='coerce').astype('Int32')\n", + " df_cleaned['value'] = pd.to_numeric(df_cleaned['value'], errors='coerce').astype(np.float32)\n", + "\n", + " # 3. Coerce datetime types\n", + " if 'created_at' in df_cleaned.columns:\n", + " df_cleaned['created_at'] = pd.to_datetime(df_cleaned['created_at'], errors='coerce')\n", + " if 'updated_at' in df_cleaned.columns:\n", + " df_cleaned['updated_at'] = pd.to_datetime(df_cleaned['updated_at'], errors='coerce')\n", + "\n", + " # 4. Replace empty strings with NaN so they are properly ignored\n", + " df_cleaned = df_cleaned.replace(r'^\\s*$', np.nan, regex=True)\n", + "\n", + " # 5. Convert other dtypes to best possible\n", + " df_cleaned = df_cleaned.convert_dtypes()\n", + " logger.info('Successfully cleaned DataFrame.')\n", + "\n", + " # 6. Convert all string data to lowercase\n", + " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + " logger.info('Converted all string data to lowercase.')\n", + " return df_cleaned\n", + "\n", + " except Exception as e:\n", + " logger.error(f'An error occurred during DataFrame cleaning: {e}', exc_info=True)\n", + " return None\n", + "\n", + " " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Data Normalization Function" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "def normalize_dataframes(dataframes, normalize_columns):\n", + " \"\"\"Normalizes a list of DataFrames by replacing name columns with foreign key IDs.\n", + "\n", + " This function iterates through a list of dataframes and, for each one, iterates\n", + " through a dictionary of columns that need to be normalized. It uses the \n", + " `replace_name_with_id_df` utility to look up or create the corresponding ID\n", + " in the database.\n", + "\n", + " Args:\n", + " dataframes (list[pd.DataFrame]): A list of DataFrames to normalize.\n", + " normalize_columns (dict): A dictionary mapping column names to SQLModel classes and attributes.\n", + "\n", + " Returns:\n", + " list[pd.DataFrame]: The list of normalized DataFrames.\n", + " \"\"\"\n", + " logger.info(f'Starting normalization process for {len(dataframes)} dataframes.')\n", + " normalized_dfs = []\n", + " try:\n", + " with Session(engine) as db:\n", + " for i, df in enumerate(dataframes):\n", + " if not isinstance(df, pd.DataFrame):\n", + " logger.warning(f'Item {i+1} is not a DataFrame, skipping.')\n", + " continue\n", + " \n", + " logger.info(f'Processing DataFrame #{i+1} with {len(df)} rows.')\n", + " df_normalized = df.copy()\n", + "\n", + " for df_col, (model, model_name_attr) in normalize_columns.items():\n", + " if df_col not in df_normalized.columns:\n", + " logger.warning(f\"Column '{df_col}' not in DataFrame #{i+1}. Skipping normalization for this column.\")\n", + " continue\n", + " \n", + " try:\n", + " # Skip normalization if the column is all NaN/None\n", + " if df_normalized[df_col].isnull().all():\n", + " logger.info(f\"Skipping normalization for column '{df_col}' as it contains only null values.\")\n", + " continue\n", + " \n", + " logger.info(f\"Normalizing column '{df_col}' using model '{model.__name__}'.\")\n", + " df_normalized, num_created = replace_name_with_id_df(\n", + " db=db,\n", + " df=df_normalized,\n", + " ref_model=model,\n", + " df_name_column=df_col,\n", + " model_name_attr=model_name_attr,\n", + " id_column_name='id',\n", + " final_column_name=f'{df_col}_id'\n", + " )\n", + " if num_created > 0:\n", + " logger.info(f\"Created {num_created} new records in '{model.__name__}' table.\")\n", + " new_col_name = f'{df_col}_id'\n", + " num_nulls = df_normalized[new_col_name].isnull().sum()\n", + " logger.info(f\"Successfully normalized '{df_col}'. New column '{new_col_name}' contains {num_nulls} null values.\")\n", + " except Exception as e:\n", + " logger.error(f\"Error normalizing column '{df_col}' in DataFrame #{i+1}: {e}\", exc_info=True)\n", + " continue # Continue to the next column\n", + " \n", + " normalized_dfs.append(df_normalized)\n", + " logger.info(f'Finished processing DataFrame #{i+1}.')\n", + " \n", + " logger.info('Committing database session.')\n", + " db.commit()\n", + " logger.info('Database commit successful.')\n", + " except Exception as e:\n", + " logger.error(f'A critical error occurred during the database session: {e}', exc_info=True)\n", + " db.rollback()\n", + " logger.info('Database session rolled back.')\n", + " \n", + " return normalized_dfs\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### ETL Execution Example" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# --- 1. Extraction ---\n", + "# In a real Prefect flow, each extraction would be a separate task.\n", + "logger.info('Starting data extraction...')\n", + "prox_df = proximate.extract(project_root=project_root)\n", + "ult_df = ultimate.extract(project_root=project_root)\n", + "cmp_df = cmpana.extract(project_root=project_root)\n", + "dataframes = [prox_df, ult_df, cmp_df]\n", + "logger.info('Data extraction complete.')\n", + "\n", + "# --- 2. Cleaning ---\n", + "# This list comprehension applies the cleaning function to each extracted dataframe.\n", + "logger.info('Starting data cleaning...')\n", + "clean_dataframes = [clean_the_gsheets(df) for df in dataframes if df is not None]\n", + "logger.info('Data cleaning complete.')\n", + "\n", + "# --- 3. Normalization ---\n", + "# This dictionary defines the columns to be normalized. \n", + "# The key is the column name in the DataFrame.\n", + "# The value is a tuple containing the corresponding SQLAlchemy model and the name of the attribute on the model to match against.\n", + "NORMALIZE_COLUMNS = {\n", + " 'resource': (Resource, 'name'),\n", + " 'prepared_sample': (PreparedSample, 'name'),\n", + " 'preparation_method': (PreparationMethod, 'name'),\n", + " 'parameter': (Parameter, 'name'),\n", + " 'unit': (Unit, 'name'),\n", + " 'analyst_email': (Contact, 'email'),\n", + " 'analysis_type': (AnalysisType, 'name'),\n", + " 'primary_ag_product': (PrimaryAgProduct, 'name')\n", + "}\n", + "\n", + "logger.info('Starting data normalization...')\n", + "normalized_dataframes = normalize_dataframes(clean_dataframes, NORMALIZE_COLUMNS)\n", + "logger.info('Data normalization complete.')\n", + "\n", + "# --- 4. Display Results ---\n", + "logger.info('Displaying results of normalization...')\n", + "for i, df in enumerate(normalized_dataframes):\n", + " print(f'--- Normalized DataFrame {i+1} ---')\n", + " display(df.head())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Deployment Plan\n", + "\n", + "The code in this notebook will be transitioned to the main ETL pipeline by following these steps:\n", + "\n", + "1. **Function Migration**: The `clean_the_gsheets` and `normalize_dataframes` functions will be moved to a new utility module, for example, `src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_utils.py`. Each function will be decorated with `@task` from Prefect to turn it into a reusable pipeline component.\n", + "2. **Flow Creation**: A new Prefect flow will be created in the `src/ca_biositing/pipeline/ca_biositing/pipeline/flows/` directory (e.g., `master_extraction_flow.py`). This flow will orchestrate the entire ETL process for a given data source.\n", + "3. **Task Integration**: The new flow will be composed of individual tasks. It will call the existing extraction tasks (`proximate.extract`, etc.), and then pass the results to the new cleaning and normalization tasks from `etl_utils.py`.\n", + "4. **Logging**: The `logging` module will be replaced with `get_run_logger()` from Prefect within the tasks to ensure logs are captured by the Prefect UI.\n", + "5. **Configuration**: The `NORMALIZE_COLUMNS` dictionary will be moved to a configuration file or defined within the relevant flow to make it easier to manage and modify without changing the code.\n", + "6. **Testing**: Unit tests will be written for the new utility functions in `etl_utils.py`. An integration test will be created for the new Prefect flow to ensure all the tasks work together correctly.\n", + "7. **Deployment**: Once the flow is complete and tested, it will be deployed to the Prefect server using the `pixi run deploy` command, making it available to be run on a schedule or manually via the UI." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.13.11" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb new file mode 100644 index 00000000..3c8228d6 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb @@ -0,0 +1,318 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## ETL Notebook for CA Biositing Project\n", + "\n", + "This notebook provides a documented walkthrough of the ETL (Extract, Transform, Load) process for the CA Biositing project. It is designed for interactive development and exploration before migrating logic into the production pipeline.\n", + "\n", + "It covers:\n", + "\n", + "1. **Setup**: Importing necessary libraries and establishing a connection to the database.\n", + "2. **Extraction**: Pulling raw data from Google Sheets.\n", + "3. **Cleaning**: Standardizing data types, handling missing values, and cleaning column names.\n", + "4. **Normalization**: Replacing human-readable names (e.g., \"Corn\") with database foreign key IDs (e.g., `resource_id: 1`).\n", + "5. **Utilities**: Common functions for data manipulation and analysis.\n", + "6. **Deployment Plan**: A step-by-step guide for moving the code from this notebook into the production ETL modules." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "import sys\n", + "import pandas as pd\n", + "import numpy as np\n", + "import janitor as jn\n", + "import logging\n", + "from IPython.display import display\n", + "from sqlalchemy.orm import Session\n", + "from sqlalchemy import select\n", + "\n", + "# --- Basic Logging Configuration for Notebook ---\n", + "# When running in a notebook, we use Python's standard logging.\n", + "# In the production pipeline, this will be replaced by Prefect's `get_run_logger()`\n", + "logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')\n", + "logger = logging.getLogger()\n", + "\n", + "# --- Robustly find the project root ---\n", + "# This ensures that the notebook can be run from any directory within the project.\n", + "path = os.getcwd()\n", + "project_root = None\n", + "while path != os.path.dirname(path):\n", + " if 'pixi.toml' in os.listdir(path):\n", + " project_root = path\n", + " break\n", + " path = os.path.dirname(path)\n", + "\n", + "if not project_root:\n", + " raise FileNotFoundError(\"Could not find project root containing 'pixi.toml'.\")\n", + "\n", + "# Add the project root to the Python path to allow for module imports\n", + "if project_root not in sys.path:\n", + " sys.path.insert(0, project_root)\n", + " logger.info(f\"Added project root '{project_root}' to sys.path\")\n", + "else:\n", + " logger.info(f\"Project root '{project_root}' is already in sys.path\")\n", + "\n", + "# --- Import project modules ---\n", + "try:\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", + " from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import replace_name_with_id_df\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate, ultimate, cmpana\n", + " logger.info('Successfully imported all project modules.')\n", + "except ImportError as e:\n", + " logger.error(f'Failed to import project modules: {e}', exc_info=True)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Data Cleaning Function" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "def clean_the_gsheets(df):\n", + " \"\"\"Cleans and standardizes a DataFrame extracted from Google Sheets.\n", + "\n", + " This function performs several key operations:\n", + " 1. Cleans column names to a standard format (snake_case).\n", + " 2. Drops rows where essential columns ('repl_no', 'value') are empty.\n", + " 3. Coerces data types for numeric and datetime columns, handling errors gracefully.\n", + " 4. Converts remaining columns to the best possible data types.\n", + "\n", + " Args:\n", + " df (pd.DataFrame): The raw DataFrame.\n", + "\n", + " Returns:\n", + " pd.DataFrame: The cleaned DataFrame.\n", + " \"\"\"\n", + " logger.info('Starting DataFrame cleaning process.')\n", + " if not isinstance(df, pd.DataFrame):\n", + " logger.error('Input is not a pandas DataFrame.')\n", + " return None\n", + " \n", + " try:\n", + " # 1. Clean names and drop rows with missing essential data\n", + " df_cleaned = df.clean_names().dropna(subset=['repl_no', 'value'])\n", + " logger.info(f'Dropped {len(df) - len(df_cleaned)} rows with missing values.')\n", + "\n", + " # 2. Coerce numeric types\n", + " df_cleaned['repl_no'] = pd.to_numeric(df_cleaned['repl_no'], errors='coerce').astype('Int32')\n", + " df_cleaned['value'] = pd.to_numeric(df_cleaned['value'], errors='coerce').astype(np.float32)\n", + "\n", + " # 3. Coerce datetime types\n", + " if 'created_at' in df_cleaned.columns:\n", + " df_cleaned['created_at'] = pd.to_datetime(df_cleaned['created_at'], errors='coerce')\n", + " if 'updated_at' in df_cleaned.columns:\n", + " df_cleaned['updated_at'] = pd.to_datetime(df_cleaned['updated_at'], errors='coerce')\n", + "\n", + " # 4. Replace empty strings with NaN so they are properly ignored\n", + " df_cleaned = df_cleaned.replace(r'^\\s*$', np.nan, regex=True)\n", + "\n", + " # 5. Convert other dtypes to best possible\n", + " df_cleaned = df_cleaned.convert_dtypes()\n", + " logger.info('Successfully cleaned DataFrame.')\n", + "\n", + " # 6. Convert all string data to lowercase\n", + " df_cleaned = df_cleaned.applymap(lambda s: s.lower() if isinstance(s, str) else s)\n", + " logger.info('Converted all string data to lowercase.')\n", + " return df_cleaned\n", + "\n", + " except Exception as e:\n", + " logger.error(f'An error occurred during DataFrame cleaning: {e}', exc_info=True)\n", + " return None\n", + "\n", + " " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Data Normalization Function" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "def normalize_dataframes(dataframes, normalize_columns):\n", + " \"\"\"Normalizes a list of DataFrames by replacing name columns with foreign key IDs.\n", + "\n", + " This function iterates through a list of dataframes and, for each one, iterates\n", + " through a dictionary of columns that need to be normalized. It uses the \n", + " `replace_name_with_id_df` utility to look up or create the corresponding ID\n", + " in the database.\n", + "\n", + " Args:\n", + " dataframes (list[pd.DataFrame]): A list of DataFrames to normalize.\n", + " normalize_columns (dict): A dictionary mapping column names to SQLModel classes and attributes.\n", + "\n", + " Returns:\n", + " list[pd.DataFrame]: The list of normalized DataFrames.\n", + " \"\"\"\n", + " logger.info(f'Starting normalization process for {len(dataframes)} dataframes.')\n", + " normalized_dfs = []\n", + " try:\n", + " with Session(engine) as db:\n", + " for i, df in enumerate(dataframes):\n", + " if not isinstance(df, pd.DataFrame):\n", + " logger.warning(f'Item {i+1} is not a DataFrame, skipping.')\n", + " continue\n", + " \n", + " logger.info(f'Processing DataFrame #{i+1} with {len(df)} rows.')\n", + " df_normalized = df.copy()\n", + "\n", + " for df_col, (model, model_name_attr) in normalize_columns.items():\n", + " if df_col not in df_normalized.columns:\n", + " logger.warning(f\"Column '{df_col}' not in DataFrame #{i+1}. Skipping normalization for this column.\")\n", + " continue\n", + " \n", + " try:\n", + " # Skip normalization if the column is all NaN/None\n", + " if df_normalized[df_col].isnull().all():\n", + " logger.info(f\"Skipping normalization for column '{df_col}' as it contains only null values.\")\n", + " continue\n", + " \n", + " logger.info(f\"Normalizing column '{df_col}' using model '{model.__name__}'.\")\n", + " df_normalized, num_created = replace_name_with_id_df(\n", + " db=db,\n", + " df=df_normalized,\n", + " ref_model=model,\n", + " df_name_column=df_col,\n", + " model_name_attr=model_name_attr,\n", + " id_column_name='id',\n", + " final_column_name=f'{df_col}_id'\n", + " )\n", + " if num_created > 0:\n", + " logger.info(f\"Created {num_created} new records in '{model.__name__}' table.\")\n", + " new_col_name = f'{df_col}_id'\n", + " num_nulls = df_normalized[new_col_name].isnull().sum()\n", + " logger.info(f\"Successfully normalized '{df_col}'. New column '{new_col_name}' contains {num_nulls} null values.\")\n", + " except Exception as e:\n", + " logger.error(f\"Error normalizing column '{df_col}' in DataFrame #{i+1}: {e}\", exc_info=True)\n", + " continue # Continue to the next column\n", + " \n", + " normalized_dfs.append(df_normalized)\n", + " logger.info(f'Finished processing DataFrame #{i+1}.')\n", + " \n", + " logger.info('Committing database session.')\n", + " db.commit()\n", + " logger.info('Database commit successful.')\n", + " except Exception as e:\n", + " logger.error(f'A critical error occurred during the database session: {e}', exc_info=True)\n", + " db.rollback()\n", + " logger.info('Database session rolled back.')\n", + " \n", + " return normalized_dfs\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### ETL Execution Example" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# --- 1. Extraction ---\n", + "# In a real Prefect flow, each extraction would be a separate task.\n", + "logger.info('Starting data extraction...')\n", + "prox_df = proximate.extract(project_root=project_root)\n", + "ult_df = ultimate.extract(project_root=project_root)\n", + "cmp_df = cmpana.extract(project_root=project_root)\n", + "dataframes = [prox_df, ult_df, cmp_df]\n", + "logger.info('Data extraction complete.')\n", + "\n", + "# --- 2. Cleaning ---\n", + "# This list comprehension applies the cleaning function to each extracted dataframe.\n", + "logger.info('Starting data cleaning...')\n", + "clean_dataframes = [clean_the_gsheets(df) for df in dataframes if df is not None]\n", + "logger.info('Data cleaning complete.')\n", + "\n", + "# --- 3. Normalization ---\n", + "# This dictionary defines the columns to be normalized. \n", + "# The key is the column name in the DataFrame.\n", + "# The value is a tuple containing the corresponding SQLAlchemy model and the name of the attribute on the model to match against.\n", + "NORMALIZE_COLUMNS = {\n", + " 'resource': (Resource, 'name'),\n", + " 'prepared_sample': (PreparedSample, 'name'),\n", + " 'preparation_method': (PreparationMethod, 'name'),\n", + " 'parameter': (Parameter, 'name'),\n", + " 'unit': (Unit, 'name'),\n", + " 'analyst_email': (Contact, 'email'),\n", + " 'analysis_type': (AnalysisType, 'name'),\n", + " 'primary_ag_product': (PrimaryAgProduct, 'name')\n", + "}\n", + "\n", + "logger.info('Starting data normalization...')\n", + "normalized_dataframes = normalize_dataframes(clean_dataframes, NORMALIZE_COLUMNS)\n", + "logger.info('Data normalization complete.')\n", + "\n", + "# --- 4. Display Results ---\n", + "logger.info('Displaying results of normalization...')\n", + "for i, df in enumerate(normalized_dataframes):\n", + " print(f'--- Normalized DataFrame {i+1} ---')\n", + " display(df.head())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Deployment Plan\n", + "\n", + "The code in this notebook will be transitioned to the main ETL pipeline by following these steps:\n", + "\n", + "1. **Function Migration**: The `clean_the_gsheets` and `normalize_dataframes` functions will be moved to a new utility module, for example, `src/ca_biositing/pipeline/ca_biositing/pipeline/utils/etl_utils.py`. Each function will be decorated with `@task` from Prefect to turn it into a reusable pipeline component.\n", + "2. **Flow Creation**: A new Prefect flow will be created in the `src/ca_biositing/pipeline/ca_biositing/pipeline/flows/` directory (e.g., `master_extraction_flow.py`). This flow will orchestrate the entire ETL process for a given data source.\n", + "3. **Task Integration**: The new flow will be composed of individual tasks. It will call the existing extraction tasks (`proximate.extract`, etc.), and then pass the results to the new cleaning and normalization tasks from `etl_utils.py`.\n", + "4. **Logging**: The `logging` module will be replaced with `get_run_logger()` from Prefect within the tasks to ensure logs are captured by the Prefect UI.\n", + "5. **Configuration**: The `NORMALIZE_COLUMNS` dictionary will be moved to a configuration file or defined within the relevant flow to make it easier to manage and modify without changing the code.\n", + "6. **Testing**: Unit tests will be written for the new utility functions in `etl_utils.py`. An integration test will be created for the new Prefect flow to ensure all the tasks work together correctly.\n", + "7. **Deployment**: Once the flow is complete and tested, it will be deployed to the Prefect server using the `pixi run deploy` command, making it available to be run on a schedule or manually via the UI." + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.13.11" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} From daa285bc4e9fb176da8dac66fe8245c6ad6d5975 Mon Sep 17 00:00:00 2001 From: Avi <32148378+avi9664@users.noreply.github.com> Date: Tue, 13 Jan 2026 18:50:34 -0800 Subject: [PATCH 77/81] feat (pipeline): extract data from infrastructure gdrive folder (push the rest) --- pixi.lock | 3146 +++++++++++++---- pixi.toml | 1 + .../basic_sample_info-checkpoint.py | 31 + .../biodiesel_plants-checkpoint.py | 34 + .../proximate-checkpoint.py | 59 + .../pipeline/etl/extract/biodiesel_plants.py | 34 + .../pipeline/etl/extract/external.py | 59 + .../Biodiesel_Plants-checkpoint.csv | 79 + .../Biodiesel_Plants.csv | 79 + .../external_etl_notebook-checkpoint.ipynb | 295 +- .../gdrive_to_pandas-checkpoint.py | 62 + .../gsheet_to_pandas-checkpoint.py | 59 + .../utils/external_etl_notebook.ipynb | 295 +- .../pipeline/utils/gdrive_to_pandas.py | 62 + 14 files changed, 3622 insertions(+), 673 deletions(-) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/basic_sample_info-checkpoint.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/biodiesel_plants-checkpoint.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/proximate-checkpoint.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/external.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/Biodiesel_Plants-checkpoint.csv create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/Biodiesel_Plants.csv create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gdrive_to_pandas-checkpoint.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gsheet_to_pandas-checkpoint.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gdrive_to_pandas.py diff --git a/pixi.lock b/pixi.lock index 5581bcfd..2b5c53ec 100644 --- a/pixi.lock +++ b/pixi.lock @@ -10,7 +10,11 @@ environments: - 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It connects to the + data source and returns the data as is, without any transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + logger.info("Extracting raw data from '01-BasicSampleInfo' worksheet...") + + GSHEET_NAME = "Aim 1-Feedstock Collection and Processing Data-BioCirV" + WORKSHEET_NAME = "01-BasicSampleInfo" + CREDENTIALS_PATH = "credentials.json" + + raw_df = gsheet_to_df(GSHEET_NAME, WORKSHEET_NAME, CREDENTIALS_PATH) + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/biodiesel_plants-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/biodiesel_plants-checkpoint.py new file mode 100644 index 00000000..c3635fcc --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/biodiesel_plants-checkpoint.py @@ -0,0 +1,34 @@ +from typing import Optional +import pandas as pd +from prefect import task, get_run_logger +from ...utils.gdrive_to_pandas import gdrive_to_df +# from resources.prefect import credentials + +@task +def extract(csv_path) -> Optional[pd.DataFrame]: + """ + Extracts raw data from a .csv file. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + + FILE_NAME = "Biodiesel_Plants.csv" + CREDENTIALS_PATH = "credentials.json" + logger.info(f"Extracting raw data from '{FILE_NAME}'...") + + # The gsheet_to_df function handles authentication, data fetching, and error handling. + raw_df = gdrive_to_pandas(FILE_NAME, CREDENTIALS_PATH) + + + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/proximate-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/proximate-checkpoint.py new file mode 100644 index 00000000..9bbaf910 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/proximate-checkpoint.py @@ -0,0 +1,59 @@ +""" +ETL Extract Template +--- + +This module provides a template for extracting data from a Google Sheet. + +To use this template: +1. Copy this file to the appropriate subdirectory in `src/etl/extract/`. + For example: `src/etl/extract/new_module/new_data.py` +2. Update the configuration constants (`GSHEET_NAME`, `WORKSHEET_NAME`). +3. Ensure the `CREDENTIALS_PATH` is correct. +""" + +from typing import Optional +import os +import pandas as pd +from prefect import task, get_run_logger +from ...utils.gsheet_to_pandas import gsheet_to_df + +# --- CONFIGURATION --- +# TODO: Replace with the name of the Google Sheet file. +GSHEET_NAME = "Aim 1-Feedstock Collection and Processing Data-BioCirV" + +# TODO: Replace with the exact name of the worksheet/tab to extract data from. +WORKSHEET_NAME = "03.1-Proximate" + +# The path to the credentials file. This is typically kept in the project root. +CREDENTIALS_PATH = "credentials.json" + + +@task +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: + """ + Extracts raw data from the specified Google Sheet worksheet. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + logger.info(f"Extracting raw data from '{WORKSHEET_NAME}' in '{GSHEET_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + + # The gsheet_to_df function handles authentication, data fetching, and error handling. + raw_df = gsheet_to_df(GSHEET_NAME, WORKSHEET_NAME, credentials_path) + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py new file mode 100644 index 00000000..c3635fcc --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py @@ -0,0 +1,34 @@ +from typing import Optional +import pandas as pd +from prefect import task, get_run_logger +from ...utils.gdrive_to_pandas import gdrive_to_df +# from resources.prefect import credentials + +@task +def extract(csv_path) -> Optional[pd.DataFrame]: + """ + Extracts raw data from a .csv file. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + + FILE_NAME = "Biodiesel_Plants.csv" + CREDENTIALS_PATH = "credentials.json" + logger.info(f"Extracting raw data from '{FILE_NAME}'...") + + # The gsheet_to_df function handles authentication, data fetching, and error handling. + raw_df = gdrive_to_pandas(FILE_NAME, CREDENTIALS_PATH) + + + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/external.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/external.py new file mode 100644 index 00000000..c7495876 --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/external.py @@ -0,0 +1,59 @@ +""" +ETL Extract Template +--- + +This module provides a template for extracting data from a Google Sheet. + +To use this template: +1. Copy this file to the appropriate subdirectory in `src/etl/extract/`. + For example: `src/etl/extract/new_module/new_data.py` +2. Update the configuration constants (`GSHEET_NAME`, `WORKSHEET_NAME`). +3. Ensure the `CREDENTIALS_PATH` is correct. +""" + +from typing import Optional +import os +import pandas as pd +from prefect import task, get_run_logger +from ...utils.gsheet_to_pandas import gsheet_to_df + +# --- CONFIGURATION --- +# TODO: Replace with the name of the Google Sheet file. +GSHEET_NAME = "Aim 1-Feedstock Collection and Processing Data-BioCirV" + +# TODO: Replace with the exact name of the worksheet/tab to extract data from. +WORKSHEET_NAME = "03.7-Ultimate" + +# The path to the credentials file. This is typically kept in the project root. +CREDENTIALS_PATH = "credentials.json" + + +@task +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: + """ + Extracts raw data from the specified Google Sheet worksheet. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + logger.info(f"Extracting raw data from '{WORKSHEET_NAME}' in '{GSHEET_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + + # The gsheet_to_df function handles authentication, data fetching, and error handling. + raw_df = gsheet_to_df(GSHEET_NAME, WORKSHEET_NAME, credentials_path) + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/Biodiesel_Plants-checkpoint.csv b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/Biodiesel_Plants-checkpoint.csv new file mode 100644 index 00000000..7a32cf9a --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/Biodiesel_Plants-checkpoint.csv @@ -0,0 +1,79 @@ +company,bbi_index,city,state,capacity_mmg_per_y,feedstock,status,address,coordinates,latitude,longitude,source +American GreenFuels,,New Haven,Connecticut,35,,,,,41.2901,-72.9029,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.15 +Down To Earth Energy LLC,,Monroe,Georgia,2,,,,,33.75717,-83.7277,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.16 +Maine Bio-Fuel Inc,,Portland,Maine,1,,,,,43.6914,-70.3281,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.17 +Cape Cod Biofuels Inc,,Sandwich,Massachusetts,1,,,,,41.7177,-70.4845,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.18 +Renewable Fuels by Peterson,,North Haverhill,New Hampshire,8,,,,,44.077,-72.0047,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.19 +Blue Ridge Biofuels LLC,,Newton,North Carolina,2,,,,,35.6058,-81.30837,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.20 +Lake Erie Biofuels LLC,,Erie,Pennsylvania,45,,,,,42.143,-80.0496,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.21 +World Energy Harrisburg LLC,,Camp Hill,Pennsylvania,19,,,,,40.2122,-76.939,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.22 +Southeast Biodiesel/South Carolina LLC,,Charleston,South Carolina,5,,,,,32.8772,-79.9698,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.23 +Virginia Biodiesel Refinery LLC,,West Point,Virginia,5,,,,,37.515,-76.8422,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.24 +Adkins Energy LLC,,Lena,Illinois,4,,,,,42.3638,-89.8039,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.25 +Incobrasa Industries Ltd,,Gilman,Illinois,62,,,,,40.7624,-88.0143,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.26 +Renewable Energy Group,,Danville,Illinois,50,,,,,40.1292,-87.6191,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.27 +Renewable Energy Group,,Seneca,Illinois,76,,,,,41.3067,-88.5902,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.28 +Alternative Fuel Solutions LLC,,Huntington,Indiana,3,,,,,40.9519,-85.4906,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.29 +Louis Dreyfus Agricultural Industries LLC,,Claypool,Indiana,99,,,,,41.123,-85.8901,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.30 +AG Processing,,Algona,Iowa,76,,,,,43.0776,-94.1875,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.31 +AG Processing,,Sgt Bluff,Iowa,76,,,,,42.3052,-96.3623,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.32 +Cargill Inc,,Iowa Falls,Iowa,70,,,,,42.5121,-93.2645,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.33 +Hero BX Clinton,,Clinton,Iowa,10,,,,,41.80113,-90.335543,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.34 +Iowa Renewable Energy LLC,,Washington,Iowa,36,,,,,41.3069,-91.6686,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.35 +Lva Crawfordsville Biofuel LLC,,Crawfordsville,Iowa,10,,,,,41.192,-91.5263,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.36 +Renewable Energy Group,,Mason City,Iowa,38,,,,,43.1344,-93.2644,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.37 +Renewable Energy Group,,Newton,Iowa,38,,,,,41.7329,-93.0194,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.38 +Renewable Energy Group,,Ralston,Iowa,49,,,,,42.0457,-94.6415,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.39 +Western Dubuque Biodiesel LLC,,Farley,Iowa,36,,,,,42.4514,-91.0218,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.40 +Western Iowa Energy LLC,,Wall Lake,Iowa,45,,,,,42.2555,-95.0911,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.41 +Cargill Inc,,Wichita,Kansas,91,,,,,37.7085,-97.3277,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.42 +Owensboro Grain Biodiesel LLC,,Owensboro,Kentucky,56,,,,,37.7852,-87.1429,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.43 +Adrian Lva Biofuel LLC,,Adrian,Michigan,15,,,,,41.8877,-84.0738,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.44 +Thumb Bioenergy LLC,,Sandusky,Michigan,1,,,,,43.4167,-82.816,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.45 +Ever Cat Fuels LLC,,Isanti,Minnesota,3,,,,,45.5006,-93.2429,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.46 +Minnesota Soybean Processors,,Brewster,Minnesota,36,,,,,43.7057,-95.4565,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.47 +Renewable Energy Group,,Albert Lea,Minnesota,46,,,,,43.5741,-93.3003,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.48 +AG Processing,,St. Joseph,Missouri,42,,,,,39.7278,-94.8736,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.49 +Deerfield Energy LLC,,Deerfield,Missouri,50,,,,,37.8347,-94.5781,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.50 +"Mid-America Biofuels, LLC",,Mexico,Missouri,50,,,,,39.1691,-91.8828,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.51 +Paseo Cargill Energy LLC,,Kansas City,Missouri,70,,,,,39.1208,-94.5551,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.52 +Seaboard Energy Missouri LLC,,St. Joseph,Missouri,35,,,,,39.7136,-94.8763,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.53 +ADM,,Velva,North Dakota,85,,,,,48.0225,-100.8837,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.54 +Seaboard Energy Oklahoma LLC,,Guymon,Oklahoma,40,,,,,36.7125,-101.4388,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.55 +Bioenergy Development Group LLC,,Memphis,Tennessee,36,,,,,35.1045,-89.9884,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.56 +Renewable Energy Group,,De Forest,Wisconsin,28,,,,,43.2553,-89.3359,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.57 +Hero Bx Alabama LLC,,Moundville,Alabama,20,,,,,33.0098,-87.6259,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.58 +Delek US,,Crossett,Arkansas,15,,,,,33.1343,-91.9434,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.59 +Futurefuel Chemical Company,,Batesville,Arkansas,60,,,,,35.7226,-91.525,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.60 +Delek US,,New Albany,Mississippi,12,,,,,34.531,-88.991,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.61 +Scott Petroleum Corporation,,Greenville,Mississippi,17,,,,,33.4246,-91.0501,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.62 +Delek US,,Cleburne,Texas,14,,,,,32.3992,-97.4305,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.63 +Eberle Biodiesel LLC,,Liverpool,Texas,0,,,,,29.3165,-95.3006,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.64 +Global Alternative Fuels LLC,,El Paso,Texas,15,,,,,31.8062,-106.5455,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.65 +Rbf Port Neches LLC,,Houston,Texas,144,,,,,29.9601,-93.9278,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.66 +Canary Renewables Corp,,Stockton,California,20,,,,,37.9561,-121.3669,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.67 +Crimson Renewable Energy LP,,Bakersfield,California,36,,,,,35.1782,-119.1583,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.68 +Imperial Western Products Inc,,Coachella,California,12,,,,,33.6577,-116.1581,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.69 +New Leaf Biofuel LLC,,San Diego,California,12,,,,,32.6953,-117.1398,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.70 +Big Island Biodiesel LLC,,Keaau,Hawaii,6,,,,,19.6336,-155.0504,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.71 +Sequential-Pacific Biodiesel LLC,,Salem,Oregon,12,,,,,44.8861,-122.9808,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.72 +Renewable Energy Group,,Hoquiam,Washington,107,,,,,46.9681,-123.8542,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.73 +Archer Daniels Midland Co. - Deerfield,5,Deerfield,MO,50,Soybean oil,Operational,"17700 South T Highway, Deerfield, MO 64741","37.834461802670596, -94.57840681274331",37.8344618,-94.57840681,https://issuu.com/bbiinternational/docs/biodieselmap-2023 +Cargill - Kansas City,12,Kansas City,MO,56,Soybean oil,Operational,"2306 Rochester Ave, Kansas City, MO 64120","39.12027064480734, -94.55522441736515",39.12027064,-94.55522442,https://issuu.com/bbiinternational/docs/biodieselmap-2026 +Genuine Bio-Fuel Inc.,19,Indiantown,FL,9,"Vegetable oils, Animal fats",Operational,"17250 SW Railroad Ave, Indiantown, FL 34956","27.032229522837042, -80.48923481662703",27.03222952,-80.48923482,https://issuu.com/bbiinternational/docs/biodieselmap-2027 +Green Biofuels Miami LLC,20,Miami,FL,7,Used cooking oil,Idle,"3123 NW 73rd St Suite A-C, Miami, FL 33147","25.84042254086944, -80.24840724548976",25.84042254,-80.24840725,https://issuu.com/bbiinternational/docs/biodieselmap-2028 +Green Energy Biofuel (GEB3),21,Warrenville,SC,40,"Fats, oils and greases",Operational,"2110 Main St, Warrenville, SC 29851","33.549574199322635, -81.81134991704775",33.5495742,-81.81134992,https://issuu.com/bbiinternational/docs/biodieselmap-2029 +Hero BX - Erie,23,Erie,PA,50,"Vegetable oils, Animal fats",Operational,"1670 E Lake Rd, Erie, PA 16511","42.14761498934528, -80.05303214686336",42.14761499,-80.05303215,https://issuu.com/bbiinternational/docs/biodieselmap-2030 +Lakeview Biodiesel LLC,29,Moberly,MO,10,Multifeedstock,Idle,"607 W Fowler Rd, Moberly, MO 65270","39.444604819389866, -92.44426790277895",39.44460482,-92.4442679,https://issuu.com/bbiinternational/docs/biodieselmap-2032 +Newport Biodiesel Inc.,34,Newport,RI,8,Yellow grease,Operational,"312 JT Connell Hwy, Newport, RI 02840","41.5155378368489, -71.3166049450345",41.51553784,-71.31660495,https://issuu.com/bbiinternational/docs/biodieselmap-2033 +Pacific Biodiesel,36,Kea`au,HI,6,Used cooking oil,Operational,"16-240 Mikahala St, Keaau, HI 96749","19.632865330590878, -155.0533710744427",19.63286533,-155.0533711,https://issuu.com/bbiinternational/docs/biodieselmap-2034 +Rio Valley Biofuels LLC,46,El Paso,TX,15,"Used cooking oil, Animal fats, Sunflower/canola oil, Soybean oil, Crude cottonseed",Operational,"3500 Doniphan Dr, El Paso, TX 79922","31.80656172095864, -106.54486984534253",31.80656172,-106.5448698,https://issuu.com/bbiinternational/docs/biodieselmap-2035 +SMES Dublin LLC,51,East Dublin,GA,5,Brown grease,Operational,"330 Dewey Warnock Rd, East Dublin, GA 31027","32.54352329686725, -82.81634183182987",32.5435233,-82.81634183,https://issuu.com/bbiinternational/docs/biodieselmap-2036 +Solfuels USA LLC,52,Helena,AR,40,"Yellow grease, Animal fats, Corn oil, Vegetable oils",Operational,"1463 AR-20, Helena, AR 72342","34.47875097553326, -90.60844354711763",34.47875098,-90.60844355,https://issuu.com/bbiinternational/docs/biodieselmap-2037 +W2Fuel - Adrian,56,Adrian,MI,15,Soybean oil,Operational,"1571 W Beecher Rd, Adrian, MI 49221","41.88787758413316, -84.07375166036492",41.88787758,-84.07375166,https://issuu.com/bbiinternational/docs/biodieselmap-2039 +W2Fuel - Crawfordsville,57,Crawfordsville,IA,10,Soybean oil,Operational,"3187 320th St, Crawfordsville, IA 52621","41.191119163585014, -91.52587113148789",41.19111916,-91.52587113,https://issuu.com/bbiinternational/docs/biodieselmap-2040 +Walsh BioFuels LLC,58,Mauston,WI,5,Distillers corn oil,Operational,"WI-80 & Mauston Rd, Mauston, WI 53948","43.777703209506015, -90.05515309603231",43.77770321,-90.0551531,https://issuu.com/bbiinternational/docs/biodieselmap-2041 +Western Iowa Energy - Agron Bioenergy,60,Watsonville,CA,15,Multifeedstock,Operational,"860 W Beach St, Watsonville, CA 95076","36.90388067222262, -121.76968983169887",36.90388067,-121.7696898,https://issuu.com/bbiinternational/docs/biodieselmap-2042 +White Mountain Biodiesel LLC,62,North Haverhill,NH,8,Yellow grease,Operational,"35 Business Pk Rd, North Haverhill, NH 03774","44.07671166339629, -72.0049135970569",44.07671166,-72.0049136,https://issuu.com/bbiinternational/docs/biodieselmap-2043 +World Energy - Natchez,65,Natchez,MS,72,Vegetable oils,Operational,"L E Barry Rd, Natchez, MS 39120","31.533227585047626, -91.4374585606938",31.53322759,-91.43745856,https://issuu.com/bbiinternational/docs/biodieselmap-2045 +World Energy - Rome,66,Rome,GA,20,Multifeedstock,Operational,"555 W Hermitage Rd NE, Rome, GA 30161","34.327173247943826, -85.0919307299404",34.32717325,-85.09193073,https://issuu.com/bbiinternational/docs/biodieselmap-2046 \ No newline at end of file diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/Biodiesel_Plants.csv b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/Biodiesel_Plants.csv new file mode 100644 index 00000000..7a32cf9a --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/Biodiesel_Plants.csv @@ -0,0 +1,79 @@ +company,bbi_index,city,state,capacity_mmg_per_y,feedstock,status,address,coordinates,latitude,longitude,source +American GreenFuels,,New Haven,Connecticut,35,,,,,41.2901,-72.9029,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.15 +Down To Earth Energy LLC,,Monroe,Georgia,2,,,,,33.75717,-83.7277,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.16 +Maine Bio-Fuel Inc,,Portland,Maine,1,,,,,43.6914,-70.3281,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.17 +Cape Cod Biofuels Inc,,Sandwich,Massachusetts,1,,,,,41.7177,-70.4845,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.18 +Renewable Fuels by Peterson,,North Haverhill,New Hampshire,8,,,,,44.077,-72.0047,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.19 +Blue Ridge Biofuels LLC,,Newton,North Carolina,2,,,,,35.6058,-81.30837,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.20 +Lake Erie Biofuels LLC,,Erie,Pennsylvania,45,,,,,42.143,-80.0496,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.21 +World Energy Harrisburg LLC,,Camp Hill,Pennsylvania,19,,,,,40.2122,-76.939,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.22 +Southeast Biodiesel/South Carolina LLC,,Charleston,South Carolina,5,,,,,32.8772,-79.9698,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.23 +Virginia Biodiesel Refinery LLC,,West Point,Virginia,5,,,,,37.515,-76.8422,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.24 +Adkins Energy LLC,,Lena,Illinois,4,,,,,42.3638,-89.8039,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.25 +Incobrasa Industries Ltd,,Gilman,Illinois,62,,,,,40.7624,-88.0143,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.26 +Renewable Energy Group,,Danville,Illinois,50,,,,,40.1292,-87.6191,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.27 +Renewable Energy Group,,Seneca,Illinois,76,,,,,41.3067,-88.5902,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.28 +Alternative Fuel Solutions LLC,,Huntington,Indiana,3,,,,,40.9519,-85.4906,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.29 +Louis Dreyfus Agricultural Industries LLC,,Claypool,Indiana,99,,,,,41.123,-85.8901,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.30 +AG Processing,,Algona,Iowa,76,,,,,43.0776,-94.1875,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.31 +AG Processing,,Sgt Bluff,Iowa,76,,,,,42.3052,-96.3623,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.32 +Cargill Inc,,Iowa Falls,Iowa,70,,,,,42.5121,-93.2645,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.33 +Hero BX Clinton,,Clinton,Iowa,10,,,,,41.80113,-90.335543,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.34 +Iowa Renewable Energy LLC,,Washington,Iowa,36,,,,,41.3069,-91.6686,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.35 +Lva Crawfordsville Biofuel LLC,,Crawfordsville,Iowa,10,,,,,41.192,-91.5263,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.36 +Renewable Energy Group,,Mason City,Iowa,38,,,,,43.1344,-93.2644,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.37 +Renewable Energy Group,,Newton,Iowa,38,,,,,41.7329,-93.0194,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.38 +Renewable Energy Group,,Ralston,Iowa,49,,,,,42.0457,-94.6415,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.39 +Western Dubuque Biodiesel LLC,,Farley,Iowa,36,,,,,42.4514,-91.0218,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.40 +Western Iowa Energy LLC,,Wall Lake,Iowa,45,,,,,42.2555,-95.0911,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.41 +Cargill Inc,,Wichita,Kansas,91,,,,,37.7085,-97.3277,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.42 +Owensboro Grain Biodiesel LLC,,Owensboro,Kentucky,56,,,,,37.7852,-87.1429,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.43 +Adrian Lva Biofuel LLC,,Adrian,Michigan,15,,,,,41.8877,-84.0738,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.44 +Thumb Bioenergy LLC,,Sandusky,Michigan,1,,,,,43.4167,-82.816,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.45 +Ever Cat Fuels LLC,,Isanti,Minnesota,3,,,,,45.5006,-93.2429,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.46 +Minnesota Soybean Processors,,Brewster,Minnesota,36,,,,,43.7057,-95.4565,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.47 +Renewable Energy Group,,Albert Lea,Minnesota,46,,,,,43.5741,-93.3003,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.48 +AG Processing,,St. Joseph,Missouri,42,,,,,39.7278,-94.8736,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.49 +Deerfield Energy LLC,,Deerfield,Missouri,50,,,,,37.8347,-94.5781,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.50 +"Mid-America Biofuels, LLC",,Mexico,Missouri,50,,,,,39.1691,-91.8828,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.51 +Paseo Cargill Energy LLC,,Kansas City,Missouri,70,,,,,39.1208,-94.5551,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.52 +Seaboard Energy Missouri LLC,,St. Joseph,Missouri,35,,,,,39.7136,-94.8763,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.53 +ADM,,Velva,North Dakota,85,,,,,48.0225,-100.8837,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.54 +Seaboard Energy Oklahoma LLC,,Guymon,Oklahoma,40,,,,,36.7125,-101.4388,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.55 +Bioenergy Development Group LLC,,Memphis,Tennessee,36,,,,,35.1045,-89.9884,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.56 +Renewable Energy Group,,De Forest,Wisconsin,28,,,,,43.2553,-89.3359,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.57 +Hero Bx Alabama LLC,,Moundville,Alabama,20,,,,,33.0098,-87.6259,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.58 +Delek US,,Crossett,Arkansas,15,,,,,33.1343,-91.9434,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.59 +Futurefuel Chemical Company,,Batesville,Arkansas,60,,,,,35.7226,-91.525,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.60 +Delek US,,New Albany,Mississippi,12,,,,,34.531,-88.991,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.61 +Scott Petroleum Corporation,,Greenville,Mississippi,17,,,,,33.4246,-91.0501,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.62 +Delek US,,Cleburne,Texas,14,,,,,32.3992,-97.4305,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.63 +Eberle Biodiesel LLC,,Liverpool,Texas,0,,,,,29.3165,-95.3006,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.64 +Global Alternative Fuels LLC,,El Paso,Texas,15,,,,,31.8062,-106.5455,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.65 +Rbf Port Neches LLC,,Houston,Texas,144,,,,,29.9601,-93.9278,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.66 +Canary Renewables Corp,,Stockton,California,20,,,,,37.9561,-121.3669,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.67 +Crimson Renewable Energy LP,,Bakersfield,California,36,,,,,35.1782,-119.1583,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.68 +Imperial Western Products Inc,,Coachella,California,12,,,,,33.6577,-116.1581,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.69 +New Leaf Biofuel LLC,,San Diego,California,12,,,,,32.6953,-117.1398,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.70 +Big Island Biodiesel LLC,,Keaau,Hawaii,6,,,,,19.6336,-155.0504,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.71 +Sequential-Pacific Biodiesel LLC,,Salem,Oregon,12,,,,,44.8861,-122.9808,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.72 +Renewable Energy Group,,Hoquiam,Washington,107,,,,,46.9681,-123.8542,https://atlas.eia.gov/datasets/79dad60ce89c47519452a2959d49acd8/explore?location=33.831237%2C-93.987910%2C4.73 +Archer Daniels Midland Co. - Deerfield,5,Deerfield,MO,50,Soybean oil,Operational,"17700 South T Highway, Deerfield, MO 64741","37.834461802670596, -94.57840681274331",37.8344618,-94.57840681,https://issuu.com/bbiinternational/docs/biodieselmap-2023 +Cargill - Kansas City,12,Kansas City,MO,56,Soybean oil,Operational,"2306 Rochester Ave, Kansas City, MO 64120","39.12027064480734, -94.55522441736515",39.12027064,-94.55522442,https://issuu.com/bbiinternational/docs/biodieselmap-2026 +Genuine Bio-Fuel Inc.,19,Indiantown,FL,9,"Vegetable oils, Animal fats",Operational,"17250 SW Railroad Ave, Indiantown, FL 34956","27.032229522837042, -80.48923481662703",27.03222952,-80.48923482,https://issuu.com/bbiinternational/docs/biodieselmap-2027 +Green Biofuels Miami LLC,20,Miami,FL,7,Used cooking oil,Idle,"3123 NW 73rd St Suite A-C, Miami, FL 33147","25.84042254086944, -80.24840724548976",25.84042254,-80.24840725,https://issuu.com/bbiinternational/docs/biodieselmap-2028 +Green Energy Biofuel (GEB3),21,Warrenville,SC,40,"Fats, oils and greases",Operational,"2110 Main St, Warrenville, SC 29851","33.549574199322635, -81.81134991704775",33.5495742,-81.81134992,https://issuu.com/bbiinternational/docs/biodieselmap-2029 +Hero BX - Erie,23,Erie,PA,50,"Vegetable oils, Animal fats",Operational,"1670 E Lake Rd, Erie, PA 16511","42.14761498934528, -80.05303214686336",42.14761499,-80.05303215,https://issuu.com/bbiinternational/docs/biodieselmap-2030 +Lakeview Biodiesel LLC,29,Moberly,MO,10,Multifeedstock,Idle,"607 W Fowler Rd, Moberly, MO 65270","39.444604819389866, -92.44426790277895",39.44460482,-92.4442679,https://issuu.com/bbiinternational/docs/biodieselmap-2032 +Newport Biodiesel Inc.,34,Newport,RI,8,Yellow grease,Operational,"312 JT Connell Hwy, Newport, RI 02840","41.5155378368489, -71.3166049450345",41.51553784,-71.31660495,https://issuu.com/bbiinternational/docs/biodieselmap-2033 +Pacific Biodiesel,36,Kea`au,HI,6,Used cooking oil,Operational,"16-240 Mikahala St, Keaau, HI 96749","19.632865330590878, -155.0533710744427",19.63286533,-155.0533711,https://issuu.com/bbiinternational/docs/biodieselmap-2034 +Rio Valley Biofuels LLC,46,El Paso,TX,15,"Used cooking oil, Animal fats, Sunflower/canola oil, Soybean oil, Crude cottonseed",Operational,"3500 Doniphan Dr, El Paso, TX 79922","31.80656172095864, -106.54486984534253",31.80656172,-106.5448698,https://issuu.com/bbiinternational/docs/biodieselmap-2035 +SMES Dublin LLC,51,East Dublin,GA,5,Brown grease,Operational,"330 Dewey Warnock Rd, East Dublin, GA 31027","32.54352329686725, -82.81634183182987",32.5435233,-82.81634183,https://issuu.com/bbiinternational/docs/biodieselmap-2036 +Solfuels USA LLC,52,Helena,AR,40,"Yellow grease, Animal fats, Corn oil, Vegetable oils",Operational,"1463 AR-20, Helena, AR 72342","34.47875097553326, -90.60844354711763",34.47875098,-90.60844355,https://issuu.com/bbiinternational/docs/biodieselmap-2037 +W2Fuel - Adrian,56,Adrian,MI,15,Soybean oil,Operational,"1571 W Beecher Rd, Adrian, MI 49221","41.88787758413316, -84.07375166036492",41.88787758,-84.07375166,https://issuu.com/bbiinternational/docs/biodieselmap-2039 +W2Fuel - Crawfordsville,57,Crawfordsville,IA,10,Soybean oil,Operational,"3187 320th St, Crawfordsville, IA 52621","41.191119163585014, -91.52587113148789",41.19111916,-91.52587113,https://issuu.com/bbiinternational/docs/biodieselmap-2040 +Walsh BioFuels LLC,58,Mauston,WI,5,Distillers corn oil,Operational,"WI-80 & Mauston Rd, Mauston, WI 53948","43.777703209506015, -90.05515309603231",43.77770321,-90.0551531,https://issuu.com/bbiinternational/docs/biodieselmap-2041 +Western Iowa Energy - Agron Bioenergy,60,Watsonville,CA,15,Multifeedstock,Operational,"860 W Beach St, Watsonville, CA 95076","36.90388067222262, -121.76968983169887",36.90388067,-121.7696898,https://issuu.com/bbiinternational/docs/biodieselmap-2042 +White Mountain Biodiesel LLC,62,North Haverhill,NH,8,Yellow grease,Operational,"35 Business Pk Rd, North Haverhill, NH 03774","44.07671166339629, -72.0049135970569",44.07671166,-72.0049136,https://issuu.com/bbiinternational/docs/biodieselmap-2043 +World Energy - Natchez,65,Natchez,MS,72,Vegetable oils,Operational,"L E Barry Rd, Natchez, MS 39120","31.533227585047626, -91.4374585606938",31.53322759,-91.43745856,https://issuu.com/bbiinternational/docs/biodieselmap-2045 +World Energy - Rome,66,Rome,GA,20,Multifeedstock,Operational,"555 W Hermitage Rd NE, Rome, GA 30161","34.327173247943826, -85.0919307299404",34.32717325,-85.09193073,https://issuu.com/bbiinternational/docs/biodieselmap-2046 \ No newline at end of file diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb index 3c8228d6..e2bf8007 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb @@ -20,9 +20,18 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 14, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2026-01-13 16:10:18,800 - INFO - Project root 'C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing' is already in sys.path\n", + "2026-01-13 16:10:18,802 - INFO - Successfully imported all project modules.\n" + ] + } + ], "source": [ "import os\n", "import sys\n", @@ -65,7 +74,7 @@ " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", " from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import replace_name_with_id_df\n", - " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate, ultimate, cmpana\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import biodiesel_plants\n", " logger.info('Successfully imported all project modules.')\n", "except ImportError as e:\n", " logger.error(f'Failed to import project modules: {e}', exc_info=True)" @@ -231,49 +240,259 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 72, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "from pydrive2.auth import GoogleAuth, AuthenticationError\n", + "from pydrive2.drive import GoogleDrive\n", + "from pydrive2.files import ApiRequestError\n", + "\n", + "def gdrive_to_df(file_name: str, mime_type: str, credentials_path: str, dataset_folder: str) -> pd.DataFrame:\n", + " \"\"\"\n", + " Extracts data from a CSV, ZIP, or GEOJSON file into a pandas DataFrame.\n", + "\n", + " Args:\n", + " file_name: The name of the requested file.\n", + " mime_type: The MIME type - according to https://mime-type.com/\n", + " credentials_path: The path to the Google Cloud service account credentials JSON file.\n", + "\n", + " Returns:\n", + " A pandas DataFrame containing the data from the specified worksheet, or None on error.\n", + " \"\"\"\n", + " try:\n", + " settings = {\n", + " \"client_config_backend\": \"service\",\n", + " \"service_config\": {\n", + " \"client_json_file_path\": credentials_path,\n", + " }\n", + " }\n", + " # Create instance of GoogleAuth\n", + " gauth = GoogleAuth(settings=settings)\n", + " gauth.ServiceAuth()\n", + " drive = GoogleDrive(gauth)\n", + "\n", + " try:\n", + " file_entries = drive.ListFile({\"q\": f\"title = '{file_name}' and mimeType= '{mime_type}'\"}).GetList()\n", + " if len(file_entries) == 0: \n", + " raise FileNotFoundError(f\"Error: File '{file_name}' not found. \\n Please make sure the spreadsheet name is correct and that you have shared it with the service account email.\")\n", + " return None\n", + " else:\n", + " file_entry = file_entries[0]\n", + " file = drive.CreateFile({'id': file_entry['id']})\n", + " file.GetContentFile(dataset_folder + file_name) # Download file\n", + " except ApiRequestError:\n", + " print(f\"An unexpected error occurred: {e}\")\n", + " return None\n", + "\n", + " # Use the first row as header and the rest as data\n", + " if mime_type == \"text/csv\":\n", + " df = pd.read_csv(dataset_folder + file_name)\n", + "\n", + " # De-duplicate columns, keeping the first occurrence\n", + " df = df.loc[:, ~df.columns.duplicated()]\n", + "\n", + " return df\n", + "\n", + " except AuthenticationError as e:\n", + " print(f\"Google Authentication Error: {e}\")\n", + " return None\n", + " except Exception as e:\n", + " print(f\"An unexpected error occurred: {e}\")\n", + " return None\n" + ] + }, + { + "cell_type": "code", + "execution_count": 73, "metadata": {}, "outputs": [], + "source": [ + "from typing import Optional\n", + "import pandas as pd\n", + "from prefect import task, get_run_logger\n", + "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", + "# from resources.prefect import credentials\n", + "\n", + "@task\n", + "def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", + " \"\"\"\n", + " Extracts raw data from a .csv file.\n", + "\n", + " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", + " to the data source and returns the data as is, without transformation.\n", + "\n", + " Returns:\n", + " A pandas DataFrame containing the raw data, or None if an error occurs.\n", + " \"\"\"\n", + " logger = get_run_logger()\n", + "\n", + " FILE_NAME = \"Biodiesel_Plants.csv\"\n", + " MIME_TYPE = \"text/csv\"\n", + " CREDENTIALS_PATH = \"credentials.json\"\n", + " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", + " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", + "\n", + " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", + " # Otherwise, use the default relative path (for the main pipeline)\n", + " credentials_path = CREDENTIALS_PATH\n", + " dataset_folder = DATASET_FOLDER\n", + " if project_root:\n", + " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", + " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", + "\n", + " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", + " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", + "\n", + " \n", + "\n", + " if raw_df is None:\n", + " logger.error(\"Failed to extract data. Aborting.\")\n", + " return None\n", + "\n", + " logger.info(\"Successfully extracted raw data.\")\n", + " return raw_df\n" + ] + }, + { + "cell_type": "code", + "execution_count": 74, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2026-01-13 18:36:20,831 - INFO - Starting data extraction...\n", + "2026-01-13 18:36:20,856 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-13 18:36:20,857 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-13 18:36:20,866 - INFO - Extracting raw data from 'Biodiesel_Plants.csv'...\n", + "2026-01-13 18:36:20,886 - INFO - Attempting refresh to obtain initial access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", + " return crypto.sign(self._key, message, 'sha256')\n", + "2026-01-13 18:36:20,889 - INFO - Refreshing access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " self.token_expiry = delta + _UTCNOW()\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " now = _UTCNOW()\n", + "2026-01-13 18:36:22,092 - INFO - Successfully extracted raw data.\n", + "2026-01-13 18:36:22,097 - INFO - Finished in state Completed()\n", + "2026-01-13 18:36:22,113 - INFO - Data extraction complete.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[ company bbi_index city \\\n", + "0 American GreenFuels NaN New Haven \n", + "1 Down To Earth Energy LLC NaN Monroe \n", + "2 Maine Bio-Fuel Inc NaN Portland \n", + "3 Cape Cod Biofuels Inc NaN Sandwich \n", + "4 Renewable Fuels by Peterson NaN North Haverhill \n", + ".. ... ... ... \n", + "73 Walsh BioFuels LLC 58.0 Mauston \n", + "74 Western Iowa Energy - Agron Bioenergy 60.0 Watsonville \n", + "75 White Mountain Biodiesel LLC 62.0 North Haverhill \n", + "76 World Energy - Natchez 65.0 Natchez \n", + "77 World Energy - Rome 66.0 Rome \n", + "\n", + " state capacity_mmg_per_y feedstock status \\\n", + "0 Connecticut 35 NaN NaN \n", + "1 Georgia 2 NaN NaN \n", + "2 Maine 1 NaN NaN \n", + "3 Massachusetts 1 NaN NaN \n", + "4 New Hampshire 8 NaN NaN \n", + ".. ... ... ... ... \n", + "73 WI 5 Distillers corn oil Operational \n", + "74 CA 15 Multifeedstock Operational \n", + "75 NH 8 Yellow grease Operational \n", + "76 MS 72 Vegetable oils Operational \n", + "77 GA 20 Multifeedstock Operational \n", + "\n", + " address \\\n", + "0 NaN \n", + "1 NaN \n", + "2 NaN \n", + "3 NaN \n", + "4 NaN \n", + ".. ... \n", + "73 WI-80 & Mauston Rd, Mauston, WI 53948 \n", + "74 860 W Beach St, Watsonville, CA 95076 \n", + "75 35 Business Pk Rd, North Haverhill, NH 03774 \n", + "76 L E Barry Rd, Natchez, MS 39120 \n", + "77 555 W Hermitage Rd NE, Rome, GA 30161 \n", + "\n", + " coordinates latitude longitude \\\n", + "0 NaN 41.290100 -72.902900 \n", + "1 NaN 33.757170 -83.727700 \n", + "2 NaN 43.691400 -70.328100 \n", + "3 NaN 41.717700 -70.484500 \n", + "4 NaN 44.077000 -72.004700 \n", + ".. ... ... ... \n", + "73 43.777703209506015, -90.05515309603231 43.777703 -90.055153 \n", + "74 36.90388067222262, -121.76968983169887 36.903881 -121.769690 \n", + "75 44.07671166339629, -72.0049135970569 44.076712 -72.004914 \n", + "76 31.533227585047626, -91.4374585606938 31.533228 -91.437459 \n", + "77 34.327173247943826, -85.0919307299404 34.327173 -85.091931 \n", + "\n", + " source \n", + "0 https://atlas.eia.gov/datasets/79dad60ce89c475... \n", + "1 https://atlas.eia.gov/datasets/79dad60ce89c475... \n", + "2 https://atlas.eia.gov/datasets/79dad60ce89c475... \n", + "3 https://atlas.eia.gov/datasets/79dad60ce89c475... \n", + "4 https://atlas.eia.gov/datasets/79dad60ce89c475... \n", + ".. ... \n", + "73 https://issuu.com/bbiinternational/docs/biodie... \n", + "74 https://issuu.com/bbiinternational/docs/biodie... \n", + "75 https://issuu.com/bbiinternational/docs/biodie... \n", + "76 https://issuu.com/bbiinternational/docs/biodie... \n", + "77 https://issuu.com/bbiinternational/docs/biodie... \n", + "\n", + "[78 rows x 12 columns]]\n" + ] + } + ], "source": [ "# --- 1. Extraction ---\n", "# In a real Prefect flow, each extraction would be a separate task.\n", "logger.info('Starting data extraction...')\n", - "prox_df = proximate.extract(project_root=project_root)\n", - "ult_df = ultimate.extract(project_root=project_root)\n", - "cmp_df = cmpana.extract(project_root=project_root)\n", - "dataframes = [prox_df, ult_df, cmp_df]\n", + "biodiesel_plants_df = extract(project_root=project_root)\n", + "dataframes = [biodiesel_plants_df]\n", + "print(dataframes)\n", "logger.info('Data extraction complete.')\n", "\n", - "# --- 2. Cleaning ---\n", - "# This list comprehension applies the cleaning function to each extracted dataframe.\n", - "logger.info('Starting data cleaning...')\n", - "clean_dataframes = [clean_the_gsheets(df) for df in dataframes if df is not None]\n", - "logger.info('Data cleaning complete.')\n", - "\n", - "# --- 3. Normalization ---\n", - "# This dictionary defines the columns to be normalized. \n", - "# The key is the column name in the DataFrame.\n", - "# The value is a tuple containing the corresponding SQLAlchemy model and the name of the attribute on the model to match against.\n", - "NORMALIZE_COLUMNS = {\n", - " 'resource': (Resource, 'name'),\n", - " 'prepared_sample': (PreparedSample, 'name'),\n", - " 'preparation_method': (PreparationMethod, 'name'),\n", - " 'parameter': (Parameter, 'name'),\n", - " 'unit': (Unit, 'name'),\n", - " 'analyst_email': (Contact, 'email'),\n", - " 'analysis_type': (AnalysisType, 'name'),\n", - " 'primary_ag_product': (PrimaryAgProduct, 'name')\n", - "}\n", - "\n", - "logger.info('Starting data normalization...')\n", - "normalized_dataframes = normalize_dataframes(clean_dataframes, NORMALIZE_COLUMNS)\n", - "logger.info('Data normalization complete.')\n", - "\n", - "# --- 4. Display Results ---\n", - "logger.info('Displaying results of normalization...')\n", - "for i, df in enumerate(normalized_dataframes):\n", - " print(f'--- Normalized DataFrame {i+1} ---')\n", - " display(df.head())" + "# # --- 2. Cleaning ---\n", + "# # This list comprehension applies the cleaning function to each extracted dataframe.\n", + "# logger.info('Starting data cleaning...')\n", + "# clean_dataframes = [clean_the_gsheets(df) for df in dataframes if df is not None]\n", + "# logger.info('Data cleaning complete.')\n", + "\n", + "# # --- 3. Normalization ---\n", + "# # This dictionary defines the columns to be normalized. \n", + "# # The key is the column name in the DataFrame.\n", + "# # The value is a tuple containing the corresponding SQLAlchemy model and the name of the attribute on the model to match against.\n", + "# NORMALIZE_COLUMNS = {\n", + "# 'resource': (Resource, 'name'),\n", + "# 'prepared_sample': (PreparedSample, 'name'),\n", + "# 'preparation_method': (PreparationMethod, 'name'),\n", + "# 'parameter': (Parameter, 'name'),\n", + "# 'unit': (Unit, 'name'),\n", + "# 'analyst_email': (Contact, 'email'),\n", + "# 'analysis_type': (AnalysisType, 'name'),\n", + "# 'primary_ag_product': (PrimaryAgProduct, 'name')\n", + "# }\n", + "\n", + "# logger.info('Starting data normalization...')\n", + "# normalized_dataframes = normalize_dataframes(clean_dataframes, NORMALIZE_COLUMNS)\n", + "# logger.info('Data normalization complete.')\n", + "\n", + "# # --- 4. Display Results ---\n", + "# logger.info('Displaying results of normalization...')\n", + "# for i, df in enumerate(normalized_dataframes):\n", + "# print(f'--- Normalized DataFrame {i+1} ---')\n", + "# display(df.head())" ] }, { diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gdrive_to_pandas-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gdrive_to_pandas-checkpoint.py new file mode 100644 index 00000000..8b083a0c --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gdrive_to_pandas-checkpoint.py @@ -0,0 +1,62 @@ +import pandas as pd +from pydrive2.auth import GoogleAuth +from pydrive2.drive import GoogleDrive + +def gdrive_to_df(file_name: str, credentials_path: str) -> pd.DataFrame: + """ + Extracts data from a CSV or GEOJSON into a pandas DataFrame. + + Args: + file_name: The name of the requested file. + credentials_path: The path to the Google Cloud service account credentials JSON file. + + Returns: + A pandas DataFrame containing the data from the specified worksheet, or None on error. + """ + try: + settings = { + "client_config_backend": "service", + "service_config": { + "client_json_file_path": credentials_path, + } + } + # Create instance of GoogleAuth + gauth = GoogleAuth(settings=settings) + gauth.ServiceAuth() + drive = GoogleDrive(gauth) + + try: + file_list = drive.ListFile().GetList() + print(file_list) + except SpreadsheetNotFound: + print(f"Error: Spreadsheet '{gsheet_name}' not found.") + print("Please make sure the spreadsheet name is correct and that you have shared it with the service account email.") + return None + + + # Get values directly to ensure we get calculated values, not formulas. + # 'FORMATTED_VALUE' gets the value as you see it in the sheet. + all_values = worksheet.get_all_values(value_render_option='FORMATTED_VALUE') + if not all_values: + return pd.DataFrame() # Return empty DataFrame if sheet is empty + + # Use the first row as header and the rest as data + df = pd.DataFrame(all_values[1:], columns=all_values[0]) + + # De-duplicate columns, keeping the first occurrence + df = df.loc[:, ~df.columns.duplicated()] + + return df + + except APIError as e: + print(f"Google API Error: {e}") + return None + except Exception as e: + print(f"An unexpected error occurred: {e}") + return None + + +if __name__ == '__main__': + # This part is for direct execution of this file, which is not the primary use case. + # The main test logic is in test_gsheet_to_pandas.py + pass diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gsheet_to_pandas-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gsheet_to_pandas-checkpoint.py new file mode 100644 index 00000000..a240c2ec --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gsheet_to_pandas-checkpoint.py @@ -0,0 +1,59 @@ +import gspread +import pandas as pd +from gspread.exceptions import SpreadsheetNotFound, WorksheetNotFound, APIError + +def gsheet_to_df(gsheet_name: str, worksheet_name: str, credentials_path: str) -> pd.DataFrame: + """ + Extracts data from a specific tab in a Google Sheet into a pandas DataFrame. + + Args: + gsheet_name: The name of the Google Sheet. + worksheet_name: The name of the worksheet/tab. + credentials_path: The path to the Google Cloud service account credentials JSON file. + + Returns: + A pandas DataFrame containing the data from the specified worksheet, or None on error. + """ + try: + gc = gspread.service_account(filename=credentials_path) + + try: + spreadsheet = gc.open(gsheet_name) + except SpreadsheetNotFound: + print(f"Error: Spreadsheet '{gsheet_name}' not found.") + print("Please make sure the spreadsheet name is correct and that you have shared it with the service account email.") + return None + + try: + worksheet = spreadsheet.worksheet(worksheet_name) + except WorksheetNotFound: + print(f"Error: Worksheet '{worksheet_name}' not found in the spreadsheet.") + print("Please make sure the worksheet name is correct.") + return None + + # Get values directly to ensure we get calculated values, not formulas. + # 'FORMATTED_VALUE' gets the value as you see it in the sheet. + all_values = worksheet.get_all_values(value_render_option='FORMATTED_VALUE') + if not all_values: + return pd.DataFrame() # Return empty DataFrame if sheet is empty + + # Use the first row as header and the rest as data + df = pd.DataFrame(all_values[1:], columns=all_values[0]) + + # De-duplicate columns, keeping the first occurrence + df = df.loc[:, ~df.columns.duplicated()] + + return df + + except APIError as e: + print(f"Google API Error: {e}") + return None + except Exception as e: + print(f"An unexpected error occurred: {e}") + return None + + +if __name__ == '__main__': + # This part is for direct execution of this file, which is not the primary use case. + # The main test logic is in test_gsheet_to_pandas.py + pass diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb index 3c8228d6..e2bf8007 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb @@ -20,9 +20,18 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 14, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2026-01-13 16:10:18,800 - INFO - Project root 'C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing' is already in sys.path\n", + "2026-01-13 16:10:18,802 - INFO - Successfully imported all project modules.\n" + ] + } + ], "source": [ "import os\n", "import sys\n", @@ -65,7 +74,7 @@ " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.engine import engine\n", " from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import replace_name_with_id_df\n", - " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import proximate, ultimate, cmpana\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import biodiesel_plants\n", " logger.info('Successfully imported all project modules.')\n", "except ImportError as e:\n", " logger.error(f'Failed to import project modules: {e}', exc_info=True)" @@ -231,49 +240,259 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 72, + "metadata": {}, + "outputs": [], + "source": [ + "import pandas as pd\n", + "from pydrive2.auth import GoogleAuth, AuthenticationError\n", + "from pydrive2.drive import GoogleDrive\n", + "from pydrive2.files import ApiRequestError\n", + "\n", + "def gdrive_to_df(file_name: str, mime_type: str, credentials_path: str, dataset_folder: str) -> pd.DataFrame:\n", + " \"\"\"\n", + " Extracts data from a CSV, ZIP, or GEOJSON file into a pandas DataFrame.\n", + "\n", + " Args:\n", + " file_name: The name of the requested file.\n", + " mime_type: The MIME type - according to https://mime-type.com/\n", + " credentials_path: The path to the Google Cloud service account credentials JSON file.\n", + "\n", + " Returns:\n", + " A pandas DataFrame containing the data from the specified worksheet, or None on error.\n", + " \"\"\"\n", + " try:\n", + " settings = {\n", + " \"client_config_backend\": \"service\",\n", + " \"service_config\": {\n", + " \"client_json_file_path\": credentials_path,\n", + " }\n", + " }\n", + " # Create instance of GoogleAuth\n", + " gauth = GoogleAuth(settings=settings)\n", + " gauth.ServiceAuth()\n", + " drive = GoogleDrive(gauth)\n", + "\n", + " try:\n", + " file_entries = drive.ListFile({\"q\": f\"title = '{file_name}' and mimeType= '{mime_type}'\"}).GetList()\n", + " if len(file_entries) == 0: \n", + " raise FileNotFoundError(f\"Error: File '{file_name}' not found. \\n Please make sure the spreadsheet name is correct and that you have shared it with the service account email.\")\n", + " return None\n", + " else:\n", + " file_entry = file_entries[0]\n", + " file = drive.CreateFile({'id': file_entry['id']})\n", + " file.GetContentFile(dataset_folder + file_name) # Download file\n", + " except ApiRequestError:\n", + " print(f\"An unexpected error occurred: {e}\")\n", + " return None\n", + "\n", + " # Use the first row as header and the rest as data\n", + " if mime_type == \"text/csv\":\n", + " df = pd.read_csv(dataset_folder + file_name)\n", + "\n", + " # De-duplicate columns, keeping the first occurrence\n", + " df = df.loc[:, ~df.columns.duplicated()]\n", + "\n", + " return df\n", + "\n", + " except AuthenticationError as e:\n", + " print(f\"Google Authentication Error: {e}\")\n", + " return None\n", + " except Exception as e:\n", + " print(f\"An unexpected error occurred: {e}\")\n", + " return None\n" + ] + }, + { + "cell_type": "code", + "execution_count": 73, "metadata": {}, "outputs": [], + "source": [ + "from typing import Optional\n", + "import pandas as pd\n", + "from prefect import task, get_run_logger\n", + "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", + "# from resources.prefect import credentials\n", + "\n", + "@task\n", + "def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", + " \"\"\"\n", + " Extracts raw data from a .csv file.\n", + "\n", + " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", + " to the data source and returns the data as is, without transformation.\n", + "\n", + " Returns:\n", + " A pandas DataFrame containing the raw data, or None if an error occurs.\n", + " \"\"\"\n", + " logger = get_run_logger()\n", + "\n", + " FILE_NAME = \"Biodiesel_Plants.csv\"\n", + " MIME_TYPE = \"text/csv\"\n", + " CREDENTIALS_PATH = \"credentials.json\"\n", + " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", + " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", + "\n", + " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", + " # Otherwise, use the default relative path (for the main pipeline)\n", + " credentials_path = CREDENTIALS_PATH\n", + " dataset_folder = DATASET_FOLDER\n", + " if project_root:\n", + " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", + " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", + "\n", + " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", + " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", + "\n", + " \n", + "\n", + " if raw_df is None:\n", + " logger.error(\"Failed to extract data. Aborting.\")\n", + " return None\n", + "\n", + " logger.info(\"Successfully extracted raw data.\")\n", + " return raw_df\n" + ] + }, + { + "cell_type": "code", + "execution_count": 74, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2026-01-13 18:36:20,831 - INFO - Starting data extraction...\n", + "2026-01-13 18:36:20,856 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-13 18:36:20,857 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-13 18:36:20,866 - INFO - Extracting raw data from 'Biodiesel_Plants.csv'...\n", + "2026-01-13 18:36:20,886 - INFO - Attempting refresh to obtain initial access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", + " return crypto.sign(self._key, message, 'sha256')\n", + "2026-01-13 18:36:20,889 - INFO - Refreshing access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " self.token_expiry = delta + _UTCNOW()\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " now = _UTCNOW()\n", + "2026-01-13 18:36:22,092 - INFO - Successfully extracted raw data.\n", + "2026-01-13 18:36:22,097 - INFO - Finished in state Completed()\n", + "2026-01-13 18:36:22,113 - INFO - Data extraction complete.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[ company bbi_index city \\\n", + "0 American GreenFuels NaN New Haven \n", + "1 Down To Earth Energy LLC NaN Monroe \n", + "2 Maine Bio-Fuel Inc NaN Portland \n", + "3 Cape Cod Biofuels Inc NaN Sandwich \n", + "4 Renewable Fuels by Peterson NaN North Haverhill \n", + ".. ... ... ... \n", + "73 Walsh BioFuels LLC 58.0 Mauston \n", + "74 Western Iowa Energy - Agron Bioenergy 60.0 Watsonville \n", + "75 White Mountain Biodiesel LLC 62.0 North Haverhill \n", + "76 World Energy - Natchez 65.0 Natchez \n", + "77 World Energy - Rome 66.0 Rome \n", + "\n", + " state capacity_mmg_per_y feedstock status \\\n", + "0 Connecticut 35 NaN NaN \n", + "1 Georgia 2 NaN NaN \n", + "2 Maine 1 NaN NaN \n", + "3 Massachusetts 1 NaN NaN \n", + "4 New Hampshire 8 NaN NaN \n", + ".. ... ... ... ... \n", + "73 WI 5 Distillers corn oil Operational \n", + "74 CA 15 Multifeedstock Operational \n", + "75 NH 8 Yellow grease Operational \n", + "76 MS 72 Vegetable oils Operational \n", + "77 GA 20 Multifeedstock Operational \n", + "\n", + " address \\\n", + "0 NaN \n", + "1 NaN \n", + "2 NaN \n", + "3 NaN \n", + "4 NaN \n", + ".. ... \n", + "73 WI-80 & Mauston Rd, Mauston, WI 53948 \n", + "74 860 W Beach St, Watsonville, CA 95076 \n", + "75 35 Business Pk Rd, North Haverhill, NH 03774 \n", + "76 L E Barry Rd, Natchez, MS 39120 \n", + "77 555 W Hermitage Rd NE, Rome, GA 30161 \n", + "\n", + " coordinates latitude longitude \\\n", + "0 NaN 41.290100 -72.902900 \n", + "1 NaN 33.757170 -83.727700 \n", + "2 NaN 43.691400 -70.328100 \n", + "3 NaN 41.717700 -70.484500 \n", + "4 NaN 44.077000 -72.004700 \n", + ".. ... ... ... \n", + "73 43.777703209506015, -90.05515309603231 43.777703 -90.055153 \n", + "74 36.90388067222262, -121.76968983169887 36.903881 -121.769690 \n", + "75 44.07671166339629, -72.0049135970569 44.076712 -72.004914 \n", + "76 31.533227585047626, -91.4374585606938 31.533228 -91.437459 \n", + "77 34.327173247943826, -85.0919307299404 34.327173 -85.091931 \n", + "\n", + " source \n", + "0 https://atlas.eia.gov/datasets/79dad60ce89c475... \n", + "1 https://atlas.eia.gov/datasets/79dad60ce89c475... \n", + "2 https://atlas.eia.gov/datasets/79dad60ce89c475... \n", + "3 https://atlas.eia.gov/datasets/79dad60ce89c475... \n", + "4 https://atlas.eia.gov/datasets/79dad60ce89c475... \n", + ".. ... \n", + "73 https://issuu.com/bbiinternational/docs/biodie... \n", + "74 https://issuu.com/bbiinternational/docs/biodie... \n", + "75 https://issuu.com/bbiinternational/docs/biodie... \n", + "76 https://issuu.com/bbiinternational/docs/biodie... \n", + "77 https://issuu.com/bbiinternational/docs/biodie... \n", + "\n", + "[78 rows x 12 columns]]\n" + ] + } + ], "source": [ "# --- 1. Extraction ---\n", "# In a real Prefect flow, each extraction would be a separate task.\n", "logger.info('Starting data extraction...')\n", - "prox_df = proximate.extract(project_root=project_root)\n", - "ult_df = ultimate.extract(project_root=project_root)\n", - "cmp_df = cmpana.extract(project_root=project_root)\n", - "dataframes = [prox_df, ult_df, cmp_df]\n", + "biodiesel_plants_df = extract(project_root=project_root)\n", + "dataframes = [biodiesel_plants_df]\n", + "print(dataframes)\n", "logger.info('Data extraction complete.')\n", "\n", - "# --- 2. Cleaning ---\n", - "# This list comprehension applies the cleaning function to each extracted dataframe.\n", - "logger.info('Starting data cleaning...')\n", - "clean_dataframes = [clean_the_gsheets(df) for df in dataframes if df is not None]\n", - "logger.info('Data cleaning complete.')\n", - "\n", - "# --- 3. Normalization ---\n", - "# This dictionary defines the columns to be normalized. \n", - "# The key is the column name in the DataFrame.\n", - "# The value is a tuple containing the corresponding SQLAlchemy model and the name of the attribute on the model to match against.\n", - "NORMALIZE_COLUMNS = {\n", - " 'resource': (Resource, 'name'),\n", - " 'prepared_sample': (PreparedSample, 'name'),\n", - " 'preparation_method': (PreparationMethod, 'name'),\n", - " 'parameter': (Parameter, 'name'),\n", - " 'unit': (Unit, 'name'),\n", - " 'analyst_email': (Contact, 'email'),\n", - " 'analysis_type': (AnalysisType, 'name'),\n", - " 'primary_ag_product': (PrimaryAgProduct, 'name')\n", - "}\n", - "\n", - "logger.info('Starting data normalization...')\n", - "normalized_dataframes = normalize_dataframes(clean_dataframes, NORMALIZE_COLUMNS)\n", - "logger.info('Data normalization complete.')\n", - "\n", - "# --- 4. Display Results ---\n", - "logger.info('Displaying results of normalization...')\n", - "for i, df in enumerate(normalized_dataframes):\n", - " print(f'--- Normalized DataFrame {i+1} ---')\n", - " display(df.head())" + "# # --- 2. Cleaning ---\n", + "# # This list comprehension applies the cleaning function to each extracted dataframe.\n", + "# logger.info('Starting data cleaning...')\n", + "# clean_dataframes = [clean_the_gsheets(df) for df in dataframes if df is not None]\n", + "# logger.info('Data cleaning complete.')\n", + "\n", + "# # --- 3. Normalization ---\n", + "# # This dictionary defines the columns to be normalized. \n", + "# # The key is the column name in the DataFrame.\n", + "# # The value is a tuple containing the corresponding SQLAlchemy model and the name of the attribute on the model to match against.\n", + "# NORMALIZE_COLUMNS = {\n", + "# 'resource': (Resource, 'name'),\n", + "# 'prepared_sample': (PreparedSample, 'name'),\n", + "# 'preparation_method': (PreparationMethod, 'name'),\n", + "# 'parameter': (Parameter, 'name'),\n", + "# 'unit': (Unit, 'name'),\n", + "# 'analyst_email': (Contact, 'email'),\n", + "# 'analysis_type': (AnalysisType, 'name'),\n", + "# 'primary_ag_product': (PrimaryAgProduct, 'name')\n", + "# }\n", + "\n", + "# logger.info('Starting data normalization...')\n", + "# normalized_dataframes = normalize_dataframes(clean_dataframes, NORMALIZE_COLUMNS)\n", + "# logger.info('Data normalization complete.')\n", + "\n", + "# # --- 4. Display Results ---\n", + "# logger.info('Displaying results of normalization...')\n", + "# for i, df in enumerate(normalized_dataframes):\n", + "# print(f'--- Normalized DataFrame {i+1} ---')\n", + "# display(df.head())" ] }, { diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gdrive_to_pandas.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gdrive_to_pandas.py new file mode 100644 index 00000000..8b083a0c --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gdrive_to_pandas.py @@ -0,0 +1,62 @@ +import pandas as pd +from pydrive2.auth import GoogleAuth +from pydrive2.drive import GoogleDrive + +def gdrive_to_df(file_name: str, credentials_path: str) -> pd.DataFrame: + """ + Extracts data from a CSV or GEOJSON into a pandas DataFrame. + + Args: + file_name: The name of the requested file. + credentials_path: The path to the Google Cloud service account credentials JSON file. + + Returns: + A pandas DataFrame containing the data from the specified worksheet, or None on error. + """ + try: + settings = { + "client_config_backend": "service", + "service_config": { + "client_json_file_path": credentials_path, + } + } + # Create instance of GoogleAuth + gauth = GoogleAuth(settings=settings) + gauth.ServiceAuth() + drive = GoogleDrive(gauth) + + try: + file_list = drive.ListFile().GetList() + print(file_list) + except SpreadsheetNotFound: + print(f"Error: Spreadsheet '{gsheet_name}' not found.") + print("Please make sure the spreadsheet name is correct and that you have shared it with the service account email.") + return None + + + # Get values directly to ensure we get calculated values, not formulas. + # 'FORMATTED_VALUE' gets the value as you see it in the sheet. + all_values = worksheet.get_all_values(value_render_option='FORMATTED_VALUE') + if not all_values: + return pd.DataFrame() # Return empty DataFrame if sheet is empty + + # Use the first row as header and the rest as data + df = pd.DataFrame(all_values[1:], columns=all_values[0]) + + # De-duplicate columns, keeping the first occurrence + df = df.loc[:, ~df.columns.duplicated()] + + return df + + except APIError as e: + print(f"Google API Error: {e}") + return None + except Exception as e: + print(f"An unexpected error occurred: {e}") + return None + + +if __name__ == '__main__': + # This part is for direct execution of this file, which is not the primary use case. + # The main test logic is in test_gsheet_to_pandas.py + pass From c34df14aae7daae1884c750f3889f460ed9b4fbd Mon Sep 17 00:00:00 2001 From: Avi <32148378+avi9664@users.noreply.github.com> Date: Wed, 14 Jan 2026 12:37:22 -0800 Subject: [PATCH 78/81] feat (pipeline): extract .zip and .geojson files from gdrive --- pixi.lock | 10353 +++++++++++++--- pixi.toml | 1 + .../biodiesel_plants-checkpoint.py | 2 +- .../pipeline/etl/extract/biodiesel_plants.py | 2 +- .../Biodiesel_Plants-checkpoint.csv | 2 +- .../CA_proc_points-checkpoint.csv | 713 ++ .../US_Freight_Terminals-checkpoint.geojson | 8 + .../US_Petroleum_Pipelines-checkpoint.geojson | 4319 +++++++ .../Biodiesel_Plants.csv | 2 +- .../temp_external_datasets/CA_proc_points.csv | 713 ++ .../temp_external_datasets/CA_proc_points.zip | Bin 0 -> 147737 bytes .../US_Freight_Terminals.geojson | 8 + .../US_Petroleum_Pipelines.geojson | 4319 +++++++ .../external_etl_notebook-checkpoint.ipynb | 322 +- .../utils/external_etl_notebook.ipynb | 322 +- 15 files changed, 19433 insertions(+), 1653 deletions(-) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/CA_proc_points-checkpoint.csv create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/US_Freight_Terminals-checkpoint.geojson create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/US_Petroleum_Pipelines-checkpoint.geojson create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/CA_proc_points.csv create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/CA_proc_points.zip create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/US_Freight_Terminals.geojson create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/US_Petroleum_Pipelines.geojson diff --git a/pixi.lock b/pixi.lock index 2b5c53ec..e9755122 100644 --- a/pixi.lock +++ b/pixi.lock @@ -28,8 +28,13 @@ environments: - 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+ if raw_df is None: logger.error("Failed to extract data. Aborting.") diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py index c3635fcc..39941ce8 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py @@ -24,7 +24,7 @@ def extract(csv_path) -> Optional[pd.DataFrame]: # The gsheet_to_df function handles authentication, data fetching, and error handling. raw_df = gdrive_to_pandas(FILE_NAME, CREDENTIALS_PATH) - + if raw_df is None: logger.error("Failed to extract data. Aborting.") diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/Biodiesel_Plants-checkpoint.csv b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/Biodiesel_Plants-checkpoint.csv index 7a32cf9a..96e7c3ee 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/Biodiesel_Plants-checkpoint.csv +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/Biodiesel_Plants-checkpoint.csv @@ -76,4 +76,4 @@ Walsh BioFuels LLC,58,Mauston,WI,5,Distillers corn oil,Operational,"WI-80 & Maus Western Iowa Energy - Agron Bioenergy,60,Watsonville,CA,15,Multifeedstock,Operational,"860 W Beach St, Watsonville, CA 95076","36.90388067222262, -121.76968983169887",36.90388067,-121.7696898,https://issuu.com/bbiinternational/docs/biodieselmap-2042 White Mountain Biodiesel LLC,62,North Haverhill,NH,8,Yellow grease,Operational,"35 Business Pk Rd, North Haverhill, NH 03774","44.07671166339629, -72.0049135970569",44.07671166,-72.0049136,https://issuu.com/bbiinternational/docs/biodieselmap-2043 World Energy - Natchez,65,Natchez,MS,72,Vegetable oils,Operational,"L E Barry Rd, Natchez, MS 39120","31.533227585047626, -91.4374585606938",31.53322759,-91.43745856,https://issuu.com/bbiinternational/docs/biodieselmap-2045 -World Energy - Rome,66,Rome,GA,20,Multifeedstock,Operational,"555 W Hermitage Rd NE, Rome, GA 30161","34.327173247943826, -85.0919307299404",34.32717325,-85.09193073,https://issuu.com/bbiinternational/docs/biodieselmap-2046 \ No newline at end of file +World Energy - Rome,66,Rome,GA,20,Multifeedstock,Operational,"555 W Hermitage Rd NE, Rome, GA 30161","34.327173247943826, -85.0919307299404",34.32717325,-85.09193073,https://issuu.com/bbiinternational/docs/biodieselmap-2046 diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/CA_proc_points-checkpoint.csv b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/CA_proc_points-checkpoint.csv new file mode 100644 index 00000000..5a46f5cf --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/CA_proc_points-checkpoint.csv @@ -0,0 +1,713 @@ +Address,COUNTY,City,Company,Join_Count,MASTERTYPE,State,Subtype,TARGET_FID,Type,Zip,TYPE,wkt_geom,geom,latitude,longitude +327 Daniels Ln,Kern,Bakersfield,Real Almond Processing,1.0,almond,CA,almond,0.0,shelling,93307,PROC,0101000020E610000090A6D5EBF1BF5DC0D652E5208DAC4140,POINT (-118.9991407 35.3480569),35.3480569,-118.9991407 +26060 Colusa Road,Fresno,Coalinga,Harris Woolf,1.0,almond,CA,almond,1.0,shelling,93210,PROC,0101000020E6100000931B45D61A175EC0EC67B114C9154240,POINT (-120.361013 36.170199),36.170199,-120.361013 +21490 Ortigalita Rd,Merced,Los Banos,Parreira Almond Processing,1.0,almond,CA,almond,2.0,shelling,93635,PROC,0101000020E610000008951348E4375EC00937B62ACB7D4240,POINT (-120.8733082 36.98276266),36.98276266,-120.8733082 +8800 S Minturn Rd,Merced,Le Grand,Minturn Nut Co Inc,1.0,almond,CA,almond,3.0,shelling,95333,PROC,0101000020E6100000E025DD3B8F115EC0B26066C8C6944240,POINT (-120.2743673 37.16231637),37.16231637,-120.2743673 +,Stanislaus,,Tree Nuts LLC,1.0,almond,CA,almond,4.0,shelling,0,PROC,0101000020E61000007CD3F4D901365EC07E37DDB243BE4240,POINT (-120.843863 37.486441),37.486441,-120.843863 +4618 N Montpelier Rd,Stanislaus,Denair,Roy Johnson Farms Inc,1.0,almond,CA,almond,5.0,shelling,95316,PROC,0101000020E61000001CB62DCAEC2C5EC0173745B20DC54240,POINT (-120.7019525 37.53948048),37.53948048,-120.7019525 +2656 House Ave,Butte,Durham,Antonowich hulling,1.0,almond,CA,almond,6.0,shelling,95938,PROC,0101000020E6100000CC7C073FF1735EC0539CFE4701D04340,POINT (-121.8115995 39.6250391),39.6250391,-121.8115995 +3190 CA 45,Glenn,Glenn,River West Processing,1.0,almond,CA,almond,7.0,shelling,95943,PROC,0101000020E6100000954330B374805EC0B266438252D14340,POINT (-122.0071228 39.63533047),39.63533047,-122.0071228 +1026 Sheridan Avenue,Butte,Chico,Western Nut Company,1.0,almond,CA,almond,8.0,shelling,95926,PROC,0101000020E61000006C0B2A0538755EC02C34C63D4CDF4340,POINT (-121.8315442 39.7445142),39.7445142,-121.8315442 +10665 E Whitmore Ave,Stanislaus,Hughson,"Hudelson Nut Company, Inc.",1.0,almond,CA,almond,9.0,shelling,95326,PROC,0101000020E6100000E8C64F3E18335EC0F4BF01D223CC4240,POINT (-120.7983547 37.59484315),37.59484315,-120.7983547 +11173 Mercedes Ave,Stanislaus,Livingston,"Hughson Nut, Inc.",1.0,almond,CA,almond,10.0,shelling,95334,PROC,0101000020E610000084B46BE7A0335EC0244F8A3D51CD4240,POINT (-120.8066958 37.60404176),37.60404176,-120.8066958 +11591 Meridian Rd.,Butte,Chico,"Fair Trade Corner, Inc.",1.0,almond,CA,almond,11.0,shelling,95973,PROC,0101000020E61000000EF049CCD87A5EC096FECAEFD9DC4340,POINT (-121.9194823 39.7254009),39.7254009,-121.9194823 +11900 E Monte Vista Ave,Stanislaus,Denair,"JD Almond Farms, Inc.",1.0,almond,CA,almond,12.0,shelling,95316,PROC,0101000020E61000006174D42CAB2D5EC0F93936E953C24240,POINT (-120.7135727 37.51818576),37.51818576,-120.7135727 +1217 Root Rd.,Stanislaus,Modesto,Circle M Nut Co.,1.0,almond,CA,almond,13.0,shelling,95357,PROC,0101000020E6100000EAF2412A20395EC01262D3EF67D44240,POINT (-120.8925882 37.6594219),37.6594219,-120.8925882 +12245 Sunny Acres Ave.,Merced,Turlock,"Sunny Acres Nut Company, Inc.",1.0,almond,CA,almond,14.0,shelling,95380,PROC,0101000020E610000094D519845E2D5EC09EDD109928BC4240,POINT (-120.7088938 37.46998895),37.46998895,-120.7088938 +1260 Muir Avenue,Butte,Chico,"Farmers International, Inc.",1.0,almond,CA,almond,15.0,shelling,95973,PROC,0101000020E6100000B72CBA50D4795EC0157FCAE7CBDF4340,POINT (-121.9035837 39.7484102),39.7484102,-121.9035837 +12700 East Graves Road,San Joaquin,Manteca,"Travaille & Phippen, Inc.",1.0,almond,CA,almond,16.0,shelling,95336,PROC,0101000020E6100000439259BDC3495EC051D8A8FBBEE34240,POINT (-121.152572 37.77926584),37.77926584,-121.152572 +1324 Dayton Rd.,Butte,Chico,Maisie Jane's,1.0,almond,CA,almond,17.0,shelling,95928,PROC,0101000020E610000041D8840F00765EC031067BB889DB4340,POINT (-121.8437537 39.7151404),39.7151404,-121.8437537 +1329 Hazeldean Rd.,Stanislaus,Hickman,Grizzly Nut LLC,1.0,almond,CA,almond,18.0,shelling,95323,PROC,0101000020E6100000B939950C002F5EC08A213999B8CF4240,POINT (-120.734378 37.622821),37.622821,-120.734378 +13646 Hwy 33,Los Angeles,Los Angeles,Wonderful Pistachios & Almonds LLC,1.0,almond,CA,almond,19.0,shelling,90064,PROC,0101000020E6100000ACA8C1340C9B5DC004029D499B044140,POINT (-118.42262 34.035989),34.035989,-118.42262 +137 North Hart Road,Stanislaus,Modesto,Fisher Nut Company,1.0,almond,CA,almond,20.0,shelling,95358,PROC,0101000020E6100000052C5ED1D2475EC080954BFCB4D14240,POINT (-121.1222423 37.63833574),37.63833574,-121.1222423 +13762 1st Avenue,Kings,Hanford,Nichols Pistachio,1.0,almond,CA,almond,21.0,shelling,93230,PROC,0101000020E61000006C651DE967DE5DC085B6F704E4224240,POINT (-119.4750922 36.2725836),36.2725836,-119.4750922 +13890 Looney Rd.,Merced,Ballico,"Hilltop Ranch, Inc.",1.0,almond,CA,almond,22.0,shelling,95303,PROC,0101000020E61000004D8578245E285EC01011CC0B0FBD4240,POINT (-120.630746 37.47702167),37.47702167,-120.630746 +13890 Looney Road,Merced,Ballico,Long Valley Organic LP,1.0,almond,CA,almond,23.0,shelling,95303,PROC,0101000020E61000004D8578245E285EC01011CC0B0FBD4240,POINT (-120.630746 37.47702167),37.47702167,-120.630746 +144 Westlake Avenue,Santa Cruz,Watsonville,Int'l Almond Exchange Inc.,1.0,almond,CA,almond,24.0,shelling,95076,PROC,0101000020E610000072158BDF14725EC008008E3D7B784240,POINT (-121.782524 36.941261),36.941261,-121.782524 +14650 Co Rd 87,Yolo,Esparto,Capay Canyon Ranch,1.0,almond,CA,almond,25.0,shelling,95627,PROC,0101000020E6100000D3A23EC91D815EC00A85083884584340,POINT (-122.017443 38.691535),38.691535,-122.017443 +14827 W. Harding Rd.,Merced,Turlock,"Select Harvest USA, LLC",1.0,almond,CA,almond,26.0,shelling,95380,PROC,0101000020E610000073405C8308305EC03F89B60040BB4240,POINT (-120.7505196 37.46289071),37.46289071,-120.7505196 +14827 W. Harding Rd.,Merced,Turlock,Spycher Brothers,1.0,almond,CA,almond,27.0,shelling,95380,PROC,0101000020E610000073405C8308305EC03F89B60040BB4240,POINT (-120.7505196 37.46289071),37.46289071,-120.7505196 +14827 W. Harding Rd.,Merced,Turlock,Trinity Nut Company,1.0,almond,CA,almond,28.0,shelling,95380,PROC,0101000020E610000073405C8308305EC03F89B60040BB4240,POINT (-120.7505196 37.46289071),37.46289071,-120.7505196 +"14900 W. Belmont Ave., #2",Fresno,Kerman,"Purity Organics, Inc.",1.0,almond,CA,almond,29.0,shelling,93630,PROC,0101000020E6100000126FF838AE035EC0F000AA132B604240,POINT (-120.0575087 36.7513146),36.7513146,-120.0575087 +1502 S. Railroad Avenue,Glenn,Orland,"T. M. Duche Nut Co., Inc.",1.0,almond,CA,almond,30.0,shelling,95963,PROC,0101000020E6100000697EEB796D8C5EC0CBF6DF5267DE4340,POINT (-122.1941819 39.73752819),39.73752819,-122.1941819 +1518 K Street,Stanislaus,Modesto,Montpelier Nut Co.,1.0,almond,CA,almond,31.0,shelling,95354,PROC,0101000020E6100000CB411A5FC53F5EC0FDC77C1F92D24240,POINT (-120.9964216 37.64508432),37.64508432,-120.9964216 +15391 Vinewood Ave,Merced,Livingston,Del Rio Nut Company,1.0,almond,CA,almond,32.0,shelling,95334,PROC,0101000020E6100000C630CCAEA0305EC0366EB5775BB14240,POINT (-120.7598073 37.38560387),37.38560387,-120.7598073 +15443 Beech Avenue,Kern,Wasco,"South Valley Almond Company, LLC",1.0,almond,CA,almond,33.0,shelling,93280,PROC,0101000020E61000008285DDC199D05DC0294AB67880CC4140,POINT (-119.2593846 35.59767064),35.59767064,-119.2593846 +1550 Industrial Dr.,San Joaquin,Stockton,"Pearl Crop, Inc.",1.0,almond,CA,almond,34.0,shelling,95206,PROC,0101000020E6100000C2E567D949505EC0517DCE7A84F44240,POINT (-121.2545074 37.91029296),37.91029296,-121.2545074 +15516 South Walnut Ave.,Fresno,Caruthers,"Almonds California Pride, Inc.",1.0,almond,CA,almond,35.0,shelling,93609,PROC,0101000020E61000000F29064834F35DC0309B00C3F2404240,POINT (-119.800066 36.5074085),36.5074085,-119.800066 +15516 South Walnut Ave.,Fresno,Caruthers,Campos Brothers,1.0,almond,CA,almond,36.0,shelling,93609,PROC,0101000020E61000000F29064834F35DC0309B00C3F2404240,POINT (-119.800066 36.5074085),36.5074085,-119.800066 +1555 Warren Rd.,San Joaquin,Ripon,"Almond Ace Packing, Inc.",1.0,almond,CA,almond,37.0,shelling,95366,PROC,0101000020E610000094D920938C485EC0D12E5351C4E04240,POINT (-121.13358 37.75599114),37.75599114,-121.13358 +16219 Western Ave,Kern,Wasco,Mandelin Inc.,1.0,almond,CA,almond,38.0,shelling,93280,PROC,0101000020E6100000D427B9C326D85DC0562DC81A1EC84140,POINT (-119.377366 35.56341872),35.56341872,-119.377366 +1640 W. Dovewood Lane,Fresno,Fresno,Jeff Curry & Associates,1.0,almond,CA,almond,39.0,shelling,93711,PROC,0101000020E61000001B5EB5D7A7F45DC0B3A3271BC5684240,POINT (-119.8227443 36.8185152),36.8185152,-119.8227443 +16471 W. Whitesbridge Rd.,Fresno,Kerman,"Schaad Family Almonds, Inc.",1.0,almond,CA,almond,40.0,shelling,93630,PROC,0101000020E61000007967A32971055EC04FA5B09CCE5D4240,POINT (-120.0850319 36.7328678),36.7328678,-120.0850319 +16897 Highway 43,Kern,Wasco,Supreme Almonds of California,1.0,almond,CA,almond,41.0,shelling,93280,PROC,0101000020E61000005A547A5C0AD55DC0B2CF8C1399C54140,POINT (-119.3287574 35.54373402),35.54373402,-119.3287574 +17495 Seidner Rd,Stanislaus,Escalon,Quality Nut Company,1.0,almond,CA,almond,42.0,shelling,95320,PROC,0101000020E61000007212EFA5153C5EC03D5B3086ACD14240,POINT (-120.9388213 37.63807752),37.63807752,-120.9388213 +1750 N Siskiyou Ave,Fresno,Kerman,"Sran Family Orchards, Inc.",1.0,almond,CA,almond,43.0,shelling,93630,PROC,0101000020E6100000A91B83A9C1045EC013FF66182D614240,POINT (-120.0743202 36.7591887),36.7591887,-120.0743202 +"1802 ""C"" St.",Sacramento,Sacramento,Blue Diamond Growers,1.0,almond,CA,almond,44.0,shelling,95814,PROC,0101000020E610000097033DD4B65E5EC04A78E7F5CC4A4340,POINT (-121.479909 38.5843799),38.5843799,-121.479909 +1825 Verduga Rd,Stanislaus,Hughson,"Hughson Nut, Inc.",1.0,almond,CA,almond,45.0,shelling,95326,PROC,0101000020E610000084B46BE7A0335EC0244F8A3D51CD4240,POINT (-120.8066958 37.60404176),37.60404176,-120.8066958 +18252 Avenue 20,Madera,Madera,"Elk Ridge Almonds, Inc.",1.0,almond,CA,almond,46.0,shelling,93637,PROC,0101000020E610000012DDB3AED10D5EC06DFA79741F854240,POINT (-120.215923 37.04002243),37.04002243,-120.215923 +18666 E. Highway 120,San Joaquin,Ripon,"A.D.P. DePalma Farms, Inc.",1.0,almond,CA,almond,47.0,shelling,95366,PROC,0101000020E6100000AAD216D7F8475EC0058A58C4B0E34240,POINT (-121.124563 37.778832),37.778832,-121.124563 +19424 Rd 13,Madera,Chowchilla,"Zinke Orchards, Inc.",1.0,almond,CA,almond,48.0,shelling,93610,PROC,0101000020E6100000CE6E2D93E1135EC01D3C34A80D844240,POINT (-120.310643 37.03166678),37.03166678,-120.310643 +20001 McHenry Ave,San Joaquin,Escalon,"Naraghi Farms, LLC",1.0,almond,CA,almond,49.0,shelling,95320,PROC,0101000020E610000048A3A76DE83F5EC01EA44C0FAFE34240,POINT (-120.9985613 37.7787799),37.7787799,-120.9985613 +2020 Esplanade,Butte,Chico,Chico Nut Company,1.0,almond,CA,almond,50.0,shelling,95926,PROC,0101000020E61000001C8645FB8E765EC0D305065ACBDF4340,POINT (-121.8524769 39.7483933),39.7483933,-121.8524769 +20282 Road 21,San Joaquin,Madera,D.V. Enterprises & Co.,1.0,almond,CA,almond,51.0,shelling,95209,PROC,0101000020E61000006B9BE27151565EC093A9825149034340,POINT (-121.348721 38.025675),38.025675,-121.348721 +21275 Simpson Road,Tehama,Corning,California Almond Packers & Exporters Inc.,1.0,almond,CA,almond,52.0,shelling,96021,PROC,0101000020E6100000F1E6BA3A918F5EC0FA8746DA3AFA4340,POINT (-122.2432391 39.95492104),39.95492104,-122.2432391 +21490 Ortigalita Rd,Merced,Los Banos,"RPAC, LLC",1.0,almond,CA,almond,53.0,shelling,93635,PROC,0101000020E610000008951348E4375EC00937B62ACB7D4240,POINT (-120.8733082 36.98276266),36.98276266,-120.8733082 +21888 Ave 14,Madera,Madera,"El Dorado Almonds, LLC",1.0,almond,CA,almond,54.0,shelling,93637,PROC,0101000020E6100000FE8EF2DD77095EC064C8D203F6794240,POINT (-120.1479411 36.95282028),36.95282028,-120.1479411 +23073 S. Frederick Rd.,San Joaquin,Ripon,"Golden Gate Nuts, Inc.",1.0,almond,CA,almond,55.0,shelling,95366,PROC,0101000020E610000043EED8BEB64A5EC0182632F7B9DF4240,POINT (-121.1674039 37.74786272),37.74786272,-121.1674039 +"23986 W Whitesbridge Ave,",Fresno,Kerman,Holland Nut Co.,1.0,almond,CA,almond,56.0,shelling,93630,PROC,0101000020E6100000894567F4FE0D5EC05BCA9EA97C5E4240,POINT (-120.2186862 36.7381794),36.7381794,-120.2186862 +240 Bunker Avenue,Stanislaus,Modesto,Wholesome Nut Company,1.0,almond,CA,almond,57.0,shelling,95351,PROC,0101000020E610000026AB22DC643F5EC0C0D8948EE6CF4240,POINT (-120.990531 37.62422354),37.62422354,-120.990531 +24341 Ave 14,Madera,Madera,Bapu Almond Co. Inc.,1.0,almond,CA,almond,58.0,shelling,93637,PROC,0101000020E61000000BCF4BC5C6065EC0C8AAEF99F8794240,POINT (-120.105882 36.95289921),36.95289921,-120.105882 +2454 E. Prestwick Ave.,Fresno,Fresno,"Verve Green, Inc.",1.0,almond,CA,almond,59.0,shelling,93730,PROC,0101000020E610000040B73C7B53EF5DC05F622CD32F724240,POINT (-119.7394703 36.8920845),36.8920845,-119.7394703 +26454 Avenue 128,Tulare,Portervile,RPC Packing Inc.,1.0,almond,CA,almond,60.0,shelling,93257,PROC,0101000020E61000005AA0DD21C5C65DC0C5877E12440A4240,POINT (-119.105782 36.0802024),36.0802024,-119.105782 +26639 Jones Rd,San Joaquin,Escalon,Roche Brothers International Family Nut Co.,1.0,almond,CA,almond,61.0,shelling,95320,PROC,0101000020E61000006D37C137CD3E5EC0B9BF40312EE34240,POINT (-120.9812755 37.77484718),37.77484718,-120.9812755 +27052 East Highway 120,San Joaquin,Escalon,Paddack Hulling & Shelling,1.0,almond,CA,almond,62.0,shelling,95320,PROC,0101000020E6100000E5637781923E5EC077A94BA5A3E54240,POINT (-120.977692 37.79405657),37.79405657,-120.977692 +27421 Avenue 12,Madera,Madera,Sun-Beam Almond Co.,1.0,almond,CA,almond,63.0,shelling,93637,PROC,0101000020E6100000FA85B24B2F035EC06781346B42764240,POINT (-120.0497617 36.92390194),36.92390194,-120.0497617 +2801 Lassiter Ln,Stanislaus,Turlock,Big Tree Organic Farms,1.0,almond,CA,almond,64.0,shelling,95380,PROC,0101000020E6100000FBF664B444385EC030EEED333ABE4240,POINT (-120.8791934 37.48615121),37.48615121,-120.8791934 +2900 Airport Dr.,Madera,Madera,The Almond Company,1.0,almond,CA,almond,65.0,shelling,93637,PROC,0101000020E6100000C0E72C58CF065EC04E0689E5FD7E4240,POINT (-120.1064053 36.99212331),36.99212331,-120.1064053 +"2909 Coffee Rd., Ste. 12B",Stanislaus,Modesto,PNC,1.0,almond,CA,almond,66.0,shelling,95355,PROC,0101000020E61000000B5751CD763E5EC0760381A525D74240,POINT (-120.9760011 37.68083638),37.68083638,-120.9760011 +2917 East Shepherd Ave.,Fresno,Clovis,"P-R Farms, Inc.",1.0,almond,CA,almond,67.0,shelling,93619,PROC,0101000020E6100000BAA3FFE5DAEE5DC075DDA51EB36E4240,POINT (-119.7321105 36.8648413),36.8648413,-119.7321105 +3006 Yosemite Blvd,Stanislaus,Modesto,Quality Nut Company,1.0,almond,CA,almond,68.0,shelling,95354,PROC,0101000020E61000007212EFA5153C5EC03D5B3086ACD14240,POINT (-120.9388213 37.63807752),37.63807752,-120.9388213 +3068 Chico Ave.,Butte,Chico,Vanella Farms,1.0,almond,CA,almond,69.0,shelling,95928,PROC,0101000020E61000000ADAE4F049785EC07C18101082D94340,POINT (-121.879513 39.6992817),39.6992817,-121.879513 +3190 Highway 45,Glenn,Glenn,"Riverwest Processing, Inc.",1.0,almond,CA,almond,70.0,shelling,95943,PROC,0101000020E6100000954330B374805EC0B266438252D14340,POINT (-122.0071228 39.63533047),39.63533047,-122.0071228 +31995 S. Chrisman Rd.,San Joaquin,Tracy,"Crown Nut Company, Inc.",1.0,almond,CA,almond,71.0,shelling,95304,PROC,0101000020E61000002354049376595EC0CAE471A4F5D44240,POINT (-121.3978622 37.66374641),37.66374641,-121.3978622 +320 E South St,Glenn,Orland,Baldwin Minkler Farms,1.0,almond,CA,almond,72.0,shelling,95963,PROC,0101000020E61000007D76C075458B5EC087E7BEFF83DE4340,POINT (-122.1761145 39.73840329),39.73840329,-122.1761145 +32331 Famoso Rd.,Kern,McFarland,"Famoso Nut Company, LLC",1.0,almond,CA,almond,73.0,shelling,93250,PROC,0101000020E6100000B2C92B2169CD5DC0DF4CD04F06CD4140,POINT (-119.2095416 35.60175512),35.60175512,-119.2095416 +3242 North Avenue,Stanislaus,Modesto,BL Nut Company,1.0,almond,CA,almond,74.0,shelling,95358,PROC,0101000020E61000008CC0B398B3435EC038350A2858D64240,POINT (-121.0578367 37.67456532),37.67456532,-121.0578367 +3242 S. Carpenter Road,Stanislaus,Turlock,"Valley Harvest Nut Co., Inc.",1.0,almond,CA,almond,75.0,shelling,95358,PROC,0101000020E61000002D358CCCED415EC044CBD31C4DCB4240,POINT (-121.0301391 37.58829079),37.58829079,-121.0301391 +3443 Montpellier Rd,Stanislaus,Hickman,"Rolling Hills Nut Company, Inc.",1.0,almond,CA,almond,76.0,shelling,95323,PROC,0101000020E6100000136635B8082F5EC0F3730137A4C84240,POINT (-120.7349072 37.56751144),37.56751144,-120.7349072 +3500 Shiells Rd.,Stanislaus,Newman,"Stewart & Jasper Marketing, Inc.",1.0,almond,CA,almond,77.0,shelling,95360,PROC,0101000020E61000000EE7D0D8CD445EC0D122FC07E8A64240,POINT (-121.0750639 37.30395603),37.30395603,-121.0750639 +"3611 West Beechwood, Suite 101",Fresno,Fresno,"Panoche Creek Packing, Inc.",1.0,almond,CA,almond,78.0,shelling,93711,PROC,0101000020E6100000931ADA00ECF65DC038BF61A2416B4240,POINT (-119.8581545 36.8379405),36.8379405,-119.8581545 +365 Ruggieri Way,Colusa,Williams,Vann Family Orchards,1.0,almond,CA,almond,79.0,shelling,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +4315 E. Childs Avenue,Merced,Merced,Central Valley Processing,1.0,almond,CA,almond,80.0,shelling,95341,PROC,0101000020E610000097546D37411A5EC071F35BAEDDA44240,POINT (-120.4102305 37.28801517),37.28801517,-120.4102305 +43940 W. North Ave.,Fresno,Firebaugh,"Silver Creek Almond Co., Inc.",1.0,almond,CA,almond,81.0,shelling,93622,PROC,0101000020E610000054E3A59BC4255EC0CB8DD8DDF2584240,POINT (-120.590125 36.6949117),36.6949117,-120.590125 +44474 West Nees Avenue,Fresno,Firebaugh,"Oro Loma Ranch, LLC",1.0,almond,CA,almond,82.0,shelling,93622,PROC,0101000020E61000006C4084B8F2255EC018BC9E9E2D6D4240,POINT (-120.5929395 36.8529547),36.8529547,-120.5929395 +4512 North Ave,Stanislaus,Modesto,Beckner Ranches,1.0,almond,CA,almond,83.0,shelling,95358,PROC,0101000020E6100000055262D7F6445EC0716BDADE51D64240,POINT (-121.077566 37.67437349),37.67437349,-121.077566 +500 North F Street,Kern,Kern,"SunnyGem, LLC",1.0,almond,CA,almond,84.0,shelling,93280,PROC,0101000020E6100000192202695AD55DC075CBCCD43DCC4140,POINT (-119.3336432 35.59563694),35.59563694,-119.3336432 +5043 N Montpelier Rd,Stanislaus,Denair,Monte Vista Farming Company,1.0,almond,CA,almond,85.0,shelling,95316,PROC,0101000020E610000059AD026B8B2D5EC0648918C025C44240,POINT (-120.7116344 37.53240205),37.53240205,-120.7116344 +5166 S. Sperry Rd.,Stanislaus,Denair,California Nut Company,1.0,almond,CA,almond,86.0,shelling,95316,PROC,0101000020E61000007D03931B45335EC009D2B5C404C84240,POINT (-120.801093 37.56264552),37.56264552,-120.801093 +518 El Roya Ave.,Stanislaus,Modesto,"California Gold Almonds, LLC",1.0,almond,CA,almond,87.0,shelling,95354,PROC,0101000020E610000063038EA9603C5EC08A7460B509D14240,POINT (-120.9433998 37.63310878),37.63310878,-120.9433998 +5600 Norris Road,Kern,Bakersfield,JSS Almonds,1.0,almond,CA,almond,88.0,shelling,93308,PROC,0101000020E6100000D580F7440DC45DC092AC6818E3B54140,POINT (-119.0633099 35.4209929),35.4209929,-119.0633099 +6183 Reddick Rd,Solano,Dixon,Rotteveel Orchards,1.0,almond,CA,almond,89.0,shelling,95620,PROC,0101000020E6100000B85043658D765EC067D13B15703A4340,POINT (-121.8523801 38.4565455),38.4565455,-121.8523801 +6303 Beckwith Road,Stanislaus,Modesto,"Twin Commodities, Inc.",1.0,almond,CA,almond,90.0,shelling,95358,PROC,0101000020E61000001EF175630B475EC04F43AF9A42D74240,POINT (-121.1100701 37.6817201),37.6817201,-121.1100701 +644 Railroad AVe.,Merced,Atwater,Valley Pride Ag Company,1.0,almond,CA,almond,91.0,shelling,95301,PROC,0101000020E610000042356FE6A1265EC033DBBA40EEAB4240,POINT (-120.6036316 37.3432084),37.3432084,-120.6036316 +6543 Vivian Road,Stanislaus,Modesto,"Athwal Almonds, Inc.",1.0,almond,CA,almond,92.0,shelling,95358,PROC,0101000020E6100000EB43CD461D435EC04FBBEBAEE4C44240,POINT (-121.0486619 37.53822886),37.53822886,-121.0486619 +6677 Hardaway Rd.,San Joaquin,Stockton,Star Nut Co.,1.0,almond,CA,almond,93.0,shelling,95215,PROC,0101000020E6100000FD46E0B4054E5EC01D9BB20D3B004340,POINT (-121.2190983 38.00180217),38.00180217,-121.2190983 +6914 Rd 160,Tulare,Earlimart,"Treehouse California Almonds, LLC",1.0,almond,CA,almond,94.0,shelling,93219,PROC,0101000020E6100000FF25A94CB1CD5DC03D6787CF08F54140,POINT (-119.2139465 35.91433138),35.91433138,-119.2139465 +7030 County Road 25,Glenn,Orland,Baugher Ranch Organics,1.0,almond,CA,almond,95.0,shelling,95963,PROC,0101000020E61000005C920376358C5EC0BE4C142175DF4340,POINT (-122.190763 39.745762),39.745762,-122.190763 +709 Dutton Street,Yolo,Winters,Mariani Nut Company,1.0,almond,CA,almond,96.0,shelling,95694,PROC,0101000020E6100000EC5113D8F77D5EC0DAAE8EEB78434340,POINT (-121.9682522 38.52712769),38.52712769,-121.9682522 +7418 County Road 24,Glenn,Orland,North Valley Nut,1.0,almond,CA,almond,97.0,shelling,95963,PROC,0101000020E6100000E1174D1D1A865EC01116789BF5DA4340,POINT (-122.0953439 39.71062034),39.71062034,-122.0953439 +850 Commerce,Madera,Madera,"Sierra Valley Almonds, LLC",1.0,almond,CA,almond,98.0,shelling,93637,PROC,0101000020E610000007F5882CAD055EC08AC91B60E6784240,POINT (-120.0886947 36.9445305),36.9445305,-120.0886947 +8618 E Whitmore Ave,Stanislaus,Hughson,California Grown Nut Company,1.0,almond,CA,almond,99.0,shelling,95326,PROC,0101000020E61000001814BCD77F355EC0756EE2FD1BCC4240,POINT (-120.8359279 37.59460424),37.59460424,-120.8359279 +862 Almond Avenue,Colusa,Arbuckle,D & K Orchards,1.0,almond,CA,almond,100.0,shelling,95912,PROC,0101000020E6100000C28476F379845EC049DD8CA220804340,POINT (-122.0699433 39.00099594),39.00099594,-122.0699433 +8800 South Minturn Road,Merced,LeGrand,Minturn Nut Company,1.0,almond,CA,almond,101.0,shelling,95333,PROC,0101000020E6100000E025DD3B8F115EC0B26066C8C6944240,POINT (-120.2743673 37.16231637),37.16231637,-120.2743673 +9441 W. Butte Rd.,Sutter,Live Oak,"Tarke Farming, Inc.",1.0,almond,CA,almond,102.0,shelling,95953,PROC,0101000020E6100000975A4AF14C775EC02C0339EE35A04340,POINT (-121.8640712 39.25164583),39.25164583,-121.8640712 +9843 Cox Rd,Stanislaus,Patterson,Del Mar Farms,1.0,almond,CA,almond,103.0,shelling,95363,PROC,0101000020E61000001B97169A904A5EC012EC4B78BAC64240,POINT (-121.1650758 37.55256561),37.55256561,-121.1650758 +988 Crane Canyon Rd,Kern,Lebec,Tejon Ranch Company,1.0,almond,CA,almond,104.0,shelling,93243,PROC,0101000020E61000009E735C32B3B65DC023AF5ADB8C694140,POINT (-118.8546873 34.82461111),34.82461111,-118.8546873 +3250 Camino Del Sol,Ventura,Oxnard,olde thompson inc,1.0,dehydrator,CA,spice vegetables,292.0,dehydrator,93030,PROC,0101000020E6100000F4B2DC88DDC85DC0EF03EB93371A4140,POINT (-119.1385214 34.2048211),34.2048211,-119.1385214 +9301 Lacey Blvd,Kings,Hanford,olam spices and vegetable ingredients,1.0,dehydrator,CA,spice vegetables,293.0,dehydrator,93230,PROC,0101000020E61000003A652431F7E75DC01BE1A3B4ED294240,POINT (-119.6244624 36.3275667),36.3275667,-119.6244624 +1445 Nebraska Ave,Fresno,Selma,Sun Maid Growers,1.0,dehydrator,CA,grape,294.0,dehydrator,93662,PROC,0101000020E610000037AA2E3B9FE65DC0A87F5A56AB474240,POINT (-119.6034687 36.5599163),36.5599163,-119.6034687 +2028 S 3rd St,Fresno,Fresno,Valley Fig Growers,1.0,dehydrator,CA,fig,295.0,dehydrator,93702,PROC,0101000020E61000000D99E1F54FF15DC001C11C3D7E5C4240,POINT (-119.7705054 36.7226025),36.7226025,-119.7705054 +47641 W Nees Ave,Fresno,Firebaugh,olam spices and vegetable ingredients,1.0,dehydrator,CA,spice vegetables,296.0,dehydrator,93622,PROC,0101000020E6100000B31078BB39295EC01004C8D0B16C4240,POINT (-120.6441487 36.8491765),36.8491765,-120.6441487 +28390 Ave 12,Madera,Madera,sunsweet dryers,1.0,dehydrator,CA,prune date fruit nut,297.0,dehydrator,93637,PROC,0101000020E610000036DABB500A025EC01E6B460639764240,POINT (-120.0318796 36.92361525),36.92361525,-120.0318796 +1350 CA 152,Santa Clara,Gilroy,Gilroy foods,1.0,dehydrator,CA,garlic onion capsicums,298.0,dehydrator,95020,PROC,0101000020E6100000AA51FEA490625EC031C1DB4965804240,POINT (-121.5400784 37.00309108),37.00309108,-121.5400784 +3324 Orestimba Rd,Stanislaus,Newman,VSP products valleysun,1.0,dehydrator,CA,tomato,299.0,dehydrator,95360,PROC,0101000020E6100000E247EB5E5D455EC00D633D7B4FA84240,POINT (-121.0838239 37.31492558),37.31492558,-121.0838239 +9984 Walnut Ave,Merced,Livingston,sensient natural ingredients,1.0,dehydrator,CA,garlic onion capsicums vegetables,300.0,dehydrator,95334,PROC,0101000020E610000082035ABA822E5EC02BC0779B37B04240,POINT (-120.726729 37.376697),37.376697,-120.726729 +151 S Walnut Rd,Stanislaus,Turlock,sensient natural ingredients,1.0,dehydrator,CA,garlic onion capsicums vegetables,301.0,dehydrator,95380,PROC,0101000020E6100000FD6DAA49CB375EC0F6D2D2E4FBBE4240,POINT (-120.8717827 37.49206219),37.49206219,-120.8717827 +2757 Rockville Rd,Solano,Fairfield,Culinary Farms,1.0,dehydrator,CA,tomatoes,302.0,dehydrator,94534,PROC,0101000020E6100000F0BCF9B2D9855EC08F1436A8A21F4340,POINT (-122.0914123 38.2471514),38.2471514,-122.0914123 +500 Crocker Dr,Solano,Vacaville,Mariani Packing,1.0,dehydrator,CA,fruit,303.0,dehydrator,95688,PROC,0101000020E61000006F5DD669C97C5EC035DC3642F5334340,POINT (-121.9497933 38.4059222),38.4059222,-121.9497933 +29485 Co Rd 27,Yolo,Winters,sunsweet dryers,1.0,dehydrator,CA,prune date fruit nut,304.0,dehydrator,95694,PROC,0101000020E610000007F01648507E5EC0D177B7B244434340,POINT (-121.97365 38.525534),38.525534,-121.97365 +1520 Terminal St,Yolo,West Sacramento,California Fire Roasted LLC,1.0,dehydrator,CA,tomato,305.0,dehydrator,95691,PROC,0101000020E6100000A1E76047AD625EC0B7BCCD76E0484340,POINT (-121.5418261 38.5693501),38.5693501,-121.5418261 +1244 E Beamer St,Yolo,Woodland,Culinary Farms,1.0,dehydrator,CA,tomatoes,306.0,dehydrator,95776,PROC,0101000020E61000004C50C3B7B0705EC0BCA24A8391574340,POINT (-121.760786 38.6841282),38.6841282,-121.760786 +901 N Walton Ave,Sutter,Yuba City,sunsweet growers,1.0,dehydrator,CA,prune date,307.0,dehydrator,95993,PROC,0101000020E61000001533672211695EC0D2EF6F8EC2914340,POINT (-121.6416708 39.13874989),39.13874989,-121.6416708 +6229 Myers Road,Colusa,Williams,olam spices and vegetable ingredients,1.0,dehydrator,CA,spice vegetables,308.0,dehydrator,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +1500 Eager Rd,Sutter,Live Oak,wilbur packing co,1.0,dehydrator,CA,prune,309.0,dehydrator,95953,PROC,0101000020E610000051BB5F05F8685EC0168B3ACE48984340,POINT (-121.640138 39.18972185),39.18972185,-121.640138 +7207 Moon Bend Rd,Colusa,Colusa,sunsweet dryers,1.0,dehydrator,CA,prune date fruit nut,310.0,dehydrator,95932,PROC,0101000020E610000022EF0B9EF87F5EC039C29AB105994340,POINT (-121.9995494 39.19548626),39.19548626,-121.9995494 +9301 9399 Larkin Rd,Sutter,Live Oak,sunsweet dryers,1.0,dehydrator,CA,prune date fruit nut,311.0,dehydrator,95953,PROC,0101000020E6100000E97E4E417E6C5EC0FC89CA8635A14340,POINT (-121.695206 39.259446),39.259446,-121.695206 +1900 Highway 99,Butte,Gridley,stapleton spense packing,1.0,dehydrator,CA,plums prunes,312.0,dehydrator,95948,PROC,0101000020E610000068565B56066C5EC09688015CDAAF4340,POINT (-121.6878868 39.3738513),39.3738513,-121.6878868 +7714 Co Rd 9,Glenn,Orland,sunsweet dryers,1.0,dehydrator,CA,prune date fruit nut,313.0,dehydrator,95963,PROC,0101000020E61000005C920376358C5EC0BE4C142175DF4340,POINT (-122.190763 39.745762),39.745762,-122.190763 +12021 Ave 328,Tulare,Visalia,Elbow Gin Inc,1.0,gin,CA,cotton,417.0,gin,93291,PROC,0101000020E61000002E84E6841AD45DC0B1702FBC54314240,POINT (-119.3141186 36.38539841),36.38539841,-119.3141186 +12095 2nd Ave,Kings,Hanford,County Line Gin Inc,1.0,gin,CA,cotton,418.0,gin,93230,PROC,0101000020E61000001CD6AFCF77DF5DC0A8F63306E7254240,POINT (-119.4916877 36.2961128),36.2961128,-119.4916877 +17053 Shafter Ave,Kern,Shafter,SJV Quality Cotton,1.0,gin,CA,cotton,419.0,gin,93263,PROC,0101000020E6100000F2B1BB40C9D15DC0751FC2F0F8C34140,POINT (-119.2779085 35.53103456),35.53103456,-119.2779085 +19813 Madison Ave,Kings,Stratford,Stratford Growers Inc,1.0,gin,CA,cotton,420.0,gin,93266,PROC,0101000020E61000004C2FD6DCF6F35DC037A5BC5642154240,POINT (-119.8119423 36.166087),36.166087,-119.8119423 +20509 Elgin Ave,Kings,Lemoore,West Island CoOp Gin,1.0,gin,CA,cotton,421.0,gin,93245,PROC,0101000020E6100000A3A025D9B4F45DC04BD933958F304240,POINT (-119.8235381 36.3793818),36.3793818,-119.8235381 +2531 Wasco Way,Kern,Buttonwillow,Farmers CoOp Gin,1.0,gin,CA,cotton,422.0,gin,93206,PROC,0101000020E610000090323DBCC2DC5DC0F3F99B2FFAB24140,POINT (-119.4493857 35.39826007000001),35.39826007000001,-119.4493857 +27519 Jackson Ave,Kings,Lemoore,Westhaven Cotton Co,1.0,gin,CA,cotton,423.0,gin,93245,PROC,0101000020E61000008C20DFEFE1FC5DC0E9D7310972204240,POINT (-119.9512901 36.2534801),36.2534801,-119.9512901 +33370 W Nebraska Ave,Fresno,Cantua Creek,Pacific Pima Gin Inc,1.0,gin,CA,cotton,424.0,gin,93608,PROC,0101000020E6100000EC53E98255195EC00DECE703B8474240,POINT (-120.3958442 36.5603032),36.5603032,-120.3958442 +40109 W Bullard Ave,Fresno,Firebaugh,Broadview Coop Gin,1.0,gin,CA,cotton,425.0,gin,93622,PROC,0101000020E61000002BA798DED9205EC0AF1B00BBE4684240,POINT (-120.5132977 36.8194803),36.8194803,-120.5132977 +43939 W. North Ave.,Fresno,Firebaugh,Silver Creek Gin,1.0,gin,CA,cotton,426.0,gin,93622,PROC,0101000020E61000006741CD3571255EC0F6E0496650584240,POINT (-120.5850348 36.68995360000001),36.68995360000001,-120.5850348 +626 W Cartmill Ave,Tulare,Tulare,Mid Valley Cotton Growers Inc,1.0,gin,CA,cotton,427.0,gin,93274,PROC,0101000020E610000009F42E83D6D65DC0F9C2BF63D31E4240,POINT (-119.3568428 36.2408261),36.2408261,-119.3568428 +7870 Hutchins Rd,Merced,Dos Palos,Dos Palos CoOp Gin Inc,1.0,gin,CA,cotton,428.0,gin,93620,PROC,0101000020E6100000D1FF177467285EC0E40DD539AB8A4240,POINT (-120.6313143 37.0833504),37.0833504,-120.6313143 +8587 S Contra Costa Rd,Fresno,Tranquillity,Westside Farmers CoOp,1.0,gin,CA,cotton,429.0,gin,93668,PROC,0101000020E61000008DC9874531105EC0F6A22C32F04D4240,POINT (-120.2530073 36.6088927),36.6088927,-120.2530073 +860 Corn Camp Rd,Kern,Buttonwillow,Buttonwillow Ginning Co,1.0,gin,CA,cotton,430.0,gin,93206,PROC,0101000020E6100000B11DE7911AE15DC0C5DE5184D0B64140,POINT (-119.5172467 35.42823843),35.42823843,-119.5172467 +9450 Agripark Dr,Sutter,Sutter,North Valley Cotton Gin,1.0,gin,CA,cotton,431.0,gin,95982,PROC,0101000020E61000001C66C3F583725EC049C0229E70934340,POINT (-121.7893042 39.15187432),39.15187432,-121.7893042 +9759 Valpredo Road,Kern,Bakersfield,Western Farmers CoOp gin,1.0,gin,CA,cotton,432.0,gin,93313,PROC,0101000020E61000009FBCD93054C35DC0D020F422C9894140,POINT (-119.0520136 35.07645070000001),35.07645070000001,-119.0520136 +9759 Valpredo Road,Kern,Bakersfield,South Valley Gin,1.0,gin,CA,cotton,433.0,gin,93313,PROC,0101000020E61000009FBCD93054C35DC0D020F422C9894140,POINT (-119.0520136 35.07645070000001),35.07645070000001,-119.0520136 +9845 Hanford Armona Rd.,Kings,Hanford Ca. 93230,Central Valley CoOp,1.0,gin,CA,cotton,434.0,gin,0,PROC,0101000020E610000018B0E42A96E85DC0170335C618284240,POINT (-119.6341655 36.31325605),36.31325605,-119.6341655 +4309 Fruitland Ave,Los Angeles,Vernon,General Mills,1.0,mill,CA,bread,435.0,milling,90058,PROC,0101000020E61000005E66D828EB8C5DC0E91505B0B7FF4040,POINT (-118.201853 33.9977932),33.9977932,-118.201853 +23865 Ave 18,Madera,Madera,Valley GrainAzteca Milling,1.0,mill,CA,corn wheat,436.0,milling,93638,PROC,0101000020E61000001DD9A6C269075EC0F24940AF6C814240,POINT (-120.1158301 37.01112929),37.01112929,-120.1158301 +20100 Fairmead Blvd,Madera,Madera,Valley GrainAzteca Milling,1.0,mill,CA,corn wheat,437.0,milling,93638,PROC,0101000020E6100000DD578A89F2095EC081B45ABB48854240,POINT (-120.1554283 37.0412821),37.0412821,-120.1554283 +13310 Nanna's Way,Nevada,Grass Valley,Grass Valley Grains Farm,1.0,mill,CA,grains,438.0,milling,95949,PROC,0101000020E6100000348BAB25F8455EC03D8E3056E5964340,POINT (-121.0932707 39.1788738),39.1788738,-121.0932707 +7770 Rd 33,Madera,Madera,ENZO Olive Oil,1.0,olive,CA,olive,467.0,olive oil,93638,PROC,0101000020E6100000382394089EFC5DC05C6D8B53296E4240,POINT (-119.9471456 36.86063618),36.86063618,-119.9471456 +13950 Thornton Rd,San Joaquin,Lodi,Calivirgin coldani olive ranch,1.0,olive,CA,olive,468.0,olive oil,95242,PROC,0101000020E610000032906797EF585EC0AA1EBCB8850D4340,POINT (-121.3896235 38.10564336),38.10564336,-121.3896235 +455 Harter Ave,Yolo,Woodland,Boundary Bend Olives,1.0,olive,CA,olive,469.0,olive oil,95776,PROC,0101000020E6100000657506A197705EC092D332ADA8584340,POINT (-121.7592547 38.6926476),38.6926476,-121.7592547 +2675 Lone Tree Rd,Butte,Oroville,California Olive Ranch,1.0,olive,CA,olive,470.0,olive oil,95965,PROC,0101000020E6100000B81E85EBD1645EC058201F99B3AE4340,POINT (-121.5753125 39.36485590000001),39.36485590000001,-121.5753125 +5945 Co Rd 35,Glenn,Artois,California Olive Ranch,1.0,olive,CA,olive,471.0,olive oil,95913,PROC,0101000020E6100000FDDAFAE93F895EC0B247A81952DD4340,POINT (-122.144526 39.729068),39.729068,-122.144526 +717 Tehama St,Glenn,Orland,west coast products,1.0,olive,CA,olives,472.0,cannery oil,95963,PROC,0101000020E6100000DB9145F5B18C5EC085D726FCEFDF4340,POINT (-122.1983617 39.74951126),39.74951126,-122.1983617 +1367 E Lassen Ave,Butte,Chico,California Olive Ranch,1.0,olive,CA,olive,473.0,olive oil,95973,PROC,0101000020E6100000301004C8D0755EC01471DF0FE4E24340,POINT (-121.840868 39.7725849),39.7725849,-121.840868 +23377 South Ave,Tehama,Corning,California Olive Ranch,1.0,olive,CA,olive,474.0,olive oil,96021,PROC,0101000020E61000000E187F364D8A5EC092AFE343F9F34340,POINT (-122.1609627 39.90604447),39.90604447,-122.1609627 +14633 CA 33,Kern,Lost Hills,Horizon Nut Co,1.0,pistachio,CA,pistachios,475.0,shelling,93249,PROC,0101000020E6100000A592F073B2F85DC08A5ABB690AD24140,POINT (-119.8858919 35.64094278),35.64094278,-119.8858919 +26487 N Highway 99,Tulare,Tulare,Horizon Nut Co,1.0,pistachio,CA,pistachios,476.0,shelling,93274,PROC,0101000020E6100000A12E52288BD65DC018526E70DC1F4240,POINT (-119.3522435 36.24891477),36.24891477,-119.3522435 +4946 4998 N Jerrold Ave,Fresno,Firebaugh,horizon nut firebaugh,1.0,pistachio,CA,pistachios,477.0,shelling,93622,PROC,0101000020E6100000BB9C121093225EC09DD5027B4C6A4240,POINT (-120.540226 36.830459),36.830459,-120.540226 +1250 W Lathrop Rd,San Joaquin,Lathrop,california natural products,1.0,rice,CA,rice,549.0,misc,95330,PROC,0101000020E6100000A9F7544E7B515EC0428FFF9F96E94240,POINT (-121.273151 37.82490921),37.82490921,-121.273151 +1800 Terminal St,Yolo,West Sacramento,Farmers Rice Cooperative,1.0,rice,CA,rice,550.0,hulling mill,95691,PROC,0101000020E6100000E865B911BB625EC010338F577B484340,POINT (-121.5426678 38.56626410000001),38.56626410000001,-121.5426678 +351 Hanson Way,Yolo,Woodland,pgp international,1.0,rice,CA,grains rice,551.0,flour mill,95776,PROC,0101000020E61000003E09C787B46D5EC0EC1FFAA4C9564340,POINT (-121.7141437 38.6780287),38.6780287,-121.7141437 +6133 Abel Rd,Colusa,Williams,American Commodity Company ACCGWG LLC Great Western Growers,1.0,rice,CA,rice,552.0,hulling mill,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +4937 CA 45,Colusa,Colusa,Farmers Rice Cooperative,1.0,rice,CA,rice,553.0,warehouse,95932,PROC,0101000020E6100000852BFB09C2815EC0BDECCF2C26AE4340,POINT (-122.0274682 39.36054001),39.36054001,-122.0274682 +1 Comet Ln,Colusa,Maxwell,California Heritage Mills,1.0,rice,CA,rice,554.0,mill,95955,PROC,0101000020E610000067BAD7497D885EC0E08096AE60A34340,POINT (-122.132647 39.276388),39.276388,-122.132647 +10400 Billings Rd,Sutter,Live Oak,Gibbs Wild Rice,1.0,rice,CA,rice,555.0,distributer,95953,PROC,0101000020E610000035DBCB6CC66C5EC0D564BE6A02A44340,POINT (-121.6996109 39.28132376),39.28132376,-121.6996109 +126 E Main St,Colusa,Colusa,PGP International,1.0,rice,CA,rice,556.0,mill,95932,PROC,0101000020E610000008F13790E47F5EC044A212CF409B4340,POINT (-121.9983254 39.21291531),39.21291531,-121.9983254 +1603 Highway 99 W,Colusa,Arbuckle,ADM Milling Co,1.0,rice,CA,rice,557.0,mill,95912,PROC,0101000020E610000038DA71C3EF805EC0302C7FBE2D844340,POINT (-122.014634 39.032646),39.032646,-122.014634 +1620 E Kentucky Ave,Yolo,Woodland,SunFoods LLC,1.0,rice,CA,rice,558.0,distributer,95776,PROC,0101000020E61000006366FA809B6F5EC0ADB9484673584340,POINT (-121.7438662 38.6910179),38.6910179,-121.7438662 +1701 Abel Rd,Colusa,Williams,Tamaki Rice Corp,1.0,rice,CA,rice,559.0,mill,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +22540 Russell Ave,Merced,South Dos Palos,Koda Farms,1.0,rice,CA,rice,560.0,mill,93665,PROC,0101000020E6100000DA441CA1D5295EC0D51B9C25547A4240,POINT (-120.6536639 36.95569296),36.95569296,-120.6536639 +2640 Hoffman Rd,Yuba,Olivehurst,Rue and Forsman Ranc Inc,1.0,rice,CA,rice,561.0,distributer,95961,PROC,0101000020E610000089D4B48B69605EC03BCFF1340D824340,POINT (-121.506442 39.01602804),39.01602804,-121.506442 +2889 Niagara Ave,Colusa,Colusa,Colusa Rice Company,1.0,rice,CA,rice,562.0,distributer,95932,PROC,0101000020E6100000255987A3AB805EC0581AF8510D9B4340,POINT (-122.010476 39.211344),39.211344,-122.010476 +3455 Nelson Rd,Butte,Durham,Far West Rice Inc,1.0,rice,CA,rice,563.0,mill,95938,PROC,0101000020E610000075A26EB16C765EC063B6645584C64340,POINT (-121.8503841 39.5509135),39.5509135,-121.8503841 +507 Bannock St,Butte,Biggs,SunWest Foods Inc,1.0,rice,CA,rice,564.0,mill,95917,PROC,0101000020E6100000BFC980FDA16D5EC0803628507AB44340,POINT (-121.7130121 39.4099827),39.4099827,-121.7130121 +5311 Midway,Butte,Richvale,Lundberg Family Farms,1.0,rice,CA,rice,565.0,mill,95974,PROC,0101000020E610000044D554BBCB6F5EC076D6B848EBBF4340,POINT (-121.7468098 39.4993678),39.4993678,-121.7468098 +6550 Struckmeyer Rd,Colusa,Arbuckle,California Family Foods Inc,1.0,rice,CA,rice,566.0,mill,95912,PROC,0101000020E610000038DA71C3EF805EC0302C7FBE2D844340,POINT (-122.014634 39.032646),39.032646,-122.014634 +7050 Eddy Rd,Colusa,Arbuckle,Sun Valley Rice Co LLC,1.0,rice,CA,rice,567.0,mill,95912,PROC,0101000020E610000095E8764023815EC0C788E1762A7B4340,POINT (-122.0177766 38.96223341),38.96223341,-122.0177766 +7875 County Road 32 1/2,Glenn,Glenn,Rice Researchers Inc,1.0,rice,CA,rice,568.0,mill,95943,PROC,0101000020E61000005299620E82825EC001B5A4E5B8D04340,POINT (-122.039188 39.63064261),39.63064261,-122.039188 +845 Kentucky Ave,Yolo,Woodland,Pacific International Rice Mills Bung,1.0,rice,CA,rice,569.0,mill,95695,PROC,0101000020E6100000D736209D15715EC09DDBDF34D8584340,POINT (-121.7669442 38.6940981),38.6940981,-121.7669442 +8969 CA-70,Yuba,Marysville,District 10 Dryers LLC,1.0,rice,CA,rice,570.0,mill,95901,PROC,0101000020E61000006FBBD05CA75D5EC07AC7293A929B4340,POINT (-121.46334 39.2154),39.2154,-121.46334 +Old Hwy 99W,Colusa,Maxwell,Polit Farms Inc,1.0,rice,CA,rice,571.0,mill,95955,PROC,0101000020E610000067BAD7497D885EC0E08096AE60A34340,POINT (-122.132647 39.276388),39.276388,-122.132647 +26069 Rd 148,Tulare,Visalia,Bock Ranch,1.0,walnut,CA,walnut,584.0,shelling,93292,PROC,0101000020E6100000365CE49EAECF5DC07BFAA5D1A6214240,POINT (-119.245033 36.26290341),36.26290341,-119.245033 +5430 Putah Creek Rd,Solano,Winters,Dixon Ridge Farms,1.0,walnut,CA,walnut,585.0,shelling,95694,PROC,0101000020E610000069290FC1A7795EC0E7A15B5430434340,POINT (-121.9008639 38.5249124),38.5249124,-121.9008639 +1501 Eager Rd,Sutter,Live Oak,wilbur packing co,1.0,walnut,CA,walnut,586.0,shelling,95953,PROC,0101000020E61000003617C9682E6A5EC02B6BDDFE43984340,POINT (-121.6590826 39.18957506),39.18957506,-121.6590826 +3230 CA 45,Glenn,Glenn,Keyawa Orchard Inc,1.0,walnut,CA,walnut,587.0,shelling,95943,PROC,0101000020E6100000CE041E7379805EC0BE8D495630D24340,POINT (-122.0074127 39.64210013),39.64210013,-122.0074127 +10695 Decker Ave,Tehama,Los Molinos,Crain Walnut Shelling,1.0,walnut,CA,walnut,588.0,shelling,96055,PROC,0101000020E61000008196AE609B875EC062305E77E30C4440,POINT (-122.1188585 40.10069172),40.10069172,-122.1188585 +1026 Sheridan Avenue,Butte,Chico,Western Nut co,1.0,walnut,CA,walnut,589.0,shelling,95926,PROC,0101000020E61000006C0B2A0538755EC02C34C63D4CDF4340,POINT (-121.8315442 39.7445142),39.7445142,-121.8315442 +1038 Larkin Road,Butte,Gridley,Golden Pacific Farms LLC,1.0,walnut,CA,walnut,590.0,shelling,95948,PROC,0101000020E6100000D6E0229C3B6A5EC0716770A5E8AB4340,POINT (-121.6598883 39.3430373),39.3430373,-121.6598883 +10660 Bryne Avenue,Tehama,Los Molinos,C R Crain Sons Inc,1.0,walnut,CA,walnut,591.0,shelling,96055,PROC,0101000020E61000006452E8610D885EC083740C23180D4440,POINT (-122.1258168 40.1022991),40.1022991,-122.1258168 +10695 Decker Avenue,Tehama,Los Molinos,Crain Walnut Shelling,1.0,walnut,CA,walnut,592.0,shelling,96055,PROC,0101000020E61000008196AE609B875EC062305E77E30C4440,POINT (-122.1188585 40.10069172),40.10069172,-122.1188585 +10830 Yosemite Blvd.,Stanislaus,Waterford,Frazier Nut Farms Inc,1.0,walnut,CA,walnut,593.0,shelling,95386,PROC,0101000020E610000090AB47D0CE325EC0F0F98292D9D04240,POINT (-120.7938729 37.63163978),37.63163978,-120.7938729 +112 Sandy Lane,Contra Costa,Oakley,Continente Nut LLC,1.0,walnut,CA,walnut,594.0,shelling,94561,PROC,0101000020E610000021C3CF24D66F5EC0C11259B535004340,POINT (-121.7474453 38.00163905),38.00163905,-121.7474453 +1190 Buena Vista Road,San Benito,Hollister,Gibson Farms,1.0,walnut,CA,walnut,595.0,shelling,95023,PROC,0101000020E61000008C6A6C0ABF5A5EC0D40E7F4DD66D4240,POINT (-121.4179102 36.8581025),36.8581025,-121.4179102 +12022 E. Comstock Rd.,San Joaquin,Stockton,Avanti Nut Co,1.0,walnut,CA,walnut,596.0,shelling,95215,PROC,0101000020E6100000B405DF8FB64A5EC0B570B43EC0044340,POINT (-121.1673927 38.03711685),38.03711685,-121.1673927 +1240 E. Caldwell Avenue,Tulare,Visalia,Atlas world food Ag,1.0,walnut,CA,walnut,597.0,shelling,93292,PROC,0101000020E610000090AE8850DBD15DC0DBABEA4031264240,POINT (-119.2790109 36.2983781),36.2983781,-119.2790109 +126 4th Street,Merced,Gustine,Pusateri Nut Company,1.0,walnut,CA,walnut,598.0,shelling,95322,PROC,0101000020E61000006F8C5363F83F5EC00296432842A14240,POINT (-120.9995354 37.25983146),37.25983146,-120.9995354 +14290 E Comstock Rd,San Joaquin,Linden,Anderson Barngrover Ranch Co Inc,1.0,walnut,CA,walnut,599.0,shelling,95236,PROC,0101000020E610000050786407F0485EC035A1830DD3044340,POINT (-121.1396502 38.03769082),38.03769082,-121.1396502 +1500 Reed Rd.,Sutter,Yuba City,Sutter Foods,1.0,walnut,CA,walnut,600.0,shelling,95993,PROC,0101000020E61000000953944BE3685EC09B515680AD8A4340,POINT (-121.638873 39.08341984),39.08341984,-121.638873 +1550 Industrial Drive,San Joaquin,Stockton,Pearl Crop Inc,1.0,walnut,CA,walnut,601.0,shelling,95206,PROC,0101000020E6100000C2E567D949505EC0517DCE7A84F44240,POINT (-121.2545074 37.91029296),37.91029296,-121.2545074 +1555 Warren Road,San Joaquin,Ripon,almond ace packing inc,1.0,walnut,CA,walnut,602.0,processor,95366,PROC,0101000020E610000094D920938C485EC0D12E5351C4E04240,POINT (-121.13358 37.75599114),37.75599114,-121.13358 +1590 Little Orchard Street,Santa Clara,San Jose,Santa Clara Nut Company,1.0,walnut,CA,walnut,603.0,shelling,95110,PROC,0101000020E61000007F726FD9FC775EC0531FED24C7A74240,POINT (-121.8748077 37.3107649),37.3107649,-121.8748077 +16200 County Road 87,Yolo,Esparto,Haag Farm,1.0,walnut,CA,walnut,604.0,shelling,95627,PROC,0101000020E6100000F7692629FA805EC0AD70892B80594340,POINT (-122.0152686 38.69922394),38.69922394,-122.0152686 +1640 State Highway 45,Glenn,Glenn,Borges of California,1.0,walnut,CA,walnut,605.0,shelling,95943,PROC,0101000020E610000081785DBF60835EC04ED1915CFECB4340,POINT (-122.05278 39.5937),39.5937,-122.05278 +1640 State Highway 45,Glenn,Glenn,Carriere Family Farms,1.0,walnut,CA,walnut,606.0,shelling,95943,PROC,0101000020E610000081785DBF60835EC04ED1915CFECB4340,POINT (-122.05278 39.5937),39.5937,-122.05278 +17071 E. Baker Road,San Joaquin,Linden,Ferrari Farms Inc,1.0,walnut,CA,walnut,607.0,shelling,95236,PROC,0101000020E61000002878AFFFDF465EC0179E346052044340,POINT (-121.1074218 38.03376391),38.03376391,-121.1074218 +1760 Main Street,San Joaquin,Escalon,The DeRuosi Group,1.0,walnut,CA,walnut,608.0,shelling,95320,PROC,0101000020E6100000D580F7448D3F5EC02932639FBAE54240,POINT (-120.9929974 37.79475777),37.79475777,-120.9929974 +18400 S. Enterprise Road,San Joaquin,Escalon,GoldRiver Orchards,1.0,walnut,CA,walnut,609.0,shelling,95320,PROC,0101000020E610000013D4F02DAC3B5EC0C1CD3D7FB5E54240,POINT (-120.932384 37.79460135),37.79460135,-120.932384 +1900 Feather River Blvd.,Yuba,Olivehurst,ShoEi Foods USA Inc,1.0,walnut,CA,walnut,610.0,shelling,95961,PROC,0101000020E61000006EC1525DC0645EC03BBEC5DC987F4340,POINT (-121.574241 38.99685249),38.99685249,-121.574241 +200 Wilkie Avenue,Sutter,Yuba City,California Valley Nut Co,1.0,walnut,CA,walnut,611.0,shelling,95991,PROC,0101000020E6100000890C063296665EC017929BFA237E4340,POINT (-121.6029172 38.98547299),38.98547299,-121.6029172 +2065 Geer Road,Stanislaus,Hughson,Mid Valley Nut Company,1.0,walnut,CA,walnut,612.0,shelling,95326,PROC,0101000020E6100000B950F9D7F2365EC05A84622B68CC4240,POINT (-120.858572 37.596929),37.596929,-120.858572 +2097 Beyer Lane,San Joaquin,Stockton,OG Nut Company,1.0,walnut,CA,walnut,613.0,shelling,95215,PROC,0101000020E6100000521F926BD44E5EC0C8DA198528FE4240,POINT (-121.2317151 37.98561157),37.98561157,-121.2317151 +2106 E. Main Street,Tulare,Visalia,Nutri Nut,1.0,walnut,CA,walnut,614.0,shelling,93292,PROC,0101000020E6100000D0DECFDF3AD15DC0614150244E2A4240,POINT (-119.2692184 36.3305097),36.3305097,-119.2692184 +21161 Ave. 160,Tulare,Porterville,RPC Packing Inc,1.0,walnut,CA,walnut,615.0,shelling,93257,PROC,0101000020E61000005AA0DD21C5C65DC0C5877E12440A4240,POINT (-119.105782 36.0802024),36.0802024,-119.105782 +2288 Geer Road,Stanislaus,Hughson,Grower Direct Nut Company,1.0,walnut,CA,walnut,616.0,shelling,95326,PROC,0101000020E6100000B950F9D7F2365EC05A84622B68CC4240,POINT (-120.858572 37.596929),37.596929,-120.858572 +240 Bunker Avenue,Stanislaus,Modesto,Wholesome Nut Company Inc,1.0,walnut,CA,walnut,617.0,shelling,95351,PROC,0101000020E610000026AB22DC643F5EC0C0D8948EE6CF4240,POINT (-120.990531 37.62422354),37.62422354,-120.990531 +24490 Joseph Avenue,Tehama,Los Molinos,California Walnut Co inc,1.0,walnut,CA,walnut,618.0,shelling,96055,PROC,0101000020E61000003711A22108885EC0887258D06A0F4440,POINT (-122.1254963 40.1204472),40.1204472,-122.1254963 +2644 Hegan Ln,Butte,Chico,Acme Walnut,1.0,walnut,CA,walnut,619.0,shelling,95928,PROC,0101000020E61000005EE7F05A53745EC03684190923DA4340,POINT (-121.8175876 39.7041942),39.7041942,-121.8175876 +26829 Road 156,Tulare,Visalia,Greggory Lamar Hart,1.0,walnut,CA,walnut,620.0,shelling,93292,PROC,0101000020E61000009B70541369CE5DC0C4739DE3AF234240,POINT (-119.2251633 36.27880521),36.27880521,-119.2251633 +29241 W. Cottonwood Road,Merced,Gustine,John B Sanfilippo Son,1.0,walnut,CA,walnut,621.0,shelling,95322,PROC,0101000020E6100000106AD0E16B415EC0A420B22705984240,POINT (-121.0222096 37.18765732),37.18765732,-121.0222096 +3050 S Hunt Rd,Merced,Gustine,Andersen Nut Co,1.0,walnut,CA,walnut,622.0,shelling,95322,PROC,0101000020E6100000A7CCCD37A23F5EC0A64D30F7249F4240,POINT (-120.994276 37.2433156),37.2433156,-120.994276 +3068 Chico Ave.,Butte,Chico,Vanella Farms,1.0,walnut,CA,walnut,623.0,processor,95928,PROC,0101000020E61000000ADAE4F049785EC07C18101082D94340,POINT (-121.879513 39.6992817),39.6992817,-121.879513 +3100 Zinfandel Rd.,Sacramento,Rancho Cordova,Agrocal Corp,1.0,walnut,CA,walnut,624.0,processor,95670,PROC,0101000020E6100000CC8D339765525EC07F801895124B4340,POINT (-121.2874506 38.58650459),38.58650459,-121.2874506 +3710 Cosby Avenue,Butte,Chico,Smith Walnut Orchards,1.0,walnut,CA,walnut,625.0,shelling,95928,PROC,0101000020E6100000A3F7D73C58775EC055078A69F0D84340,POINT (-121.8647606 39.6948368),39.6948368,-121.8647606 +400 D Street,Stanislaus,Turlock,Turlock Walnut Company Inc,1.0,walnut,CA,walnut,626.0,shelling,95380,PROC,0101000020E6100000A062E64C24365EC01986B8075BBE4240,POINT (-120.8459656 37.48715302),37.48715302,-120.8459656 +40897 Road 120,Tulare,Orosi,GSF Nut Company LLC,1.0,walnut,CA,walnut,627.0,shelling,93647,PROC,0101000020E61000005A29A9B896D35DC045253B5710444240,POINT (-119.3060743 36.53174868),36.53174868,-119.3060743 +411 Orchard Road,San Benito,Hollister,Lomanto Nut Shelling,1.0,walnut,CA,walnut,628.0,shelling,95023,PROC,0101000020E6100000EC25D75E55585EC055682096CD774240,POINT (-121.3802106 36.9359615),36.9359615,-121.3802106 +4302 N. Beecher Lane,San Joaquin,Stockton,Beecher Lane Walnut,1.0,walnut,CA,walnut,629.0,shelling,95215,PROC,0101000020E61000007528F9C7B14A5EC087E26D2990014340,POINT (-121.1671009 38.01221197),38.01221197,-121.1671009 +4530 Rowles Rd,Tehama,Vina,Andersen Sons Shelling,1.0,walnut,CA,walnut,630.0,shelling,96092,PROC,0101000020E610000083B57B035D835EC03AA50F9FECF64340,POINT (-122.0525521 39.92909611),39.92909611,-122.0525521 +50 Guynn Bridge Ct.,Butte,Chico,Red Barn Walnut Co,1.0,walnut,CA,walnut,631.0,shelling,95926,PROC,0101000020E61000008457DCC9F1775EC044C18C2958DF4340,POINT (-121.8741326 39.744878),39.744878,-121.8741326 +500 N. Jack Tone Road,San Joaquin,Stockon,Morada Nut Company,1.0,walnut,CA,walnut,632.0,processor,95215,PROC,0101000020E6100000F2FD1E0684495EC01ED623268BFC4240,POINT (-121.1486831 37.97299649),37.97299649,-121.1486831 +5414 E. Floral Avenue,Fresno,Selma,Poindexter Nut Company,1.0,walnut,CA,walnut,633.0,shelling,93662,PROC,0101000020E6100000B442ECA75AEC5DC0F8C96A1DC9494240,POINT (-119.6930332 36.57645004),36.57645004,-119.6930332 +5640 River Road,Stanislaus,Oakdale,Gambini Nut Company Inc,1.0,walnut,CA,walnut,634.0,shelling,95361,PROC,0101000020E61000009C84775E4F395EC07808E3A771E34240,POINT (-120.8954693 37.776906),37.776906,-120.8954693 +6100 Wilson Landing Road,Butte,Chico,Berberian Nut Co,1.0,walnut,CA,walnut,635.0,shelling,95973,PROC,0101000020E6100000FEC5223C907E5EC0AB2924F48EE64340,POINT (-121.9775534 39.8012376),39.8012376,-121.9775534 +6215 South George Washington Blvd.,Sutter,Yuba City,Valley Dried Fruit,1.0,walnut,CA,walnut,636.0,shelling,95993,PROC,0101000020E6100000E7CB6669026B5EC004281D171B844340,POINT (-121.6720222 39.03207673),39.03207673,-121.6720222 +6413 E Keyes Rd,Stanislaus,Hughson,Alpine Pacific Nut Co,1.0,walnut,CA,walnut,637.0,shelling,95326,PROC,0101000020E61000006446D33403385EC0803DECA690C64240,POINT (-120.8751957 37.55128943),37.55128943,-120.8751957 +6677 E. Hardaway Rd.,San Joaquin,Stockton,Star Nut Co,1.0,walnut,CA,walnut,638.0,processor,95215,PROC,0101000020E6100000FD46E0B4054E5EC01D9BB20D3B004340,POINT (-121.2190983 38.00180217),38.00180217,-121.2190983 +7229 Moon Bend Rd.,Colusa,Colusa,Empire Nut Company LLC,1.0,walnut,CA,walnut,639.0,shelling,95932,PROC,0101000020E6100000E10DC40DD37F5EC0C0B7237B08994340,POINT (-121.9972567 39.19557132),39.19557132,-121.9972567 +7233 County Rd. 24,Glenn,Orland,Omega Walnut Inc,1.0,walnut,CA,walnut,640.0,shelling,95963,PROC,0101000020E61000005479F1344F875EC0BC3E10ACECDA4340,POINT (-122.1142094 39.71034766),39.71034766,-122.1142094 +8000 N. Podesta Ln.,San Joaquin,Linden,Podesta Packing,1.0,walnut,CA,walnut,641.0,shelling,95236,PROC,0101000020E6100000D6F21483D1415EC0581E628BF6054340,POINT (-121.0284126 38.04658644),38.04658644,-121.0284126 +833 Tudor Road,Sutter,Yuba City,Sacramento Packing Inc,1.0,walnut,CA,walnut,642.0,processor,95991,PROC,0101000020E6100000D2623ABE07685EC0DBB232D0EB804340,POINT (-121.6254726 39.00719645),39.00719645,-121.6254726 +8540 Garden Highway,Sutter,Yuba City,Stephens Ranch Inc,1.0,walnut,CA,walnut,643.0,shelling,95991,PROC,0101000020E6100000064A0A2C00675EC058FA965A6B804340,POINT (-121.6093855 39.00327618),39.00327618,-121.6093855 +896 O'Banion Road,Sutter,Yuba City,Sacramento Valley Walnut Growers LLC,1.0,walnut,CA,walnut,644.0,shelling,95991,PROC,0101000020E6100000AE7FD767CE675EC0CF328B506C7F4340,POINT (-121.621973 38.995493),38.995493,-121.621973 +9457 River Road,Butte,Chico,Bremner Farms,1.0,walnut,CA,walnut,645.0,shelling,95928,PROC,0101000020E6100000474E70FBAF7C5EC0B60600D8CAD24340,POINT (-121.9482411 39.6468153),39.6468153,-121.9482411 +9839 Hutchinson Road,San Joaquin,Manteca,River Oak Orchards,1.0,walnut,CA,walnut,646.0,shelling,95337,PROC,0101000020E610000046274BADF74B5EC0DA835A1DCADC4240,POINT (-121.186992 37.72491805),37.72491805,-121.186992 +9979 Tyler Road,Tehama,Gerber,Haleakala Walnut Shelling Inc,1.0,walnut,CA,walnut,647.0,shelling,96035,PROC,0101000020E61000009B9E6637E9895EC0B30BE5C8730A4440,POINT (-122.1548594 40.08165847),40.08165847,-122.1548594 +Cherokee Business Park,San Joaquin,Stockton,Cal Ranch Inc,1.0,walnut,CA,walnut,648.0,shelling,95205,PROC,0101000020E61000002995F0845E4E5EC07B4FE5B4A7FA4240,POINT (-121.224519 37.958243),37.958243,-121.224519 +2069 Aldergrove Ave,0,Escondido,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,92029,PROC,0101000020E610000025E99AC937475DC0C67012D6088F4040,POINT (-117.11278 33.11745716),33.11745716,-117.11278 +2825 La Mirada Dr,0,Vista,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,92081,PROC,0101000020E6100000C972124ADF4D5DC02BE8EE21FE924040,POINT (-117.2167535 33.14838051),33.14838051,-117.2167535 +7700 Irvine Center Dr 500,0,Irvine,Interstate Brands Corp Hostess,0.0,bakery,CA,bread,0.0,bakery,92618,PROC,0101000020E61000001CBE3BE848705DC0AE5DA0C5CED44040,POINT (-117.7544499 33.66256018),33.66256018,-117.7544499 +26962 Vista Terrace,0,Lake Forest,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,92630,PROC,0101000020E610000088049D5A476A5DC01FEAA99B2CD54040,POINT (-117.6606051 33.66542383),33.66542383,-117.6606051 +44655 Jackson St,0,Indio,Interstate Brands Corp Hostess,0.0,bakery,CA,bread,0.0,bakery,92201,PROC,0101000020E610000065CAE259DD0D5DC0BB698E07B6DC4040,POINT (-116.2166352 33.7243051),33.7243051,-116.2166352 +19251 Ruppert,0,Thousand Palms,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,92276,PROC,0101000020E6100000D237691A14185DC05BEECC04C3E74040,POINT (-116.376227 33.810639),33.810639,-116.376227 +1500 Francisco St,0,Torrance,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,90501,PROC,0101000020E6100000BA53951172935DC0D59233B9BDEC4040,POINT (-118.3038372 33.8495399),33.8495399,-118.3038372 +366 S Acacia Ave,0,Fullerton,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,92831,PROC,0101000020E6100000AF2A56687B795DC09D5B53E607EF4040,POINT (-117.8981572 33.86742858),33.86742858,-117.8981572 +1055 Sandhill Ave,0,Carson,General Mills,0.0,bakery,CA,bread,0.0,milling,90746,PROC,0101000020E6100000681316CB63905DC06C66E37789F04040,POINT (-118.2560909 33.8791952),33.8791952,-118.2560909 +16701 Trojan Way,0,La Mirada,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,90638,PROC,0101000020E6100000B1EC38341B815DC04DE13942A3F04040,POINT (-118.0172854 33.87998226),33.87998226,-118.0172854 +8049 Somerset Blvd,0,Paramount,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,90723,PROC,0101000020E6100000B5728AE91D8A5DC03D45ED02CEF24040,POINT (-118.1580757 33.89691197),33.89691197,-118.1580757 +1493 E 6th St,0,Beaumont,Interstate Brands Corp Hostess,0.0,bakery,CA,bread,0.0,bakery,92223,PROC,0101000020E610000070B614EB2F3D5DC0A29520C8E6F64040,POINT (-116.9560497 33.9289179),33.9289179,-116.9560497 +5200 Alameda St,0,Vernon,Sara Lee Fresh Inc,0.0,bakery,CA,bread,0.0,bakery,90058,PROC,0101000020E6100000600FDC372D8F5DC0BF9F75E84FFF4040,POINT (-118.2371349 33.9946261),33.9946261,-118.2371349 +5200 S Alameda St,0,Vernon,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,90058,PROC,0101000020E6100000600FDC372D8F5DC0BF9F75E84FFF4040,POINT (-118.2371349 33.9946261),33.9946261,-118.2371349 +5471 Ferguson Dr,0,Commerce,General Mills,0.0,bakery,CA,bread,0.0,distributor,90022,PROC,0101000020E610000085494CABFC895DC0C163D3A55A014140,POINT (-118.1560467 34.01057885000001),34.01057885000001,-118.1560467 +10820 San Sevaine Way,0,Mira Loma,Cajoleben Inc Galassos Bakery DBA,0.0,bakery,CA,bread,0.0,bakery,91752,PROC,0101000020E6100000130544D238615DC0BA652C3F15024140,POINT (-117.5190931 34.0162734),34.0162734,-117.5190931 +635 W Valley Blvd,0,Bloomington,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,92316,PROC,0101000020E6100000186426AC68585DC02E3807F803094140,POINT (-117.3813887 34.07043362),34.07043362,-117.3813887 +9535 Archibald Ave,0,Rancho Cucamonga,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,91730,PROC,0101000020E61000007B6D910FD5655DC0EB01F390290A4140,POINT (-117.5911292 34.0793935),34.0793935,-117.5911292 +5341 Derry Ave,0,Agoura Hills,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,91301,PROC,0101000020E6100000E36A099EE7AF5DC0F3E8C21FB0124140,POINT (-118.7485118 34.14599988),34.14599988,-118.7485118 +9822 Glenoaks Blvd,0,Sun Valley,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,91352,PROC,0101000020E6100000C8EF6DFAB3985DC031AE3C71CE1F4140,POINT (-118.385985 34.24848762),34.24848762,-118.385985 +4535 Dupont Ct,0,Ventura,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93003,PROC,0101000020E6100000C2E2CB9FCACE5DC07AB4273740204140,POINT (-119.2311172 34.2519597),34.2519597,-119.2311172 +17365 Jasmine St,0,Victorville,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,92395,PROC,0101000020E6100000E11813AC3B525DC071917BBABA3C4140,POINT (-117.2848921 34.4744485),34.4744485,-117.2848921 +751 W Ave L8,0,Lancaster,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93534,PROC,0101000020E61000008E9F7C305F895DC0993FCF349B534140,POINT (-118.1464349 34.65317402),34.65317402,-118.1464349 +2220 Hutton Rd,0,Nipomo,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93444,PROC,0101000020E6100000E9CEB815E71B5EC01ABBE93B647F4140,POINT (-120.4359793 34.9952464),34.9952464,-120.4359793 +6320 District Blvd,0,Bakersfield,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93313,PROC,0101000020E6100000C6DD205AABC45DC007126FF838A84140,POINT (-119.0729585 35.3142386),35.3142386,-119.0729585 +2309 E Brundage Ln C,0,Bakersfield,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,93307,PROC,0101000020E610000049D345AFABBE5DC0EA46B30D37AD4140,POINT (-118.9792288 35.3532426),35.3532426,-118.9792288 +28801 CA 58,0,Bakersfield,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93314,PROC,0101000020E6100000572426A8E1CA5DC090300C5872B14140,POINT (-119.170023 35.386302),35.386302,-119.170023 +712 W California Ave A,0,Ridgecrest,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93555,PROC,0101000020E6100000BE1D9727C66B5DC0560DA1CE85CF4140,POINT (-117.6839694 35.62127097),35.62127097,-117.6839694 +1323 E Inyokern Rd,0,Ridgecrest,Interstate Brands Corp Hostess,0.0,bakery,CA,bread,0.0,bakery,93555,PROC,0101000020E61000006765564AAA6C5DC0F5A7E8A367D34140,POINT (-117.6978937 35.65160035),35.65160035,-117.6978937 +8316 Elowin Ct,0,Visalia,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93291,PROC,0101000020E6100000534F30AD97D85DC0CF9552E1192C4240,POINT (-119.3842576 36.3445398),36.3445398,-119.3842576 +1355 Burton Ave,0,Salinas,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93901,PROC,0101000020E6100000271AFF991C685EC0F779E7AB3F534240,POINT (-121.6267457 36.6503806),36.6503806,-121.6267457 +3630 N Hazel Ave,0,Fresno,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93722,PROC,0101000020E6100000364C7ED55BF65DC04302469737654240,POINT (-119.8493551 36.790759),36.790759,-119.8493551 +120 Lee Rd A,0,Watsonville,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95076,PROC,0101000020E61000003EA0223DFB715EC0B2E4E088A4734240,POINT (-121.7809594 36.9034587),36.9034587,-121.7809594 +865 Beechcraft Ave,0,Merced,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95341,PROC,0101000020E61000001A68E32DFC205EC0F35EADC118A64240,POINT (-120.5153918 37.29763051),37.29763051,-120.5153918 +1160 W 13th St,0,Merced,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95341,PROC,0101000020E6100000FF31BE79BB1F5EC0498E6C957DA64240,POINT (-120.4958176 37.30070751),37.30070751,-120.4958176 +1791 Sycamore Ave,0,Atwater,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95301,PROC,0101000020E6100000465B954476275EC0E621955A56AC4240,POINT (-120.6165935 37.34638531),37.34638531,-120.6165935 +890 Service St G,0,San Jose,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95112,PROC,0101000020E6100000B7C5466AEB785EC0AD73C23A44AF4240,POINT (-121.8893686 37.3692697),37.3692697,-121.8893686 +1711 Junction Ct 370,0,San Jose,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95112,PROC,0101000020E61000003B14AA40D2795EC0CDDF298991AF4240,POINT (-121.9034578 37.3716289),37.3716289,-121.9034578 +456 W Maude Ave,0,Sunnyvale,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94085,PROC,0101000020E6100000EB5795D810825EC0143D9578E5B14240,POINT (-122.0322782 37.3898154),37.3898154,-122.0322782 +600 Garner Rd,0,Modesto,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95357,PROC,0101000020E6100000900A0852CE3A5EC0135FB37DC4D04240,POINT (-120.9188428 37.63099643),37.63099643,-120.9188428 +305 Codoni Ave,0,Modesto,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95357,PROC,0101000020E61000001041D5E8553A5EC0BDDC2FB849D14240,POINT (-120.9114935 37.63506224),37.63506224,-120.9114935 +475 S Canal St,0,South San Francisco,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94080,PROC,0101000020E6100000314F9DFDB79A5EC001E49DA643D34240,POINT (-122.4174799 37.65050204),37.65050204,-122.4174799 +151 W Hill Pl,0,Brisbane,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,94005,PROC,0101000020E610000049827005149B5EC0DEE8633EA0D84240,POINT (-122.423097 37.69239025),37.69239025,-122.423097 +1450 S Loop Rd,0,Alameda,FritoLay Distribution Center,0.0,bakery,CA,bakery,0.0,distributor,94502,PROC,0101000020E6100000C9B0E5F0248F5EC0143DF03158DC4240,POINT (-122.2366297 37.7214415),37.7214415,-122.2366297 +937 66th Ave,0,Oakland,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94621,PROC,0101000020E6100000AF29EB92CC8C5EC0EE45CDBAF3E04240,POINT (-122.1999862 37.75743804),37.75743804,-122.1999862 +901 King St,0,Oakland,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94606,PROC,0101000020E6100000BA4DB857668F5EC0EB15BB229DE34240,POINT (-122.2406215 37.7782329),37.7782329,-122.2406215 +1190 Spreckels Ave,0,Manteca,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95336,PROC,0101000020E61000005CD71EACB54C5EC09584C0A1A2E44240,POINT (-121.1985884 37.78621313),37.78621313,-121.1985884 +4020 Nelson Ave,0,Concord,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94520,PROC,0101000020E6100000BAD1110ADB825EC079CE71C9CC004340,POINT (-122.0446191 38.0062496),38.0062496,-122.0446191 +2201 Verne Roberts Cir,0,Antioch,Costco Bakery,0.0,bakery,CA,bread,0.0,bakery,94509,PROC,0101000020E6100000D30F8F6992755EC06F00EC9227014340,POINT (-121.8370613 38.0090202),38.0090202,-121.8370613 +5045 Forni Dr,0,Concord,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,94520,PROC,0101000020E6100000FA9F57972E825EC08F55A58867024340,POINT (-122.0340937 38.0187846),38.0187846,-122.0340937 +2245 CA 49,0,Angels Camp,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95222,PROC,0101000020E610000000E65AB400285EC011E15F048D094340,POINT (-120.625043 38.074616),38.074616,-120.625043 +2445 S Watney Way A,0,Fairfield,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94533,PROC,0101000020E61000008276E2CDF5845EC09DBAF2599E1D4340,POINT (-122.0775027 38.231395),38.231395,-122.0775027 +2500 Crocker Cir,0,Fairfield,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,94533,PROC,0101000020E610000001A1F5F0E57E5EC0B9B8D7930A234340,POINT (-121.9827845 38.2737603),38.2737603,-121.9827845 +10115 Iron Rock Way 1,0,Elk Grove,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95624,PROC,0101000020E6100000A245B6F3FD565EC0402ACDFF0E324340,POINT (-121.35925 38.39108274),38.39108274,-121.35925 +7601 Wilbur Way,0,Sacramento,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95828,PROC,0101000020E6100000358EA2186A595EC0CC13DFBB933D4340,POINT (-121.3971006 38.48107098),38.48107098,-121.3971006 +3810 Seaport Blvd,0,West Sacramento,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95691,PROC,0101000020E61000001D44C6FE8D645EC09545E54F69484340,POINT (-121.5711667 38.56571387),38.56571387,-121.5711667 +781 Bevins St,0,Lakeport,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95453,PROC,0101000020E6100000596375502EBB5EC0904C242414854340,POINT (-122.9247018 39.03967716),39.03967716,-122.9247018 +401 Burns Dr,0,Yuba City,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95991,PROC,0101000020E61000004DB049C851675EC03AD7C5A7DF8D4340,POINT (-121.6143666 39.10838792),39.10838792,-121.6143666 +3001 S State St,0,Ukiah,Earthgrains Co,0.0,bakery,CA,bread,0.0,bakery,95482,PROC,0101000020E6100000AE02C64494CC5EC0A37C399A408E4340,POINT (-123.1965496 39.11134651),39.11134651,-123.1965496 +22601 CA 1,0,Fort Bragg,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95437,PROC,0101000020E6100000190A8E812BF35EC0C14858E928BC4340,POINT (-123.7995304 39.46999852),39.46999852,-123.7995304 +1801 Idora St,0,Oroville,Delallo Italian,0.0,bakery,CA,pasta bread,0.0,bakery,95966,PROC,0101000020E610000015E7035D56635EC0C91759D70DBF4340,POINT (-121.5521462 39.4926099),39.4926099,-121.5521462 +741 Oroville Chico Hwy,0,Durham,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95938,PROC,0101000020E6100000C55FEEEE5C6E5EC063BA6B64B2D24340,POINT (-121.7244222 39.6460691),39.6460691,-121.7244222 +20196 Charlanne Dr,0,Redding,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,96002,PROC,0101000020E61000002B68FFA872935EC04E870442A1454440,POINT (-122.3038733 40.5439837),40.5439837,-122.3038733 +69 W 3rd St,0,Eureka,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95501,PROC,0101000020E61000003CF9F4D8160B5FC04A6C2D82B5664440,POINT (-124.1732695 40.8024142),40.8024142,-124.1732695 +1525 Lucas Rd G,0,Yreka,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,96097,PROC,0101000020E61000002B1895D409A85EC0567DAEB662DD4440,POINT (-122.6256 41.729575),41.729575,-122.6256 +1348 47th St,0,San Diego,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,92102,PROC,0101000020E61000007EC6850321465DC0141F44D72A5C4040,POINT (-117.095765 32.7200574),32.7200574,-117.095765 +7995 Armour St,0,San Diego,Pepsi Co Bottling Group,0.0,beverage,CA,beverage,0.0,manufacturer,92111,PROC,0101000020E61000006313F472B3495DC0B9E2E2A8DC684040,POINT (-117.1515777 32.819234),32.819234,-117.1515777 +27442 Portola Pkwy,0,Foothill Ranch,Pepsi Cola Co,0.0,beverage,CA,beverage,0.0,manufacturer,92610,PROC,0101000020E6100000D7FDBEDAAC695DC09E6CB9E985D54040,POINT (-117.6511752 33.6681492),33.6681492,-117.6511752 +2603 Camino Ramon 550,0,San Ramon,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,94583,PROC,0101000020E6100000364877C6AD755DC03D22AEB5DAD64040,POINT (-117.8387314 33.67854949),33.67854949,-117.8387314 +83801 Citrus Ave,0,Indio,Pepsi Co,0.0,beverage,CA,beverage,0.0,distribution,92201,PROC,0101000020E61000002B0F779AF10C5DC029C9DF62EADB4040,POINT (-116.2022463 33.7180904),33.7180904,-116.2022463 +2121 E Winston Rd,0,Anaheim,Coca Cola water,0.0,beverage,CA,water,0.0,distribution,92806,PROC,0101000020E6100000652E15C0B9785DC021A92AD956E84040,POINT (-117.8863373 33.8151504),33.8151504,-117.8863373 +961 E 4th St,0,Los Angeles,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,90013,PROC,0101000020E610000042453069E7925DC0FA30B58400ED4040,POINT (-118.2953742 33.85157832),33.85157832,-118.2953742 +6200 Caballero Blvd,0,Buena Park,CorruKraft Inc,0.0,beverage,CA,beverage,0.0,distributor,90620,PROC,0101000020E61000002A8E03AF96815DC0E746A2E1DEEE4040,POINT (-118.024822 33.8661768),33.8661768,-118.024822 +4701 Park Rd,0,Benicia,Pepsi Co Bottling Group,0.0,beverage,CA,beverage,0.0,manufacturer,94510,PROC,0101000020E61000005494A69C8A815DC0FC427EECE4EE4040,POINT (-118.0240852 33.8663612),33.8663612,-118.0240852 +14326 Monte Vista Ave,0,Chino,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,91710,PROC,0101000020E6100000274EEE77A86C5DC0BA94250020FF4040,POINT (-117.6977825 33.99316408),33.99316408,-117.6977825 +2095 S Archibald Ave,0,Ontario,Pepsi Cola Sales Distribution,0.0,beverage,CA,beverage,0.0,distribution,91761,PROC,0101000020E6100000BAD1110ADB655DC03D1059A489044140,POINT (-117.5914941 34.0354505),34.0354505,-117.5914941 +1560 E 20th St,0,Los Angeles,Nestle Waters,0.0,beverage,CA,water,0.0,water,90011,PROC,0101000020E610000052BC259499925DC03075A103DC044140,POINT (-118.2906237 34.0379643),34.0379643,-118.2906237 +3 Park Plaza 600,0,Irvine,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,92614,PROC,0101000020E6100000A477E052048F5DC0ABD82D3C8E054140,POINT (-118.2346389 34.04340317),34.04340317,-118.2346389 +1650 S Vintage Ave,0,Ontario,Coca Cola Ontario Syrup,0.0,beverage,CA,sugar,0.0,syrup,91761,PROC,0101000020E6100000BFC1CD9838625DC0E0FDA7D19A054140,POINT (-117.5347044 34.0437872),34.0437872,-117.5347044 +10670 6th St,0,Rancho Cucamonga,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,91730,PROC,0101000020E61000007352F3B0AB645DC09CB34F11F10A4140,POINT (-117.5729792 34.0854818),34.0854818,-117.5729792 +4416 Azusa Canyon Rd,0,Irwindale,Pepsi Co Bottling Group,0.0,beverage,CA,beverage,0.0,distributor,91706,PROC,0101000020E61000000EAB2E96587C5DC0EC378F9AE10B4140,POINT (-117.9429069 34.09282238),34.09282238,-117.9429069 +1200 Arroyo St,0,San Fernando,Pepsi Co,0.0,beverage,CA,beverage,0.0,distributor,91340,PROC,0101000020E6100000BEFD1422BB9A5DC068222A5C28254140,POINT (-118.4176717 34.29029419),34.29029419,-118.4176717 +12925 Bradley Ave,0,Sylmar,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,91342,PROC,0101000020E6100000D24A6B1D669D5DC098F67244E3264140,POINT (-118.4593576 34.30381065),34.30381065,-118.4593576 +4375 N Ventura Ave,0,Ventura,Pepsi Co,0.0,beverage,CA,beverage,0.0,distribution,93001,PROC,0101000020E6100000BD2DA237A6D25DC0FE9F1E36EC294140,POINT (-119.2913951 34.3275211),34.3275211,-119.2913951 +715 Vandenberg St,0,Salinas,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,93905,PROC,0101000020E6100000CFEFA07EBC665EC09DC9480735544240,POINT (-121.6052548 36.6578683),36.6578683,-121.6052548 +3220 E Malaga Ave,0,Fresno,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,93725,PROC,0101000020E6100000BF7FF3E2C4EE5DC0F69100DAFB554240,POINT (-119.730767 36.6717484),36.6717484,-119.730767 +1555 Old Bayshore Hwy,0,San Jose,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,95112,PROC,0101000020E6100000BAC95EA5F1795EC0BF1D13EF21AF4240,POINT (-121.9053739 37.36822308),37.36822308,-121.9053739 +1733 Morgan Rd,0,Modesto,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,95358,PROC,0101000020E6100000BDC282FB813E5EC0BE94EC9E5DCD4240,POINT (-120.9766835 37.60441958),37.60441958,-120.9766835 +29000 Hesperian Blvd,0,Hayward,Pepsi Co,0.0,beverage,CA,beverage,0.0,distributor,94544,PROC,0101000020E61000008E23319C46855EC01B09D91E62CE4240,POINT (-122.0824347 37.6123694),37.6123694,-122.0824347 +14655 Wicks Blvd,0,San Leandro,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,94577,PROC,0101000020E610000041518F238C8A5EC0B7CC8EF925D94240,POINT (-122.1648034 37.6964714),37.6964714,-122.1648034 +1565 N MacArthur Dr 500,0,Tracy,Pepsi Co,0.0,beverage,CA,beverage,0.0,distributor,95376,PROC,0101000020E6100000A16FC108505A5EC031F1A20A5ADF4240,POINT (-121.4111349 37.74493535),37.74493535,-121.4111349 +19875 Pacific Gateway Dr,0,Torrance,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,90502,PROC,0101000020E610000025F37E92717D5EC0C580579172E24240,POINT (-121.9600569 37.76912133),37.76912133,-121.9600569 +4225 Pepsi Pl,0,Stockton,Pepsi Co,0.0,beverage,CA,beverage,0.0,manufacturer,95215,PROC,0101000020E6100000F82A4366F84F5EC01244C46A7FFE4240,POINT (-121.2495361 37.98826346),37.98826346,-121.2495361 +6261 Caballero Blvd,0,Buena Park,Pepsi Co Bottling Group,0.0,beverage,CA,beverage,0.0,manufacturer,90620,PROC,0101000020E610000014ECBFCECD875EC0D5157D4FF6094340,POINT (-122.1219365 38.0778293),38.0778293,-122.1219365 +650 Babcock Ln,0,Ukiah,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,95482,PROC,0101000020E6100000F52D73BA2CCC5EC01B56448F90914340,POINT (-123.19023 39.13722411),39.13722411,-123.19023 +15801 W 1st St,0,Irwindale,Miller Coors LLC,0.0,brewery,CA,grains,0.0,brewery,91706,PROC,0101000020E61000004CDF6B080E7C5DC0D17AB616FF0F4140,POINT (-117.9383565 34.12497219),34.12497219,-117.9383565 +912 Gilman St,0,Berkeley,Gilman Brewery Company,0.0,brewery,CA,grains,0.0,brewery,94710,PROC,0101000020E6100000541FA3972C935EC0D9846A3986F04240,POINT (-122.2995967 37.8790962),37.8790962,-122.2995967 +3101 Busch Dr,0,Fairfield,AnheuserBusch LLC LA or Solano,0.0,brewery,CA,grains,0.0,brewery,94534,PROC,0101000020E6100000F804E4A6E1855EC020F35C3A411E4340,POINT (-122.0918977 38.2363656),38.2363656,-122.0918977 +1201 K St 730,0,Sacramento,AnheuserBusch LLC LA or Solano,0.0,brewery,CA,grains,0.0,brewery,95814,PROC,0101000020E610000025462AE7665F5EC091C8252B124A4340,POINT (-121.4906557 38.57867946),38.57867946,-121.4906557 +17700 Boonville Rd,0,Boonville,Anderson Valley Brewery,0.0,brewery,CA,grains,0.0,brewery,95415,PROC,0101000020E6100000769E1D15A4D65EC0839596D316804340,POINT (-123.3537648 39.00069661),39.00069661,-123.3537648 +1075 E 20th St,0,Chico,Sierra Nevada Brewery,0.0,brewery,CA,grains,0.0,brewery,95928,PROC,0101000020E61000002A9D595C2D745EC0D6427F57BADC4340,POINT (-121.8152686 39.7244367),39.7244367,-121.8152686 +10051 Old Grove Rd,0,San Diego,Ballast Point Brewing,0.0,brewery,CA,distillers grain,0.0,brewery distillery,92131,PROC,0101000020E61000005D8AABCA3E475DC064CDA7120E734040,POINT (-117.1132075 32.89886697),32.89886697,-117.1132075 +8680 Miralani Dr #120,0,San Diego,Setting Sun Sake Brewing Co,0.0,brewery,CA,distillers grain,0.0,brewery,92126,PROC,0101000020E610000074565579CC485DC01F8357C3AC724040,POINT (-117.1374801 32.89589731),32.89589731,-117.1374801 +12132 Knott St,0,Garden Grove,Guilianos Specialty Foods,0.0,cannery,CA,olive capsicum,0.0,cannery,92841,PROC,0101000020E6100000A98E0BBDB4805DC0B05A36C690E44040,POINT (-118.0110314 33.78566816),33.78566816,-118.0110314 +5821 Wilderness Ave,0,Riverside,triple h food processors,0.0,cannery,CA,tomato fruit vegetable misc,0.0,cannery,92504,PROC,0101000020E6100000775FDF98AF5C5DC0E9EEDF617FFB4040,POINT (-117.4482176 33.9648249),33.9648249,-117.4482176 +5650 E Santa Ana St,0,Ontario,Mizkan America,0.0,cannery,CA,grapes vegetables,0.0,cannery,91761,PROC,0101000020E61000002E156580D5615DC0C0A78306AC064140,POINT (-117.5286561 34.0521248),34.0521248,-117.5286561 +315 E. Fourth St.,0,Ontario,cc graber co,0.0,cannery,CA,olives,0.0,cannery,91764,PROC,0101000020E61000001385F12E72695DC08E89DEF30D0A4140,POINT (-117.6475942 34.0785508),34.0785508,-117.6475942 +10037 8th St,0,Rancho Cucamonga,Mizkan America,0.0,cannery,CA,grapes vegetables,0.0,cannery,91730,PROC,0101000020E610000047F1E0DD80655DC03731C96DA00B4140,POINT (-117.5859904 34.0908334),34.0908334,-117.5859904 +Dock 1 Berth 3,0,Port Hueneme,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,93041,PROC,0101000020E6100000A5BDC11726CC5DC06D1CB1169F144140,POINT (-119.189825 34.161105),34.161105,-119.189825 +800 Commercial Ave,0,Oxnard,smucker fruit processing co,0.0,cannery,CA,fruit,0.0,cannery,93030,PROC,0101000020E61000001CFC0E8F0ECB5DC06BC6585CD2184140,POINT (-119.1727636 34.1939197),34.1939197,-119.1727636 +554 Todd Rd,0,Santa Paula,saticoy food corp,0.0,cannery,CA,vegetables,0.0,cannery,93060,PROC,0101000020E61000009BC8CC052EC75DC049D9226937284140,POINT (-119.112184 34.314191),34.314191,-119.112184 +19800 W Gale Ave,0,Huron,Los Gatos Tomato Products,0.0,cannery,CA,tomato,0.0,cannery,93234,PROC,0101000020E6100000767F06E5C7095EC027953A1279174240,POINT (-120.1528256 36.1833823),36.1833823,-120.1528256 +10652 Jackson Ave,0,Hanford,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,93230,PROC,0101000020E61000002C1E28017BE95DC0D19CAB9CAC204240,POINT (-119.6481326 36.2552677),36.2552677,-119.6481326 +1913 Industrial Way,0,Sanger,initiative foods,0.0,cannery,CA,fruit and vegetables,0.0,cannery,93657,PROC,0101000020E6100000E3A2FF8A21E35DC00FC86F1B57584240,POINT (-119.5489223 36.6901583),36.6901583,-119.5489223 +1810 Academy Ave,0,Sanger,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,93657,PROC,0101000020E610000007EBFF1C66E35DC0CC8D339765584240,POINT (-119.5531075 36.6906003),36.6906003,-119.5531075 +2502 N St,0,Firebaugh,the neil jones food company,0.0,cannery,CA,tomato,0.0,cannery,93622,PROC,0101000020E61000002E3D9AEAC91C5EC051FA9D81EC6A4240,POINT (-120.449824 36.8353426),36.8353426,-120.449824 +2502 N St,0,Firebaugh,TomaTek Inc tomato,0.0,cannery,CA,tomato,0.0,cannery,93622,PROC,0101000020E61000002E3D9AEAC91C5EC051FA9D81EC6A4240,POINT (-120.449824 36.8353426),36.8353426,-120.449824 +110 Hawkins St,0,Hollister,the neil jones food company,0.0,cannery,CA,tomato,0.0,cannery,95023,PROC,0101000020E6100000BDEB223BA5595EC0E33F93B3666C4240,POINT (-121.4007099 36.8468842),36.8468842,-121.4007099 +865 East,0,Hollister,san benito foods,0.0,cannery,CA,tomato,0.0,cannery,95023,PROC,0101000020E61000003752B648DA585EC0C4978922A46C4240,POINT (-121.388323 36.848759),36.848759,-121.388323 +46 Walker St,0,Watsonville,Mizkan America,0.0,cannery,CA,apple cider mill,0.0,cannery,95076,PROC,0101000020E6100000A6327B8F69705EC0DDD8A2BBDA734240,POINT (-121.7564429 36.9051127),36.9051127,-121.7564429 +233 Peckham Rd,0,Watsonville,BellCarter Lindsay,0.0,cannery,CA,olive,0.0,cannery,95076,PROC,0101000020E61000002A841FE65C6D5EC03ACD02ED0E7A4240,POINT (-121.7087951 36.9535805),36.9535805,-121.7087951 +6580 Furlong Ave,0,Gilroy,Del Monte farm,0.0,cannery,CA,fruit vegetable,0.0,cannery,95020,PROC,0101000020E61000003E7D5FB763615EC0A1E760472D814240,POINT (-121.5217112 37.0091943),37.0091943,-121.5217112 +12045 Ingomar Grade,0,Los Banos,Liberty Packing Co Morning Star,0.0,cannery,CA,tomato,0.0,cannery,93635,PROC,0101000020E610000059A4897780365EC0FB5DD89AAD864240,POINT (-120.851591 37.052173),37.052173,-120.851591 +333 Johnson Rd,0,Los Banos,Kagome,0.0,cannery,CA,tomato dairy vegetable,0.0,cannery,93635,PROC,0101000020E6100000221B48171B375EC05685611BCC884240,POINT (-120.8610285 37.06872885),37.06872885,-120.8610285 +13448 Volta Rd,0,Los Banos,Morning Star Packing Co,0.0,cannery,CA,tomato,0.0,cannery,93635,PROC,0101000020E6100000D0B359F5393B5EC050327BD1058C4240,POINT (-120.9254125 37.09392756),37.09392756,-120.9254125 +901 Packers St,0,Atwater,teasdale foods inc,0.0,cannery,CA,vegetable bean,0.0,cannery,95301,PROC,0101000020E6100000788E1205C4265EC025C700FDFCAB4240,POINT (-120.6057141 37.34365809),37.34365809,-120.6057141 +2801 Finch Rd,0,Modesto,seneca foods corp,0.0,cannery,CA,apricots peaches pears,0.0,cannery,95354,PROC,0101000020E6100000C17861C66F3C5EC02766625FD7CF4240,POINT (-120.9443222 37.62376015),37.62376015,-120.9443222 +4000 Yosemite Blvd,0,Modesto,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,95357,PROC,0101000020E61000009D514E0FE53A5EC0FBF045DE66D14240,POINT (-120.9202307 37.63595179),37.63595179,-120.9202307 +1202 D St,0,Modesto,stanislaus food pr,0.0,cannery,CA,tomato,0.0,cannery,95354,PROC,0101000020E61000000510E3DA753F5EC018865D4E68D14240,POINT (-120.9915683 37.63599567),37.63599567,-120.9915683 +17950 Via Nicolo Rd,0,Tracy,Musco Olive Products Inc,0.0,cannery,CA,olive,0.0,cannery,95377,PROC,0101000020E6100000436271EEE5615EC0D03860992FDB4240,POINT (-121.5296589 37.71239011),37.71239011,-121.5296589 +2 Nestle Way,0,Lathrop,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,95330,PROC,0101000020E610000037B75384E5525EC0F45FD67AF5E54240,POINT (-121.2952586 37.79655395),37.79655395,-121.2952586 +1 Maritime Plaza,0,San Francisco,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,94111,PROC,0101000020E6100000062AE3DF67995EC0C3F0113125E64240,POINT (-122.396965 37.79801),37.79801,-122.396965 +760 Industrial Dr,0,Stockton,Campbell Soup,0.0,cannery,CA,misc,0.0,cannery,95206,PROC,0101000020E610000009597105EF505EC078D6C97443F44240,POINT (-121.2645887 37.9083086),37.9083086,-121.2645887 +3151 Regatta Blvd,0,Richmond,Del Monte fresh,0.0,cannery,CA,fruit vegetable,0.0,cannery,94804,PROC,0101000020E61000000070ECD973955EC04A9869FB57F64240,POINT (-122.335196 37.92456),37.92456,-122.335196 +205 N Wiget Ln,0,Walnut Creek,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,94598,PROC,0101000020E6100000BCBA1924B3815EC03443B299A6F64240,POINT (-122.0265589 37.92695924),37.92695924,-122.0265589 +3003 Oak Rd,0,Walnut Creek,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,94597,PROC,0101000020E610000003C9E0CDBF835EC0A766C526E8F64240,POINT (-122.0585818 37.9289597),37.9289597,-122.0585818 +4136 Lakeside Dr,0,San Pablo,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,94806,PROC,0101000020E6100000B7A4598F31955EC091D26C1E87FE4240,POINT (-122.3311499 37.9884985),37.9884985,-122.3311499 +650 S Guild Ave,0,Lodi,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95240,PROC,0101000020E61000007D6B71D7DC4F5EC0D54864828E0F4340,POINT (-121.2478541 38.12153654),38.12153654,-121.2478541 +741 S Stockton St,0,Lodi,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95240,PROC,0101000020E610000031CB434B43515EC02A90B84B0B104340,POINT (-121.2697323 38.12534472),38.12534472,-121.2697323 +631 N Cluff Ave,0,Lodi,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95240,PROC,0101000020E6100000C67E60D82B505EC0B9F9889021124340,POINT (-121.2526761 38.14164931),38.14164931,-121.2526761 +14531 Walnut Grove Thornton Rd,0,Walnut Grove,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,95690,PROC,0101000020E61000002827DA55C8605EC00775F46C141D4340,POINT (-121.5122275 38.22718584),38.22718584,-121.5122275 +1520 Terminal St,0,West Sacramento,California Fire Roasted LLC,0.0,cannery,CA,tomato,0.0,cannery,95691,PROC,0101000020E6100000A1E76047AD625EC0B7BCCD76E0484340,POINT (-121.5418261 38.5693501),38.5693501,-121.5418261 +1376 Lemen Ave,0,Woodland,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95776,PROC,0101000020E6100000BD35B05582705EC06B065D67E8564340,POINT (-121.757955 38.6789674),38.6789674,-121.757955 +455 Harter Ave,0,Woodland,Boundary Bend Olives,0.0,cannery,CA,olive,0.0,cannery,95776,PROC,0101000020E6100000657506A197705EC092D332ADA8584340,POINT (-121.7592547 38.6926476),38.6926476,-121.7592547 +9950 S. Ingomar Grade,0,Los Banos,Ingomar Packing Company,0.0,cannery,CA,tomato,0.0,cannery,95635,PROC,0101000020E610000058CA32C4B1395EC009FD4CBD6E754340,POINT (-120.901475 38.917442),38.917442,-120.901475 +6005 CA 99,0,Live Oak,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95953,PROC,0101000020E61000005CC246FE05695EC0517E7B6C059C4340,POINT (-121.6409908 39.21891552),39.21891552,-121.6409908 +1901 Highway 99,0,Gridley,stapleton spense packing,0.0,cannery,CA,plums prunes,0.0,cannery,95948,PROC,0101000020E610000067391AD1076C5EC090347691DBAF4340,POINT (-121.6879771 39.37388819),39.37388819,-121.6879771 +1800 Idora St,0,Oroville,Delallo Italian,0.0,cannery,CA,olive tomato,0.0,cannery,95966,PROC,0101000020E6100000A1F65B3B51635EC0807C53A236BF4340,POINT (-121.551833 39.49385480000001),39.49385480000001,-121.551833 +1601 Mitchell Ave,0,Oroville,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95965,PROC,0101000020E61000003DC967C3AB635EC011BF0754A4C04340,POINT (-121.5573586 39.5050149),39.5050149,-121.5573586 +1012 2nd St,0,Corning,BellCarter Lindsay,0.0,cannery,CA,olive,0.0,cannery,96021,PROC,0101000020E610000070FFDB766B8B5EC0E2C0F57269F64340,POINT (-122.1784341 39.92509305),39.92509305,-122.1784341 +981 Fig St,0,Corning,BellCarter Lindsay,0.0,cannery,CA,olive,0.0,cannery,96021,PROC,0101000020E610000044C4CDA9E48A5EC06EA8529279F64340,POINT (-122.1702065 39.92558507),39.92558507,-122.1702065 +6 Washinigton Ave,0,San Leandro,Maxwell House,0.0,coffee,CA,coffee,0.0,coffee,94578,PROC,0101000020E61000007A17EFC7ED875EC02ECBD765F8D94240,POINT (-122.123888 37.702893),37.702893,-122.123888 +11709 Artesia Blvd,0,Artesia,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,90701,PROC,0101000020E61000008FC8D2E267855DC0DBAC5516E0EF4040,POINT (-118.0844657 33.8740261),33.8740261,-118.0844657 +5611 Imperial Hwy,0,South Gate,Saputo Cheese USA Inc,0.0,dairy,CA,cheese,0.0,dairy,90270,PROC,0101000020E61000000C3B8C49FF8A5DC0AE37BDCD13F74040,POINT (-118.1718315 33.93029186),33.93029186,-118.1718315 +6401 Knudsen Dr,0,Bakersfield,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,93308,PROC,0101000020E610000026F67585E3C35DC0D3C66C2464B54140,POINT (-119.0607618 35.4171186),35.4171186,-119.0607618 +11894 Ave 120,0,Pixley,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,93256,PROC,0101000020E6100000ADF078A48BD45DC0D6D148B600014240,POINT (-119.3210231 36.00783423),36.00783423,-119.3210231 +10833 Octol Ave,0,Tulare,kraft,0.0,dairy,CA,dairy,0.0,dairy,93274,PROC,0101000020E6100000FDD8C985EFD45DC0FB5E9E29CF0F4240,POINT (-119.3271193 36.1235096),36.1235096,-119.3271193 +10800 Ave 184,0,Tulare,Kraft Hinez Qinc,0.0,dairy,CA,dairy,0.0,dairy,93274,PROC,0101000020E610000017E98F7A19D55DC0CEED9028D50F4240,POINT (-119.3296801 36.12369258),36.12369258,-119.3296801 +800 E Paige Ave,0,Tulare,Saputo Cheese USA Inc,0.0,dairy,CA,cheese,0.0,dairy,93274,PROC,0101000020E6100000C669882A7CD55DC04C4CBCA882174240,POINT (-119.3357035 36.1836749),36.1836749,-119.3357035 +970 E Continental Ave,0,Tulare,Nestle Dreyers,0.0,dairy,CA,frozen,0.0,dairy,93274,PROC,0101000020E6100000C991CEC048D55DC086E1C8A8D7174240,POINT (-119.3325655 36.1862689),36.1862689,-119.3325655 +901 E Levin Ave,0,Tulare,Saputo Cheese USA Inc,0.0,dairy,CA,cheese,0.0,dairy,93274,PROC,0101000020E61000008164952D6DD55DC04065A1421A184240,POINT (-119.3347887 36.1883014),36.1883014,-119.3347887 +1025 E Bardsley Ave,0,Tulare,Saputo Cheese USA Inc,0.0,dairy,CA,cheese,0.0,dairy,93274,PROC,0101000020E610000086B3B68457D55DC0A7F24D0522194240,POINT (-119.3334667 36.19635073),36.19635073,-119.3334667 +400 S M St,0,Tulare,Land O Lakes,0.0,dairy,CA,dairy,0.0,distributor,93274,PROC,0101000020E6100000181C6F3CE9D55DC0290F666E191A4240,POINT (-119.3423606 36.2039011),36.2039011,-119.3423606 +605 N J St,0,Tulare,Saputo Dairy Foods USA,0.0,dairy,CA,dairy,0.0,distributor,93274,PROC,0101000020E61000002526039B4ED65DC0AA99B514901B4240,POINT (-119.3485477 36.2153345),36.2153345,-119.3485477 +2000 N Plaza Dr,0,Visalia,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,93291,PROC,0101000020E61000003A32A0281AD95DC0C246FE05272C4240,POINT (-119.3922216 36.3449409),36.3449409,-119.3922216 +21890 Rosehart Way,0,Salinas,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,distributor,93908,PROC,0101000020E6100000EAE0AAFC7C635EC07E2DF9E9894D4240,POINT (-121.5545036 36.6057713),36.6057713,-121.5545036 +755 F St,0,Fresno,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,93706,PROC,0101000020E61000005378D0ECBAF25DC0FF3C0D18245D4240,POINT (-119.792659 36.727664),36.727664,-119.792659 +3380 W Ashlan Ave,0,Fresno,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,93722,PROC,0101000020E61000008A517C2189F65DC031AE5D7FB7654240,POINT (-119.8521198 36.7946624),36.7946624,-119.8521198 +255 Ford St,0,Watsonville,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,95076,PROC,0101000020E6100000BFA0E0BDFE705EC054D7EB27AD744240,POINT (-121.7655482 36.9115343),36.9115343,-121.7655482 +1160 G St,0,Los Banos,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,93635,PROC,0101000020E6100000B9574167AD355EC09787D031B5874240,POINT (-120.8387087 37.06021712),37.06021712,-120.8387087 +691 Inyo Ave,0,Newman,Saputo Cheese USA Inc,0.0,dairy,CA,cheese,0.0,dairy,95360,PROC,0101000020E61000000DD4731C09415EC082E0B742D4A74240,POINT (-121.0161811 37.31116518),37.31116518,-121.0161811 +8901 North Lander Avenue,0,Hilmar,Hilmar Cheese Company,0.0,dairy,CA,cheese,0.0,dairy,95324,PROC,0101000020E61000007E607DF266365EC0A0B7C2056AB54240,POINT (-120.8500334 37.41729805),37.41729805,-120.8500334 +475 S Tegner Rd,0,Turlock,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,95380,PROC,0101000020E61000003DF779E7AB385EC0B07567F5A7BE4240,POINT (-120.8854922 37.48950069),37.48950069,-120.8854922 +3600 W Canal Dr,0,Turlock,Hilmar Cheese Company,0.0,dairy,CA,cheese,0.0,dairy,95380,PROC,0101000020E61000002331410DDF365EC0A1664815C5BF4240,POINT (-120.857364 37.498202),37.498202,-120.857364 +6321 E Monte Vista Ave,0,Denair,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,95316,PROC,0101000020E6100000D291B7B7B6315EC0DB8DDBBBC8C24240,POINT (-120.7767772 37.52175091),37.52175091,-120.7767772 +2343 Hickman Rd,0,Hickman,Foster Farms Dairy Crystal,0.0,dairy,CA,dairy,0.0,dairy,95323,PROC,0101000020E61000006B5CA4F55C305EC005E485536ACC4240,POINT (-120.7556738 37.59699482),37.59699482,-120.7556738 +2843 Illinois Ave,0,Modesto,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,95358,PROC,0101000020E61000001D88D11852445EC0F42287467FCC4240,POINT (-121.0675108 37.59763414),37.59763414,-121.0675108 +1472 Hall Rd,0,Hickman,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,95323,PROC,0101000020E6100000C06268D02B2F5EC0C9E5FD870DCE4240,POINT (-120.7370492 37.60978794),37.60978794,-120.7370492 +736 Garner Rd,0,Modesto,Nestle Prepared Foods,0.0,dairy,CA,milk,0.0,dairy,95357,PROC,0101000020E61000000A37740EF93A5EC0018E350A66D04240,POINT (-120.9214512 37.62811401),37.62811401,-120.9214512 +3440 Enterprise Ave,0,Hayward,Foster Farms Dairy Crystal,0.0,dairy,CA,dairy,0.0,dairy,94545,PROC,0101000020E610000064A82FF001885EC0266195C107D14240,POINT (-122.1251183 37.6330492),37.6330492,-122.1251183 +1270 N Shaw Rd,0,Stockton,Humboldt Creamery,0.0,dairy,CA,dairy,0.0,dairy,95215,PROC,0101000020E6100000D93D1E9FB54F5EC0A5560C15EBFC4240,POINT (-121.2454603 37.97592414),37.97592414,-121.2454603 +441 Houser St,0,Cotati,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,94931,PROC,0101000020E61000001CAD0F90D4AD5EC02C216981872B4340,POINT (-122.7160988 38.3400728),38.3400728,-122.7160988 +3960 Channel Dr,0,West Sacramento,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,95691,PROC,0101000020E6100000E5828EB1EE645EC0B8E9CF7EA4474340,POINT (-121.5770687 38.5597075),38.5597075,-121.5770687 +3601 Co Rd C,0,Orland,Land O Lakes cheese,0.0,dairy,CA,cheese,0.0,dairy,95963,PROC,0101000020E61000005C920376358C5EC0BE4C142175DF4340,POINT (-122.190763 39.745762),39.745762,-122.190763 +,0,Fortuna,Foster Farms Dairy Crystal,0.0,dairy,CA,dairy,0.0,dairy,95540,PROC,0101000020E6100000F8359204E1085FC0488C9E5BE84A4440,POINT (-124.138734 40.585216),40.585216,-124.138734 +572 Fernbridge Dr,0,Fortuna,Humboldt Creamery,0.0,dairy,CA,dairy,0.0,dairy,95540,PROC,0101000020E6100000C4C1EFF0E80C5FC040984659E04E4440,POINT (-124.2017176 40.61622158),40.61622158,-124.2017176 +1555 Tahoe Ct,0,Redding,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,96003,PROC,0101000020E6100000EBAA402D86985EC0F5503640C4504440,POINT (-122.3831895 40.6309891),40.6309891,-122.3831895 +3250 Camino Del Sol,0,Oxnard,olde thompson inc,0.0,dehydrator,CA,spice vegetables,0.0,dehydrator,93030,PROC,0101000020E6100000F4B2DC88DDC85DC0EF03EB93371A4140,POINT (-119.1385214 34.2048211),34.2048211,-119.1385214 +9301 Lacey Blvd,0,Hanford,olam spices and vegetable ingredients,0.0,dehydrator,CA,spice vegetables,0.0,dehydrator,93230,PROC,0101000020E61000003A652431F7E75DC01BE1A3B4ED294240,POINT (-119.6244624 36.3275667),36.3275667,-119.6244624 +1445 Nebraska Ave,0,Selma,Sun Maid Growers,0.0,dehydrator,CA,grape,0.0,dehydrator,93662,PROC,0101000020E610000037AA2E3B9FE65DC0A87F5A56AB474240,POINT (-119.6034687 36.5599163),36.5599163,-119.6034687 +2028 S 3rd St,0,Fresno,Valley Fig Growers,0.0,dehydrator,CA,fig,0.0,dehydrator,93702,PROC,0101000020E61000000D99E1F54FF15DC001C11C3D7E5C4240,POINT (-119.7705054 36.7226025),36.7226025,-119.7705054 +47641 W Nees Ave,0,Firebaugh,olam spices and vegetable ingredients,0.0,dehydrator,CA,spice vegetables,0.0,dehydrator,93622,PROC,0101000020E6100000B31078BB39295EC01004C8D0B16C4240,POINT (-120.6441487 36.8491765),36.8491765,-120.6441487 +28390 Ave 12,0,Madera,sunsweet dryers,0.0,dehydrator,CA,prune date fruit nut,0.0,dehydrator,93637,PROC,0101000020E610000036DABB500A025EC01E6B460639764240,POINT (-120.0318796 36.92361525),36.92361525,-120.0318796 +1350 CA 152,0,Gilroy,Gilroy foods,0.0,dehydrator,CA,garlic onion capsicums,0.0,dehydrator,95020,PROC,0101000020E6100000AA51FEA490625EC031C1DB4965804240,POINT (-121.5400784 37.00309108),37.00309108,-121.5400784 +3324 Orestimba Rd,0,Newman,VSP products valleysun,0.0,dehydrator,CA,tomato,0.0,dehydrator,95360,PROC,0101000020E6100000E247EB5E5D455EC00D633D7B4FA84240,POINT (-121.0838239 37.31492558),37.31492558,-121.0838239 +9984 Walnut Ave,0,Livingston,sensient natural ingredients,0.0,dehydrator,CA,garlic onion capsicums vegetables,0.0,dehydrator,95334,PROC,0101000020E610000082035ABA822E5EC02BC0779B37B04240,POINT (-120.726729 37.376697),37.376697,-120.726729 +151 S Walnut Rd,0,Turlock,sensient natural ingredients,0.0,dehydrator,CA,garlic onion capsicums vegetables,0.0,dehydrator,95380,PROC,0101000020E6100000FD6DAA49CB375EC0F6D2D2E4FBBE4240,POINT (-120.8717827 37.49206219),37.49206219,-120.8717827 +2757 Rockville Rd,0,Fairfield,Culinary Farms,0.0,dehydrator,CA,tomatoes,0.0,dehydrator,94534,PROC,0101000020E6100000F0BCF9B2D9855EC08F1436A8A21F4340,POINT (-122.0914123 38.2471514),38.2471514,-122.0914123 +500 Crocker Dr,0,Vacaville,Mariani Packing,0.0,dehydrator,CA,fruit,0.0,dehydrator,95688,PROC,0101000020E61000006F5DD669C97C5EC035DC3642F5334340,POINT (-121.9497933 38.4059222),38.4059222,-121.9497933 +29485 Co Rd 27,0,Winters,sunsweet dryers,0.0,dehydrator,CA,prune date fruit nut,0.0,dehydrator,95694,PROC,0101000020E610000007F01648507E5EC0D177B7B244434340,POINT (-121.97365 38.525534),38.525534,-121.97365 +1520 Terminal St,0,West Sacramento,California Fire Roasted LLC,0.0,dehydrator,CA,tomato,0.0,dehydrator,95691,PROC,0101000020E6100000A1E76047AD625EC0B7BCCD76E0484340,POINT (-121.5418261 38.5693501),38.5693501,-121.5418261 +1244 E Beamer St,0,Woodland,Culinary Farms,0.0,dehydrator,CA,tomatoes,0.0,dehydrator,95776,PROC,0101000020E61000004C50C3B7B0705EC0BCA24A8391574340,POINT (-121.760786 38.6841282),38.6841282,-121.760786 +901 N Walton Ave,0,Yuba City,sunsweet growers,0.0,dehydrator,CA,prune date,0.0,dehydrator,95993,PROC,0101000020E61000001533672211695EC0D2EF6F8EC2914340,POINT (-121.6416708 39.13874989),39.13874989,-121.6416708 +6229 Myers Road,0,Williams,olam spices and vegetable ingredients,0.0,dehydrator,CA,spice vegetables,0.0,dehydrator,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +1500 Eager Rd,0,Live Oak,wilbur packing co,0.0,dehydrator,CA,prune,0.0,dehydrator,95953,PROC,0101000020E610000051BB5F05F8685EC0168B3ACE48984340,POINT (-121.640138 39.18972185),39.18972185,-121.640138 +7207 Moon Bend Rd,0,Colusa,sunsweet dryers,0.0,dehydrator,CA,prune date fruit nut,0.0,dehydrator,95932,PROC,0101000020E610000022EF0B9EF87F5EC039C29AB105994340,POINT (-121.9995494 39.19548626),39.19548626,-121.9995494 +9301 9399 Larkin Rd,0,Live Oak,sunsweet dryers,0.0,dehydrator,CA,prune date fruit nut,0.0,dehydrator,95953,PROC,0101000020E6100000E97E4E417E6C5EC0FC89CA8635A14340,POINT (-121.695206 39.259446),39.259446,-121.695206 +1900 Highway 99,0,Gridley,stapleton spense packing,0.0,dehydrator,CA,plums prunes,0.0,dehydrator,95948,PROC,0101000020E610000068565B56066C5EC09688015CDAAF4340,POINT (-121.6878868 39.3738513),39.3738513,-121.6878868 +7714 Co Rd 9,0,Orland,sunsweet dryers,0.0,dehydrator,CA,prune date fruit nut,0.0,dehydrator,95963,PROC,0101000020E61000005C920376358C5EC0BE4C142175DF4340,POINT (-122.190763 39.745762),39.745762,-122.190763 +101 Larkspur Landing Cir # 350,0,Larkspur,ONeill Vintners Distillers,0.0,distillery,CA,distillers grain,0.0,distillery,94939,PROC,0101000020E6100000BE1182FABBA05EC0C218ECE126F94240,POINT (-122.5114733 37.9464991),37.9464991,-122.5114733 +103 Harvard Ave #4,0,Half Moon Bay,Half Moon Bay Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,94019,PROC,0101000020E61000005DEEDD309B9F5EC0F8929DE96BC04240,POINT (-122.4938471 37.50329323),37.50329323,-122.4938471 +10400 US-101,0,Hopland,Jaxon Keys Winery Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95449,PROC,0101000020E6100000C1E270E657C75EC0BA8102EFE47D4340,POINT (-123.11474 38.983549),38.983549,-123.11474 +1042 McCall Ave,0,Sanger,E J Gallo Mc Call Winery,0.0,distillery,CA,distillers grain,0.0,distillery,93657,PROC,0101000020E6100000CCCF0D4DD9E65DC0CDA90947355C4240,POINT (-119.607013 36.7203759),36.7203759,-119.607013 +108 Dodd Ct,0,American Canyon,Loch Union Distilling,0.0,distillery,CA,distillers grain,0.0,distillery,94503,PROC,0101000020E6100000094E7D2079905EC0449DA0EAE3184340,POINT (-122.257393 38.19445546),38.19445546,-122.257393 +10960 Wheatlands Ave,0,Santee,BNS Brewing and Distilling Co,0.0,distillery,CA,distillers grain,0.0,distillery,92071,PROC,0101000020E6100000BEAA0E14533D5DC049360D40596C4040,POINT (-116.9581957 32.8464737),32.8464737,-116.9581957 +1121 Palmetto Ave,0,Pacifica,The Tripp Distillery LLC,0.0,distillery,CA,distillers grain,0.0,distillery,94044,PROC,0101000020E6100000040A50AE849F5EC0A44F2F2134D24240,POINT (-122.4924732 37.64221587),37.64221587,-122.4924732 +11460 Sunrise Gold Cir c,0,Rancho Cordova,Gold River Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95742,PROC,0101000020E610000076887FD8D2505EC01ED0255E964C4340,POINT (-121.262869 38.59833886),38.59833886,-121.262869 +121 Industrial Way #4,0,Belmont,Old World Spirits LLC,0.0,distillery,CA,distillers grain,0.0,distillery,94002,PROC,0101000020E6100000E6CAA0DAE0995EC0BFCB56A8FFD34240,POINT (-122.404349 37.65623955),37.65623955,-122.404349 +12205 Locksley Ln #11,0,Auburn,California Distilled Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,95602,PROC,0101000020E610000060F591A520465EC046C4FFE3A5794340,POINT (-121.0957426 38.95037508),38.95037508,-121.0957426 +1260 Lincoln Ave #1100,0,Pasadena,Stark Spirits Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,91103,PROC,0101000020E61000004E5FCFD72C8A5DC0A46E675F79154140,POINT (-118.158987 34.1677665),34.1677665,-118.158987 +1300 Factory Pl,0,Los Angeles,loft bear,0.0,distillery,CA,distillers grain,0.0,distillery,90013,PROC,0101000020E6100000E02BBAF51A8F5DC00FCAE29BF9044140,POINT (-118.2360205 34.03886746),34.03886746,-118.2360205 +1320 Scott St,0,Petaluma,Griffo Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,94954,PROC,0101000020E61000006EA301BC85AA5EC008C7D1C19F224340,POINT (-122.6644125 38.2705004),38.2705004,-122.6644125 +137 Anacapa St,0,Santa Barbara,Cutlers Artisan Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,93101,PROC,0101000020E6100000BA15C26A2CEC5DC096129BF215354140,POINT (-119.690211 34.41473229),34.41473229,-119.690211 +1439 Egbert Ave,0,San Francisco,Seven Stills Brewery Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,94124,PROC,0101000020E61000001B5B199E28995EC08173EBDA83DC4240,POINT (-122.3931041 37.7227739),37.7227739,-122.3931041 +1477 University Ave,0,San Diego,FruitCraft Fermentery Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,92103,PROC,0101000020E61000004B32BCA390495DC00147A753C35F4040,POINT (-117.1494531 32.7481484),32.7481484,-117.1494531 +1495 G St,0,San Diego,You Yours Distilling Co,0.0,distillery,CA,distillers grain,0.0,distillery,92101,PROC,0101000020E6100000666DAEF5A0495DC0DFBB7262345B4040,POINT (-117.1504492 32.71253615),32.71253615,-117.1504492 +1705 Mariposa St,0,San Francisco,Anchor Brewers Distillers,0.0,distillery,CA,distillers grain,0.0,distillery,94107,PROC,0101000020E610000038712832A9995EC04EB857E6ADE14240,POINT (-122.4009519 37.7631195),37.7631195,-122.4009519 +200 Yosemite Blvd,0,Modesto,E J Gallo Brandy Plant,0.0,distillery,CA,distillers grain,0.0,distillery,95354,PROC,0101000020E6100000C481EBE5523F5EC06551B73768D14240,POINT (-120.9894347 37.63599297),37.63599297,-120.9894347 +201 Industrial Way,0,Buellton,Brothers Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,93427,PROC,0101000020E610000011CE0248C80C5EC0AA5DB818A84E4140,POINT (-120.1997242 34.6145049),34.6145049,-120.1997242 +2174 CA-46,0,Paso Robles,KroBar Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,93446,PROC,0101000020E610000066DB696B442C5EC0290989B48DD14140,POINT (-120.691676 35.637137),35.637137,-120.691676 +23570 Arnold Dr,0,Sonoma,HelloCello Proh Sprits Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95476,PROC,0101000020E6100000E85729F3459D5EC05F11FC6F251D4340,POINT (-122.4573944 38.22770500000001),38.22770500000001,-122.4573944 +2420 Park Ave,0,Chico,Hooker Oak Distillery LLC,0.0,distillery,CA,distillers grain,0.0,distillery,95928,PROC,0101000020E61000003F0C63C133745EC03C35F2D47EDB4340,POINT (-121.8156589 39.7148081),39.7148081,-121.8156589 +2455 Huntington Dr,0,Fairfield,FrankLin Distillers Products Ltd,0.0,distillery,CA,distillers grain,0.0,distillery,94533,PROC,0101000020E6100000407B3F7FEB7E5EC0E08ABC93EC224340,POINT (-121.9831236 38.27284476),38.27284476,-121.9831236 +2459 E 8th St,0,Los Angeles,Greenbar Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,90021,PROC,0101000020E61000004D8F5CED978E5DC079B4CC7DCD034140,POINT (-118.2280229 34.0297086),34.0297086,-118.2280229 +2505 Monarch St,0,Alameda,Hangar 1 Vodka,0.0,distillery,CA,distillers grain,0.0,distillery,94501,PROC,0101000020E610000071917BBABA935EC0C0538EEAF0E44240,POINT (-122.308272 37.78860218),37.78860218,-122.308272 +2601 Monarch St,0,Alameda,St George Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,94501,PROC,0101000020E6100000106CA68CC9935EC05AF10D85CFE44240,POINT (-122.3091766 37.787583),37.787583,-122.3091766 +270 17th St,0,San Diego,Old Harbor Distilling Co,0.0,distillery,CA,distillers grain,0.0,distillery,92101,PROC,0101000020E61000004C04053983495DC0B4299123A15A4040,POINT (-117.1486342 32.70804257),32.70804257,-117.1486342 +2725 Adelaida Rd,0,Paso Robles,Villicana Winery refind Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,93446,PROC,0101000020E6100000EFF08DD7722F5EC06A1FE16A53D34140,POINT (-120.7413844 35.6509832),35.6509832,-120.7413844 +2739 Via Orange Way Suite 110,0,Spring Valley,Liberty Call Distilling LLC,0.0,distillery,CA,distillers grain,0.0,distillery,91978,PROC,0101000020E6100000C2A15CBF053E5DC03AF2F6D6765D4040,POINT (-116.9691008 32.7301892),32.7301892,-116.9691008 +2766 Via Orange Way h,0,Spring Valley,San Diego Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,91978,PROC,0101000020E6100000DAFDCF06053E5DC0054E3ABA5F5D4040,POINT (-116.9690568 32.72948387),32.72948387,-116.9690568 +3064 Limestone Way,0,Paso Robles,Wine Shine,0.0,distillery,CA,distillers grain,0.0,distillery,93446,PROC,0101000020E610000066DB696B442C5EC0290989B48DD14140,POINT (-120.691676 35.637137),35.637137,-120.691676 +3073 Newtown Rd,0,Placerville,1848 Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95667,PROC,0101000020E61000007288B839952F5EC0D70BECCEE65D4340,POINT (-120.743483 38.73360621),38.73360621,-120.743483 +3173 Del Este,0,Modesto,Do Good Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95354,PROC,0101000020E610000047ACC5A7003E5EC0BF0F070951D24240,POINT (-120.96879 37.643098),37.643098,-120.96879 +3189 Independence Dr,0,Livermore,Sutherland Distilling Company,0.0,distillery,CA,distillers grain,0.0,distillery,94551,PROC,0101000020E6100000DE58501814745EC0A374E95F92DA4240,POINT (-121.8137265 37.707592),37.707592,-121.8137265 +3230 Riverside Ave,0,Paso Robles,Azeo Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,93446,PROC,0101000020E610000004D48A251B2C5EC0A8BD2DFDF0D24140,POINT (-120.6891569 35.6479794),35.6479794,-120.6891569 +3701 Collins Ave,0,Richmond,Falcon Spirits Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,94806,PROC,0101000020E61000008FA1084EA2965EC05E363AE7A7FD4240,POINT (-122.3536563 37.98168650000001),37.98168650000001,-122.3536563 +382 Enterprise St Ste 104,0,San Marcos,California Spitirs Co,0.0,distillery,CA,distillers grain,0.0,distillery,92078,PROC,0101000020E610000063CF4312E2495DC02DC3C9479C914040,POINT (-117.1544233 33.1375818),33.1375818,-117.1544233 +3891 N Ventura Ave,0,Ventura,Ventura Spirits Company,0.0,distillery,CA,distillers grain,0.0,distillery,93001,PROC,0101000020E61000006F7374A69AD25DC05C69633612294140,POINT (-119.2906891 34.3208683),34.3208683,-119.2906891 +4001 Spring Mountain Rd,0,St Helena,Charbay Winery Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,94574,PROC,0101000020E61000007FF8F9EFC1A25EC07B67178084424340,POINT (-122.543087 38.51966859),38.51966859,-122.543087 +40300 Greenwood Way,0,Oakhurst,Oakhurst Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,93644,PROC,0101000020E6100000E6CB0BB08FE95DC0460FD7C5C8AA4240,POINT (-119.649395 37.3342521),37.3342521,-119.649395 +40880 County Center Dr,0,Temecula,Kalifornia Distilleries Inc,0.0,distillery,CA,distillers grain,0.0,distillery,92591,PROC,0101000020E6100000ECF021F2274A5DC09466987F99C34040,POINT (-117.1586881 33.5281219),33.5281219,-117.1586881 +411 Broadway St,0,Fresno,411 Broadway Ales Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,93721,PROC,0101000020E6100000F6B8CA6E41F25DC07C97F7DD195D4240,POINT (-119.7852437 36.7273519),36.7273519,-119.7852437 +425 Alta St #15,0,Gonzales,Fogs End Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,93926,PROC,0101000020E61000006E73BE33B55C5EC0F67CCD72D9404240,POINT (-121.4485597 36.506636),36.506636,-121.4485597 +427 Swift St A,0,Santa Cruz,Venus Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,95060,PROC,0101000020E61000001CC0119326835EC0516452E8617A4240,POINT (-122.0492294 36.9561129),36.9561129,-122.0492294 +477 25th St,0,Oakland,Crooked City Cider,0.0,distillery,CA,distillers grain,0.0,distillery,94612,PROC,0101000020E6100000E5E2B9081D915EC06B8F28FE39E84240,POINT (-122.2673971 37.8142698),37.8142698,-122.2673971 +5050 Robert J Mathews Pkwy,0,El Dorado Hills,Dry Diggings Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95762,PROC,0101000020E6100000B52B3E4FCD435EC00BA8AAAFB24F4340,POINT (-121.0594061 38.62264057000001),38.62264057000001,-121.0594061 +5216 Arboga Rd,0,Olivehurst,CaliShine Distillery Co,0.0,distillery,CA,distillers grain,0.0,distillery,95961,PROC,0101000020E61000003153A40CE6635EC0E54A56A8628D4340,POINT (-121.5609161 39.10457329),39.10457329,-121.5609161 +555 Avacado Rd,0,Oroville,Cobble Ridge Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95966,PROC,0101000020E6100000878A71FE265F5EC0FF7A8505F7BD4340,POINT (-121.486755 39.484101),39.484101,-121.486755 +5579 Soquel San Jose Rd,0,Soquel,Osocalis Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95073,PROC,0101000020E61000007E78F1D9957C5EC02D74CA4862874240,POINT (-121.9466462 37.0576869),37.0576869,-121.9466462 +5625 State Farm Dr #18,0,Rohnert Park,Sonoma County Distilling Co,0.0,distillery,CA,distillers grain,0.0,distillery,94928,PROC,0101000020E61000000FA6176B6EAD5EC0A28B97B89F2D4340,POINT (-122.7098644 38.3564368),38.3564368,-122.7098644 +611 2nd St,0,Petaluma,Sweetwater Distillers,0.0,distillery,CA,distillers grain,0.0,distillery,94952,PROC,0101000020E610000096B9540067A85EC07016A36C991D4340,POINT (-122.6312867 38.23124464),38.23124464,-122.6312867 +6790 McKinley St,0,Sebastopol,Spirit Works Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95472,PROC,0101000020E6100000DCD6169E97B45EC077B00FFCB9334340,POINT (-122.821754 38.4041133),38.4041133,-122.821754 +721 Nevada Street #206B,0,Redlands,J Riley Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,92373,PROC,0101000020E61000001767672CF54D5DC06BE9769BDC074140,POINT (-117.2180892 34.0614199),34.0614199,-117.2180892 +7759 Bell Rd,0,Windsor,Sonoma Brothers Distilling,0.0,distillery,CA,distillers grain,0.0,distillery,95492,PROC,0101000020E61000008C2FDAE385B35EC04166C28AAE444340,POINT (-122.805047 38.5365766),38.5365766,-122.805047 +802 E Washington Ave,0,Santa Ana,Blinky Owl Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,92701,PROC,0101000020E6100000C2A1B778F8765DC07F7FEFDBB5E04040,POINT (-117.8589155 33.7555499),33.7555499,-117.8589155 +8418 S Lac Jac Ave,0,Parlier,Oneill Beverages Co LLC,0.0,distillery,CA,distillers grain,0.0,distillery,93648,PROC,0101000020E6100000CB619C64D0DE5DC00162B774714E4240,POINT (-119.4814693 36.6128374),36.6128374,-119.4814693 +8650 Hayden Pl,0,Culver City,Bavarian Breweries Distilleries,0.0,distillery,CA,distillers grain,0.0,distillery,90232,PROC,0101000020E6100000B61902DB9C985DC0AE994208C4024140,POINT (-118.3845737 34.02160743),34.02160743,-118.3845737 +8706 Production Ave,0,San Diego,Malahat Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,92121,PROC,0101000020E6100000D185A28AAC4A5DC0955BFF5316714040,POINT (-117.1667811 32.8834939),32.8834939,-117.1667811 +8733 Magnolia Ave Ste. 126,0,Santee,Copper Collar Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,92071,PROC,0101000020E6100000F87F1F1FBE3D5DC0D2F701E5C26A4040,POINT (-116.9647291 32.83407271),32.83407271,-116.9647291 +909 E El Segundo Blvd,0,El Segundo,Rob Rubens Distilling and Brewing,0.0,distillery,CA,distillers grain,0.0,distillery,90245,PROC,0101000020E6100000BB062230FB995DC03F6AFA8956F54040,POINT (-118.4059563 33.91670346),33.91670346,-118.4059563 +915 S Santa Fe Ave,0,Los Angeles,Our/Los Angeles Vodka,0.0,distillery,CA,distillers grain,0.0,distillery,90021,PROC,0101000020E6100000184CB2C4B98E5DC0B612572127044140,POINT (-118.2300884 34.03244416),34.03244416,-118.2300884 +9275 Midway,0,Durham,Almendra Winery Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95938,PROC,0101000020E6100000DAB6DE2527735EC042CAF4F00AD24340,POINT (-121.7992644 39.6409589),39.6409589,-121.7992644 +9750 Distribution Ave,0,San Diego,Cutwater Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,92121,PROC,0101000020E61000005C1B2AC6794A5DC08F238C5539714040,POINT (-117.1636825 32.8845622),32.8845622,-117.1636825 +E South St,0,Bishop,Owens Valley Distilling Co,0.0,distillery,CA,distillers grain,0.0,distillery,93514,PROC,0101000020E6100000323B8BDEA99A5DC0B439CE6DC2AD4240,POINT (-118.416618 37.357496),37.357496,-118.416618 +Pier 50 Shed B,0,San Francisco,Distillery No 209,0.0,distillery,CA,distillers grain,0.0,distillery,94158,PROC,0101000020E61000002A58E36C3A995EC05512D90759E24240,POINT (-122.394191 37.768342),37.768342,-122.394191 +10441 Stanford Ave,0,Garden Grove,Darling International Inc,0.0,fog,CA,fog,0.0,distributor,92842,PROC,0101000020E6100000C729DFD8D87C5DC07591214B8FE34040,POINT (-117.9507353 33.77781047),33.77781047,-117.9507353 +11947 S Carpenter Rd,0,Crows Landing,Darling International Inc,0.0,fog,CA,fog,0.0,recycling,95313,PROC,0101000020E6100000DDB243FCC3425EC098DC28B2D6B64240,POINT (-121.043212 37.428427),37.428427,-121.043212 +11946 S Carpenter Rd,0,Crows Landing,Darling International Inc,0.0,fog,CA,fog,0.0,meat,95313,PROC,0101000020E610000098D7B6CDF9415EC006B86277E8BC4240,POINT (-121.0308718 37.47584431),37.47584431,-121.0308718 +7878 Airway Rd,0,San Diego,Heinz Frozen Food Co,0.0,freshfrozen,CA,misc,0.0,frozen,92154,PROC,0101000020E61000008AE59656433E5DC0E3363BCEC4474040,POINT (-116.97286 32.56069353),32.56069353,-116.97286 +2105 Anderholt Rd,0,Holtville,Grimmway Farm,0.0,freshfrozen,CA,misc carrot,0.0,farm,92250,PROC,0101000020E610000058E36C3A02D85CC03B6EF8DD74674040,POINT (-115.375136 32.808254),32.808254,-115.375136 +1051 Pacific Ave,0,Oxnard,Gills Onions,0.0,freshfrozen,CA,onion,0.0,fresh,93030,PROC,0101000020E6100000070951BEA0CA5DC0AAE8595A57184140,POINT (-119.166061 34.1901658),34.1901658,-119.166061 +1250 E Third St,0,Oxnard,tree top,0.0,freshfrozen,CA,fruit,0.0,frozen,93030,PROC,0101000020E61000007F0173E34CCB5DC0DB178EEFA4194140,POINT (-119.1765679 34.20034594),34.20034594,-119.1765679 +CA 166,0,New Cuyama,Grimmway Farm,0.0,freshfrozen,CA,misc carrot,0.0,farm,93254,PROC,0101000020E6100000F96706F181EA5DC06D1CB1169F784140,POINT (-119.664181 34.942355),34.942355,-119.664181 +830 Sycamore Rd,0,Arvin,Grimmway Arvin Organic,0.0,freshfrozen,CA,vegetables,0.0,distributor,93203,PROC,0101000020E61000006F7143424AB45DC0075E6F9338994140,POINT (-118.8170324 35.19703906),35.19703906,-118.8170324 +12000 Main St,0,Lamont,CalOrganic Farms,0.0,freshfrozen,CA,vegetables,0.0,farm,93241,PROC,0101000020E610000081EB8A19E1BA5DC0ED139BEA249F4140,POINT (-118.919989 35.2433141),35.2433141,-118.919989 +14141 Di Giorgio Rd,0,Arvin,Grimmway Farm,0.0,freshfrozen,CA,misc carrot,0.0,farm,93203,PROC,0101000020E61000002909E46D80B75DC03026052FDD9F4140,POINT (-118.8672137 35.24893749),35.24893749,-118.8672137 +12495 Di Giorgio Rd,0,Arvin,Grimmway Farm,0.0,freshfrozen,CA,misc carrot,0.0,farm,93203,PROC,0101000020E61000009040CDDA37B75DC0CA69D301DE9F4140,POINT (-118.8627841 35.24896262),35.24896262,-118.8627841 +11412 Malaga Rd,0,Arvin,Grimmway Farm,0.0,freshfrozen,CA,misc carrot,0.0,farm,93203,PROC,0101000020E61000005576B0B442B75DC09A4074B553A04140,POINT (-118.8634464 35.25255459),35.25255459,-118.8634464 +14322 Di Giorgio Rd,0,Arvin,Green Valley Packers LLC,0.0,freshfrozen,CA,fruit vegetable,0.0,distributor,93203,PROC,0101000020E6100000AE5EEA8C14B65DC069B2DA5779A04140,POINT (-118.8450043 35.2537031),35.2537031,-118.8450043 +6900 Mountain View Rd,0,Bakersfield,Grimmway Enterprises,0.0,freshfrozen,CA,misc carrot,0.0,farm,93307,PROC,0101000020E610000055E0BFD42ABB5DC07DCF488446A44140,POINT (-118.9244892 35.283402),35.283402,-118.9244892 +7200 E Brundage Ln,0,Bakersfield,Bolthouse,0.0,freshfrozen,CA,fruit vegetable,0.0,beverage,93306,PROC,0101000020E61000003A419B1C3EBB5DC0E6D308A293AD4140,POINT (-118.925666 35.35606790000001),35.35606790000001,-118.925666 +33540 CA 58,0,Buttonwillow,Bolthouse,0.0,freshfrozen,CA,fruit vegetable,0.0,farm,93206,PROC,0101000020E61000006B0F7BA100D85DC0CAF474430DB34140,POINT (-119.3750385 35.39884227),35.39884227,-119.3750385 +6301 S Zerker Rd,0,Shafter,Grimmway Citrus,0.0,freshfrozen,CA,citrus,0.0,farm,93263,PROC,0101000020E6100000B610E4A084D25DC0DAE731CA33BF4140,POINT (-119.289345 35.493768),35.493768,-119.289345 +11888 E Clarkson Ave,0,Kingsburg,sunsweet fresh,0.0,freshfrozen,CA,prune date,0.0,fresh,93631,PROC,0101000020E6100000FCBB8800F1E45DC00B4DC8BDAF404240,POINT (-119.5772096 36.5053632),36.5053632,-119.5772096 +16429 W Kamm Ave,0,Helm,ConAgra Foods,0.0,freshfrozen,CA,tomato misc,0.0,distributor,93627,PROC,0101000020E610000090DD054A8A055EC0E7DE686C54434240,POINT (-120.0865655 36.5260139),36.5260139,-120.0865655 +12133 Avenue 408,0,Cutler,wawona frozen foods,0.0,freshfrozen,CA,fruit,0.0,frozen,93615,PROC,0101000020E61000004D3A803452D35DC0F8D6D182E1434240,POINT (-119.3018924 36.53031955),36.53031955,-119.3018924 +2202 S Cedar Ave,0,Fresno,wawona frozen foods,0.0,freshfrozen,CA,fruit,0.0,frozen,93725,PROC,0101000020E610000089C8FA1752F05DC0F4C70FF0FF5B4240,POINT (-119.7550106 36.7187481),36.7187481,-119.7550106 +5626 E Shields Ave,0,Fresno,ConAgra Foods,0.0,freshfrozen,CA,tomato misc,0.0,distributor,93727,PROC,0101000020E6100000355F251FBBEC5DC05960D916AF634240,POINT (-119.698921 36.7787808),36.7787808,-119.698921 +100 W Alluvial Ave,0,Clovis,wawona frozen foods,0.0,freshfrozen,CA,fruit,0.0,frozen,93611,PROC,0101000020E6100000DA88CC01A7ED5DC04E41237DFF6B4240,POINT (-119.7133183 36.8437344),36.8437344,-119.7133183 +1265 N Minnewawa Ave,0,Clovis,wawona frozen foods,0.0,freshfrozen,CA,fruit,0.0,frozen,93619,PROC,0101000020E61000000C37853A51ED5DC01FB127CB5A6D4240,POINT (-119.7080828 36.8543333),36.8543333,-119.7080828 +1720 Beach Rd,0,Watsonville,Del Mar Foods,0.0,freshfrozen,CA,apple peach apricot blackberries strawberries brussel sprouts bell pepers spinach,0.0,frozen,95076,PROC,0101000020E6100000CA1F67F5E9715EC02992544BDF724240,POINT (-121.7799047 36.8974394),36.8974394,-121.7799047 +120 Dubois St,0,Santa Cruz,Odwalla Juices,0.0,freshfrozen,CA,fruit vegetable,0.0,misc,95060,PROC,0101000020E610000025CB49287D825EC0B756C565267E4240,POINT (-122.038889 36.9855468),36.9855468,-122.038889 +2525 Cooper Ave,0,Merced,white oaks frozen foods,0.0,freshfrozen,CA,vegetables,0.0,frozen,95348,PROC,0101000020E61000000E6F319AF0205EC06BABC40280A84240,POINT (-120.5146852 37.31640658),37.31640658,-120.5146852 +1805 Las Plumas Ave,0,San Jose,Odwalla Juices,0.0,freshfrozen,CA,fruit vegetable,0.0,misc,95133,PROC,0101000020E6100000837BAF6B45775EC0DC2C5E2C8CAE4240,POINT (-121.8636121 37.36365275),37.36365275,-121.8636121 +120 Stone Pine Rd,0,Half Moon Bay,Odwalla Juices,0.0,freshfrozen,CA,fruit vegetable,0.0,misc,94019,PROC,0101000020E6100000E344AADE509B5EC0B7B2E9ADA6BB4240,POINT (-122.4268109 37.46602415),37.46602415,-122.4268109 +300 Dianne Dr,0,Turlock,supherb farms,0.0,freshfrozen,CA,vegetable herb,0.0,fresh frozen,95380,PROC,0101000020E6100000B261F2AB5E385EC02D9A290879BF4240,POINT (-120.8807783 37.4958811),37.4958811,-120.8807783 +1010 Twin Cities Rd,0,Courtland,seneca foods corp,0.0,freshfrozen,CA,apricots peaches pears,0.0,distributor,95615,PROC,0101000020E6100000E3A430EF71635EC00EBDC5C37B284340,POINT (-121.553829 38.316277),38.316277,-121.553829 +2327 Chester Dr,0,Penngrove,Morning Star Packing Co,0.0,freshfrozen,CA,tomato,0.0,distributor,94951,PROC,0101000020E6100000B8E11C1A3BAA5EC0374A03E4F02A4340,POINT (-122.6598573 38.3354764),38.3354764,-122.6598573 +345 Sutton Pl,0,Santa Rosa,Odwalla Juices,0.0,freshfrozen,CA,fruit vegetable,0.0,misc,95407,PROC,0101000020E6100000EDDBA4FD6AAE5EC02D1911D610324340,POINT (-122.7252802 38.3911388),38.3911388,-122.7252802 +826 National Dr 200,0,Sacramento,Odwalla Juices,0.0,freshfrozen,CA,fruit vegetable,0.0,misc,95834,PROC,0101000020E6100000EFB490DB0A5F5EC0123F106AD0534340,POINT (-121.4850377 38.6547978),38.6547978,-121.4850377 +724 Main St 202,0,Woodland,Morning Star Packing Co,0.0,freshfrozen,CA,tomato,0.0,distributor,95695,PROC,0101000020E6100000572426A861715EC086E2F161B4564340,POINT (-121.7715855 38.67737984),38.67737984,-121.7715855 +2211 Old Highway 99W,0,Williams,Morning Star Packing Co,0.0,freshfrozen,CA,tomato,0.0,distributor,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +7545 Irvine Center Dr,0,Irvine,kraft,0.0,misc,CA,misc dairy meat bakery,0.0,distributor,92618,PROC,0101000020E610000085BB69E940705DC015BBA6D5CAD44040,POINT (-117.7539619 33.66244002),33.66244002,-117.7539619 +18301 Von Karman Ave 1100,0,Irvine,Golden State Foods,0.0,misc,CA,meat dairy vegetables,0.0,distribution,92612,PROC,0101000020E61000002558C1148A765DC053D62D0AD4D64040,POINT (-117.8521778 33.67834594000001),33.67834594000001,-117.8521778 +1500 E Walnut Ave,0,Fullerton,kraft,0.0,misc,CA,misc dairy meat bakery,0.0,misc,92831,PROC,0101000020E610000050BA3EBDE3795DC059D40E1C23EF4040,POINT (-117.9045251 33.86825896),33.86825896,-117.9045251 +12801 Excelsior Dr,0,Santa Fe Springs,Safeway Distribution,0.0,misc,CA,misc,0.0,distributor,90670,PROC,0101000020E6100000EE9D2C1018845DC03E0801F992F24040,POINT (-118.0639687 33.89511025),33.89511025,-118.0639687 +19317 Arenth Ave,0,City of Industry,Golden State Foods,0.0,misc,CA,meat dairy vegetables,0.0,distribution,91748,PROC,0101000020E61000003F4C0C1357785DC012D3CFE517004140,POINT (-117.8803146 34.0007293),34.0007293,-117.8803146 +21489 Baker Pkwy,0,City of Industry,Golden State Foods,0.0,misc,CA,meat dairy vegetables,0.0,distribution,91789,PROC,0101000020E61000006F6D3C339C755DC0B735D88A6C014140,POINT (-117.8376587 34.01112495),34.01112495,-117.8376587 +11600 Riverside Dr,0,Mira Loma,Costco Depot,0.0,misc,CA,misc,0.0,distributor,91752,PROC,0101000020E6100000FAFD518A8C625DC07BC9B557D5014140,POINT (-117.5398279 34.0143232),34.0143232,-117.5398279 +3450 Dulles Dr,0,Mira Loma,Nestle Prepared Foods,0.0,misc,CA,food beverage,0.0,distributor,91752,PROC,0101000020E6100000F45723160C615DC0180F4AF322034140,POINT (-117.5163627 34.0245041),34.0245041,-117.5163627 +640 S 6th Ave,0,City of Industry,Golden State Foods,0.0,misc,CA,meat dairy vegetables,0.0,distribution,91746,PROC,0101000020E6100000DDBCCC0B0B7F5DC039E53C29B4034140,POINT (-117.9850492 34.02893558),34.02893558,-117.9850492 +5650 E Santa Ana St,0,Ontario,GEODIS distribution,0.0,misc,CA,misc,0.0,shipping,91761,PROC,0101000020E61000002E156580D5615DC0C0A78306AC064140,POINT (-117.5286561 34.0521248),34.0521248,-117.5286561 +3392 N Mike Daley Dr,0,San Bernardino,heinz,0.0,misc,CA,misc dairy meat bakery,0.0,distributor,92407,PROC,0101000020E6100000B53286DE07555DC01F752ACF72134140,POINT (-117.3286053 34.1519412),34.1519412,-117.3286053 +950 Mountain View Ave,0,Oxnard,pacific coast produce,0.0,misc,CA,misc fruit meat dairy,0.0,distribution,93030,PROC,0101000020E6100000FE2B2B4DCACA5DC00A4F43AF9A184140,POINT (-119.1685975 34.1922206),34.1922206,-119.1685975 +21101 Bear Mountain Blvd,0,Bakersfield,J G Boswell Co,0.0,misc,CA,onion tomato wheat cotton alfalfa,0.0,farm,93311,PROC,0101000020E6100000628CA3CDCCCC5DC0D3E2E71AC19A4140,POINT (-119.2000002 35.2090181),35.2090181,-119.2000002 +Ashe Rd,0,Bakersfield,J G Boswell Co,0.0,misc,CA,onion tomato wheat cotton alfalfa,0.0,farm,93313,PROC,0101000020E6100000A33CF372D8C35DC03048FAB48AA04140,POINT (-119.060086 35.254233),35.254233,-119.060086 +36889 CA 58,0,Buttonwillow,J G Boswell Tomato Co,0.0,misc,CA,onion tomato wheat cotton alfalfa,0.0,misc,93206,PROC,0101000020E6100000CB0EF10F5BDC5DC04015376E31B34140,POINT (-119.443058 35.399946),35.399946,-119.443058 +7835 Estrella Rd,0,San Miguel,Star Farms,0.0,misc,CA,misc,0.0,farm,93451,PROC,0101000020E6100000D7F03ED8F3295EC06A73524E6ADC4140,POINT (-120.6555081 35.7219942),35.7219942,-120.6555081 +28001 Dairy Ave,0,Corcoran,J G Boswell Co,0.0,misc,CA,onion tomato wheat cotton alfalfa,0.0,misc,93212,PROC,0101000020E610000005508C2C99E45DC007BCC43F09064240,POINT (-119.571849 36.04715726),36.04715726,-119.571849 +710 Bainum Ave,0,Corcoran,J G Boswell Co,0.0,misc,CA,onion tomato wheat cotton alfalfa,0.0,misc,93212,PROC,0101000020E61000008E0244C18CE35DC045CFD2BAB20B4240,POINT (-119.555466 36.0913919),36.0913919,-119.555466 +18900 Gayle Ave,0,Huron,Woolf Enterprises,0.0,misc,CA,almond pistachio wheat garlic hay onion tomato grape walnut,0.0,farm,93234,PROC,0101000020E61000002C2CB81FF0055EC03B6D8D08C6174240,POINT (-120.092781 36.185731),36.185731,-120.092781 +2494 S Orange Ave,0,Fresno,kraft,0.0,misc,CA,misc dairy meat bakery,0.0,misc,93725,PROC,0101000020E6100000D136A38BF2F05DC06878B306EF5A4240,POINT (-119.7648038 36.7104195),36.7104195,-119.7648038 +6205 Engle Way E,0,Gilroy,Nestle Prepared Foods,0.0,misc,CA,misc,0.0,misc,95020,PROC,0101000020E610000070FD05CC8D635EC0BFE0890FA27E4240,POINT (-121.5555296 36.9893207),36.9893207,-121.5555296 +1125 Paulson Rd,0,Turlock,Land O Lakes Purina Feed,0.0,misc,CA,misc,0.0,misc,95380,PROC,0101000020E6100000E89491C45C355EC0ED5FBC930DBE4240,POINT (-120.8337871 37.48478934),37.48478934,-120.8337871 +16900 W Schulte Rd,0,Tracy,Safeway Distribution,0.0,misc,CA,misc,0.0,distributor,95377,PROC,0101000020E61000007BF3C06C27615EC032DDB1F9B4DB4240,POINT (-121.5180313 37.71646043),37.71646043,-121.5180313 +25862 S Schulte Ct,0,Tracy,Costco Depot,0.0,misc,CA,misc,0.0,distributor,95377,PROC,0101000020E61000001C977153035D5EC0F88903E8F7DB4240,POINT (-121.453328 37.718503),37.718503,-121.453328 +3000 Executive Pkwy,0,San Ramon,The Kraft Heinz Co,0.0,misc,CA,misc dairy meat bakery,0.0,distributor,94583,PROC,0101000020E6100000A4B38295F97D5EC03F24326255E24240,POINT (-121.9683584 37.7682307),37.7682307,-121.9683584 +2603 Camino Ramon 180,0,San Ramon,hj heinz co,0.0,misc,CA,misc dairy meat bakery,0.0,distributor,94583,PROC,0101000020E610000025F37E92717D5EC0C580579172E24240,POINT (-121.9600569 37.76912133),37.76912133,-121.9600569 +12667 Alcosta Blvd,0,San Ramon,kraft,0.0,misc,CA,misc dairy meat bakery,0.0,distributor,94583,PROC,0101000020E610000042542B5D8B7D5EC0AA549ADE0FE34240,POINT (-121.9616311 37.7739218),37.7739218,-121.9616311 +3656 Perlman Dr,0,Stockton,Hormel Foods Corp,0.0,misc,CA,misc meat,0.0,distributor,95206,PROC,0101000020E6100000F42675B80C515EC034C65E5A1AF54240,POINT (-121.2664014 37.91486673),37.91486673,-121.2664014 +7770 Rd 33,0,Madera,ENZO Olive Oil,0.0,olive,CA,olive,0.0,olive oil,93638,PROC,0101000020E6100000382394089EFC5DC05C6D8B53296E4240,POINT (-119.9471456 36.86063618),36.86063618,-119.9471456 +13950 Thornton Rd,0,Lodi,Calivirgin coldani olive ranch,0.0,olive,CA,olive,0.0,olive oil,95242,PROC,0101000020E610000032906797EF585EC0AA1EBCB8850D4340,POINT (-121.3896235 38.10564336),38.10564336,-121.3896235 +455 Harter Ave,0,Woodland,Boundary Bend Olives,0.0,olive,CA,olive,0.0,olive oil,95776,PROC,0101000020E6100000657506A197705EC092D332ADA8584340,POINT (-121.7592547 38.6926476),38.6926476,-121.7592547 +2675 Lone Tree Rd,0,Oroville,California Olive Ranch,0.0,olive,CA,olive,0.0,olive oil,95965,PROC,0101000020E6100000B81E85EBD1645EC058201F99B3AE4340,POINT (-121.5753125 39.36485590000001),39.36485590000001,-121.5753125 +5945 Co Rd 35,0,Artois,California Olive Ranch,0.0,olive,CA,olive,0.0,olive oil,95913,PROC,0101000020E6100000FDDAFAE93F895EC0B247A81952DD4340,POINT (-122.144526 39.729068),39.729068,-122.144526 +717 Tehama St,0,Orland,west coast products,0.0,olive,CA,olives,0.0,cannery oil,95963,PROC,0101000020E6100000DB9145F5B18C5EC085D726FCEFDF4340,POINT (-122.1983617 39.74951126),39.74951126,-122.1983617 +1367 E Lassen Ave,0,Chico,California Olive Ranch,0.0,olive,CA,olive,0.0,olive oil,95973,PROC,0101000020E6100000301004C8D0755EC01471DF0FE4E24340,POINT (-121.840868 39.7725849),39.7725849,-121.840868 +23377 South Ave,0,Corning,California Olive Ranch,0.0,olive,CA,olive,0.0,olive oil,96021,PROC,0101000020E61000000E187F364D8A5EC092AFE343F9F34340,POINT (-122.1609627 39.90604447),39.90604447,-122.1609627 +770 N Plano St,0,Porterville,Foster Farms,0.0,poultrymeat,CA,poultry,0.0,poultry,93257,PROC,0101000020E610000081DA5EC16CC05DC0ABAE4335250A4240,POINT (-119.0066379 36.0792605),36.0792605,-119.0066379 +2960 S Cherry Ave,0,Fresno,Foster Farms,0.0,poultrymeat,CA,poultry,0.0,poultry,93706,PROC,0101000020E6100000D01154E817F35DC004B5CEAE31594240,POINT (-119.7983342 36.6968287),36.6968287,-119.7983342 +5763 E Shields Ave,0,Fresno,Foster Farms Turkey Hatchery,0.0,poultrymeat,CA,turkey,0.0,poultry,93727,PROC,0101000020E61000002738503B57EC5DC0A98999D8D7634240,POINT (-119.6928242 36.7800246),36.7800246,-119.6928242 +18305 1st Ave,0,Stevinson,Foster Farms,0.0,poultrymeat,CA,poultry,0.0,poultry,95374,PROC,0101000020E6100000EE073C3080345EC079FB9C50C2AB4240,POINT (-120.820324 37.34186752),37.34186752,-120.820324 +1033 S Center St,0,Turlock,Foster Farms,0.0,poultrymeat,CA,poultry,0.0,poultry,95380,PROC,0101000020E61000007BE4C57883355EC0F65C2A5F65BE4240,POINT (-120.8361494 37.48746862),37.48746862,-120.8361494 +17880 W Schulte Rd,0,Tracy,Costco Meat Factory,0.0,poultrymeat,CA,poultry,0.0,poultry,95377,PROC,0101000020E6100000D4997B48F8615EC08513C93E65DC4240,POINT (-121.530779 37.72183976),37.72183976,-121.530779 +1500 Cader Ln,0,Petaluma,Petaluma poultry processors,0.0,poultrymeat,CA,chicken,0.0,poultry,94954,PROC,0101000020E6100000CE8536A5E1A55EC0A4062EEAEE1D4340,POINT (-122.5918973 38.2338536),38.2338536,-122.5918973 +4816 Long Beach Ave,0,Los Angeles,Los Angeles Poultry Co,0.0,poultrymeat,CA,poultry,0.0,processor,90058,PROC,0101000020E6100000C627AE74888F5DC0EE7043A5F4FF4040,POINT (-118.2427036 33.99965349),33.99965349,-118.2427036 +57 Shank Rd,0,Brawley,National Beef LP,0.0,redmeat,CA,beef,0.0,distributer,92227,PROC,0101000020E610000047681547AFE15CC09DC520EA1D804040,POINT (-115.5263231 33.00091292),33.00091292,-115.5263231 +2 Venture 250,0,Irvine,Hormel Foods Corp,0.0,redmeat,CA,misc meat,0.0,meat,92618,PROC,0101000020E6100000D68D774746705DC0D559B1E86BD44040,POINT (-117.7542895 33.65954312),33.65954312,-117.7542895 +3163 E Vernon Ave,0,Vernon,Clougherty Packing LLC Hormel Foods Corp farmer john,0.0,redmeat,CA,pork,0.0,distributor,90058,PROC,0101000020E6100000FB7B84F5DA8D5DC0B2BAD573D2004140,POINT (-118.2164892 34.0064225),34.0064225,-118.2164892 +145 S Hill Dr,0,Brisbane,Del Monte meat co,0.0,redmeat,CA,meat misc,0.0,meat,94005,PROC,0101000020E6100000325871AAB59A5EC0D58BCA1B1AD84240,POINT (-122.417338 37.68829677),37.68829677,-122.417338 +401 Jackson St,0,Oakland,Del Monte meat co,0.0,redmeat,CA,meat misc,0.0,meat,94607,PROC,0101000020E61000006740626042915EC08F464FDBD0E54240,POINT (-122.2696763 37.7954363),37.7954363,-122.2696763 +251 D'Arcy Pkwy,0,Lathrop,Swiss American Sausage Co,0.0,redmeat,CA,meat,0.0,distributor,95330,PROC,0101000020E610000032112510E5525EC0F66758EFE4E64240,POINT (-121.2952309 37.80386154),37.80386154,-121.2952309 +1000 Davis St,0,Livingston,Foster Farms Inc,0.0,redmeat,CA,meat,0.0,processor,95334,PROC,0101000020E6100000BAD4AD435A2E5EC0E714CBCA02B24240,POINT (-120.7242593 37.39071021),37.39071021,-120.7242593 +1210 66th St,0,Sacramento,Reeds Gormet Meat Co,0.0,redmeat,CA,meat,0.0,processor,95819,PROC,0101000020E6100000EB5EDD674B5B5EC0EDABBC2E0D474340,POINT (-121.4264774 38.5550898),38.5550898,-121.4264774 +12136 California Route 2,0,Los Angeles,Star Kosher Meat Market,0.0,redmeat,CA,meat,0.0,processor,90025,PROC,0101000020E6100000795D1A1AAA9D5DC0853A93D32A054140,POINT (-118.4635072 34.04036946),34.04036946,-118.4635072 +1219 N Carpenter Rd,0,Modesto,Ziadeh Meat Market,0.0,redmeat,CA,meat,0.0,processor,95351,PROC,0101000020E610000002EA72EF06425EC02D61E95379D34240,POINT (-121.0316733 37.65214013),37.65214013,-121.0316733 +1220 South Ave,0,Turlock,Sanders Meat Services,0.0,redmeat,CA,meat,0.0,distributer,95380,PROC,0101000020E610000000091E3A18375EC0DEEF48A31FBE4240,POINT (-120.8608537 37.48534051),37.48534051,-120.8608537 +12210 Michigan St #13,0,Grand Terrace,Exotic meat Market,0.0,redmeat,CA,meat,0.0,processor,92313,PROC,0101000020E6100000BB3E181DB5545DC06ED4546012044140,POINT (-117.3235543 34.0318108),34.0318108,-117.3235543 +1301 Rocky Point Dr,0,Oceanside,Olli Salumeria,0.0,redmeat,CA,meat,0.0,processor,92056,PROC,0101000020E6100000B62A2E3391525DC07A56D28A6F9B4040,POINT (-117.2901123 33.2143415),33.2143415,-117.2901123 +140 E Palm St,0,Exeter,Exeter Meats,0.0,redmeat,CA,meat,0.0,processor,93221,PROC,0101000020E6100000A4C8B5FC1BC95DC00F9BC8CC05264240,POINT (-119.1423332 36.297052),36.297052,-119.1423332 +1411 E Baseline St,0,San Bernardino,Nagle Veal and Quality Meats Inc,0.0,redmeat,CA,meat,0.0,distribution,92410,PROC,0101000020E6100000BC653D6B6D505DC0E67D7786840F4140,POINT (-117.2566784 34.12123185),34.12123185,-117.2566784 +1420 S Myrtle Ave,0,Monrovia,Burnett and Son Meat Co Inc,0.0,redmeat,CA,meat,0.0,processor,91016,PROC,0101000020E610000006AFA7670B805DC0540FC1067E114140,POINT (-118.0006961 34.13665852),34.13665852,-118.0006961 +14250 Lomitas Ave,0,City of Industry,Pocino Foods Co,0.0,redmeat,CA,meat,0.0,processor,91746,PROC,0101000020E6100000D718CFFB5A7F5DC086032159C0034140,POINT (-117.9899282 34.0293075),34.0293075,-117.9899282 +1471 Atteberry Ln,0,San Jose,Jims Wholesale Meats,0.0,redmeat,CA,meat,0.0,distribution,95131,PROC,0101000020E610000085D8F4FBD9795EC03F7F901B34B34240,POINT (-121.9039297 37.4000277),37.4000277,-121.9039297 +1480 Drew Ave,0,Davis,Superior Farms Inc,0.0,redmeat,CA,meat,0.0,processor,95618,PROC,0101000020E6100000FAA4C97B8B6E5EC07C03BC9A76454340,POINT (-121.7272634 38.54268202),38.54268202,-121.7272634 +1660 Old Bayshore Hwy,0,San Jose,Mohawk Packing Co,0.0,redmeat,CA,meat,0.0,distributer,95112,PROC,0101000020E6100000CA59338D017A5EC02306B2853DAF4240,POINT (-121.9063447 37.36906501000001),37.36906501000001,-121.9063447 +16691 Hale Ave,0,Irvine,sysco newport meat co,0.0,redmeat,CA,meat,0.0,processor,92606,PROC,0101000020E6100000CEC133A149755DC059F6A8E8DDD84040,POINT (-117.832619 33.69427212),33.69427212,-117.832619 +18256 CA-108,0,Jamestown,Raw Hide Meats,0.0,redmeat,CA,meat,0.0,processor,95327,PROC,0101000020E61000001EA4A7C8211C5EC0029D499BAAF54240,POINT (-120.439562 37.919269),37.919269,-120.439562 +1828 E Hedges Ave,0,Fresno,Valley Protein Inc,0.0,redmeat,CA,red meat poultry,0.0,processor,93703,PROC,0101000020E610000032207BBD7BF25DC0E3E423CE2F614240,POINT (-119.7888025 36.75927140000001),36.75927140000001,-119.7888025 +19455 E Clausen Rd,0,Turlock,Clausen Meat Co,0.0,redmeat,CA,meat,0.0,distribution,95380,PROC,0101000020E610000042EFE8DA72355EC027CBFF9A62BA4240,POINT (-120.8351352 37.4561342),37.4561342,-120.8351352 +2102 W Chestnut Ave,0,Santa Ana,California Sausage Inc,0.0,redmeat,CA,meat,0.0,distributer,92703,PROC,0101000020E6100000122E895869795DC00F234A9C11DF4040,POINT (-117.8970548 33.74272493),33.74272493,-117.8970548 +2300 Hoover Ave,0,Modesto,California Meat Distributing,0.0,redmeat,CA,meat,0.0,processor,95354,PROC,0101000020E610000023CED435243D5EC0EA6D3B862AD14240,POINT (-120.9553351 37.63411024),37.63411024,-120.9553351 +2316 S Fruit Ave,0,Fresno,Ortegas Meat Distribution Inc,0.0,redmeat,CA,meat,0.0,processor,93706,PROC,0101000020E6100000FBDAE9BD67F45DC0461850B9D35B4240,POINT (-119.8188319 36.7173988),36.7173988,-119.8188319 +2443 E 27th St,0,Los Angeles,K and M Food Service,0.0,redmeat,CA,meat,0.0,distributer,90058,PROC,0101000020E6100000201219B1AA8E5DC0D0C8CE78AE014140,POINT (-118.2291682 34.01313696),34.01313696,-118.2291682 +2533 Folex Way,0,Spring Valley,Seaport Meat Co,0.0,redmeat,CA,meat,0.0,distribution,91978,PROC,0101000020E6100000955FABA9D13D5DC079BB140D085D4040,POINT (-116.9659218 32.7268082),32.7268082,-116.9659218 +2550 Britannia Blvd #101,0,San Diego,Jensen Meat Co,0.0,redmeat,CA,meat,0.0,distributer,92154,PROC,0101000020E610000043BD2A61B73E5DC07834A359B8464040,POINT (-116.9799426 32.55250092),32.55250092,-116.9799426 +2900 Ayers Ave,0,Vernon,Harvest Meat Co Inc,0.0,redmeat,CA,meat,0.0,warehouse,90058,PROC,0101000020E610000045AD7A0ACA8B5DC03D15CB88E6FF4040,POINT (-118.1842066 33.99922285),33.99922285,-118.1842066 +299 W Main St,0,Brawley,Brandt Beef LLC,0.0,redmeat,CA,meat,0.0,processor,92227,PROC,0101000020E610000080B74082E2E25CC03BB79E5B477D4040,POINT (-115.545075 32.97874017),32.97874017,-115.545075 +30248 Santucci Ct,0,Hayward,Bay Area Seafood Inc,0.0,redmeat,CA,meat,0.0,processor,94544,PROC,0101000020E6100000820B68D85E835EC005F86EF3C6CF4240,POINT (-122.0526639 37.623259),37.623259,-122.0526639 +3049 E Vernon Ave,0,Los Angeles,Farmer John,0.0,redmeat,CA,meat,0.0,distributer,90058,PROC,0101000020E61000001146FD3F188E5DC01497A1F9B5004140,POINT (-118.2202301 34.00555344),34.00555344,-118.2202301 +3189 W Dakota Ave,0,Fresno,Golden California Meat Packers,0.0,redmeat,CA,beef,0.0,distributer,93722,PROC,0101000020E6100000F2947ABB4AF65DC0B73C7BD399644240,POINT (-119.8483113 36.7859444),36.7859444,-119.8483113 +3196 Bird St,0,Livingston,Mayars Halal Meat,0.0,redmeat,CA,meat,0.0,processor,95334,PROC,0101000020E610000082035ABA822E5EC02BC0779B37B04240,POINT (-120.726729 37.376697),37.376697,-120.726729 +333 Clay St,0,Oakland,Allied Pringle Food Sales,0.0,redmeat,CA,meat,0.0,distributer,94607,PROC,0101000020E610000042DAB573D0915EC025B07B2321E64240,POINT (-122.2783479 37.79788631),37.79788631,-122.2783479 +3336 Fruitland Ave,0,Vernon,Jobbers Meat Packing Co,0.0,redmeat,CA,meat,0.0,distribution,90058,PROC,0101000020E61000004C0EE9013D8D5DC07C3D88328EFF4040,POINT (-118.2068486 33.99652702),33.99652702,-118.2068486 +3421 Guerneville Rd,0,Santa Rosa,Willowside Meats Inc,0.0,redmeat,CA,meat,0.0,processor,95401,PROC,0101000020E6100000AAA6DA5D56B35EC01421753BFB394340,POINT (-122.8021464 38.4529795),38.4529795,-122.8021464 +344 Cliffwood Park St,0,Brea,West Coast Prime Meats,0.0,redmeat,CA,meat,0.0,processor,92821,PROC,0101000020E6100000BB7372D0EF785DC0ACC79EB95EF64040,POINT (-117.8896371 33.92476578),33.92476578,-117.8896371 +3450 Riverside Ave,0,Paso Robles,J and R natural meat and sausage,0.0,redmeat,CA,meat,0.0,processor,93446,PROC,0101000020E610000066DB696B442C5EC0290989B48DD14140,POINT (-120.691676 35.637137),35.637137,-120.691676 +3461 Main St,0,Chula Vista,Heartland Meat Co,0.0,redmeat,CA,meat,0.0,processor,91911,PROC,0101000020E6100000B97768B3C5435DC074B8F3501D4C4040,POINT (-117.0589417 32.59464466),32.59464466,-117.0589417 +3530 Arden Rd,0,Hayward,Grand Food Meat Wholesale,0.0,redmeat,CA,meat,0.0,distribution,94545,PROC,0101000020E6100000AB5736188F875EC0A3F034F4AACF4240,POINT (-122.1181088 37.6224046),37.6224046,-122.1181088 +4215 Exchange Ave,0,Vernon,King Meat Service Inc,0.0,redmeat,CA,meat,0.0,processor,90058,PROC,0101000020E61000003E4ADBAE068D5DC0C02FC3B965004140,POINT (-118.2035329 34.00310442),34.00310442,-118.2035329 +4276 N Tracy Blvd,0,Tracy,American Custom Meats,0.0,redmeat,CA,meat,0.0,processor,95304,PROC,0101000020E61000007392F7BBC15B5EC0DCC9F15451E24240,POINT (-121.4336996 37.76810705),37.76810705,-121.4336996 +4586 E Commerce Ave,0,Fresno,Certified Meat Products,0.0,redmeat,CA,meat,0.0,distribution,93725,PROC,0101000020E6100000E4DDEC6ACDEF5DC01953550D67594240,POINT (-119.7469127 36.6984574),36.6984574,-119.7469127 +5030 Gifford Ave,0,Vernon,Premier Meat Co,0.0,redmeat,CA,meat,0.0,processor,90058,PROC,0101000020E6100000046D173F328C5DC01448C30865FF4040,POINT (-118.1905668 33.99527082),33.99527082,-118.1905668 +511 W North Ave,0,Fresno,Fresno Grind,0.0,redmeat,CA,meat,0.0,processor,93706,PROC,0101000020E6100000BF092A4F45F35DC07613211A82584240,POINT (-119.8011053 36.6914704),36.6914704,-119.8011053 +5151 Alcoa Ave,0,Vernon,Rose and Shore Inc,0.0,redmeat,CA,meat,0.0,processor,90058,PROC,0101000020E6100000F6F873C0648D5DC0A2A476757DFF4040,POINT (-118.2092744 33.9960162),33.9960162,-118.2092744 +5217 Industry Ave,0,Pico Rivera,Daniels Western Meat Packers,0.0,redmeat,CA,meat,0.0,distributer,90660,PROC,0101000020E6100000FF64428218865DC09DAB9CAC87004140,POINT (-118.0952459 34.00414045),34.00414045,-118.0952459 +601 Zeff Rd,0,Modesto,Yosemite Meat Co Inc,0.0,redmeat,CA,meat,0.0,distribution,95351,PROC,0101000020E6100000437B50ABC33F5EC0E87981A3AECF4240,POINT (-120.9963177 37.62251705),37.62251705,-120.9963177 +6114 Scott Way,0,Commerce,Sterling Pacific Meat Co,0.0,redmeat,CA,meat,0.0,distribution,90040,PROC,0101000020E6100000D2510E6693895DC0A4C0F16B5AFD4040,POINT (-118.1496215 33.97932195000001),33.97932195000001,-118.1496215 +6621 Midway Rd,0,Dixon,Superior Farms,0.0,redmeat,CA,meat,0.0,processor,95620,PROC,0101000020E61000002705CC327A745EC0BED32A1B52354340,POINT (-121.8199584 38.41656818),38.41656818,-121.8199584 +6969 Clark Ave,0,Newark,Harvest Meat Co,0.0,redmeat,CA,meat,0.0,distribution,94560,PROC,0101000020E61000001BA6118EB47B5DC0DB93B875D4104140,POINT (-117.9328952 34.13148376),34.13148376,-117.9328952 +730 Spreckels Ave,0,Manteca,Cargill Food Distribution,0.0,redmeat,CA,meat,0.0,processor,95336,PROC,0101000020E6100000F401DC87974C5EC0A94F517964E54240,POINT (-121.1967487 37.79212872),37.79212872,-121.1967487 +7310 Pine Ave,0,Chino,Lizze Custom Processing,0.0,redmeat,CA,meat,0.0,distribution,91708,PROC,0101000020E61000009B6736D950695DC053509B8246FA4040,POINT (-117.6455596 33.9552768),33.9552768,-117.6455596 +769 Caudill St,0,San Luis Obispo,Cattaneo Brothers Inc,0.0,redmeat,CA,meat,0.0,processor,93401,PROC,0101000020E61000003E2C8A0DCC295EC06BDF92D222A24140,POINT (-120.6530794 35.2666877),35.2666877,-120.6530794 +7750 Petaluma Hill Rd,0,Penngrove,Buds Custom Meats,0.0,redmeat,CA,meat,0.0,processor,94951,PROC,0101000020E6100000150AC7E26DAA5EC08A856BFF14294340,POINT (-122.6629569 38.3209533),38.3209533,-122.6629569 +850 E Bidwell St,0,Folsom,Adams Meat Shop,0.0,redmeat,CA,meat,0.0,processor,95630,PROC,0101000020E610000026BD14C3FA495EC08529A99708564340,POINT (-121.1559303 38.67213722),38.67213722,-121.1559303 +9531 Beverly Rd,0,Pico Rivera,Manning Beef LLC,0.0,redmeat,CA,meat,0.0,processor,90660,PROC,0101000020E61000009AFE36D5A4845DC0A0F2F972B0004140,POINT (-118.0725606 34.0053848),34.0053848,-118.0725606 +960 S Sanborn Rd,0,Salinas,Monterey Fish Co,0.0,redmeat,CA,meat,0.0,distribution,93901,PROC,0101000020E6100000D8F0F44A59765EC0FAEDEBC0394B4240,POINT (-121.8492 36.5877),36.5877,-121.8492 +970 E Sandy Mush Rd,0,Merced,Yosemite Valley Beef,0.0,redmeat,CA,meat,0.0,processor,95341,PROC,0101000020E6100000C5BA021BA11E5EC0D4BBF406CA974240,POINT (-120.4785831 37.18585288),37.18585288,-120.4785831 +,0,Commerce,AA Meat Products Inc,0.0,redmeat,CA,beef,0.0,processor,90040,PROC,0101000020E6100000AA9A20EA3E885DC04C6C3EAE0DFD4040,POINT (-118.12884 33.97698),33.97698,-118.12884 +160 Municipal Wharf 2,0,Monterey,Monterey Fish Co,0.0,seafood,CA,seafood,0.0,distribution,93940,PROC,0101000020E6100000D8F0F44A59765EC0FAEDEBC0394B4240,POINT (-121.8492 36.5877),36.5877,-121.8492 +2500 Francisco Blvd,0,Pacifica,Stuckeys Sustainable,0.0,seafood,CA,seafood,0.0,processor,94044,PROC,0101000020E610000036012B2C5D9F5EC02D635CD49BD04240,POINT (-122.4900618 37.62975554),37.62975554,-122.4900618 +6520 Irwindale Ave,0,Irwindale,Harvest Meat Co,0.0,seafood,CA,seafood,0.0,warehouse,91702,PROC,0101000020E61000001BA6118EB47B5DC0DB93B875D4104140,POINT (-117.9328952 34.13148376),34.13148376,-117.9328952 +395 W Keystone Rd,0,Brawley,spreckels sugar co,0.0,sugarbeat,CA,sugar beet,0.0,sugar,92227,PROC,0101000020E61000006227614B34E45CC038718B5CE4734040,POINT (-115.5656918 32.90540654),32.90540654,-115.5656918 +29400 W Whitesbridge Ave,0,Mendota,spreckels sugar co,0.0,sugarbeat,CA,sugar beet,0.0,sugar,93640,PROC,0101000020E6100000B62110F9F8145EC0C8F54AB43F5E4240,POINT (-120.3276961 36.7363191),36.7363191,-120.3276961 +16150 Stephens St,0,City of Industry,Snak King Corp,0.0,tortilla,CA,tortilla,0.0,bakery,91745,PROC,0101000020E61000001C936A44D57C5DC071C4FFC297014140,POINT (-117.9505168 34.0124439),34.0124439,-117.9505168 +11559 Jersey Blvd,0,Rancho Cucamonga,GrumaMissions Food Corp,0.0,tortilla,CA,tortilla,0.0,bakery,91730,PROC,0101000020E6100000245A97BF67635DC0A2BB7F87FD0B4140,POINT (-117.5532073 34.0936746),34.0936746,-117.5532073 +14200 Arminta St,0,Panorama City,Mission Foods,0.0,tortilla,CA,tortilla,0.0,bakery,91402,PROC,0101000020E610000020D4A0C3579C5DC0EA74C531371B4140,POINT (-118.4428567 34.2126219),34.2126219,-118.4428567 +1153 Madison Ln,0,Salinas,Mission Foods,0.0,tortilla,CA,tortilla,0.0,distributor,93907,PROC,0101000020E6100000E523CE2F6F6B5EC073CCC353D9584240,POINT (-121.6786613 36.6941323),36.6941323,-121.6786613 +2849 E Edgar Ave,0,Fresno,Mission Foods,0.0,tortilla,CA,tortilla,0.0,distributor,93706,PROC,0101000020E6100000F97F7AD8B0F15DC06A1327F73B594240,POINT (-119.7764188 36.6971425),36.6971425,-119.7764188 +410 E Trimble Rd,0,San Jose,Mission Foods,0.0,tortilla,CA,tortilla,0.0,distributor,95131,PROC,0101000020E61000007E891D320A7B5EC02E3D79DCE0B14240,POINT (-121.9224973 37.38967472),37.38967472,-121.9224973 +23415 Cabot Blvd,0,Hayward,Mission Foods,0.0,tortilla,CA,tortilla,0.0,distributor,94545,PROC,0101000020E610000074F112F7B3885EC00E02E1F9FBD14240,POINT (-122.1359842 37.6405022),37.6405022,-122.1359842 +4120 Indian Ave,0,Perris,General Mills,0.0,warehouse,CA,bread,0.0,warehouse,92571,PROC,0101000020E6100000A3DE9DC6074F5DC0385211024DEC4040,POINT (-117.2348496 33.8461001),33.8461001,-117.2348496 +1375 Beachey Pl,0,Carson,General Mills,0.0,warehouse,CA,bread,0.0,warehouse,90746,PROC,0101000020E61000008FADC2C1B98F5DC0EABD8CBD72EE4040,POINT (-118.2457127 33.86287660000001),33.86287660000001,-118.2457127 +14344 Carmenita Rd,0,Norwalk,Mission Foods,0.0,warehouse,CA,tortilla,0.0,warehouse,90650,PROC,0101000020E6100000EC1DC940F9825DC0DE39F7CB65F34040,POINT (-118.0464632 33.90154409),33.90154409,-118.0464632 +14600 Proctor Ave,0,City of Industry,FritoLay,0.0,warehouse,CA,bakery,0.0,warehouse,91746,PROC,0101000020E6100000C30FCEA78E7E5DC0477F8183EA034140,POINT (-117.977457 34.03059429),34.03059429,-117.977457 +13508 Marlay Ave,0,Fontana,CocoCola Fontana Warehouse,0.0,warehouse,CA,beverage,0.0,warehouse,92337,PROC,0101000020E610000012CB1C81AE605DC0680EFF9F79054140,POINT (-117.5106509 34.0427742),34.0427742,-117.5106509 +3971 E Airport Dr,0,Ontario,Kraft Foods Warehouse,0.0,warehouse,CA,misc dairy meat bakery,0.0,warehouse,91761,PROC,0101000020E610000032A0281A35645DC067D1E05BFD074140,POINT (-117.5657411 34.0624194),34.0624194,-117.5657411 +1650 E Central Ave,0,San Bernardino,Pepsi Co,0.0,warehouse,CA,beverage,0.0,warehouse,92408,PROC,0101000020E61000009EA3440111505DC01074B4AA250B4140,POINT (-117.2510379 34.087087),34.087087,-117.2510379 +14069 Balboa Blvd,0,Sylmar,FritoLay,0.0,warehouse,CA,bakery,0.0,warehouse,91342,PROC,0101000020E6100000D22FB6B52A9F5DC0CDC11A0429294140,POINT (-118.4869818 34.32156421),34.32156421,-118.4869818 +1055 E North Ave,0,Fresno,Kraft Foods Distribution Center,0.0,warehouse,CA,misc dairy meat bakery,0.0,warehouse,93725,PROC,0101000020E61000003DF207034FF15DC0DEFD96A542584240,POINT (-119.7704475 36.6895339),36.6895339,-119.7704475 +6300 Cameron Blvd,0,Gilroy,Pepsi Co,0.0,warehouse,CA,beverage,0.0,warehouse,95020,PROC,0101000020E6100000EB94A2F0B4625EC0321180C9D77F4240,POINT (-121.5422937 36.9987728),36.9987728,-121.5422937 +2748 W Winton Ave,0,Hayward,Mission Foods,0.0,warehouse,CA,tortilla,0.0,warehouse,94545,PROC,0101000020E61000006E5B4A4C06895EC0782C1103B8D24240,POINT (-122.1410094 37.6462406),37.6462406,-122.1410094 +4718 Newcastle 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-93.196716291478708, 45.024094588300535 ], [ -93.263835999690585, 44.979964999645212 ] ] ] } } +] +} diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/Biodiesel_Plants.csv b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/Biodiesel_Plants.csv index 7a32cf9a..96e7c3ee 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/Biodiesel_Plants.csv +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/Biodiesel_Plants.csv @@ -76,4 +76,4 @@ Walsh BioFuels LLC,58,Mauston,WI,5,Distillers corn oil,Operational,"WI-80 & Maus Western Iowa Energy - Agron Bioenergy,60,Watsonville,CA,15,Multifeedstock,Operational,"860 W Beach St, Watsonville, CA 95076","36.90388067222262, -121.76968983169887",36.90388067,-121.7696898,https://issuu.com/bbiinternational/docs/biodieselmap-2042 White Mountain Biodiesel LLC,62,North Haverhill,NH,8,Yellow grease,Operational,"35 Business Pk Rd, North Haverhill, NH 03774","44.07671166339629, -72.0049135970569",44.07671166,-72.0049136,https://issuu.com/bbiinternational/docs/biodieselmap-2043 World Energy - Natchez,65,Natchez,MS,72,Vegetable oils,Operational,"L E Barry Rd, Natchez, MS 39120","31.533227585047626, -91.4374585606938",31.53322759,-91.43745856,https://issuu.com/bbiinternational/docs/biodieselmap-2045 -World Energy - Rome,66,Rome,GA,20,Multifeedstock,Operational,"555 W Hermitage Rd NE, Rome, GA 30161","34.327173247943826, -85.0919307299404",34.32717325,-85.09193073,https://issuu.com/bbiinternational/docs/biodieselmap-2046 \ No newline at end of file +World Energy - Rome,66,Rome,GA,20,Multifeedstock,Operational,"555 W Hermitage Rd NE, Rome, GA 30161","34.327173247943826, -85.0919307299404",34.32717325,-85.09193073,https://issuu.com/bbiinternational/docs/biodieselmap-2046 diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/CA_proc_points.csv b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/CA_proc_points.csv new file mode 100644 index 00000000..5a46f5cf --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/CA_proc_points.csv @@ -0,0 +1,713 @@ +Address,COUNTY,City,Company,Join_Count,MASTERTYPE,State,Subtype,TARGET_FID,Type,Zip,TYPE,wkt_geom,geom,latitude,longitude +327 Daniels Ln,Kern,Bakersfield,Real Almond Processing,1.0,almond,CA,almond,0.0,shelling,93307,PROC,0101000020E610000090A6D5EBF1BF5DC0D652E5208DAC4140,POINT (-118.9991407 35.3480569),35.3480569,-118.9991407 +26060 Colusa Road,Fresno,Coalinga,Harris Woolf,1.0,almond,CA,almond,1.0,shelling,93210,PROC,0101000020E6100000931B45D61A175EC0EC67B114C9154240,POINT (-120.361013 36.170199),36.170199,-120.361013 +21490 Ortigalita Rd,Merced,Los Banos,Parreira Almond Processing,1.0,almond,CA,almond,2.0,shelling,93635,PROC,0101000020E610000008951348E4375EC00937B62ACB7D4240,POINT (-120.8733082 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Pistachio,1.0,almond,CA,almond,21.0,shelling,93230,PROC,0101000020E61000006C651DE967DE5DC085B6F704E4224240,POINT (-119.4750922 36.2725836),36.2725836,-119.4750922 +13890 Looney Rd.,Merced,Ballico,"Hilltop Ranch, Inc.",1.0,almond,CA,almond,22.0,shelling,95303,PROC,0101000020E61000004D8578245E285EC01011CC0B0FBD4240,POINT (-120.630746 37.47702167),37.47702167,-120.630746 +13890 Looney Road,Merced,Ballico,Long Valley Organic LP,1.0,almond,CA,almond,23.0,shelling,95303,PROC,0101000020E61000004D8578245E285EC01011CC0B0FBD4240,POINT (-120.630746 37.47702167),37.47702167,-120.630746 +144 Westlake Avenue,Santa Cruz,Watsonville,Int'l Almond Exchange Inc.,1.0,almond,CA,almond,24.0,shelling,95076,PROC,0101000020E610000072158BDF14725EC008008E3D7B784240,POINT (-121.782524 36.941261),36.941261,-121.782524 +14650 Co Rd 87,Yolo,Esparto,Capay Canyon Ranch,1.0,almond,CA,almond,25.0,shelling,95627,PROC,0101000020E6100000D3A23EC91D815EC00A85083884584340,POINT (-122.017443 38.691535),38.691535,-122.017443 +14827 W. Harding Rd.,Merced,Turlock,"Select Harvest USA, LLC",1.0,almond,CA,almond,26.0,shelling,95380,PROC,0101000020E610000073405C8308305EC03F89B60040BB4240,POINT (-120.7505196 37.46289071),37.46289071,-120.7505196 +14827 W. Harding Rd.,Merced,Turlock,Spycher Brothers,1.0,almond,CA,almond,27.0,shelling,95380,PROC,0101000020E610000073405C8308305EC03F89B60040BB4240,POINT (-120.7505196 37.46289071),37.46289071,-120.7505196 +14827 W. Harding Rd.,Merced,Turlock,Trinity Nut Company,1.0,almond,CA,almond,28.0,shelling,95380,PROC,0101000020E610000073405C8308305EC03F89B60040BB4240,POINT (-120.7505196 37.46289071),37.46289071,-120.7505196 +"14900 W. Belmont Ave., #2",Fresno,Kerman,"Purity Organics, Inc.",1.0,almond,CA,almond,29.0,shelling,93630,PROC,0101000020E6100000126FF838AE035EC0F000AA132B604240,POINT (-120.0575087 36.7513146),36.7513146,-120.0575087 +1502 S. Railroad Avenue,Glenn,Orland,"T. M. Duche Nut Co., Inc.",1.0,almond,CA,almond,30.0,shelling,95963,PROC,0101000020E6100000697EEB796D8C5EC0CBF6DF5267DE4340,POINT (-122.1941819 39.73752819),39.73752819,-122.1941819 +1518 K Street,Stanislaus,Modesto,Montpelier Nut Co.,1.0,almond,CA,almond,31.0,shelling,95354,PROC,0101000020E6100000CB411A5FC53F5EC0FDC77C1F92D24240,POINT (-120.9964216 37.64508432),37.64508432,-120.9964216 +15391 Vinewood Ave,Merced,Livingston,Del Rio Nut Company,1.0,almond,CA,almond,32.0,shelling,95334,PROC,0101000020E6100000C630CCAEA0305EC0366EB5775BB14240,POINT (-120.7598073 37.38560387),37.38560387,-120.7598073 +15443 Beech Avenue,Kern,Wasco,"South Valley Almond Company, LLC",1.0,almond,CA,almond,33.0,shelling,93280,PROC,0101000020E61000008285DDC199D05DC0294AB67880CC4140,POINT (-119.2593846 35.59767064),35.59767064,-119.2593846 +1550 Industrial Dr.,San Joaquin,Stockton,"Pearl Crop, Inc.",1.0,almond,CA,almond,34.0,shelling,95206,PROC,0101000020E6100000C2E567D949505EC0517DCE7A84F44240,POINT (-121.2545074 37.91029296),37.91029296,-121.2545074 +15516 South Walnut Ave.,Fresno,Caruthers,"Almonds California Pride, Inc.",1.0,almond,CA,almond,35.0,shelling,93609,PROC,0101000020E61000000F29064834F35DC0309B00C3F2404240,POINT (-119.800066 36.5074085),36.5074085,-119.800066 +15516 South Walnut Ave.,Fresno,Caruthers,Campos Brothers,1.0,almond,CA,almond,36.0,shelling,93609,PROC,0101000020E61000000F29064834F35DC0309B00C3F2404240,POINT (-119.800066 36.5074085),36.5074085,-119.800066 +1555 Warren Rd.,San Joaquin,Ripon,"Almond Ace Packing, Inc.",1.0,almond,CA,almond,37.0,shelling,95366,PROC,0101000020E610000094D920938C485EC0D12E5351C4E04240,POINT (-121.13358 37.75599114),37.75599114,-121.13358 +16219 Western Ave,Kern,Wasco,Mandelin Inc.,1.0,almond,CA,almond,38.0,shelling,93280,PROC,0101000020E6100000D427B9C326D85DC0562DC81A1EC84140,POINT (-119.377366 35.56341872),35.56341872,-119.377366 +1640 W. Dovewood Lane,Fresno,Fresno,Jeff Curry & Associates,1.0,almond,CA,almond,39.0,shelling,93711,PROC,0101000020E61000001B5EB5D7A7F45DC0B3A3271BC5684240,POINT (-119.8227443 36.8185152),36.8185152,-119.8227443 +16471 W. Whitesbridge Rd.,Fresno,Kerman,"Schaad Family Almonds, Inc.",1.0,almond,CA,almond,40.0,shelling,93630,PROC,0101000020E61000007967A32971055EC04FA5B09CCE5D4240,POINT (-120.0850319 36.7328678),36.7328678,-120.0850319 +16897 Highway 43,Kern,Wasco,Supreme Almonds of California,1.0,almond,CA,almond,41.0,shelling,93280,PROC,0101000020E61000005A547A5C0AD55DC0B2CF8C1399C54140,POINT (-119.3287574 35.54373402),35.54373402,-119.3287574 +17495 Seidner Rd,Stanislaus,Escalon,Quality Nut Company,1.0,almond,CA,almond,42.0,shelling,95320,PROC,0101000020E61000007212EFA5153C5EC03D5B3086ACD14240,POINT (-120.9388213 37.63807752),37.63807752,-120.9388213 +1750 N Siskiyou Ave,Fresno,Kerman,"Sran Family Orchards, Inc.",1.0,almond,CA,almond,43.0,shelling,93630,PROC,0101000020E6100000A91B83A9C1045EC013FF66182D614240,POINT (-120.0743202 36.7591887),36.7591887,-120.0743202 +"1802 ""C"" St.",Sacramento,Sacramento,Blue Diamond Growers,1.0,almond,CA,almond,44.0,shelling,95814,PROC,0101000020E610000097033DD4B65E5EC04A78E7F5CC4A4340,POINT (-121.479909 38.5843799),38.5843799,-121.479909 +1825 Verduga Rd,Stanislaus,Hughson,"Hughson Nut, Inc.",1.0,almond,CA,almond,45.0,shelling,95326,PROC,0101000020E610000084B46BE7A0335EC0244F8A3D51CD4240,POINT (-120.8066958 37.60404176),37.60404176,-120.8066958 +18252 Avenue 20,Madera,Madera,"Elk Ridge Almonds, Inc.",1.0,almond,CA,almond,46.0,shelling,93637,PROC,0101000020E610000012DDB3AED10D5EC06DFA79741F854240,POINT (-120.215923 37.04002243),37.04002243,-120.215923 +18666 E. Highway 120,San Joaquin,Ripon,"A.D.P. DePalma Farms, Inc.",1.0,almond,CA,almond,47.0,shelling,95366,PROC,0101000020E6100000AAD216D7F8475EC0058A58C4B0E34240,POINT (-121.124563 37.778832),37.778832,-121.124563 +19424 Rd 13,Madera,Chowchilla,"Zinke Orchards, Inc.",1.0,almond,CA,almond,48.0,shelling,93610,PROC,0101000020E6100000CE6E2D93E1135EC01D3C34A80D844240,POINT (-120.310643 37.03166678),37.03166678,-120.310643 +20001 McHenry Ave,San Joaquin,Escalon,"Naraghi Farms, LLC",1.0,almond,CA,almond,49.0,shelling,95320,PROC,0101000020E610000048A3A76DE83F5EC01EA44C0FAFE34240,POINT (-120.9985613 37.7787799),37.7787799,-120.9985613 +2020 Esplanade,Butte,Chico,Chico Nut Company,1.0,almond,CA,almond,50.0,shelling,95926,PROC,0101000020E61000001C8645FB8E765EC0D305065ACBDF4340,POINT (-121.8524769 39.7483933),39.7483933,-121.8524769 +20282 Road 21,San Joaquin,Madera,D.V. Enterprises & Co.,1.0,almond,CA,almond,51.0,shelling,95209,PROC,0101000020E61000006B9BE27151565EC093A9825149034340,POINT (-121.348721 38.025675),38.025675,-121.348721 +21275 Simpson Road,Tehama,Corning,California Almond Packers & Exporters Inc.,1.0,almond,CA,almond,52.0,shelling,96021,PROC,0101000020E6100000F1E6BA3A918F5EC0FA8746DA3AFA4340,POINT (-122.2432391 39.95492104),39.95492104,-122.2432391 +21490 Ortigalita Rd,Merced,Los Banos,"RPAC, LLC",1.0,almond,CA,almond,53.0,shelling,93635,PROC,0101000020E610000008951348E4375EC00937B62ACB7D4240,POINT (-120.8733082 36.98276266),36.98276266,-120.8733082 +21888 Ave 14,Madera,Madera,"El Dorado Almonds, LLC",1.0,almond,CA,almond,54.0,shelling,93637,PROC,0101000020E6100000FE8EF2DD77095EC064C8D203F6794240,POINT (-120.1479411 36.95282028),36.95282028,-120.1479411 +23073 S. Frederick Rd.,San Joaquin,Ripon,"Golden Gate Nuts, Inc.",1.0,almond,CA,almond,55.0,shelling,95366,PROC,0101000020E610000043EED8BEB64A5EC0182632F7B9DF4240,POINT (-121.1674039 37.74786272),37.74786272,-121.1674039 +"23986 W Whitesbridge Ave,",Fresno,Kerman,Holland Nut Co.,1.0,almond,CA,almond,56.0,shelling,93630,PROC,0101000020E6100000894567F4FE0D5EC05BCA9EA97C5E4240,POINT (-120.2186862 36.7381794),36.7381794,-120.2186862 +240 Bunker Avenue,Stanislaus,Modesto,Wholesome Nut Company,1.0,almond,CA,almond,57.0,shelling,95351,PROC,0101000020E610000026AB22DC643F5EC0C0D8948EE6CF4240,POINT (-120.990531 37.62422354),37.62422354,-120.990531 +24341 Ave 14,Madera,Madera,Bapu Almond Co. Inc.,1.0,almond,CA,almond,58.0,shelling,93637,PROC,0101000020E61000000BCF4BC5C6065EC0C8AAEF99F8794240,POINT (-120.105882 36.95289921),36.95289921,-120.105882 +2454 E. Prestwick Ave.,Fresno,Fresno,"Verve Green, Inc.",1.0,almond,CA,almond,59.0,shelling,93730,PROC,0101000020E610000040B73C7B53EF5DC05F622CD32F724240,POINT (-119.7394703 36.8920845),36.8920845,-119.7394703 +26454 Avenue 128,Tulare,Portervile,RPC Packing Inc.,1.0,almond,CA,almond,60.0,shelling,93257,PROC,0101000020E61000005AA0DD21C5C65DC0C5877E12440A4240,POINT (-119.105782 36.0802024),36.0802024,-119.105782 +26639 Jones Rd,San Joaquin,Escalon,Roche Brothers International Family Nut Co.,1.0,almond,CA,almond,61.0,shelling,95320,PROC,0101000020E61000006D37C137CD3E5EC0B9BF40312EE34240,POINT (-120.9812755 37.77484718),37.77484718,-120.9812755 +27052 East Highway 120,San Joaquin,Escalon,Paddack Hulling & Shelling,1.0,almond,CA,almond,62.0,shelling,95320,PROC,0101000020E6100000E5637781923E5EC077A94BA5A3E54240,POINT (-120.977692 37.79405657),37.79405657,-120.977692 +27421 Avenue 12,Madera,Madera,Sun-Beam Almond Co.,1.0,almond,CA,almond,63.0,shelling,93637,PROC,0101000020E6100000FA85B24B2F035EC06781346B42764240,POINT (-120.0497617 36.92390194),36.92390194,-120.0497617 +2801 Lassiter Ln,Stanislaus,Turlock,Big Tree Organic Farms,1.0,almond,CA,almond,64.0,shelling,95380,PROC,0101000020E6100000FBF664B444385EC030EEED333ABE4240,POINT (-120.8791934 37.48615121),37.48615121,-120.8791934 +2900 Airport Dr.,Madera,Madera,The Almond Company,1.0,almond,CA,almond,65.0,shelling,93637,PROC,0101000020E6100000C0E72C58CF065EC04E0689E5FD7E4240,POINT (-120.1064053 36.99212331),36.99212331,-120.1064053 +"2909 Coffee Rd., Ste. 12B",Stanislaus,Modesto,PNC,1.0,almond,CA,almond,66.0,shelling,95355,PROC,0101000020E61000000B5751CD763E5EC0760381A525D74240,POINT (-120.9760011 37.68083638),37.68083638,-120.9760011 +2917 East Shepherd Ave.,Fresno,Clovis,"P-R Farms, Inc.",1.0,almond,CA,almond,67.0,shelling,93619,PROC,0101000020E6100000BAA3FFE5DAEE5DC075DDA51EB36E4240,POINT (-119.7321105 36.8648413),36.8648413,-119.7321105 +3006 Yosemite Blvd,Stanislaus,Modesto,Quality Nut Company,1.0,almond,CA,almond,68.0,shelling,95354,PROC,0101000020E61000007212EFA5153C5EC03D5B3086ACD14240,POINT (-120.9388213 37.63807752),37.63807752,-120.9388213 +3068 Chico Ave.,Butte,Chico,Vanella Farms,1.0,almond,CA,almond,69.0,shelling,95928,PROC,0101000020E61000000ADAE4F049785EC07C18101082D94340,POINT (-121.879513 39.6992817),39.6992817,-121.879513 +3190 Highway 45,Glenn,Glenn,"Riverwest Processing, Inc.",1.0,almond,CA,almond,70.0,shelling,95943,PROC,0101000020E6100000954330B374805EC0B266438252D14340,POINT (-122.0071228 39.63533047),39.63533047,-122.0071228 +31995 S. Chrisman Rd.,San Joaquin,Tracy,"Crown Nut Company, Inc.",1.0,almond,CA,almond,71.0,shelling,95304,PROC,0101000020E61000002354049376595EC0CAE471A4F5D44240,POINT (-121.3978622 37.66374641),37.66374641,-121.3978622 +320 E South St,Glenn,Orland,Baldwin Minkler Farms,1.0,almond,CA,almond,72.0,shelling,95963,PROC,0101000020E61000007D76C075458B5EC087E7BEFF83DE4340,POINT (-122.1761145 39.73840329),39.73840329,-122.1761145 +32331 Famoso Rd.,Kern,McFarland,"Famoso Nut Company, LLC",1.0,almond,CA,almond,73.0,shelling,93250,PROC,0101000020E6100000B2C92B2169CD5DC0DF4CD04F06CD4140,POINT (-119.2095416 35.60175512),35.60175512,-119.2095416 +3242 North Avenue,Stanislaus,Modesto,BL Nut Company,1.0,almond,CA,almond,74.0,shelling,95358,PROC,0101000020E61000008CC0B398B3435EC038350A2858D64240,POINT (-121.0578367 37.67456532),37.67456532,-121.0578367 +3242 S. Carpenter Road,Stanislaus,Turlock,"Valley Harvest Nut Co., Inc.",1.0,almond,CA,almond,75.0,shelling,95358,PROC,0101000020E61000002D358CCCED415EC044CBD31C4DCB4240,POINT (-121.0301391 37.58829079),37.58829079,-121.0301391 +3443 Montpellier Rd,Stanislaus,Hickman,"Rolling Hills Nut Company, Inc.",1.0,almond,CA,almond,76.0,shelling,95323,PROC,0101000020E6100000136635B8082F5EC0F3730137A4C84240,POINT (-120.7349072 37.56751144),37.56751144,-120.7349072 +3500 Shiells Rd.,Stanislaus,Newman,"Stewart & Jasper Marketing, Inc.",1.0,almond,CA,almond,77.0,shelling,95360,PROC,0101000020E61000000EE7D0D8CD445EC0D122FC07E8A64240,POINT (-121.0750639 37.30395603),37.30395603,-121.0750639 +"3611 West Beechwood, Suite 101",Fresno,Fresno,"Panoche Creek Packing, Inc.",1.0,almond,CA,almond,78.0,shelling,93711,PROC,0101000020E6100000931ADA00ECF65DC038BF61A2416B4240,POINT (-119.8581545 36.8379405),36.8379405,-119.8581545 +365 Ruggieri Way,Colusa,Williams,Vann Family Orchards,1.0,almond,CA,almond,79.0,shelling,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +4315 E. Childs Avenue,Merced,Merced,Central Valley Processing,1.0,almond,CA,almond,80.0,shelling,95341,PROC,0101000020E610000097546D37411A5EC071F35BAEDDA44240,POINT (-120.4102305 37.28801517),37.28801517,-120.4102305 +43940 W. North Ave.,Fresno,Firebaugh,"Silver Creek Almond Co., Inc.",1.0,almond,CA,almond,81.0,shelling,93622,PROC,0101000020E610000054E3A59BC4255EC0CB8DD8DDF2584240,POINT (-120.590125 36.6949117),36.6949117,-120.590125 +44474 West Nees Avenue,Fresno,Firebaugh,"Oro Loma Ranch, LLC",1.0,almond,CA,almond,82.0,shelling,93622,PROC,0101000020E61000006C4084B8F2255EC018BC9E9E2D6D4240,POINT (-120.5929395 36.8529547),36.8529547,-120.5929395 +4512 North Ave,Stanislaus,Modesto,Beckner Ranches,1.0,almond,CA,almond,83.0,shelling,95358,PROC,0101000020E6100000055262D7F6445EC0716BDADE51D64240,POINT (-121.077566 37.67437349),37.67437349,-121.077566 +500 North F Street,Kern,Kern,"SunnyGem, LLC",1.0,almond,CA,almond,84.0,shelling,93280,PROC,0101000020E6100000192202695AD55DC075CBCCD43DCC4140,POINT (-119.3336432 35.59563694),35.59563694,-119.3336432 +5043 N Montpelier Rd,Stanislaus,Denair,Monte Vista Farming Company,1.0,almond,CA,almond,85.0,shelling,95316,PROC,0101000020E610000059AD026B8B2D5EC0648918C025C44240,POINT (-120.7116344 37.53240205),37.53240205,-120.7116344 +5166 S. Sperry Rd.,Stanislaus,Denair,California Nut Company,1.0,almond,CA,almond,86.0,shelling,95316,PROC,0101000020E61000007D03931B45335EC009D2B5C404C84240,POINT (-120.801093 37.56264552),37.56264552,-120.801093 +518 El Roya Ave.,Stanislaus,Modesto,"California Gold Almonds, LLC",1.0,almond,CA,almond,87.0,shelling,95354,PROC,0101000020E610000063038EA9603C5EC08A7460B509D14240,POINT (-120.9433998 37.63310878),37.63310878,-120.9433998 +5600 Norris Road,Kern,Bakersfield,JSS Almonds,1.0,almond,CA,almond,88.0,shelling,93308,PROC,0101000020E6100000D580F7440DC45DC092AC6818E3B54140,POINT (-119.0633099 35.4209929),35.4209929,-119.0633099 +6183 Reddick Rd,Solano,Dixon,Rotteveel Orchards,1.0,almond,CA,almond,89.0,shelling,95620,PROC,0101000020E6100000B85043658D765EC067D13B15703A4340,POINT (-121.8523801 38.4565455),38.4565455,-121.8523801 +6303 Beckwith Road,Stanislaus,Modesto,"Twin Commodities, Inc.",1.0,almond,CA,almond,90.0,shelling,95358,PROC,0101000020E61000001EF175630B475EC04F43AF9A42D74240,POINT (-121.1100701 37.6817201),37.6817201,-121.1100701 +644 Railroad AVe.,Merced,Atwater,Valley Pride Ag Company,1.0,almond,CA,almond,91.0,shelling,95301,PROC,0101000020E610000042356FE6A1265EC033DBBA40EEAB4240,POINT (-120.6036316 37.3432084),37.3432084,-120.6036316 +6543 Vivian Road,Stanislaus,Modesto,"Athwal Almonds, Inc.",1.0,almond,CA,almond,92.0,shelling,95358,PROC,0101000020E6100000EB43CD461D435EC04FBBEBAEE4C44240,POINT (-121.0486619 37.53822886),37.53822886,-121.0486619 +6677 Hardaway Rd.,San Joaquin,Stockton,Star Nut Co.,1.0,almond,CA,almond,93.0,shelling,95215,PROC,0101000020E6100000FD46E0B4054E5EC01D9BB20D3B004340,POINT (-121.2190983 38.00180217),38.00180217,-121.2190983 +6914 Rd 160,Tulare,Earlimart,"Treehouse California Almonds, LLC",1.0,almond,CA,almond,94.0,shelling,93219,PROC,0101000020E6100000FF25A94CB1CD5DC03D6787CF08F54140,POINT (-119.2139465 35.91433138),35.91433138,-119.2139465 +7030 County Road 25,Glenn,Orland,Baugher Ranch Organics,1.0,almond,CA,almond,95.0,shelling,95963,PROC,0101000020E61000005C920376358C5EC0BE4C142175DF4340,POINT (-122.190763 39.745762),39.745762,-122.190763 +709 Dutton Street,Yolo,Winters,Mariani Nut Company,1.0,almond,CA,almond,96.0,shelling,95694,PROC,0101000020E6100000EC5113D8F77D5EC0DAAE8EEB78434340,POINT (-121.9682522 38.52712769),38.52712769,-121.9682522 +7418 County Road 24,Glenn,Orland,North Valley Nut,1.0,almond,CA,almond,97.0,shelling,95963,PROC,0101000020E6100000E1174D1D1A865EC01116789BF5DA4340,POINT (-122.0953439 39.71062034),39.71062034,-122.0953439 +850 Commerce,Madera,Madera,"Sierra Valley Almonds, LLC",1.0,almond,CA,almond,98.0,shelling,93637,PROC,0101000020E610000007F5882CAD055EC08AC91B60E6784240,POINT (-120.0886947 36.9445305),36.9445305,-120.0886947 +8618 E Whitmore Ave,Stanislaus,Hughson,California Grown Nut Company,1.0,almond,CA,almond,99.0,shelling,95326,PROC,0101000020E61000001814BCD77F355EC0756EE2FD1BCC4240,POINT (-120.8359279 37.59460424),37.59460424,-120.8359279 +862 Almond Avenue,Colusa,Arbuckle,D & K Orchards,1.0,almond,CA,almond,100.0,shelling,95912,PROC,0101000020E6100000C28476F379845EC049DD8CA220804340,POINT (-122.0699433 39.00099594),39.00099594,-122.0699433 +8800 South Minturn Road,Merced,LeGrand,Minturn Nut Company,1.0,almond,CA,almond,101.0,shelling,95333,PROC,0101000020E6100000E025DD3B8F115EC0B26066C8C6944240,POINT (-120.2743673 37.16231637),37.16231637,-120.2743673 +9441 W. Butte Rd.,Sutter,Live Oak,"Tarke Farming, Inc.",1.0,almond,CA,almond,102.0,shelling,95953,PROC,0101000020E6100000975A4AF14C775EC02C0339EE35A04340,POINT (-121.8640712 39.25164583),39.25164583,-121.8640712 +9843 Cox Rd,Stanislaus,Patterson,Del Mar Farms,1.0,almond,CA,almond,103.0,shelling,95363,PROC,0101000020E61000001B97169A904A5EC012EC4B78BAC64240,POINT (-121.1650758 37.55256561),37.55256561,-121.1650758 +988 Crane Canyon Rd,Kern,Lebec,Tejon Ranch Company,1.0,almond,CA,almond,104.0,shelling,93243,PROC,0101000020E61000009E735C32B3B65DC023AF5ADB8C694140,POINT (-118.8546873 34.82461111),34.82461111,-118.8546873 +3250 Camino Del Sol,Ventura,Oxnard,olde thompson inc,1.0,dehydrator,CA,spice vegetables,292.0,dehydrator,93030,PROC,0101000020E6100000F4B2DC88DDC85DC0EF03EB93371A4140,POINT (-119.1385214 34.2048211),34.2048211,-119.1385214 +9301 Lacey Blvd,Kings,Hanford,olam spices and vegetable ingredients,1.0,dehydrator,CA,spice vegetables,293.0,dehydrator,93230,PROC,0101000020E61000003A652431F7E75DC01BE1A3B4ED294240,POINT (-119.6244624 36.3275667),36.3275667,-119.6244624 +1445 Nebraska Ave,Fresno,Selma,Sun Maid Growers,1.0,dehydrator,CA,grape,294.0,dehydrator,93662,PROC,0101000020E610000037AA2E3B9FE65DC0A87F5A56AB474240,POINT (-119.6034687 36.5599163),36.5599163,-119.6034687 +2028 S 3rd St,Fresno,Fresno,Valley Fig Growers,1.0,dehydrator,CA,fig,295.0,dehydrator,93702,PROC,0101000020E61000000D99E1F54FF15DC001C11C3D7E5C4240,POINT (-119.7705054 36.7226025),36.7226025,-119.7705054 +47641 W Nees Ave,Fresno,Firebaugh,olam spices and vegetable ingredients,1.0,dehydrator,CA,spice vegetables,296.0,dehydrator,93622,PROC,0101000020E6100000B31078BB39295EC01004C8D0B16C4240,POINT (-120.6441487 36.8491765),36.8491765,-120.6441487 +28390 Ave 12,Madera,Madera,sunsweet dryers,1.0,dehydrator,CA,prune date fruit nut,297.0,dehydrator,93637,PROC,0101000020E610000036DABB500A025EC01E6B460639764240,POINT (-120.0318796 36.92361525),36.92361525,-120.0318796 +1350 CA 152,Santa Clara,Gilroy,Gilroy foods,1.0,dehydrator,CA,garlic onion capsicums,298.0,dehydrator,95020,PROC,0101000020E6100000AA51FEA490625EC031C1DB4965804240,POINT (-121.5400784 37.00309108),37.00309108,-121.5400784 +3324 Orestimba Rd,Stanislaus,Newman,VSP products valleysun,1.0,dehydrator,CA,tomato,299.0,dehydrator,95360,PROC,0101000020E6100000E247EB5E5D455EC00D633D7B4FA84240,POINT (-121.0838239 37.31492558),37.31492558,-121.0838239 +9984 Walnut Ave,Merced,Livingston,sensient natural ingredients,1.0,dehydrator,CA,garlic onion capsicums vegetables,300.0,dehydrator,95334,PROC,0101000020E610000082035ABA822E5EC02BC0779B37B04240,POINT (-120.726729 37.376697),37.376697,-120.726729 +151 S Walnut Rd,Stanislaus,Turlock,sensient natural ingredients,1.0,dehydrator,CA,garlic onion capsicums vegetables,301.0,dehydrator,95380,PROC,0101000020E6100000FD6DAA49CB375EC0F6D2D2E4FBBE4240,POINT (-120.8717827 37.49206219),37.49206219,-120.8717827 +2757 Rockville Rd,Solano,Fairfield,Culinary Farms,1.0,dehydrator,CA,tomatoes,302.0,dehydrator,94534,PROC,0101000020E6100000F0BCF9B2D9855EC08F1436A8A21F4340,POINT (-122.0914123 38.2471514),38.2471514,-122.0914123 +500 Crocker Dr,Solano,Vacaville,Mariani Packing,1.0,dehydrator,CA,fruit,303.0,dehydrator,95688,PROC,0101000020E61000006F5DD669C97C5EC035DC3642F5334340,POINT (-121.9497933 38.4059222),38.4059222,-121.9497933 +29485 Co Rd 27,Yolo,Winters,sunsweet dryers,1.0,dehydrator,CA,prune date fruit nut,304.0,dehydrator,95694,PROC,0101000020E610000007F01648507E5EC0D177B7B244434340,POINT (-121.97365 38.525534),38.525534,-121.97365 +1520 Terminal St,Yolo,West Sacramento,California Fire Roasted LLC,1.0,dehydrator,CA,tomato,305.0,dehydrator,95691,PROC,0101000020E6100000A1E76047AD625EC0B7BCCD76E0484340,POINT (-121.5418261 38.5693501),38.5693501,-121.5418261 +1244 E Beamer St,Yolo,Woodland,Culinary Farms,1.0,dehydrator,CA,tomatoes,306.0,dehydrator,95776,PROC,0101000020E61000004C50C3B7B0705EC0BCA24A8391574340,POINT (-121.760786 38.6841282),38.6841282,-121.760786 +901 N Walton Ave,Sutter,Yuba City,sunsweet growers,1.0,dehydrator,CA,prune date,307.0,dehydrator,95993,PROC,0101000020E61000001533672211695EC0D2EF6F8EC2914340,POINT (-121.6416708 39.13874989),39.13874989,-121.6416708 +6229 Myers Road,Colusa,Williams,olam spices and vegetable ingredients,1.0,dehydrator,CA,spice vegetables,308.0,dehydrator,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +1500 Eager Rd,Sutter,Live Oak,wilbur packing co,1.0,dehydrator,CA,prune,309.0,dehydrator,95953,PROC,0101000020E610000051BB5F05F8685EC0168B3ACE48984340,POINT (-121.640138 39.18972185),39.18972185,-121.640138 +7207 Moon Bend Rd,Colusa,Colusa,sunsweet dryers,1.0,dehydrator,CA,prune date fruit nut,310.0,dehydrator,95932,PROC,0101000020E610000022EF0B9EF87F5EC039C29AB105994340,POINT (-121.9995494 39.19548626),39.19548626,-121.9995494 +9301 9399 Larkin Rd,Sutter,Live Oak,sunsweet dryers,1.0,dehydrator,CA,prune date fruit nut,311.0,dehydrator,95953,PROC,0101000020E6100000E97E4E417E6C5EC0FC89CA8635A14340,POINT (-121.695206 39.259446),39.259446,-121.695206 +1900 Highway 99,Butte,Gridley,stapleton spense packing,1.0,dehydrator,CA,plums prunes,312.0,dehydrator,95948,PROC,0101000020E610000068565B56066C5EC09688015CDAAF4340,POINT (-121.6878868 39.3738513),39.3738513,-121.6878868 +7714 Co Rd 9,Glenn,Orland,sunsweet dryers,1.0,dehydrator,CA,prune date fruit nut,313.0,dehydrator,95963,PROC,0101000020E61000005C920376358C5EC0BE4C142175DF4340,POINT (-122.190763 39.745762),39.745762,-122.190763 +12021 Ave 328,Tulare,Visalia,Elbow Gin Inc,1.0,gin,CA,cotton,417.0,gin,93291,PROC,0101000020E61000002E84E6841AD45DC0B1702FBC54314240,POINT (-119.3141186 36.38539841),36.38539841,-119.3141186 +12095 2nd Ave,Kings,Hanford,County Line Gin Inc,1.0,gin,CA,cotton,418.0,gin,93230,PROC,0101000020E61000001CD6AFCF77DF5DC0A8F63306E7254240,POINT (-119.4916877 36.2961128),36.2961128,-119.4916877 +17053 Shafter Ave,Kern,Shafter,SJV Quality Cotton,1.0,gin,CA,cotton,419.0,gin,93263,PROC,0101000020E6100000F2B1BB40C9D15DC0751FC2F0F8C34140,POINT (-119.2779085 35.53103456),35.53103456,-119.2779085 +19813 Madison Ave,Kings,Stratford,Stratford Growers Inc,1.0,gin,CA,cotton,420.0,gin,93266,PROC,0101000020E61000004C2FD6DCF6F35DC037A5BC5642154240,POINT (-119.8119423 36.166087),36.166087,-119.8119423 +20509 Elgin Ave,Kings,Lemoore,West Island CoOp Gin,1.0,gin,CA,cotton,421.0,gin,93245,PROC,0101000020E6100000A3A025D9B4F45DC04BD933958F304240,POINT (-119.8235381 36.3793818),36.3793818,-119.8235381 +2531 Wasco Way,Kern,Buttonwillow,Farmers CoOp Gin,1.0,gin,CA,cotton,422.0,gin,93206,PROC,0101000020E610000090323DBCC2DC5DC0F3F99B2FFAB24140,POINT (-119.4493857 35.39826007000001),35.39826007000001,-119.4493857 +27519 Jackson Ave,Kings,Lemoore,Westhaven Cotton Co,1.0,gin,CA,cotton,423.0,gin,93245,PROC,0101000020E61000008C20DFEFE1FC5DC0E9D7310972204240,POINT (-119.9512901 36.2534801),36.2534801,-119.9512901 +33370 W Nebraska Ave,Fresno,Cantua Creek,Pacific Pima Gin Inc,1.0,gin,CA,cotton,424.0,gin,93608,PROC,0101000020E6100000EC53E98255195EC00DECE703B8474240,POINT (-120.3958442 36.5603032),36.5603032,-120.3958442 +40109 W Bullard Ave,Fresno,Firebaugh,Broadview Coop Gin,1.0,gin,CA,cotton,425.0,gin,93622,PROC,0101000020E61000002BA798DED9205EC0AF1B00BBE4684240,POINT (-120.5132977 36.8194803),36.8194803,-120.5132977 +43939 W. North Ave.,Fresno,Firebaugh,Silver Creek Gin,1.0,gin,CA,cotton,426.0,gin,93622,PROC,0101000020E61000006741CD3571255EC0F6E0496650584240,POINT (-120.5850348 36.68995360000001),36.68995360000001,-120.5850348 +626 W Cartmill Ave,Tulare,Tulare,Mid Valley Cotton Growers Inc,1.0,gin,CA,cotton,427.0,gin,93274,PROC,0101000020E610000009F42E83D6D65DC0F9C2BF63D31E4240,POINT (-119.3568428 36.2408261),36.2408261,-119.3568428 +7870 Hutchins Rd,Merced,Dos Palos,Dos Palos CoOp Gin Inc,1.0,gin,CA,cotton,428.0,gin,93620,PROC,0101000020E6100000D1FF177467285EC0E40DD539AB8A4240,POINT (-120.6313143 37.0833504),37.0833504,-120.6313143 +8587 S Contra Costa Rd,Fresno,Tranquillity,Westside Farmers CoOp,1.0,gin,CA,cotton,429.0,gin,93668,PROC,0101000020E61000008DC9874531105EC0F6A22C32F04D4240,POINT (-120.2530073 36.6088927),36.6088927,-120.2530073 +860 Corn Camp Rd,Kern,Buttonwillow,Buttonwillow Ginning Co,1.0,gin,CA,cotton,430.0,gin,93206,PROC,0101000020E6100000B11DE7911AE15DC0C5DE5184D0B64140,POINT (-119.5172467 35.42823843),35.42823843,-119.5172467 +9450 Agripark Dr,Sutter,Sutter,North Valley Cotton Gin,1.0,gin,CA,cotton,431.0,gin,95982,PROC,0101000020E61000001C66C3F583725EC049C0229E70934340,POINT (-121.7893042 39.15187432),39.15187432,-121.7893042 +9759 Valpredo Road,Kern,Bakersfield,Western Farmers CoOp gin,1.0,gin,CA,cotton,432.0,gin,93313,PROC,0101000020E61000009FBCD93054C35DC0D020F422C9894140,POINT (-119.0520136 35.07645070000001),35.07645070000001,-119.0520136 +9759 Valpredo Road,Kern,Bakersfield,South Valley Gin,1.0,gin,CA,cotton,433.0,gin,93313,PROC,0101000020E61000009FBCD93054C35DC0D020F422C9894140,POINT (-119.0520136 35.07645070000001),35.07645070000001,-119.0520136 +9845 Hanford Armona Rd.,Kings,Hanford Ca. 93230,Central Valley CoOp,1.0,gin,CA,cotton,434.0,gin,0,PROC,0101000020E610000018B0E42A96E85DC0170335C618284240,POINT (-119.6341655 36.31325605),36.31325605,-119.6341655 +4309 Fruitland Ave,Los Angeles,Vernon,General Mills,1.0,mill,CA,bread,435.0,milling,90058,PROC,0101000020E61000005E66D828EB8C5DC0E91505B0B7FF4040,POINT (-118.201853 33.9977932),33.9977932,-118.201853 +23865 Ave 18,Madera,Madera,Valley GrainAzteca Milling,1.0,mill,CA,corn wheat,436.0,milling,93638,PROC,0101000020E61000001DD9A6C269075EC0F24940AF6C814240,POINT (-120.1158301 37.01112929),37.01112929,-120.1158301 +20100 Fairmead Blvd,Madera,Madera,Valley GrainAzteca Milling,1.0,mill,CA,corn wheat,437.0,milling,93638,PROC,0101000020E6100000DD578A89F2095EC081B45ABB48854240,POINT (-120.1554283 37.0412821),37.0412821,-120.1554283 +13310 Nanna's Way,Nevada,Grass Valley,Grass Valley Grains Farm,1.0,mill,CA,grains,438.0,milling,95949,PROC,0101000020E6100000348BAB25F8455EC03D8E3056E5964340,POINT (-121.0932707 39.1788738),39.1788738,-121.0932707 +7770 Rd 33,Madera,Madera,ENZO Olive Oil,1.0,olive,CA,olive,467.0,olive oil,93638,PROC,0101000020E6100000382394089EFC5DC05C6D8B53296E4240,POINT (-119.9471456 36.86063618),36.86063618,-119.9471456 +13950 Thornton Rd,San Joaquin,Lodi,Calivirgin coldani olive ranch,1.0,olive,CA,olive,468.0,olive oil,95242,PROC,0101000020E610000032906797EF585EC0AA1EBCB8850D4340,POINT (-121.3896235 38.10564336),38.10564336,-121.3896235 +455 Harter Ave,Yolo,Woodland,Boundary Bend Olives,1.0,olive,CA,olive,469.0,olive oil,95776,PROC,0101000020E6100000657506A197705EC092D332ADA8584340,POINT (-121.7592547 38.6926476),38.6926476,-121.7592547 +2675 Lone Tree Rd,Butte,Oroville,California Olive Ranch,1.0,olive,CA,olive,470.0,olive oil,95965,PROC,0101000020E6100000B81E85EBD1645EC058201F99B3AE4340,POINT (-121.5753125 39.36485590000001),39.36485590000001,-121.5753125 +5945 Co Rd 35,Glenn,Artois,California Olive Ranch,1.0,olive,CA,olive,471.0,olive oil,95913,PROC,0101000020E6100000FDDAFAE93F895EC0B247A81952DD4340,POINT (-122.144526 39.729068),39.729068,-122.144526 +717 Tehama St,Glenn,Orland,west coast products,1.0,olive,CA,olives,472.0,cannery oil,95963,PROC,0101000020E6100000DB9145F5B18C5EC085D726FCEFDF4340,POINT (-122.1983617 39.74951126),39.74951126,-122.1983617 +1367 E Lassen Ave,Butte,Chico,California Olive Ranch,1.0,olive,CA,olive,473.0,olive oil,95973,PROC,0101000020E6100000301004C8D0755EC01471DF0FE4E24340,POINT (-121.840868 39.7725849),39.7725849,-121.840868 +23377 South Ave,Tehama,Corning,California Olive Ranch,1.0,olive,CA,olive,474.0,olive oil,96021,PROC,0101000020E61000000E187F364D8A5EC092AFE343F9F34340,POINT (-122.1609627 39.90604447),39.90604447,-122.1609627 +14633 CA 33,Kern,Lost Hills,Horizon Nut Co,1.0,pistachio,CA,pistachios,475.0,shelling,93249,PROC,0101000020E6100000A592F073B2F85DC08A5ABB690AD24140,POINT (-119.8858919 35.64094278),35.64094278,-119.8858919 +26487 N Highway 99,Tulare,Tulare,Horizon Nut Co,1.0,pistachio,CA,pistachios,476.0,shelling,93274,PROC,0101000020E6100000A12E52288BD65DC018526E70DC1F4240,POINT (-119.3522435 36.24891477),36.24891477,-119.3522435 +4946 4998 N Jerrold Ave,Fresno,Firebaugh,horizon nut firebaugh,1.0,pistachio,CA,pistachios,477.0,shelling,93622,PROC,0101000020E6100000BB9C121093225EC09DD5027B4C6A4240,POINT (-120.540226 36.830459),36.830459,-120.540226 +1250 W Lathrop Rd,San Joaquin,Lathrop,california natural products,1.0,rice,CA,rice,549.0,misc,95330,PROC,0101000020E6100000A9F7544E7B515EC0428FFF9F96E94240,POINT (-121.273151 37.82490921),37.82490921,-121.273151 +1800 Terminal St,Yolo,West Sacramento,Farmers Rice Cooperative,1.0,rice,CA,rice,550.0,hulling mill,95691,PROC,0101000020E6100000E865B911BB625EC010338F577B484340,POINT (-121.5426678 38.56626410000001),38.56626410000001,-121.5426678 +351 Hanson Way,Yolo,Woodland,pgp international,1.0,rice,CA,grains rice,551.0,flour mill,95776,PROC,0101000020E61000003E09C787B46D5EC0EC1FFAA4C9564340,POINT (-121.7141437 38.6780287),38.6780287,-121.7141437 +6133 Abel Rd,Colusa,Williams,American Commodity Company ACCGWG LLC Great Western Growers,1.0,rice,CA,rice,552.0,hulling mill,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +4937 CA 45,Colusa,Colusa,Farmers Rice Cooperative,1.0,rice,CA,rice,553.0,warehouse,95932,PROC,0101000020E6100000852BFB09C2815EC0BDECCF2C26AE4340,POINT (-122.0274682 39.36054001),39.36054001,-122.0274682 +1 Comet Ln,Colusa,Maxwell,California Heritage Mills,1.0,rice,CA,rice,554.0,mill,95955,PROC,0101000020E610000067BAD7497D885EC0E08096AE60A34340,POINT (-122.132647 39.276388),39.276388,-122.132647 +10400 Billings Rd,Sutter,Live Oak,Gibbs Wild Rice,1.0,rice,CA,rice,555.0,distributer,95953,PROC,0101000020E610000035DBCB6CC66C5EC0D564BE6A02A44340,POINT (-121.6996109 39.28132376),39.28132376,-121.6996109 +126 E Main St,Colusa,Colusa,PGP International,1.0,rice,CA,rice,556.0,mill,95932,PROC,0101000020E610000008F13790E47F5EC044A212CF409B4340,POINT (-121.9983254 39.21291531),39.21291531,-121.9983254 +1603 Highway 99 W,Colusa,Arbuckle,ADM Milling Co,1.0,rice,CA,rice,557.0,mill,95912,PROC,0101000020E610000038DA71C3EF805EC0302C7FBE2D844340,POINT (-122.014634 39.032646),39.032646,-122.014634 +1620 E Kentucky Ave,Yolo,Woodland,SunFoods LLC,1.0,rice,CA,rice,558.0,distributer,95776,PROC,0101000020E61000006366FA809B6F5EC0ADB9484673584340,POINT (-121.7438662 38.6910179),38.6910179,-121.7438662 +1701 Abel Rd,Colusa,Williams,Tamaki Rice Corp,1.0,rice,CA,rice,559.0,mill,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +22540 Russell Ave,Merced,South Dos Palos,Koda Farms,1.0,rice,CA,rice,560.0,mill,93665,PROC,0101000020E6100000DA441CA1D5295EC0D51B9C25547A4240,POINT (-120.6536639 36.95569296),36.95569296,-120.6536639 +2640 Hoffman Rd,Yuba,Olivehurst,Rue and Forsman Ranc Inc,1.0,rice,CA,rice,561.0,distributer,95961,PROC,0101000020E610000089D4B48B69605EC03BCFF1340D824340,POINT (-121.506442 39.01602804),39.01602804,-121.506442 +2889 Niagara Ave,Colusa,Colusa,Colusa Rice Company,1.0,rice,CA,rice,562.0,distributer,95932,PROC,0101000020E6100000255987A3AB805EC0581AF8510D9B4340,POINT (-122.010476 39.211344),39.211344,-122.010476 +3455 Nelson Rd,Butte,Durham,Far West Rice Inc,1.0,rice,CA,rice,563.0,mill,95938,PROC,0101000020E610000075A26EB16C765EC063B6645584C64340,POINT (-121.8503841 39.5509135),39.5509135,-121.8503841 +507 Bannock St,Butte,Biggs,SunWest Foods Inc,1.0,rice,CA,rice,564.0,mill,95917,PROC,0101000020E6100000BFC980FDA16D5EC0803628507AB44340,POINT (-121.7130121 39.4099827),39.4099827,-121.7130121 +5311 Midway,Butte,Richvale,Lundberg Family Farms,1.0,rice,CA,rice,565.0,mill,95974,PROC,0101000020E610000044D554BBCB6F5EC076D6B848EBBF4340,POINT (-121.7468098 39.4993678),39.4993678,-121.7468098 +6550 Struckmeyer Rd,Colusa,Arbuckle,California Family Foods Inc,1.0,rice,CA,rice,566.0,mill,95912,PROC,0101000020E610000038DA71C3EF805EC0302C7FBE2D844340,POINT (-122.014634 39.032646),39.032646,-122.014634 +7050 Eddy Rd,Colusa,Arbuckle,Sun Valley Rice Co LLC,1.0,rice,CA,rice,567.0,mill,95912,PROC,0101000020E610000095E8764023815EC0C788E1762A7B4340,POINT (-122.0177766 38.96223341),38.96223341,-122.0177766 +7875 County Road 32 1/2,Glenn,Glenn,Rice Researchers Inc,1.0,rice,CA,rice,568.0,mill,95943,PROC,0101000020E61000005299620E82825EC001B5A4E5B8D04340,POINT (-122.039188 39.63064261),39.63064261,-122.039188 +845 Kentucky Ave,Yolo,Woodland,Pacific International Rice Mills Bung,1.0,rice,CA,rice,569.0,mill,95695,PROC,0101000020E6100000D736209D15715EC09DDBDF34D8584340,POINT (-121.7669442 38.6940981),38.6940981,-121.7669442 +8969 CA-70,Yuba,Marysville,District 10 Dryers LLC,1.0,rice,CA,rice,570.0,mill,95901,PROC,0101000020E61000006FBBD05CA75D5EC07AC7293A929B4340,POINT (-121.46334 39.2154),39.2154,-121.46334 +Old Hwy 99W,Colusa,Maxwell,Polit Farms Inc,1.0,rice,CA,rice,571.0,mill,95955,PROC,0101000020E610000067BAD7497D885EC0E08096AE60A34340,POINT (-122.132647 39.276388),39.276388,-122.132647 +26069 Rd 148,Tulare,Visalia,Bock Ranch,1.0,walnut,CA,walnut,584.0,shelling,93292,PROC,0101000020E6100000365CE49EAECF5DC07BFAA5D1A6214240,POINT (-119.245033 36.26290341),36.26290341,-119.245033 +5430 Putah Creek Rd,Solano,Winters,Dixon Ridge Farms,1.0,walnut,CA,walnut,585.0,shelling,95694,PROC,0101000020E610000069290FC1A7795EC0E7A15B5430434340,POINT (-121.9008639 38.5249124),38.5249124,-121.9008639 +1501 Eager Rd,Sutter,Live Oak,wilbur packing co,1.0,walnut,CA,walnut,586.0,shelling,95953,PROC,0101000020E61000003617C9682E6A5EC02B6BDDFE43984340,POINT (-121.6590826 39.18957506),39.18957506,-121.6590826 +3230 CA 45,Glenn,Glenn,Keyawa Orchard Inc,1.0,walnut,CA,walnut,587.0,shelling,95943,PROC,0101000020E6100000CE041E7379805EC0BE8D495630D24340,POINT (-122.0074127 39.64210013),39.64210013,-122.0074127 +10695 Decker Ave,Tehama,Los Molinos,Crain Walnut Shelling,1.0,walnut,CA,walnut,588.0,shelling,96055,PROC,0101000020E61000008196AE609B875EC062305E77E30C4440,POINT (-122.1188585 40.10069172),40.10069172,-122.1188585 +1026 Sheridan Avenue,Butte,Chico,Western Nut co,1.0,walnut,CA,walnut,589.0,shelling,95926,PROC,0101000020E61000006C0B2A0538755EC02C34C63D4CDF4340,POINT (-121.8315442 39.7445142),39.7445142,-121.8315442 +1038 Larkin Road,Butte,Gridley,Golden Pacific Farms LLC,1.0,walnut,CA,walnut,590.0,shelling,95948,PROC,0101000020E6100000D6E0229C3B6A5EC0716770A5E8AB4340,POINT (-121.6598883 39.3430373),39.3430373,-121.6598883 +10660 Bryne Avenue,Tehama,Los Molinos,C R Crain Sons Inc,1.0,walnut,CA,walnut,591.0,shelling,96055,PROC,0101000020E61000006452E8610D885EC083740C23180D4440,POINT (-122.1258168 40.1022991),40.1022991,-122.1258168 +10695 Decker Avenue,Tehama,Los Molinos,Crain Walnut Shelling,1.0,walnut,CA,walnut,592.0,shelling,96055,PROC,0101000020E61000008196AE609B875EC062305E77E30C4440,POINT (-122.1188585 40.10069172),40.10069172,-122.1188585 +10830 Yosemite Blvd.,Stanislaus,Waterford,Frazier Nut Farms Inc,1.0,walnut,CA,walnut,593.0,shelling,95386,PROC,0101000020E610000090AB47D0CE325EC0F0F98292D9D04240,POINT (-120.7938729 37.63163978),37.63163978,-120.7938729 +112 Sandy Lane,Contra Costa,Oakley,Continente Nut LLC,1.0,walnut,CA,walnut,594.0,shelling,94561,PROC,0101000020E610000021C3CF24D66F5EC0C11259B535004340,POINT (-121.7474453 38.00163905),38.00163905,-121.7474453 +1190 Buena Vista Road,San Benito,Hollister,Gibson Farms,1.0,walnut,CA,walnut,595.0,shelling,95023,PROC,0101000020E61000008C6A6C0ABF5A5EC0D40E7F4DD66D4240,POINT (-121.4179102 36.8581025),36.8581025,-121.4179102 +12022 E. Comstock Rd.,San Joaquin,Stockton,Avanti Nut Co,1.0,walnut,CA,walnut,596.0,shelling,95215,PROC,0101000020E6100000B405DF8FB64A5EC0B570B43EC0044340,POINT (-121.1673927 38.03711685),38.03711685,-121.1673927 +1240 E. Caldwell Avenue,Tulare,Visalia,Atlas world food Ag,1.0,walnut,CA,walnut,597.0,shelling,93292,PROC,0101000020E610000090AE8850DBD15DC0DBABEA4031264240,POINT (-119.2790109 36.2983781),36.2983781,-119.2790109 +126 4th Street,Merced,Gustine,Pusateri Nut Company,1.0,walnut,CA,walnut,598.0,shelling,95322,PROC,0101000020E61000006F8C5363F83F5EC00296432842A14240,POINT (-120.9995354 37.25983146),37.25983146,-120.9995354 +14290 E Comstock Rd,San Joaquin,Linden,Anderson Barngrover Ranch Co Inc,1.0,walnut,CA,walnut,599.0,shelling,95236,PROC,0101000020E610000050786407F0485EC035A1830DD3044340,POINT (-121.1396502 38.03769082),38.03769082,-121.1396502 +1500 Reed Rd.,Sutter,Yuba City,Sutter Foods,1.0,walnut,CA,walnut,600.0,shelling,95993,PROC,0101000020E61000000953944BE3685EC09B515680AD8A4340,POINT (-121.638873 39.08341984),39.08341984,-121.638873 +1550 Industrial Drive,San Joaquin,Stockton,Pearl Crop Inc,1.0,walnut,CA,walnut,601.0,shelling,95206,PROC,0101000020E6100000C2E567D949505EC0517DCE7A84F44240,POINT (-121.2545074 37.91029296),37.91029296,-121.2545074 +1555 Warren Road,San Joaquin,Ripon,almond ace packing inc,1.0,walnut,CA,walnut,602.0,processor,95366,PROC,0101000020E610000094D920938C485EC0D12E5351C4E04240,POINT (-121.13358 37.75599114),37.75599114,-121.13358 +1590 Little Orchard Street,Santa Clara,San Jose,Santa Clara Nut Company,1.0,walnut,CA,walnut,603.0,shelling,95110,PROC,0101000020E61000007F726FD9FC775EC0531FED24C7A74240,POINT (-121.8748077 37.3107649),37.3107649,-121.8748077 +16200 County Road 87,Yolo,Esparto,Haag Farm,1.0,walnut,CA,walnut,604.0,shelling,95627,PROC,0101000020E6100000F7692629FA805EC0AD70892B80594340,POINT (-122.0152686 38.69922394),38.69922394,-122.0152686 +1640 State Highway 45,Glenn,Glenn,Borges of California,1.0,walnut,CA,walnut,605.0,shelling,95943,PROC,0101000020E610000081785DBF60835EC04ED1915CFECB4340,POINT (-122.05278 39.5937),39.5937,-122.05278 +1640 State Highway 45,Glenn,Glenn,Carriere Family Farms,1.0,walnut,CA,walnut,606.0,shelling,95943,PROC,0101000020E610000081785DBF60835EC04ED1915CFECB4340,POINT (-122.05278 39.5937),39.5937,-122.05278 +17071 E. Baker Road,San Joaquin,Linden,Ferrari Farms Inc,1.0,walnut,CA,walnut,607.0,shelling,95236,PROC,0101000020E61000002878AFFFDF465EC0179E346052044340,POINT (-121.1074218 38.03376391),38.03376391,-121.1074218 +1760 Main Street,San Joaquin,Escalon,The DeRuosi Group,1.0,walnut,CA,walnut,608.0,shelling,95320,PROC,0101000020E6100000D580F7448D3F5EC02932639FBAE54240,POINT (-120.9929974 37.79475777),37.79475777,-120.9929974 +18400 S. Enterprise Road,San Joaquin,Escalon,GoldRiver Orchards,1.0,walnut,CA,walnut,609.0,shelling,95320,PROC,0101000020E610000013D4F02DAC3B5EC0C1CD3D7FB5E54240,POINT (-120.932384 37.79460135),37.79460135,-120.932384 +1900 Feather River Blvd.,Yuba,Olivehurst,ShoEi Foods USA Inc,1.0,walnut,CA,walnut,610.0,shelling,95961,PROC,0101000020E61000006EC1525DC0645EC03BBEC5DC987F4340,POINT (-121.574241 38.99685249),38.99685249,-121.574241 +200 Wilkie Avenue,Sutter,Yuba City,California Valley Nut Co,1.0,walnut,CA,walnut,611.0,shelling,95991,PROC,0101000020E6100000890C063296665EC017929BFA237E4340,POINT (-121.6029172 38.98547299),38.98547299,-121.6029172 +2065 Geer Road,Stanislaus,Hughson,Mid Valley Nut Company,1.0,walnut,CA,walnut,612.0,shelling,95326,PROC,0101000020E6100000B950F9D7F2365EC05A84622B68CC4240,POINT (-120.858572 37.596929),37.596929,-120.858572 +2097 Beyer Lane,San Joaquin,Stockton,OG Nut Company,1.0,walnut,CA,walnut,613.0,shelling,95215,PROC,0101000020E6100000521F926BD44E5EC0C8DA198528FE4240,POINT (-121.2317151 37.98561157),37.98561157,-121.2317151 +2106 E. Main Street,Tulare,Visalia,Nutri Nut,1.0,walnut,CA,walnut,614.0,shelling,93292,PROC,0101000020E6100000D0DECFDF3AD15DC0614150244E2A4240,POINT (-119.2692184 36.3305097),36.3305097,-119.2692184 +21161 Ave. 160,Tulare,Porterville,RPC Packing Inc,1.0,walnut,CA,walnut,615.0,shelling,93257,PROC,0101000020E61000005AA0DD21C5C65DC0C5877E12440A4240,POINT (-119.105782 36.0802024),36.0802024,-119.105782 +2288 Geer Road,Stanislaus,Hughson,Grower Direct Nut Company,1.0,walnut,CA,walnut,616.0,shelling,95326,PROC,0101000020E6100000B950F9D7F2365EC05A84622B68CC4240,POINT (-120.858572 37.596929),37.596929,-120.858572 +240 Bunker Avenue,Stanislaus,Modesto,Wholesome Nut Company Inc,1.0,walnut,CA,walnut,617.0,shelling,95351,PROC,0101000020E610000026AB22DC643F5EC0C0D8948EE6CF4240,POINT (-120.990531 37.62422354),37.62422354,-120.990531 +24490 Joseph Avenue,Tehama,Los Molinos,California Walnut Co inc,1.0,walnut,CA,walnut,618.0,shelling,96055,PROC,0101000020E61000003711A22108885EC0887258D06A0F4440,POINT (-122.1254963 40.1204472),40.1204472,-122.1254963 +2644 Hegan Ln,Butte,Chico,Acme Walnut,1.0,walnut,CA,walnut,619.0,shelling,95928,PROC,0101000020E61000005EE7F05A53745EC03684190923DA4340,POINT (-121.8175876 39.7041942),39.7041942,-121.8175876 +26829 Road 156,Tulare,Visalia,Greggory Lamar Hart,1.0,walnut,CA,walnut,620.0,shelling,93292,PROC,0101000020E61000009B70541369CE5DC0C4739DE3AF234240,POINT (-119.2251633 36.27880521),36.27880521,-119.2251633 +29241 W. Cottonwood Road,Merced,Gustine,John B Sanfilippo Son,1.0,walnut,CA,walnut,621.0,shelling,95322,PROC,0101000020E6100000106AD0E16B415EC0A420B22705984240,POINT (-121.0222096 37.18765732),37.18765732,-121.0222096 +3050 S Hunt Rd,Merced,Gustine,Andersen Nut Co,1.0,walnut,CA,walnut,622.0,shelling,95322,PROC,0101000020E6100000A7CCCD37A23F5EC0A64D30F7249F4240,POINT (-120.994276 37.2433156),37.2433156,-120.994276 +3068 Chico Ave.,Butte,Chico,Vanella Farms,1.0,walnut,CA,walnut,623.0,processor,95928,PROC,0101000020E61000000ADAE4F049785EC07C18101082D94340,POINT (-121.879513 39.6992817),39.6992817,-121.879513 +3100 Zinfandel Rd.,Sacramento,Rancho Cordova,Agrocal Corp,1.0,walnut,CA,walnut,624.0,processor,95670,PROC,0101000020E6100000CC8D339765525EC07F801895124B4340,POINT (-121.2874506 38.58650459),38.58650459,-121.2874506 +3710 Cosby Avenue,Butte,Chico,Smith Walnut Orchards,1.0,walnut,CA,walnut,625.0,shelling,95928,PROC,0101000020E6100000A3F7D73C58775EC055078A69F0D84340,POINT (-121.8647606 39.6948368),39.6948368,-121.8647606 +400 D Street,Stanislaus,Turlock,Turlock Walnut Company Inc,1.0,walnut,CA,walnut,626.0,shelling,95380,PROC,0101000020E6100000A062E64C24365EC01986B8075BBE4240,POINT (-120.8459656 37.48715302),37.48715302,-120.8459656 +40897 Road 120,Tulare,Orosi,GSF Nut Company LLC,1.0,walnut,CA,walnut,627.0,shelling,93647,PROC,0101000020E61000005A29A9B896D35DC045253B5710444240,POINT (-119.3060743 36.53174868),36.53174868,-119.3060743 +411 Orchard Road,San Benito,Hollister,Lomanto Nut Shelling,1.0,walnut,CA,walnut,628.0,shelling,95023,PROC,0101000020E6100000EC25D75E55585EC055682096CD774240,POINT (-121.3802106 36.9359615),36.9359615,-121.3802106 +4302 N. Beecher Lane,San Joaquin,Stockton,Beecher Lane Walnut,1.0,walnut,CA,walnut,629.0,shelling,95215,PROC,0101000020E61000007528F9C7B14A5EC087E26D2990014340,POINT (-121.1671009 38.01221197),38.01221197,-121.1671009 +4530 Rowles Rd,Tehama,Vina,Andersen Sons Shelling,1.0,walnut,CA,walnut,630.0,shelling,96092,PROC,0101000020E610000083B57B035D835EC03AA50F9FECF64340,POINT (-122.0525521 39.92909611),39.92909611,-122.0525521 +50 Guynn Bridge Ct.,Butte,Chico,Red Barn Walnut Co,1.0,walnut,CA,walnut,631.0,shelling,95926,PROC,0101000020E61000008457DCC9F1775EC044C18C2958DF4340,POINT (-121.8741326 39.744878),39.744878,-121.8741326 +500 N. Jack Tone Road,San Joaquin,Stockon,Morada Nut Company,1.0,walnut,CA,walnut,632.0,processor,95215,PROC,0101000020E6100000F2FD1E0684495EC01ED623268BFC4240,POINT (-121.1486831 37.97299649),37.97299649,-121.1486831 +5414 E. Floral Avenue,Fresno,Selma,Poindexter Nut Company,1.0,walnut,CA,walnut,633.0,shelling,93662,PROC,0101000020E6100000B442ECA75AEC5DC0F8C96A1DC9494240,POINT (-119.6930332 36.57645004),36.57645004,-119.6930332 +5640 River Road,Stanislaus,Oakdale,Gambini Nut Company Inc,1.0,walnut,CA,walnut,634.0,shelling,95361,PROC,0101000020E61000009C84775E4F395EC07808E3A771E34240,POINT (-120.8954693 37.776906),37.776906,-120.8954693 +6100 Wilson Landing Road,Butte,Chico,Berberian Nut Co,1.0,walnut,CA,walnut,635.0,shelling,95973,PROC,0101000020E6100000FEC5223C907E5EC0AB2924F48EE64340,POINT (-121.9775534 39.8012376),39.8012376,-121.9775534 +6215 South George Washington Blvd.,Sutter,Yuba City,Valley Dried Fruit,1.0,walnut,CA,walnut,636.0,shelling,95993,PROC,0101000020E6100000E7CB6669026B5EC004281D171B844340,POINT (-121.6720222 39.03207673),39.03207673,-121.6720222 +6413 E Keyes Rd,Stanislaus,Hughson,Alpine Pacific Nut Co,1.0,walnut,CA,walnut,637.0,shelling,95326,PROC,0101000020E61000006446D33403385EC0803DECA690C64240,POINT (-120.8751957 37.55128943),37.55128943,-120.8751957 +6677 E. Hardaway Rd.,San Joaquin,Stockton,Star Nut Co,1.0,walnut,CA,walnut,638.0,processor,95215,PROC,0101000020E6100000FD46E0B4054E5EC01D9BB20D3B004340,POINT (-121.2190983 38.00180217),38.00180217,-121.2190983 +7229 Moon Bend Rd.,Colusa,Colusa,Empire Nut Company LLC,1.0,walnut,CA,walnut,639.0,shelling,95932,PROC,0101000020E6100000E10DC40DD37F5EC0C0B7237B08994340,POINT (-121.9972567 39.19557132),39.19557132,-121.9972567 +7233 County Rd. 24,Glenn,Orland,Omega Walnut Inc,1.0,walnut,CA,walnut,640.0,shelling,95963,PROC,0101000020E61000005479F1344F875EC0BC3E10ACECDA4340,POINT (-122.1142094 39.71034766),39.71034766,-122.1142094 +8000 N. Podesta Ln.,San Joaquin,Linden,Podesta Packing,1.0,walnut,CA,walnut,641.0,shelling,95236,PROC,0101000020E6100000D6F21483D1415EC0581E628BF6054340,POINT (-121.0284126 38.04658644),38.04658644,-121.0284126 +833 Tudor Road,Sutter,Yuba City,Sacramento Packing Inc,1.0,walnut,CA,walnut,642.0,processor,95991,PROC,0101000020E6100000D2623ABE07685EC0DBB232D0EB804340,POINT (-121.6254726 39.00719645),39.00719645,-121.6254726 +8540 Garden Highway,Sutter,Yuba City,Stephens Ranch Inc,1.0,walnut,CA,walnut,643.0,shelling,95991,PROC,0101000020E6100000064A0A2C00675EC058FA965A6B804340,POINT (-121.6093855 39.00327618),39.00327618,-121.6093855 +896 O'Banion Road,Sutter,Yuba City,Sacramento Valley Walnut Growers LLC,1.0,walnut,CA,walnut,644.0,shelling,95991,PROC,0101000020E6100000AE7FD767CE675EC0CF328B506C7F4340,POINT (-121.621973 38.995493),38.995493,-121.621973 +9457 River Road,Butte,Chico,Bremner Farms,1.0,walnut,CA,walnut,645.0,shelling,95928,PROC,0101000020E6100000474E70FBAF7C5EC0B60600D8CAD24340,POINT (-121.9482411 39.6468153),39.6468153,-121.9482411 +9839 Hutchinson Road,San Joaquin,Manteca,River Oak Orchards,1.0,walnut,CA,walnut,646.0,shelling,95337,PROC,0101000020E610000046274BADF74B5EC0DA835A1DCADC4240,POINT (-121.186992 37.72491805),37.72491805,-121.186992 +9979 Tyler Road,Tehama,Gerber,Haleakala Walnut Shelling Inc,1.0,walnut,CA,walnut,647.0,shelling,96035,PROC,0101000020E61000009B9E6637E9895EC0B30BE5C8730A4440,POINT (-122.1548594 40.08165847),40.08165847,-122.1548594 +Cherokee Business Park,San Joaquin,Stockton,Cal Ranch Inc,1.0,walnut,CA,walnut,648.0,shelling,95205,PROC,0101000020E61000002995F0845E4E5EC07B4FE5B4A7FA4240,POINT (-121.224519 37.958243),37.958243,-121.224519 +2069 Aldergrove Ave,0,Escondido,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,92029,PROC,0101000020E610000025E99AC937475DC0C67012D6088F4040,POINT (-117.11278 33.11745716),33.11745716,-117.11278 +2825 La Mirada Dr,0,Vista,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,92081,PROC,0101000020E6100000C972124ADF4D5DC02BE8EE21FE924040,POINT (-117.2167535 33.14838051),33.14838051,-117.2167535 +7700 Irvine Center Dr 500,0,Irvine,Interstate Brands Corp Hostess,0.0,bakery,CA,bread,0.0,bakery,92618,PROC,0101000020E61000001CBE3BE848705DC0AE5DA0C5CED44040,POINT (-117.7544499 33.66256018),33.66256018,-117.7544499 +26962 Vista Terrace,0,Lake Forest,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,92630,PROC,0101000020E610000088049D5A476A5DC01FEAA99B2CD54040,POINT (-117.6606051 33.66542383),33.66542383,-117.6606051 +44655 Jackson St,0,Indio,Interstate Brands Corp Hostess,0.0,bakery,CA,bread,0.0,bakery,92201,PROC,0101000020E610000065CAE259DD0D5DC0BB698E07B6DC4040,POINT (-116.2166352 33.7243051),33.7243051,-116.2166352 +19251 Ruppert,0,Thousand Palms,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,92276,PROC,0101000020E6100000D237691A14185DC05BEECC04C3E74040,POINT (-116.376227 33.810639),33.810639,-116.376227 +1500 Francisco St,0,Torrance,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,90501,PROC,0101000020E6100000BA53951172935DC0D59233B9BDEC4040,POINT (-118.3038372 33.8495399),33.8495399,-118.3038372 +366 S Acacia Ave,0,Fullerton,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,92831,PROC,0101000020E6100000AF2A56687B795DC09D5B53E607EF4040,POINT (-117.8981572 33.86742858),33.86742858,-117.8981572 +1055 Sandhill Ave,0,Carson,General Mills,0.0,bakery,CA,bread,0.0,milling,90746,PROC,0101000020E6100000681316CB63905DC06C66E37789F04040,POINT (-118.2560909 33.8791952),33.8791952,-118.2560909 +16701 Trojan Way,0,La Mirada,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,90638,PROC,0101000020E6100000B1EC38341B815DC04DE13942A3F04040,POINT (-118.0172854 33.87998226),33.87998226,-118.0172854 +8049 Somerset Blvd,0,Paramount,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,90723,PROC,0101000020E6100000B5728AE91D8A5DC03D45ED02CEF24040,POINT (-118.1580757 33.89691197),33.89691197,-118.1580757 +1493 E 6th St,0,Beaumont,Interstate Brands Corp Hostess,0.0,bakery,CA,bread,0.0,bakery,92223,PROC,0101000020E610000070B614EB2F3D5DC0A29520C8E6F64040,POINT (-116.9560497 33.9289179),33.9289179,-116.9560497 +5200 Alameda St,0,Vernon,Sara Lee Fresh Inc,0.0,bakery,CA,bread,0.0,bakery,90058,PROC,0101000020E6100000600FDC372D8F5DC0BF9F75E84FFF4040,POINT (-118.2371349 33.9946261),33.9946261,-118.2371349 +5200 S Alameda St,0,Vernon,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,90058,PROC,0101000020E6100000600FDC372D8F5DC0BF9F75E84FFF4040,POINT (-118.2371349 33.9946261),33.9946261,-118.2371349 +5471 Ferguson Dr,0,Commerce,General Mills,0.0,bakery,CA,bread,0.0,distributor,90022,PROC,0101000020E610000085494CABFC895DC0C163D3A55A014140,POINT (-118.1560467 34.01057885000001),34.01057885000001,-118.1560467 +10820 San Sevaine Way,0,Mira Loma,Cajoleben Inc Galassos Bakery DBA,0.0,bakery,CA,bread,0.0,bakery,91752,PROC,0101000020E6100000130544D238615DC0BA652C3F15024140,POINT (-117.5190931 34.0162734),34.0162734,-117.5190931 +635 W Valley Blvd,0,Bloomington,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,92316,PROC,0101000020E6100000186426AC68585DC02E3807F803094140,POINT (-117.3813887 34.07043362),34.07043362,-117.3813887 +9535 Archibald Ave,0,Rancho Cucamonga,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,91730,PROC,0101000020E61000007B6D910FD5655DC0EB01F390290A4140,POINT (-117.5911292 34.0793935),34.0793935,-117.5911292 +5341 Derry Ave,0,Agoura Hills,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,91301,PROC,0101000020E6100000E36A099EE7AF5DC0F3E8C21FB0124140,POINT (-118.7485118 34.14599988),34.14599988,-118.7485118 +9822 Glenoaks Blvd,0,Sun Valley,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,91352,PROC,0101000020E6100000C8EF6DFAB3985DC031AE3C71CE1F4140,POINT (-118.385985 34.24848762),34.24848762,-118.385985 +4535 Dupont Ct,0,Ventura,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93003,PROC,0101000020E6100000C2E2CB9FCACE5DC07AB4273740204140,POINT (-119.2311172 34.2519597),34.2519597,-119.2311172 +17365 Jasmine St,0,Victorville,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,92395,PROC,0101000020E6100000E11813AC3B525DC071917BBABA3C4140,POINT (-117.2848921 34.4744485),34.4744485,-117.2848921 +751 W Ave L8,0,Lancaster,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93534,PROC,0101000020E61000008E9F7C305F895DC0993FCF349B534140,POINT (-118.1464349 34.65317402),34.65317402,-118.1464349 +2220 Hutton Rd,0,Nipomo,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93444,PROC,0101000020E6100000E9CEB815E71B5EC01ABBE93B647F4140,POINT (-120.4359793 34.9952464),34.9952464,-120.4359793 +6320 District Blvd,0,Bakersfield,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93313,PROC,0101000020E6100000C6DD205AABC45DC007126FF838A84140,POINT (-119.0729585 35.3142386),35.3142386,-119.0729585 +2309 E Brundage Ln C,0,Bakersfield,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,93307,PROC,0101000020E610000049D345AFABBE5DC0EA46B30D37AD4140,POINT (-118.9792288 35.3532426),35.3532426,-118.9792288 +28801 CA 58,0,Bakersfield,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93314,PROC,0101000020E6100000572426A8E1CA5DC090300C5872B14140,POINT (-119.170023 35.386302),35.386302,-119.170023 +712 W California Ave A,0,Ridgecrest,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93555,PROC,0101000020E6100000BE1D9727C66B5DC0560DA1CE85CF4140,POINT (-117.6839694 35.62127097),35.62127097,-117.6839694 +1323 E Inyokern Rd,0,Ridgecrest,Interstate Brands Corp Hostess,0.0,bakery,CA,bread,0.0,bakery,93555,PROC,0101000020E61000006765564AAA6C5DC0F5A7E8A367D34140,POINT (-117.6978937 35.65160035),35.65160035,-117.6978937 +8316 Elowin Ct,0,Visalia,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93291,PROC,0101000020E6100000534F30AD97D85DC0CF9552E1192C4240,POINT (-119.3842576 36.3445398),36.3445398,-119.3842576 +1355 Burton Ave,0,Salinas,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93901,PROC,0101000020E6100000271AFF991C685EC0F779E7AB3F534240,POINT (-121.6267457 36.6503806),36.6503806,-121.6267457 +3630 N Hazel Ave,0,Fresno,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,93722,PROC,0101000020E6100000364C7ED55BF65DC04302469737654240,POINT (-119.8493551 36.790759),36.790759,-119.8493551 +120 Lee Rd A,0,Watsonville,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95076,PROC,0101000020E61000003EA0223DFB715EC0B2E4E088A4734240,POINT (-121.7809594 36.9034587),36.9034587,-121.7809594 +865 Beechcraft Ave,0,Merced,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95341,PROC,0101000020E61000001A68E32DFC205EC0F35EADC118A64240,POINT (-120.5153918 37.29763051),37.29763051,-120.5153918 +1160 W 13th St,0,Merced,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95341,PROC,0101000020E6100000FF31BE79BB1F5EC0498E6C957DA64240,POINT (-120.4958176 37.30070751),37.30070751,-120.4958176 +1791 Sycamore Ave,0,Atwater,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95301,PROC,0101000020E6100000465B954476275EC0E621955A56AC4240,POINT (-120.6165935 37.34638531),37.34638531,-120.6165935 +890 Service St G,0,San Jose,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95112,PROC,0101000020E6100000B7C5466AEB785EC0AD73C23A44AF4240,POINT (-121.8893686 37.3692697),37.3692697,-121.8893686 +1711 Junction Ct 370,0,San Jose,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95112,PROC,0101000020E61000003B14AA40D2795EC0CDDF298991AF4240,POINT (-121.9034578 37.3716289),37.3716289,-121.9034578 +456 W Maude Ave,0,Sunnyvale,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94085,PROC,0101000020E6100000EB5795D810825EC0143D9578E5B14240,POINT (-122.0322782 37.3898154),37.3898154,-122.0322782 +600 Garner Rd,0,Modesto,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95357,PROC,0101000020E6100000900A0852CE3A5EC0135FB37DC4D04240,POINT (-120.9188428 37.63099643),37.63099643,-120.9188428 +305 Codoni Ave,0,Modesto,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95357,PROC,0101000020E61000001041D5E8553A5EC0BDDC2FB849D14240,POINT (-120.9114935 37.63506224),37.63506224,-120.9114935 +475 S Canal St,0,South San Francisco,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94080,PROC,0101000020E6100000314F9DFDB79A5EC001E49DA643D34240,POINT (-122.4174799 37.65050204),37.65050204,-122.4174799 +151 W Hill Pl,0,Brisbane,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,94005,PROC,0101000020E610000049827005149B5EC0DEE8633EA0D84240,POINT (-122.423097 37.69239025),37.69239025,-122.423097 +1450 S Loop Rd,0,Alameda,FritoLay Distribution Center,0.0,bakery,CA,bakery,0.0,distributor,94502,PROC,0101000020E6100000C9B0E5F0248F5EC0143DF03158DC4240,POINT (-122.2366297 37.7214415),37.7214415,-122.2366297 +937 66th Ave,0,Oakland,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94621,PROC,0101000020E6100000AF29EB92CC8C5EC0EE45CDBAF3E04240,POINT (-122.1999862 37.75743804),37.75743804,-122.1999862 +901 King St,0,Oakland,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94606,PROC,0101000020E6100000BA4DB857668F5EC0EB15BB229DE34240,POINT (-122.2406215 37.7782329),37.7782329,-122.2406215 +1190 Spreckels Ave,0,Manteca,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95336,PROC,0101000020E61000005CD71EACB54C5EC09584C0A1A2E44240,POINT (-121.1985884 37.78621313),37.78621313,-121.1985884 +4020 Nelson Ave,0,Concord,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94520,PROC,0101000020E6100000BAD1110ADB825EC079CE71C9CC004340,POINT (-122.0446191 38.0062496),38.0062496,-122.0446191 +2201 Verne Roberts Cir,0,Antioch,Costco Bakery,0.0,bakery,CA,bread,0.0,bakery,94509,PROC,0101000020E6100000D30F8F6992755EC06F00EC9227014340,POINT (-121.8370613 38.0090202),38.0090202,-121.8370613 +5045 Forni Dr,0,Concord,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,94520,PROC,0101000020E6100000FA9F57972E825EC08F55A58867024340,POINT (-122.0340937 38.0187846),38.0187846,-122.0340937 +2245 CA 49,0,Angels Camp,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95222,PROC,0101000020E610000000E65AB400285EC011E15F048D094340,POINT (-120.625043 38.074616),38.074616,-120.625043 +2445 S Watney Way A,0,Fairfield,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,94533,PROC,0101000020E61000008276E2CDF5845EC09DBAF2599E1D4340,POINT (-122.0775027 38.231395),38.231395,-122.0775027 +2500 Crocker Cir,0,Fairfield,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,94533,PROC,0101000020E610000001A1F5F0E57E5EC0B9B8D7930A234340,POINT (-121.9827845 38.2737603),38.2737603,-121.9827845 +10115 Iron Rock Way 1,0,Elk Grove,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95624,PROC,0101000020E6100000A245B6F3FD565EC0402ACDFF0E324340,POINT (-121.35925 38.39108274),38.39108274,-121.35925 +7601 Wilbur Way,0,Sacramento,Bimbo Bakeries,0.0,bakery,CA,bread,0.0,bakery,95828,PROC,0101000020E6100000358EA2186A595EC0CC13DFBB933D4340,POINT (-121.3971006 38.48107098),38.48107098,-121.3971006 +3810 Seaport Blvd,0,West Sacramento,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95691,PROC,0101000020E61000001D44C6FE8D645EC09545E54F69484340,POINT (-121.5711667 38.56571387),38.56571387,-121.5711667 +781 Bevins St,0,Lakeport,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95453,PROC,0101000020E6100000596375502EBB5EC0904C242414854340,POINT (-122.9247018 39.03967716),39.03967716,-122.9247018 +401 Burns Dr,0,Yuba City,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95991,PROC,0101000020E61000004DB049C851675EC03AD7C5A7DF8D4340,POINT (-121.6143666 39.10838792),39.10838792,-121.6143666 +3001 S State St,0,Ukiah,Earthgrains Co,0.0,bakery,CA,bread,0.0,bakery,95482,PROC,0101000020E6100000AE02C64494CC5EC0A37C399A408E4340,POINT (-123.1965496 39.11134651),39.11134651,-123.1965496 +22601 CA 1,0,Fort Bragg,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95437,PROC,0101000020E6100000190A8E812BF35EC0C14858E928BC4340,POINT (-123.7995304 39.46999852),39.46999852,-123.7995304 +1801 Idora St,0,Oroville,Delallo Italian,0.0,bakery,CA,pasta bread,0.0,bakery,95966,PROC,0101000020E610000015E7035D56635EC0C91759D70DBF4340,POINT (-121.5521462 39.4926099),39.4926099,-121.5521462 +741 Oroville Chico Hwy,0,Durham,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95938,PROC,0101000020E6100000C55FEEEE5C6E5EC063BA6B64B2D24340,POINT (-121.7244222 39.6460691),39.6460691,-121.7244222 +20196 Charlanne Dr,0,Redding,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,96002,PROC,0101000020E61000002B68FFA872935EC04E870442A1454440,POINT (-122.3038733 40.5439837),40.5439837,-122.3038733 +69 W 3rd St,0,Eureka,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,95501,PROC,0101000020E61000003CF9F4D8160B5FC04A6C2D82B5664440,POINT (-124.1732695 40.8024142),40.8024142,-124.1732695 +1525 Lucas Rd G,0,Yreka,FritoLay,0.0,bakery,CA,bakery,0.0,distributor,96097,PROC,0101000020E61000002B1895D409A85EC0567DAEB662DD4440,POINT (-122.6256 41.729575),41.729575,-122.6256 +1348 47th St,0,San Diego,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,92102,PROC,0101000020E61000007EC6850321465DC0141F44D72A5C4040,POINT (-117.095765 32.7200574),32.7200574,-117.095765 +7995 Armour St,0,San Diego,Pepsi Co Bottling Group,0.0,beverage,CA,beverage,0.0,manufacturer,92111,PROC,0101000020E61000006313F472B3495DC0B9E2E2A8DC684040,POINT (-117.1515777 32.819234),32.819234,-117.1515777 +27442 Portola Pkwy,0,Foothill Ranch,Pepsi Cola Co,0.0,beverage,CA,beverage,0.0,manufacturer,92610,PROC,0101000020E6100000D7FDBEDAAC695DC09E6CB9E985D54040,POINT (-117.6511752 33.6681492),33.6681492,-117.6511752 +2603 Camino Ramon 550,0,San Ramon,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,94583,PROC,0101000020E6100000364877C6AD755DC03D22AEB5DAD64040,POINT (-117.8387314 33.67854949),33.67854949,-117.8387314 +83801 Citrus Ave,0,Indio,Pepsi Co,0.0,beverage,CA,beverage,0.0,distribution,92201,PROC,0101000020E61000002B0F779AF10C5DC029C9DF62EADB4040,POINT (-116.2022463 33.7180904),33.7180904,-116.2022463 +2121 E Winston Rd,0,Anaheim,Coca Cola water,0.0,beverage,CA,water,0.0,distribution,92806,PROC,0101000020E6100000652E15C0B9785DC021A92AD956E84040,POINT (-117.8863373 33.8151504),33.8151504,-117.8863373 +961 E 4th St,0,Los Angeles,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,90013,PROC,0101000020E610000042453069E7925DC0FA30B58400ED4040,POINT (-118.2953742 33.85157832),33.85157832,-118.2953742 +6200 Caballero Blvd,0,Buena Park,CorruKraft Inc,0.0,beverage,CA,beverage,0.0,distributor,90620,PROC,0101000020E61000002A8E03AF96815DC0E746A2E1DEEE4040,POINT (-118.024822 33.8661768),33.8661768,-118.024822 +4701 Park Rd,0,Benicia,Pepsi Co Bottling Group,0.0,beverage,CA,beverage,0.0,manufacturer,94510,PROC,0101000020E61000005494A69C8A815DC0FC427EECE4EE4040,POINT (-118.0240852 33.8663612),33.8663612,-118.0240852 +14326 Monte Vista Ave,0,Chino,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,91710,PROC,0101000020E6100000274EEE77A86C5DC0BA94250020FF4040,POINT (-117.6977825 33.99316408),33.99316408,-117.6977825 +2095 S Archibald Ave,0,Ontario,Pepsi Cola Sales Distribution,0.0,beverage,CA,beverage,0.0,distribution,91761,PROC,0101000020E6100000BAD1110ADB655DC03D1059A489044140,POINT (-117.5914941 34.0354505),34.0354505,-117.5914941 +1560 E 20th St,0,Los Angeles,Nestle Waters,0.0,beverage,CA,water,0.0,water,90011,PROC,0101000020E610000052BC259499925DC03075A103DC044140,POINT (-118.2906237 34.0379643),34.0379643,-118.2906237 +3 Park Plaza 600,0,Irvine,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,92614,PROC,0101000020E6100000A477E052048F5DC0ABD82D3C8E054140,POINT (-118.2346389 34.04340317),34.04340317,-118.2346389 +1650 S Vintage Ave,0,Ontario,Coca Cola Ontario Syrup,0.0,beverage,CA,sugar,0.0,syrup,91761,PROC,0101000020E6100000BFC1CD9838625DC0E0FDA7D19A054140,POINT (-117.5347044 34.0437872),34.0437872,-117.5347044 +10670 6th St,0,Rancho Cucamonga,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,91730,PROC,0101000020E61000007352F3B0AB645DC09CB34F11F10A4140,POINT (-117.5729792 34.0854818),34.0854818,-117.5729792 +4416 Azusa Canyon Rd,0,Irwindale,Pepsi Co Bottling Group,0.0,beverage,CA,beverage,0.0,distributor,91706,PROC,0101000020E61000000EAB2E96587C5DC0EC378F9AE10B4140,POINT (-117.9429069 34.09282238),34.09282238,-117.9429069 +1200 Arroyo St,0,San Fernando,Pepsi Co,0.0,beverage,CA,beverage,0.0,distributor,91340,PROC,0101000020E6100000BEFD1422BB9A5DC068222A5C28254140,POINT (-118.4176717 34.29029419),34.29029419,-118.4176717 +12925 Bradley Ave,0,Sylmar,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,91342,PROC,0101000020E6100000D24A6B1D669D5DC098F67244E3264140,POINT (-118.4593576 34.30381065),34.30381065,-118.4593576 +4375 N Ventura Ave,0,Ventura,Pepsi Co,0.0,beverage,CA,beverage,0.0,distribution,93001,PROC,0101000020E6100000BD2DA237A6D25DC0FE9F1E36EC294140,POINT (-119.2913951 34.3275211),34.3275211,-119.2913951 +715 Vandenberg St,0,Salinas,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,93905,PROC,0101000020E6100000CFEFA07EBC665EC09DC9480735544240,POINT (-121.6052548 36.6578683),36.6578683,-121.6052548 +3220 E Malaga Ave,0,Fresno,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,93725,PROC,0101000020E6100000BF7FF3E2C4EE5DC0F69100DAFB554240,POINT (-119.730767 36.6717484),36.6717484,-119.730767 +1555 Old Bayshore Hwy,0,San Jose,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,95112,PROC,0101000020E6100000BAC95EA5F1795EC0BF1D13EF21AF4240,POINT (-121.9053739 37.36822308),37.36822308,-121.9053739 +1733 Morgan Rd,0,Modesto,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,95358,PROC,0101000020E6100000BDC282FB813E5EC0BE94EC9E5DCD4240,POINT (-120.9766835 37.60441958),37.60441958,-120.9766835 +29000 Hesperian Blvd,0,Hayward,Pepsi Co,0.0,beverage,CA,beverage,0.0,distributor,94544,PROC,0101000020E61000008E23319C46855EC01B09D91E62CE4240,POINT (-122.0824347 37.6123694),37.6123694,-122.0824347 +14655 Wicks Blvd,0,San Leandro,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,94577,PROC,0101000020E610000041518F238C8A5EC0B7CC8EF925D94240,POINT (-122.1648034 37.6964714),37.6964714,-122.1648034 +1565 N MacArthur Dr 500,0,Tracy,Pepsi Co,0.0,beverage,CA,beverage,0.0,distributor,95376,PROC,0101000020E6100000A16FC108505A5EC031F1A20A5ADF4240,POINT (-121.4111349 37.74493535),37.74493535,-121.4111349 +19875 Pacific Gateway Dr,0,Torrance,Coca Cola,0.0,beverage,CA,beverage,0.0,manufacturer,90502,PROC,0101000020E610000025F37E92717D5EC0C580579172E24240,POINT (-121.9600569 37.76912133),37.76912133,-121.9600569 +4225 Pepsi Pl,0,Stockton,Pepsi Co,0.0,beverage,CA,beverage,0.0,manufacturer,95215,PROC,0101000020E6100000F82A4366F84F5EC01244C46A7FFE4240,POINT (-121.2495361 37.98826346),37.98826346,-121.2495361 +6261 Caballero Blvd,0,Buena Park,Pepsi Co Bottling Group,0.0,beverage,CA,beverage,0.0,manufacturer,90620,PROC,0101000020E610000014ECBFCECD875EC0D5157D4FF6094340,POINT (-122.1219365 38.0778293),38.0778293,-122.1219365 +650 Babcock Ln,0,Ukiah,Coca Cola bottling,0.0,beverage,CA,beverage,0.0,distribution,95482,PROC,0101000020E6100000F52D73BA2CCC5EC01B56448F90914340,POINT (-123.19023 39.13722411),39.13722411,-123.19023 +15801 W 1st St,0,Irwindale,Miller Coors LLC,0.0,brewery,CA,grains,0.0,brewery,91706,PROC,0101000020E61000004CDF6B080E7C5DC0D17AB616FF0F4140,POINT (-117.9383565 34.12497219),34.12497219,-117.9383565 +912 Gilman St,0,Berkeley,Gilman Brewery Company,0.0,brewery,CA,grains,0.0,brewery,94710,PROC,0101000020E6100000541FA3972C935EC0D9846A3986F04240,POINT (-122.2995967 37.8790962),37.8790962,-122.2995967 +3101 Busch Dr,0,Fairfield,AnheuserBusch LLC LA or Solano,0.0,brewery,CA,grains,0.0,brewery,94534,PROC,0101000020E6100000F804E4A6E1855EC020F35C3A411E4340,POINT (-122.0918977 38.2363656),38.2363656,-122.0918977 +1201 K St 730,0,Sacramento,AnheuserBusch LLC LA or Solano,0.0,brewery,CA,grains,0.0,brewery,95814,PROC,0101000020E610000025462AE7665F5EC091C8252B124A4340,POINT (-121.4906557 38.57867946),38.57867946,-121.4906557 +17700 Boonville Rd,0,Boonville,Anderson Valley Brewery,0.0,brewery,CA,grains,0.0,brewery,95415,PROC,0101000020E6100000769E1D15A4D65EC0839596D316804340,POINT (-123.3537648 39.00069661),39.00069661,-123.3537648 +1075 E 20th St,0,Chico,Sierra Nevada Brewery,0.0,brewery,CA,grains,0.0,brewery,95928,PROC,0101000020E61000002A9D595C2D745EC0D6427F57BADC4340,POINT (-121.8152686 39.7244367),39.7244367,-121.8152686 +10051 Old Grove Rd,0,San Diego,Ballast Point Brewing,0.0,brewery,CA,distillers grain,0.0,brewery distillery,92131,PROC,0101000020E61000005D8AABCA3E475DC064CDA7120E734040,POINT (-117.1132075 32.89886697),32.89886697,-117.1132075 +8680 Miralani Dr #120,0,San Diego,Setting Sun Sake Brewing Co,0.0,brewery,CA,distillers grain,0.0,brewery,92126,PROC,0101000020E610000074565579CC485DC01F8357C3AC724040,POINT (-117.1374801 32.89589731),32.89589731,-117.1374801 +12132 Knott St,0,Garden Grove,Guilianos Specialty Foods,0.0,cannery,CA,olive capsicum,0.0,cannery,92841,PROC,0101000020E6100000A98E0BBDB4805DC0B05A36C690E44040,POINT (-118.0110314 33.78566816),33.78566816,-118.0110314 +5821 Wilderness Ave,0,Riverside,triple h food processors,0.0,cannery,CA,tomato fruit vegetable misc,0.0,cannery,92504,PROC,0101000020E6100000775FDF98AF5C5DC0E9EEDF617FFB4040,POINT (-117.4482176 33.9648249),33.9648249,-117.4482176 +5650 E Santa Ana St,0,Ontario,Mizkan America,0.0,cannery,CA,grapes vegetables,0.0,cannery,91761,PROC,0101000020E61000002E156580D5615DC0C0A78306AC064140,POINT (-117.5286561 34.0521248),34.0521248,-117.5286561 +315 E. Fourth St.,0,Ontario,cc graber co,0.0,cannery,CA,olives,0.0,cannery,91764,PROC,0101000020E61000001385F12E72695DC08E89DEF30D0A4140,POINT (-117.6475942 34.0785508),34.0785508,-117.6475942 +10037 8th St,0,Rancho Cucamonga,Mizkan America,0.0,cannery,CA,grapes vegetables,0.0,cannery,91730,PROC,0101000020E610000047F1E0DD80655DC03731C96DA00B4140,POINT (-117.5859904 34.0908334),34.0908334,-117.5859904 +Dock 1 Berth 3,0,Port Hueneme,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,93041,PROC,0101000020E6100000A5BDC11726CC5DC06D1CB1169F144140,POINT (-119.189825 34.161105),34.161105,-119.189825 +800 Commercial Ave,0,Oxnard,smucker fruit processing co,0.0,cannery,CA,fruit,0.0,cannery,93030,PROC,0101000020E61000001CFC0E8F0ECB5DC06BC6585CD2184140,POINT (-119.1727636 34.1939197),34.1939197,-119.1727636 +554 Todd Rd,0,Santa Paula,saticoy food corp,0.0,cannery,CA,vegetables,0.0,cannery,93060,PROC,0101000020E61000009BC8CC052EC75DC049D9226937284140,POINT (-119.112184 34.314191),34.314191,-119.112184 +19800 W Gale Ave,0,Huron,Los Gatos Tomato Products,0.0,cannery,CA,tomato,0.0,cannery,93234,PROC,0101000020E6100000767F06E5C7095EC027953A1279174240,POINT (-120.1528256 36.1833823),36.1833823,-120.1528256 +10652 Jackson Ave,0,Hanford,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,93230,PROC,0101000020E61000002C1E28017BE95DC0D19CAB9CAC204240,POINT (-119.6481326 36.2552677),36.2552677,-119.6481326 +1913 Industrial Way,0,Sanger,initiative foods,0.0,cannery,CA,fruit and vegetables,0.0,cannery,93657,PROC,0101000020E6100000E3A2FF8A21E35DC00FC86F1B57584240,POINT (-119.5489223 36.6901583),36.6901583,-119.5489223 +1810 Academy Ave,0,Sanger,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,93657,PROC,0101000020E610000007EBFF1C66E35DC0CC8D339765584240,POINT (-119.5531075 36.6906003),36.6906003,-119.5531075 +2502 N St,0,Firebaugh,the neil jones food company,0.0,cannery,CA,tomato,0.0,cannery,93622,PROC,0101000020E61000002E3D9AEAC91C5EC051FA9D81EC6A4240,POINT (-120.449824 36.8353426),36.8353426,-120.449824 +2502 N St,0,Firebaugh,TomaTek Inc tomato,0.0,cannery,CA,tomato,0.0,cannery,93622,PROC,0101000020E61000002E3D9AEAC91C5EC051FA9D81EC6A4240,POINT (-120.449824 36.8353426),36.8353426,-120.449824 +110 Hawkins St,0,Hollister,the neil jones food company,0.0,cannery,CA,tomato,0.0,cannery,95023,PROC,0101000020E6100000BDEB223BA5595EC0E33F93B3666C4240,POINT (-121.4007099 36.8468842),36.8468842,-121.4007099 +865 East,0,Hollister,san benito foods,0.0,cannery,CA,tomato,0.0,cannery,95023,PROC,0101000020E61000003752B648DA585EC0C4978922A46C4240,POINT (-121.388323 36.848759),36.848759,-121.388323 +46 Walker St,0,Watsonville,Mizkan America,0.0,cannery,CA,apple cider mill,0.0,cannery,95076,PROC,0101000020E6100000A6327B8F69705EC0DDD8A2BBDA734240,POINT (-121.7564429 36.9051127),36.9051127,-121.7564429 +233 Peckham Rd,0,Watsonville,BellCarter Lindsay,0.0,cannery,CA,olive,0.0,cannery,95076,PROC,0101000020E61000002A841FE65C6D5EC03ACD02ED0E7A4240,POINT (-121.7087951 36.9535805),36.9535805,-121.7087951 +6580 Furlong Ave,0,Gilroy,Del Monte farm,0.0,cannery,CA,fruit vegetable,0.0,cannery,95020,PROC,0101000020E61000003E7D5FB763615EC0A1E760472D814240,POINT (-121.5217112 37.0091943),37.0091943,-121.5217112 +12045 Ingomar Grade,0,Los Banos,Liberty Packing Co Morning Star,0.0,cannery,CA,tomato,0.0,cannery,93635,PROC,0101000020E610000059A4897780365EC0FB5DD89AAD864240,POINT (-120.851591 37.052173),37.052173,-120.851591 +333 Johnson Rd,0,Los Banos,Kagome,0.0,cannery,CA,tomato dairy vegetable,0.0,cannery,93635,PROC,0101000020E6100000221B48171B375EC05685611BCC884240,POINT (-120.8610285 37.06872885),37.06872885,-120.8610285 +13448 Volta Rd,0,Los Banos,Morning Star Packing Co,0.0,cannery,CA,tomato,0.0,cannery,93635,PROC,0101000020E6100000D0B359F5393B5EC050327BD1058C4240,POINT (-120.9254125 37.09392756),37.09392756,-120.9254125 +901 Packers St,0,Atwater,teasdale foods inc,0.0,cannery,CA,vegetable bean,0.0,cannery,95301,PROC,0101000020E6100000788E1205C4265EC025C700FDFCAB4240,POINT (-120.6057141 37.34365809),37.34365809,-120.6057141 +2801 Finch Rd,0,Modesto,seneca foods corp,0.0,cannery,CA,apricots peaches pears,0.0,cannery,95354,PROC,0101000020E6100000C17861C66F3C5EC02766625FD7CF4240,POINT (-120.9443222 37.62376015),37.62376015,-120.9443222 +4000 Yosemite Blvd,0,Modesto,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,95357,PROC,0101000020E61000009D514E0FE53A5EC0FBF045DE66D14240,POINT (-120.9202307 37.63595179),37.63595179,-120.9202307 +1202 D St,0,Modesto,stanislaus food pr,0.0,cannery,CA,tomato,0.0,cannery,95354,PROC,0101000020E61000000510E3DA753F5EC018865D4E68D14240,POINT (-120.9915683 37.63599567),37.63599567,-120.9915683 +17950 Via Nicolo Rd,0,Tracy,Musco Olive Products Inc,0.0,cannery,CA,olive,0.0,cannery,95377,PROC,0101000020E6100000436271EEE5615EC0D03860992FDB4240,POINT (-121.5296589 37.71239011),37.71239011,-121.5296589 +2 Nestle Way,0,Lathrop,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,95330,PROC,0101000020E610000037B75384E5525EC0F45FD67AF5E54240,POINT (-121.2952586 37.79655395),37.79655395,-121.2952586 +1 Maritime Plaza,0,San Francisco,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,94111,PROC,0101000020E6100000062AE3DF67995EC0C3F0113125E64240,POINT (-122.396965 37.79801),37.79801,-122.396965 +760 Industrial Dr,0,Stockton,Campbell Soup,0.0,cannery,CA,misc,0.0,cannery,95206,PROC,0101000020E610000009597105EF505EC078D6C97443F44240,POINT (-121.2645887 37.9083086),37.9083086,-121.2645887 +3151 Regatta Blvd,0,Richmond,Del Monte fresh,0.0,cannery,CA,fruit vegetable,0.0,cannery,94804,PROC,0101000020E61000000070ECD973955EC04A9869FB57F64240,POINT (-122.335196 37.92456),37.92456,-122.335196 +205 N Wiget Ln,0,Walnut Creek,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,94598,PROC,0101000020E6100000BCBA1924B3815EC03443B299A6F64240,POINT (-122.0265589 37.92695924),37.92695924,-122.0265589 +3003 Oak Rd,0,Walnut Creek,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,94597,PROC,0101000020E610000003C9E0CDBF835EC0A766C526E8F64240,POINT (-122.0585818 37.9289597),37.9289597,-122.0585818 +4136 Lakeside Dr,0,San Pablo,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,94806,PROC,0101000020E6100000B7A4598F31955EC091D26C1E87FE4240,POINT (-122.3311499 37.9884985),37.9884985,-122.3311499 +650 S Guild Ave,0,Lodi,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95240,PROC,0101000020E61000007D6B71D7DC4F5EC0D54864828E0F4340,POINT (-121.2478541 38.12153654),38.12153654,-121.2478541 +741 S Stockton St,0,Lodi,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95240,PROC,0101000020E610000031CB434B43515EC02A90B84B0B104340,POINT (-121.2697323 38.12534472),38.12534472,-121.2697323 +631 N Cluff Ave,0,Lodi,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95240,PROC,0101000020E6100000C67E60D82B505EC0B9F9889021124340,POINT (-121.2526761 38.14164931),38.14164931,-121.2526761 +14531 Walnut Grove Thornton Rd,0,Walnut Grove,Del Monte,0.0,cannery,CA,fruit vegetable,0.0,cannery,95690,PROC,0101000020E61000002827DA55C8605EC00775F46C141D4340,POINT (-121.5122275 38.22718584),38.22718584,-121.5122275 +1520 Terminal St,0,West Sacramento,California Fire Roasted LLC,0.0,cannery,CA,tomato,0.0,cannery,95691,PROC,0101000020E6100000A1E76047AD625EC0B7BCCD76E0484340,POINT (-121.5418261 38.5693501),38.5693501,-121.5418261 +1376 Lemen Ave,0,Woodland,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95776,PROC,0101000020E6100000BD35B05582705EC06B065D67E8564340,POINT (-121.757955 38.6789674),38.6789674,-121.757955 +455 Harter Ave,0,Woodland,Boundary Bend Olives,0.0,cannery,CA,olive,0.0,cannery,95776,PROC,0101000020E6100000657506A197705EC092D332ADA8584340,POINT (-121.7592547 38.6926476),38.6926476,-121.7592547 +9950 S. Ingomar Grade,0,Los Banos,Ingomar Packing Company,0.0,cannery,CA,tomato,0.0,cannery,95635,PROC,0101000020E610000058CA32C4B1395EC009FD4CBD6E754340,POINT (-120.901475 38.917442),38.917442,-120.901475 +6005 CA 99,0,Live Oak,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95953,PROC,0101000020E61000005CC246FE05695EC0517E7B6C059C4340,POINT (-121.6409908 39.21891552),39.21891552,-121.6409908 +1901 Highway 99,0,Gridley,stapleton spense packing,0.0,cannery,CA,plums prunes,0.0,cannery,95948,PROC,0101000020E610000067391AD1076C5EC090347691DBAF4340,POINT (-121.6879771 39.37388819),39.37388819,-121.6879771 +1800 Idora St,0,Oroville,Delallo Italian,0.0,cannery,CA,olive tomato,0.0,cannery,95966,PROC,0101000020E6100000A1F65B3B51635EC0807C53A236BF4340,POINT (-121.551833 39.49385480000001),39.49385480000001,-121.551833 +1601 Mitchell Ave,0,Oroville,pacific coast producers,0.0,cannery,CA,fruit tomato,0.0,cannery,95965,PROC,0101000020E61000003DC967C3AB635EC011BF0754A4C04340,POINT (-121.5573586 39.5050149),39.5050149,-121.5573586 +1012 2nd St,0,Corning,BellCarter Lindsay,0.0,cannery,CA,olive,0.0,cannery,96021,PROC,0101000020E610000070FFDB766B8B5EC0E2C0F57269F64340,POINT (-122.1784341 39.92509305),39.92509305,-122.1784341 +981 Fig St,0,Corning,BellCarter Lindsay,0.0,cannery,CA,olive,0.0,cannery,96021,PROC,0101000020E610000044C4CDA9E48A5EC06EA8529279F64340,POINT (-122.1702065 39.92558507),39.92558507,-122.1702065 +6 Washinigton Ave,0,San Leandro,Maxwell House,0.0,coffee,CA,coffee,0.0,coffee,94578,PROC,0101000020E61000007A17EFC7ED875EC02ECBD765F8D94240,POINT (-122.123888 37.702893),37.702893,-122.123888 +11709 Artesia Blvd,0,Artesia,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,90701,PROC,0101000020E61000008FC8D2E267855DC0DBAC5516E0EF4040,POINT (-118.0844657 33.8740261),33.8740261,-118.0844657 +5611 Imperial Hwy,0,South Gate,Saputo Cheese USA Inc,0.0,dairy,CA,cheese,0.0,dairy,90270,PROC,0101000020E61000000C3B8C49FF8A5DC0AE37BDCD13F74040,POINT (-118.1718315 33.93029186),33.93029186,-118.1718315 +6401 Knudsen Dr,0,Bakersfield,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,93308,PROC,0101000020E610000026F67585E3C35DC0D3C66C2464B54140,POINT (-119.0607618 35.4171186),35.4171186,-119.0607618 +11894 Ave 120,0,Pixley,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,93256,PROC,0101000020E6100000ADF078A48BD45DC0D6D148B600014240,POINT (-119.3210231 36.00783423),36.00783423,-119.3210231 +10833 Octol Ave,0,Tulare,kraft,0.0,dairy,CA,dairy,0.0,dairy,93274,PROC,0101000020E6100000FDD8C985EFD45DC0FB5E9E29CF0F4240,POINT (-119.3271193 36.1235096),36.1235096,-119.3271193 +10800 Ave 184,0,Tulare,Kraft Hinez Qinc,0.0,dairy,CA,dairy,0.0,dairy,93274,PROC,0101000020E610000017E98F7A19D55DC0CEED9028D50F4240,POINT (-119.3296801 36.12369258),36.12369258,-119.3296801 +800 E Paige Ave,0,Tulare,Saputo Cheese USA Inc,0.0,dairy,CA,cheese,0.0,dairy,93274,PROC,0101000020E6100000C669882A7CD55DC04C4CBCA882174240,POINT (-119.3357035 36.1836749),36.1836749,-119.3357035 +970 E Continental Ave,0,Tulare,Nestle Dreyers,0.0,dairy,CA,frozen,0.0,dairy,93274,PROC,0101000020E6100000C991CEC048D55DC086E1C8A8D7174240,POINT (-119.3325655 36.1862689),36.1862689,-119.3325655 +901 E Levin Ave,0,Tulare,Saputo Cheese USA Inc,0.0,dairy,CA,cheese,0.0,dairy,93274,PROC,0101000020E61000008164952D6DD55DC04065A1421A184240,POINT (-119.3347887 36.1883014),36.1883014,-119.3347887 +1025 E Bardsley Ave,0,Tulare,Saputo Cheese USA Inc,0.0,dairy,CA,cheese,0.0,dairy,93274,PROC,0101000020E610000086B3B68457D55DC0A7F24D0522194240,POINT (-119.3334667 36.19635073),36.19635073,-119.3334667 +400 S M St,0,Tulare,Land O Lakes,0.0,dairy,CA,dairy,0.0,distributor,93274,PROC,0101000020E6100000181C6F3CE9D55DC0290F666E191A4240,POINT (-119.3423606 36.2039011),36.2039011,-119.3423606 +605 N J St,0,Tulare,Saputo Dairy Foods USA,0.0,dairy,CA,dairy,0.0,distributor,93274,PROC,0101000020E61000002526039B4ED65DC0AA99B514901B4240,POINT (-119.3485477 36.2153345),36.2153345,-119.3485477 +2000 N Plaza Dr,0,Visalia,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,93291,PROC,0101000020E61000003A32A0281AD95DC0C246FE05272C4240,POINT (-119.3922216 36.3449409),36.3449409,-119.3922216 +21890 Rosehart Way,0,Salinas,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,distributor,93908,PROC,0101000020E6100000EAE0AAFC7C635EC07E2DF9E9894D4240,POINT (-121.5545036 36.6057713),36.6057713,-121.5545036 +755 F St,0,Fresno,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,93706,PROC,0101000020E61000005378D0ECBAF25DC0FF3C0D18245D4240,POINT (-119.792659 36.727664),36.727664,-119.792659 +3380 W Ashlan Ave,0,Fresno,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,93722,PROC,0101000020E61000008A517C2189F65DC031AE5D7FB7654240,POINT (-119.8521198 36.7946624),36.7946624,-119.8521198 +255 Ford St,0,Watsonville,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,95076,PROC,0101000020E6100000BFA0E0BDFE705EC054D7EB27AD744240,POINT (-121.7655482 36.9115343),36.9115343,-121.7655482 +1160 G St,0,Los Banos,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,93635,PROC,0101000020E6100000B9574167AD355EC09787D031B5874240,POINT (-120.8387087 37.06021712),37.06021712,-120.8387087 +691 Inyo Ave,0,Newman,Saputo Cheese USA Inc,0.0,dairy,CA,cheese,0.0,dairy,95360,PROC,0101000020E61000000DD4731C09415EC082E0B742D4A74240,POINT (-121.0161811 37.31116518),37.31116518,-121.0161811 +8901 North Lander Avenue,0,Hilmar,Hilmar Cheese Company,0.0,dairy,CA,cheese,0.0,dairy,95324,PROC,0101000020E61000007E607DF266365EC0A0B7C2056AB54240,POINT (-120.8500334 37.41729805),37.41729805,-120.8500334 +475 S Tegner Rd,0,Turlock,California Dairies Inc,0.0,dairy,CA,dairy,0.0,distributor,95380,PROC,0101000020E61000003DF779E7AB385EC0B07567F5A7BE4240,POINT (-120.8854922 37.48950069),37.48950069,-120.8854922 +3600 W Canal Dr,0,Turlock,Hilmar Cheese Company,0.0,dairy,CA,cheese,0.0,dairy,95380,PROC,0101000020E61000002331410DDF365EC0A1664815C5BF4240,POINT (-120.857364 37.498202),37.498202,-120.857364 +6321 E Monte Vista Ave,0,Denair,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,95316,PROC,0101000020E6100000D291B7B7B6315EC0DB8DDBBBC8C24240,POINT (-120.7767772 37.52175091),37.52175091,-120.7767772 +2343 Hickman Rd,0,Hickman,Foster Farms Dairy Crystal,0.0,dairy,CA,dairy,0.0,dairy,95323,PROC,0101000020E61000006B5CA4F55C305EC005E485536ACC4240,POINT (-120.7556738 37.59699482),37.59699482,-120.7556738 +2843 Illinois Ave,0,Modesto,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,95358,PROC,0101000020E61000001D88D11852445EC0F42287467FCC4240,POINT (-121.0675108 37.59763414),37.59763414,-121.0675108 +1472 Hall Rd,0,Hickman,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,95323,PROC,0101000020E6100000C06268D02B2F5EC0C9E5FD870DCE4240,POINT (-120.7370492 37.60978794),37.60978794,-120.7370492 +736 Garner Rd,0,Modesto,Nestle Prepared Foods,0.0,dairy,CA,milk,0.0,dairy,95357,PROC,0101000020E61000000A37740EF93A5EC0018E350A66D04240,POINT (-120.9214512 37.62811401),37.62811401,-120.9214512 +3440 Enterprise Ave,0,Hayward,Foster Farms Dairy Crystal,0.0,dairy,CA,dairy,0.0,dairy,94545,PROC,0101000020E610000064A82FF001885EC0266195C107D14240,POINT (-122.1251183 37.6330492),37.6330492,-122.1251183 +1270 N Shaw Rd,0,Stockton,Humboldt Creamery,0.0,dairy,CA,dairy,0.0,dairy,95215,PROC,0101000020E6100000D93D1E9FB54F5EC0A5560C15EBFC4240,POINT (-121.2454603 37.97592414),37.97592414,-121.2454603 +441 Houser St,0,Cotati,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,94931,PROC,0101000020E61000001CAD0F90D4AD5EC02C216981872B4340,POINT (-122.7160988 38.3400728),38.3400728,-122.7160988 +3960 Channel Dr,0,West Sacramento,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,95691,PROC,0101000020E6100000E5828EB1EE645EC0B8E9CF7EA4474340,POINT (-121.5770687 38.5597075),38.5597075,-121.5770687 +3601 Co Rd C,0,Orland,Land O Lakes cheese,0.0,dairy,CA,cheese,0.0,dairy,95963,PROC,0101000020E61000005C920376358C5EC0BE4C142175DF4340,POINT (-122.190763 39.745762),39.745762,-122.190763 +,0,Fortuna,Foster Farms Dairy Crystal,0.0,dairy,CA,dairy,0.0,dairy,95540,PROC,0101000020E6100000F8359204E1085FC0488C9E5BE84A4440,POINT (-124.138734 40.585216),40.585216,-124.138734 +572 Fernbridge Dr,0,Fortuna,Humboldt Creamery,0.0,dairy,CA,dairy,0.0,dairy,95540,PROC,0101000020E6100000C4C1EFF0E80C5FC040984659E04E4440,POINT (-124.2017176 40.61622158),40.61622158,-124.2017176 +1555 Tahoe Ct,0,Redding,Foster Farms Dairy,0.0,dairy,CA,dairy,0.0,dairy,96003,PROC,0101000020E6100000EBAA402D86985EC0F5503640C4504440,POINT (-122.3831895 40.6309891),40.6309891,-122.3831895 +3250 Camino Del Sol,0,Oxnard,olde thompson inc,0.0,dehydrator,CA,spice vegetables,0.0,dehydrator,93030,PROC,0101000020E6100000F4B2DC88DDC85DC0EF03EB93371A4140,POINT (-119.1385214 34.2048211),34.2048211,-119.1385214 +9301 Lacey Blvd,0,Hanford,olam spices and vegetable ingredients,0.0,dehydrator,CA,spice vegetables,0.0,dehydrator,93230,PROC,0101000020E61000003A652431F7E75DC01BE1A3B4ED294240,POINT (-119.6244624 36.3275667),36.3275667,-119.6244624 +1445 Nebraska Ave,0,Selma,Sun Maid Growers,0.0,dehydrator,CA,grape,0.0,dehydrator,93662,PROC,0101000020E610000037AA2E3B9FE65DC0A87F5A56AB474240,POINT (-119.6034687 36.5599163),36.5599163,-119.6034687 +2028 S 3rd St,0,Fresno,Valley Fig Growers,0.0,dehydrator,CA,fig,0.0,dehydrator,93702,PROC,0101000020E61000000D99E1F54FF15DC001C11C3D7E5C4240,POINT (-119.7705054 36.7226025),36.7226025,-119.7705054 +47641 W Nees Ave,0,Firebaugh,olam spices and vegetable ingredients,0.0,dehydrator,CA,spice vegetables,0.0,dehydrator,93622,PROC,0101000020E6100000B31078BB39295EC01004C8D0B16C4240,POINT (-120.6441487 36.8491765),36.8491765,-120.6441487 +28390 Ave 12,0,Madera,sunsweet dryers,0.0,dehydrator,CA,prune date fruit nut,0.0,dehydrator,93637,PROC,0101000020E610000036DABB500A025EC01E6B460639764240,POINT (-120.0318796 36.92361525),36.92361525,-120.0318796 +1350 CA 152,0,Gilroy,Gilroy foods,0.0,dehydrator,CA,garlic onion capsicums,0.0,dehydrator,95020,PROC,0101000020E6100000AA51FEA490625EC031C1DB4965804240,POINT (-121.5400784 37.00309108),37.00309108,-121.5400784 +3324 Orestimba Rd,0,Newman,VSP products valleysun,0.0,dehydrator,CA,tomato,0.0,dehydrator,95360,PROC,0101000020E6100000E247EB5E5D455EC00D633D7B4FA84240,POINT (-121.0838239 37.31492558),37.31492558,-121.0838239 +9984 Walnut Ave,0,Livingston,sensient natural ingredients,0.0,dehydrator,CA,garlic onion capsicums vegetables,0.0,dehydrator,95334,PROC,0101000020E610000082035ABA822E5EC02BC0779B37B04240,POINT (-120.726729 37.376697),37.376697,-120.726729 +151 S Walnut Rd,0,Turlock,sensient natural ingredients,0.0,dehydrator,CA,garlic onion capsicums vegetables,0.0,dehydrator,95380,PROC,0101000020E6100000FD6DAA49CB375EC0F6D2D2E4FBBE4240,POINT (-120.8717827 37.49206219),37.49206219,-120.8717827 +2757 Rockville Rd,0,Fairfield,Culinary Farms,0.0,dehydrator,CA,tomatoes,0.0,dehydrator,94534,PROC,0101000020E6100000F0BCF9B2D9855EC08F1436A8A21F4340,POINT (-122.0914123 38.2471514),38.2471514,-122.0914123 +500 Crocker Dr,0,Vacaville,Mariani Packing,0.0,dehydrator,CA,fruit,0.0,dehydrator,95688,PROC,0101000020E61000006F5DD669C97C5EC035DC3642F5334340,POINT (-121.9497933 38.4059222),38.4059222,-121.9497933 +29485 Co Rd 27,0,Winters,sunsweet dryers,0.0,dehydrator,CA,prune date fruit nut,0.0,dehydrator,95694,PROC,0101000020E610000007F01648507E5EC0D177B7B244434340,POINT (-121.97365 38.525534),38.525534,-121.97365 +1520 Terminal St,0,West Sacramento,California Fire Roasted LLC,0.0,dehydrator,CA,tomato,0.0,dehydrator,95691,PROC,0101000020E6100000A1E76047AD625EC0B7BCCD76E0484340,POINT (-121.5418261 38.5693501),38.5693501,-121.5418261 +1244 E Beamer St,0,Woodland,Culinary Farms,0.0,dehydrator,CA,tomatoes,0.0,dehydrator,95776,PROC,0101000020E61000004C50C3B7B0705EC0BCA24A8391574340,POINT (-121.760786 38.6841282),38.6841282,-121.760786 +901 N Walton Ave,0,Yuba City,sunsweet growers,0.0,dehydrator,CA,prune date,0.0,dehydrator,95993,PROC,0101000020E61000001533672211695EC0D2EF6F8EC2914340,POINT (-121.6416708 39.13874989),39.13874989,-121.6416708 +6229 Myers Road,0,Williams,olam spices and vegetable ingredients,0.0,dehydrator,CA,spice vegetables,0.0,dehydrator,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +1500 Eager Rd,0,Live Oak,wilbur packing co,0.0,dehydrator,CA,prune,0.0,dehydrator,95953,PROC,0101000020E610000051BB5F05F8685EC0168B3ACE48984340,POINT (-121.640138 39.18972185),39.18972185,-121.640138 +7207 Moon Bend Rd,0,Colusa,sunsweet dryers,0.0,dehydrator,CA,prune date fruit nut,0.0,dehydrator,95932,PROC,0101000020E610000022EF0B9EF87F5EC039C29AB105994340,POINT (-121.9995494 39.19548626),39.19548626,-121.9995494 +9301 9399 Larkin Rd,0,Live Oak,sunsweet dryers,0.0,dehydrator,CA,prune date fruit nut,0.0,dehydrator,95953,PROC,0101000020E6100000E97E4E417E6C5EC0FC89CA8635A14340,POINT (-121.695206 39.259446),39.259446,-121.695206 +1900 Highway 99,0,Gridley,stapleton spense packing,0.0,dehydrator,CA,plums prunes,0.0,dehydrator,95948,PROC,0101000020E610000068565B56066C5EC09688015CDAAF4340,POINT (-121.6878868 39.3738513),39.3738513,-121.6878868 +7714 Co Rd 9,0,Orland,sunsweet dryers,0.0,dehydrator,CA,prune date fruit nut,0.0,dehydrator,95963,PROC,0101000020E61000005C920376358C5EC0BE4C142175DF4340,POINT (-122.190763 39.745762),39.745762,-122.190763 +101 Larkspur Landing Cir # 350,0,Larkspur,ONeill Vintners Distillers,0.0,distillery,CA,distillers grain,0.0,distillery,94939,PROC,0101000020E6100000BE1182FABBA05EC0C218ECE126F94240,POINT (-122.5114733 37.9464991),37.9464991,-122.5114733 +103 Harvard Ave #4,0,Half Moon Bay,Half Moon Bay Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,94019,PROC,0101000020E61000005DEEDD309B9F5EC0F8929DE96BC04240,POINT (-122.4938471 37.50329323),37.50329323,-122.4938471 +10400 US-101,0,Hopland,Jaxon Keys Winery Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95449,PROC,0101000020E6100000C1E270E657C75EC0BA8102EFE47D4340,POINT (-123.11474 38.983549),38.983549,-123.11474 +1042 McCall Ave,0,Sanger,E J Gallo Mc Call Winery,0.0,distillery,CA,distillers grain,0.0,distillery,93657,PROC,0101000020E6100000CCCF0D4DD9E65DC0CDA90947355C4240,POINT (-119.607013 36.7203759),36.7203759,-119.607013 +108 Dodd Ct,0,American Canyon,Loch Union Distilling,0.0,distillery,CA,distillers grain,0.0,distillery,94503,PROC,0101000020E6100000094E7D2079905EC0449DA0EAE3184340,POINT (-122.257393 38.19445546),38.19445546,-122.257393 +10960 Wheatlands Ave,0,Santee,BNS Brewing and Distilling Co,0.0,distillery,CA,distillers grain,0.0,distillery,92071,PROC,0101000020E6100000BEAA0E14533D5DC049360D40596C4040,POINT (-116.9581957 32.8464737),32.8464737,-116.9581957 +1121 Palmetto Ave,0,Pacifica,The Tripp Distillery LLC,0.0,distillery,CA,distillers grain,0.0,distillery,94044,PROC,0101000020E6100000040A50AE849F5EC0A44F2F2134D24240,POINT (-122.4924732 37.64221587),37.64221587,-122.4924732 +11460 Sunrise Gold Cir c,0,Rancho Cordova,Gold River Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95742,PROC,0101000020E610000076887FD8D2505EC01ED0255E964C4340,POINT (-121.262869 38.59833886),38.59833886,-121.262869 +121 Industrial Way #4,0,Belmont,Old World Spirits LLC,0.0,distillery,CA,distillers grain,0.0,distillery,94002,PROC,0101000020E6100000E6CAA0DAE0995EC0BFCB56A8FFD34240,POINT (-122.404349 37.65623955),37.65623955,-122.404349 +12205 Locksley Ln #11,0,Auburn,California Distilled Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,95602,PROC,0101000020E610000060F591A520465EC046C4FFE3A5794340,POINT (-121.0957426 38.95037508),38.95037508,-121.0957426 +1260 Lincoln Ave #1100,0,Pasadena,Stark Spirits Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,91103,PROC,0101000020E61000004E5FCFD72C8A5DC0A46E675F79154140,POINT (-118.158987 34.1677665),34.1677665,-118.158987 +1300 Factory Pl,0,Los Angeles,loft bear,0.0,distillery,CA,distillers grain,0.0,distillery,90013,PROC,0101000020E6100000E02BBAF51A8F5DC00FCAE29BF9044140,POINT (-118.2360205 34.03886746),34.03886746,-118.2360205 +1320 Scott St,0,Petaluma,Griffo Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,94954,PROC,0101000020E61000006EA301BC85AA5EC008C7D1C19F224340,POINT (-122.6644125 38.2705004),38.2705004,-122.6644125 +137 Anacapa St,0,Santa Barbara,Cutlers Artisan Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,93101,PROC,0101000020E6100000BA15C26A2CEC5DC096129BF215354140,POINT (-119.690211 34.41473229),34.41473229,-119.690211 +1439 Egbert Ave,0,San Francisco,Seven Stills Brewery Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,94124,PROC,0101000020E61000001B5B199E28995EC08173EBDA83DC4240,POINT (-122.3931041 37.7227739),37.7227739,-122.3931041 +1477 University Ave,0,San Diego,FruitCraft Fermentery Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,92103,PROC,0101000020E61000004B32BCA390495DC00147A753C35F4040,POINT (-117.1494531 32.7481484),32.7481484,-117.1494531 +1495 G St,0,San Diego,You Yours Distilling Co,0.0,distillery,CA,distillers grain,0.0,distillery,92101,PROC,0101000020E6100000666DAEF5A0495DC0DFBB7262345B4040,POINT (-117.1504492 32.71253615),32.71253615,-117.1504492 +1705 Mariposa St,0,San Francisco,Anchor Brewers Distillers,0.0,distillery,CA,distillers grain,0.0,distillery,94107,PROC,0101000020E610000038712832A9995EC04EB857E6ADE14240,POINT (-122.4009519 37.7631195),37.7631195,-122.4009519 +200 Yosemite Blvd,0,Modesto,E J Gallo Brandy Plant,0.0,distillery,CA,distillers grain,0.0,distillery,95354,PROC,0101000020E6100000C481EBE5523F5EC06551B73768D14240,POINT (-120.9894347 37.63599297),37.63599297,-120.9894347 +201 Industrial Way,0,Buellton,Brothers Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,93427,PROC,0101000020E610000011CE0248C80C5EC0AA5DB818A84E4140,POINT (-120.1997242 34.6145049),34.6145049,-120.1997242 +2174 CA-46,0,Paso Robles,KroBar Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,93446,PROC,0101000020E610000066DB696B442C5EC0290989B48DD14140,POINT (-120.691676 35.637137),35.637137,-120.691676 +23570 Arnold Dr,0,Sonoma,HelloCello Proh Sprits Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95476,PROC,0101000020E6100000E85729F3459D5EC05F11FC6F251D4340,POINT (-122.4573944 38.22770500000001),38.22770500000001,-122.4573944 +2420 Park Ave,0,Chico,Hooker Oak Distillery LLC,0.0,distillery,CA,distillers grain,0.0,distillery,95928,PROC,0101000020E61000003F0C63C133745EC03C35F2D47EDB4340,POINT (-121.8156589 39.7148081),39.7148081,-121.8156589 +2455 Huntington Dr,0,Fairfield,FrankLin Distillers Products Ltd,0.0,distillery,CA,distillers grain,0.0,distillery,94533,PROC,0101000020E6100000407B3F7FEB7E5EC0E08ABC93EC224340,POINT (-121.9831236 38.27284476),38.27284476,-121.9831236 +2459 E 8th St,0,Los Angeles,Greenbar Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,90021,PROC,0101000020E61000004D8F5CED978E5DC079B4CC7DCD034140,POINT (-118.2280229 34.0297086),34.0297086,-118.2280229 +2505 Monarch St,0,Alameda,Hangar 1 Vodka,0.0,distillery,CA,distillers grain,0.0,distillery,94501,PROC,0101000020E610000071917BBABA935EC0C0538EEAF0E44240,POINT (-122.308272 37.78860218),37.78860218,-122.308272 +2601 Monarch St,0,Alameda,St George Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,94501,PROC,0101000020E6100000106CA68CC9935EC05AF10D85CFE44240,POINT (-122.3091766 37.787583),37.787583,-122.3091766 +270 17th St,0,San Diego,Old Harbor Distilling Co,0.0,distillery,CA,distillers grain,0.0,distillery,92101,PROC,0101000020E61000004C04053983495DC0B4299123A15A4040,POINT (-117.1486342 32.70804257),32.70804257,-117.1486342 +2725 Adelaida Rd,0,Paso Robles,Villicana Winery refind Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,93446,PROC,0101000020E6100000EFF08DD7722F5EC06A1FE16A53D34140,POINT (-120.7413844 35.6509832),35.6509832,-120.7413844 +2739 Via Orange Way Suite 110,0,Spring Valley,Liberty Call Distilling LLC,0.0,distillery,CA,distillers grain,0.0,distillery,91978,PROC,0101000020E6100000C2A15CBF053E5DC03AF2F6D6765D4040,POINT (-116.9691008 32.7301892),32.7301892,-116.9691008 +2766 Via Orange Way h,0,Spring Valley,San Diego Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,91978,PROC,0101000020E6100000DAFDCF06053E5DC0054E3ABA5F5D4040,POINT (-116.9690568 32.72948387),32.72948387,-116.9690568 +3064 Limestone Way,0,Paso Robles,Wine Shine,0.0,distillery,CA,distillers grain,0.0,distillery,93446,PROC,0101000020E610000066DB696B442C5EC0290989B48DD14140,POINT (-120.691676 35.637137),35.637137,-120.691676 +3073 Newtown Rd,0,Placerville,1848 Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95667,PROC,0101000020E61000007288B839952F5EC0D70BECCEE65D4340,POINT (-120.743483 38.73360621),38.73360621,-120.743483 +3173 Del Este,0,Modesto,Do Good Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95354,PROC,0101000020E610000047ACC5A7003E5EC0BF0F070951D24240,POINT (-120.96879 37.643098),37.643098,-120.96879 +3189 Independence Dr,0,Livermore,Sutherland Distilling Company,0.0,distillery,CA,distillers grain,0.0,distillery,94551,PROC,0101000020E6100000DE58501814745EC0A374E95F92DA4240,POINT (-121.8137265 37.707592),37.707592,-121.8137265 +3230 Riverside Ave,0,Paso Robles,Azeo Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,93446,PROC,0101000020E610000004D48A251B2C5EC0A8BD2DFDF0D24140,POINT (-120.6891569 35.6479794),35.6479794,-120.6891569 +3701 Collins Ave,0,Richmond,Falcon Spirits Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,94806,PROC,0101000020E61000008FA1084EA2965EC05E363AE7A7FD4240,POINT (-122.3536563 37.98168650000001),37.98168650000001,-122.3536563 +382 Enterprise St Ste 104,0,San Marcos,California Spitirs Co,0.0,distillery,CA,distillers grain,0.0,distillery,92078,PROC,0101000020E610000063CF4312E2495DC02DC3C9479C914040,POINT (-117.1544233 33.1375818),33.1375818,-117.1544233 +3891 N Ventura Ave,0,Ventura,Ventura Spirits Company,0.0,distillery,CA,distillers grain,0.0,distillery,93001,PROC,0101000020E61000006F7374A69AD25DC05C69633612294140,POINT (-119.2906891 34.3208683),34.3208683,-119.2906891 +4001 Spring Mountain Rd,0,St Helena,Charbay Winery Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,94574,PROC,0101000020E61000007FF8F9EFC1A25EC07B67178084424340,POINT (-122.543087 38.51966859),38.51966859,-122.543087 +40300 Greenwood Way,0,Oakhurst,Oakhurst Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,93644,PROC,0101000020E6100000E6CB0BB08FE95DC0460FD7C5C8AA4240,POINT (-119.649395 37.3342521),37.3342521,-119.649395 +40880 County Center Dr,0,Temecula,Kalifornia Distilleries Inc,0.0,distillery,CA,distillers grain,0.0,distillery,92591,PROC,0101000020E6100000ECF021F2274A5DC09466987F99C34040,POINT (-117.1586881 33.5281219),33.5281219,-117.1586881 +411 Broadway St,0,Fresno,411 Broadway Ales Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,93721,PROC,0101000020E6100000F6B8CA6E41F25DC07C97F7DD195D4240,POINT (-119.7852437 36.7273519),36.7273519,-119.7852437 +425 Alta St #15,0,Gonzales,Fogs End Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,93926,PROC,0101000020E61000006E73BE33B55C5EC0F67CCD72D9404240,POINT (-121.4485597 36.506636),36.506636,-121.4485597 +427 Swift St A,0,Santa Cruz,Venus Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,95060,PROC,0101000020E61000001CC0119326835EC0516452E8617A4240,POINT (-122.0492294 36.9561129),36.9561129,-122.0492294 +477 25th St,0,Oakland,Crooked City Cider,0.0,distillery,CA,distillers grain,0.0,distillery,94612,PROC,0101000020E6100000E5E2B9081D915EC06B8F28FE39E84240,POINT (-122.2673971 37.8142698),37.8142698,-122.2673971 +5050 Robert J Mathews Pkwy,0,El Dorado Hills,Dry Diggings Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95762,PROC,0101000020E6100000B52B3E4FCD435EC00BA8AAAFB24F4340,POINT (-121.0594061 38.62264057000001),38.62264057000001,-121.0594061 +5216 Arboga Rd,0,Olivehurst,CaliShine Distillery Co,0.0,distillery,CA,distillers grain,0.0,distillery,95961,PROC,0101000020E61000003153A40CE6635EC0E54A56A8628D4340,POINT (-121.5609161 39.10457329),39.10457329,-121.5609161 +555 Avacado Rd,0,Oroville,Cobble Ridge Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95966,PROC,0101000020E6100000878A71FE265F5EC0FF7A8505F7BD4340,POINT (-121.486755 39.484101),39.484101,-121.486755 +5579 Soquel San Jose Rd,0,Soquel,Osocalis Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95073,PROC,0101000020E61000007E78F1D9957C5EC02D74CA4862874240,POINT (-121.9466462 37.0576869),37.0576869,-121.9466462 +5625 State Farm Dr #18,0,Rohnert Park,Sonoma County Distilling Co,0.0,distillery,CA,distillers grain,0.0,distillery,94928,PROC,0101000020E61000000FA6176B6EAD5EC0A28B97B89F2D4340,POINT (-122.7098644 38.3564368),38.3564368,-122.7098644 +611 2nd St,0,Petaluma,Sweetwater Distillers,0.0,distillery,CA,distillers grain,0.0,distillery,94952,PROC,0101000020E610000096B9540067A85EC07016A36C991D4340,POINT (-122.6312867 38.23124464),38.23124464,-122.6312867 +6790 McKinley St,0,Sebastopol,Spirit Works Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95472,PROC,0101000020E6100000DCD6169E97B45EC077B00FFCB9334340,POINT (-122.821754 38.4041133),38.4041133,-122.821754 +721 Nevada Street #206B,0,Redlands,J Riley Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,92373,PROC,0101000020E61000001767672CF54D5DC06BE9769BDC074140,POINT (-117.2180892 34.0614199),34.0614199,-117.2180892 +7759 Bell Rd,0,Windsor,Sonoma Brothers Distilling,0.0,distillery,CA,distillers grain,0.0,distillery,95492,PROC,0101000020E61000008C2FDAE385B35EC04166C28AAE444340,POINT (-122.805047 38.5365766),38.5365766,-122.805047 +802 E Washington Ave,0,Santa Ana,Blinky Owl Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,92701,PROC,0101000020E6100000C2A1B778F8765DC07F7FEFDBB5E04040,POINT (-117.8589155 33.7555499),33.7555499,-117.8589155 +8418 S Lac Jac Ave,0,Parlier,Oneill Beverages Co LLC,0.0,distillery,CA,distillers grain,0.0,distillery,93648,PROC,0101000020E6100000CB619C64D0DE5DC00162B774714E4240,POINT (-119.4814693 36.6128374),36.6128374,-119.4814693 +8650 Hayden Pl,0,Culver City,Bavarian Breweries Distilleries,0.0,distillery,CA,distillers grain,0.0,distillery,90232,PROC,0101000020E6100000B61902DB9C985DC0AE994208C4024140,POINT (-118.3845737 34.02160743),34.02160743,-118.3845737 +8706 Production Ave,0,San Diego,Malahat Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,92121,PROC,0101000020E6100000D185A28AAC4A5DC0955BFF5316714040,POINT (-117.1667811 32.8834939),32.8834939,-117.1667811 +8733 Magnolia Ave Ste. 126,0,Santee,Copper Collar Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,92071,PROC,0101000020E6100000F87F1F1FBE3D5DC0D2F701E5C26A4040,POINT (-116.9647291 32.83407271),32.83407271,-116.9647291 +909 E El Segundo Blvd,0,El Segundo,Rob Rubens Distilling and Brewing,0.0,distillery,CA,distillers grain,0.0,distillery,90245,PROC,0101000020E6100000BB062230FB995DC03F6AFA8956F54040,POINT (-118.4059563 33.91670346),33.91670346,-118.4059563 +915 S Santa Fe Ave,0,Los Angeles,Our/Los Angeles Vodka,0.0,distillery,CA,distillers grain,0.0,distillery,90021,PROC,0101000020E6100000184CB2C4B98E5DC0B612572127044140,POINT (-118.2300884 34.03244416),34.03244416,-118.2300884 +9275 Midway,0,Durham,Almendra Winery Distillery,0.0,distillery,CA,distillers grain,0.0,distillery,95938,PROC,0101000020E6100000DAB6DE2527735EC042CAF4F00AD24340,POINT (-121.7992644 39.6409589),39.6409589,-121.7992644 +9750 Distribution Ave,0,San Diego,Cutwater Spirits,0.0,distillery,CA,distillers grain,0.0,distillery,92121,PROC,0101000020E61000005C1B2AC6794A5DC08F238C5539714040,POINT (-117.1636825 32.8845622),32.8845622,-117.1636825 +E South St,0,Bishop,Owens Valley Distilling Co,0.0,distillery,CA,distillers grain,0.0,distillery,93514,PROC,0101000020E6100000323B8BDEA99A5DC0B439CE6DC2AD4240,POINT (-118.416618 37.357496),37.357496,-118.416618 +Pier 50 Shed B,0,San Francisco,Distillery No 209,0.0,distillery,CA,distillers grain,0.0,distillery,94158,PROC,0101000020E61000002A58E36C3A995EC05512D90759E24240,POINT (-122.394191 37.768342),37.768342,-122.394191 +10441 Stanford Ave,0,Garden Grove,Darling International Inc,0.0,fog,CA,fog,0.0,distributor,92842,PROC,0101000020E6100000C729DFD8D87C5DC07591214B8FE34040,POINT (-117.9507353 33.77781047),33.77781047,-117.9507353 +11947 S Carpenter Rd,0,Crows Landing,Darling International Inc,0.0,fog,CA,fog,0.0,recycling,95313,PROC,0101000020E6100000DDB243FCC3425EC098DC28B2D6B64240,POINT (-121.043212 37.428427),37.428427,-121.043212 +11946 S Carpenter Rd,0,Crows Landing,Darling International Inc,0.0,fog,CA,fog,0.0,meat,95313,PROC,0101000020E610000098D7B6CDF9415EC006B86277E8BC4240,POINT (-121.0308718 37.47584431),37.47584431,-121.0308718 +7878 Airway Rd,0,San Diego,Heinz Frozen Food Co,0.0,freshfrozen,CA,misc,0.0,frozen,92154,PROC,0101000020E61000008AE59656433E5DC0E3363BCEC4474040,POINT (-116.97286 32.56069353),32.56069353,-116.97286 +2105 Anderholt Rd,0,Holtville,Grimmway Farm,0.0,freshfrozen,CA,misc carrot,0.0,farm,92250,PROC,0101000020E610000058E36C3A02D85CC03B6EF8DD74674040,POINT (-115.375136 32.808254),32.808254,-115.375136 +1051 Pacific Ave,0,Oxnard,Gills Onions,0.0,freshfrozen,CA,onion,0.0,fresh,93030,PROC,0101000020E6100000070951BEA0CA5DC0AAE8595A57184140,POINT (-119.166061 34.1901658),34.1901658,-119.166061 +1250 E Third St,0,Oxnard,tree top,0.0,freshfrozen,CA,fruit,0.0,frozen,93030,PROC,0101000020E61000007F0173E34CCB5DC0DB178EEFA4194140,POINT (-119.1765679 34.20034594),34.20034594,-119.1765679 +CA 166,0,New Cuyama,Grimmway Farm,0.0,freshfrozen,CA,misc carrot,0.0,farm,93254,PROC,0101000020E6100000F96706F181EA5DC06D1CB1169F784140,POINT (-119.664181 34.942355),34.942355,-119.664181 +830 Sycamore Rd,0,Arvin,Grimmway Arvin Organic,0.0,freshfrozen,CA,vegetables,0.0,distributor,93203,PROC,0101000020E61000006F7143424AB45DC0075E6F9338994140,POINT (-118.8170324 35.19703906),35.19703906,-118.8170324 +12000 Main St,0,Lamont,CalOrganic Farms,0.0,freshfrozen,CA,vegetables,0.0,farm,93241,PROC,0101000020E610000081EB8A19E1BA5DC0ED139BEA249F4140,POINT (-118.919989 35.2433141),35.2433141,-118.919989 +14141 Di Giorgio Rd,0,Arvin,Grimmway Farm,0.0,freshfrozen,CA,misc carrot,0.0,farm,93203,PROC,0101000020E61000002909E46D80B75DC03026052FDD9F4140,POINT (-118.8672137 35.24893749),35.24893749,-118.8672137 +12495 Di Giorgio Rd,0,Arvin,Grimmway Farm,0.0,freshfrozen,CA,misc carrot,0.0,farm,93203,PROC,0101000020E61000009040CDDA37B75DC0CA69D301DE9F4140,POINT (-118.8627841 35.24896262),35.24896262,-118.8627841 +11412 Malaga Rd,0,Arvin,Grimmway Farm,0.0,freshfrozen,CA,misc carrot,0.0,farm,93203,PROC,0101000020E61000005576B0B442B75DC09A4074B553A04140,POINT (-118.8634464 35.25255459),35.25255459,-118.8634464 +14322 Di Giorgio Rd,0,Arvin,Green Valley Packers LLC,0.0,freshfrozen,CA,fruit vegetable,0.0,distributor,93203,PROC,0101000020E6100000AE5EEA8C14B65DC069B2DA5779A04140,POINT (-118.8450043 35.2537031),35.2537031,-118.8450043 +6900 Mountain View Rd,0,Bakersfield,Grimmway Enterprises,0.0,freshfrozen,CA,misc carrot,0.0,farm,93307,PROC,0101000020E610000055E0BFD42ABB5DC07DCF488446A44140,POINT (-118.9244892 35.283402),35.283402,-118.9244892 +7200 E Brundage Ln,0,Bakersfield,Bolthouse,0.0,freshfrozen,CA,fruit vegetable,0.0,beverage,93306,PROC,0101000020E61000003A419B1C3EBB5DC0E6D308A293AD4140,POINT (-118.925666 35.35606790000001),35.35606790000001,-118.925666 +33540 CA 58,0,Buttonwillow,Bolthouse,0.0,freshfrozen,CA,fruit vegetable,0.0,farm,93206,PROC,0101000020E61000006B0F7BA100D85DC0CAF474430DB34140,POINT (-119.3750385 35.39884227),35.39884227,-119.3750385 +6301 S Zerker Rd,0,Shafter,Grimmway Citrus,0.0,freshfrozen,CA,citrus,0.0,farm,93263,PROC,0101000020E6100000B610E4A084D25DC0DAE731CA33BF4140,POINT (-119.289345 35.493768),35.493768,-119.289345 +11888 E Clarkson Ave,0,Kingsburg,sunsweet fresh,0.0,freshfrozen,CA,prune date,0.0,fresh,93631,PROC,0101000020E6100000FCBB8800F1E45DC00B4DC8BDAF404240,POINT (-119.5772096 36.5053632),36.5053632,-119.5772096 +16429 W Kamm Ave,0,Helm,ConAgra Foods,0.0,freshfrozen,CA,tomato misc,0.0,distributor,93627,PROC,0101000020E610000090DD054A8A055EC0E7DE686C54434240,POINT (-120.0865655 36.5260139),36.5260139,-120.0865655 +12133 Avenue 408,0,Cutler,wawona frozen foods,0.0,freshfrozen,CA,fruit,0.0,frozen,93615,PROC,0101000020E61000004D3A803452D35DC0F8D6D182E1434240,POINT (-119.3018924 36.53031955),36.53031955,-119.3018924 +2202 S Cedar Ave,0,Fresno,wawona frozen foods,0.0,freshfrozen,CA,fruit,0.0,frozen,93725,PROC,0101000020E610000089C8FA1752F05DC0F4C70FF0FF5B4240,POINT (-119.7550106 36.7187481),36.7187481,-119.7550106 +5626 E Shields Ave,0,Fresno,ConAgra Foods,0.0,freshfrozen,CA,tomato misc,0.0,distributor,93727,PROC,0101000020E6100000355F251FBBEC5DC05960D916AF634240,POINT (-119.698921 36.7787808),36.7787808,-119.698921 +100 W Alluvial Ave,0,Clovis,wawona frozen foods,0.0,freshfrozen,CA,fruit,0.0,frozen,93611,PROC,0101000020E6100000DA88CC01A7ED5DC04E41237DFF6B4240,POINT (-119.7133183 36.8437344),36.8437344,-119.7133183 +1265 N Minnewawa Ave,0,Clovis,wawona frozen foods,0.0,freshfrozen,CA,fruit,0.0,frozen,93619,PROC,0101000020E61000000C37853A51ED5DC01FB127CB5A6D4240,POINT (-119.7080828 36.8543333),36.8543333,-119.7080828 +1720 Beach Rd,0,Watsonville,Del Mar Foods,0.0,freshfrozen,CA,apple peach apricot blackberries strawberries brussel sprouts bell pepers spinach,0.0,frozen,95076,PROC,0101000020E6100000CA1F67F5E9715EC02992544BDF724240,POINT (-121.7799047 36.8974394),36.8974394,-121.7799047 +120 Dubois St,0,Santa Cruz,Odwalla Juices,0.0,freshfrozen,CA,fruit vegetable,0.0,misc,95060,PROC,0101000020E610000025CB49287D825EC0B756C565267E4240,POINT (-122.038889 36.9855468),36.9855468,-122.038889 +2525 Cooper Ave,0,Merced,white oaks frozen foods,0.0,freshfrozen,CA,vegetables,0.0,frozen,95348,PROC,0101000020E61000000E6F319AF0205EC06BABC40280A84240,POINT (-120.5146852 37.31640658),37.31640658,-120.5146852 +1805 Las Plumas Ave,0,San Jose,Odwalla Juices,0.0,freshfrozen,CA,fruit vegetable,0.0,misc,95133,PROC,0101000020E6100000837BAF6B45775EC0DC2C5E2C8CAE4240,POINT (-121.8636121 37.36365275),37.36365275,-121.8636121 +120 Stone Pine Rd,0,Half Moon Bay,Odwalla Juices,0.0,freshfrozen,CA,fruit vegetable,0.0,misc,94019,PROC,0101000020E6100000E344AADE509B5EC0B7B2E9ADA6BB4240,POINT (-122.4268109 37.46602415),37.46602415,-122.4268109 +300 Dianne Dr,0,Turlock,supherb farms,0.0,freshfrozen,CA,vegetable herb,0.0,fresh frozen,95380,PROC,0101000020E6100000B261F2AB5E385EC02D9A290879BF4240,POINT (-120.8807783 37.4958811),37.4958811,-120.8807783 +1010 Twin Cities Rd,0,Courtland,seneca foods corp,0.0,freshfrozen,CA,apricots peaches pears,0.0,distributor,95615,PROC,0101000020E6100000E3A430EF71635EC00EBDC5C37B284340,POINT (-121.553829 38.316277),38.316277,-121.553829 +2327 Chester Dr,0,Penngrove,Morning Star Packing Co,0.0,freshfrozen,CA,tomato,0.0,distributor,94951,PROC,0101000020E6100000B8E11C1A3BAA5EC0374A03E4F02A4340,POINT (-122.6598573 38.3354764),38.3354764,-122.6598573 +345 Sutton Pl,0,Santa Rosa,Odwalla Juices,0.0,freshfrozen,CA,fruit vegetable,0.0,misc,95407,PROC,0101000020E6100000EDDBA4FD6AAE5EC02D1911D610324340,POINT (-122.7252802 38.3911388),38.3911388,-122.7252802 +826 National Dr 200,0,Sacramento,Odwalla Juices,0.0,freshfrozen,CA,fruit vegetable,0.0,misc,95834,PROC,0101000020E6100000EFB490DB0A5F5EC0123F106AD0534340,POINT (-121.4850377 38.6547978),38.6547978,-121.4850377 +724 Main St 202,0,Woodland,Morning Star Packing Co,0.0,freshfrozen,CA,tomato,0.0,distributor,95695,PROC,0101000020E6100000572426A861715EC086E2F161B4564340,POINT (-121.7715855 38.67737984),38.67737984,-121.7715855 +2211 Old Highway 99W,0,Williams,Morning Star Packing Co,0.0,freshfrozen,CA,tomato,0.0,distributor,95987,PROC,0101000020E6100000DC0E0D8B51895EC0840F255AF2924340,POINT (-122.145602 39.148021),39.148021,-122.145602 +7545 Irvine Center Dr,0,Irvine,kraft,0.0,misc,CA,misc dairy meat bakery,0.0,distributor,92618,PROC,0101000020E610000085BB69E940705DC015BBA6D5CAD44040,POINT (-117.7539619 33.66244002),33.66244002,-117.7539619 +18301 Von Karman Ave 1100,0,Irvine,Golden State Foods,0.0,misc,CA,meat dairy vegetables,0.0,distribution,92612,PROC,0101000020E61000002558C1148A765DC053D62D0AD4D64040,POINT (-117.8521778 33.67834594000001),33.67834594000001,-117.8521778 +1500 E Walnut Ave,0,Fullerton,kraft,0.0,misc,CA,misc dairy meat bakery,0.0,misc,92831,PROC,0101000020E610000050BA3EBDE3795DC059D40E1C23EF4040,POINT (-117.9045251 33.86825896),33.86825896,-117.9045251 +12801 Excelsior Dr,0,Santa Fe Springs,Safeway Distribution,0.0,misc,CA,misc,0.0,distributor,90670,PROC,0101000020E6100000EE9D2C1018845DC03E0801F992F24040,POINT (-118.0639687 33.89511025),33.89511025,-118.0639687 +19317 Arenth Ave,0,City of Industry,Golden State Foods,0.0,misc,CA,meat dairy vegetables,0.0,distribution,91748,PROC,0101000020E61000003F4C0C1357785DC012D3CFE517004140,POINT (-117.8803146 34.0007293),34.0007293,-117.8803146 +21489 Baker Pkwy,0,City of Industry,Golden State Foods,0.0,misc,CA,meat dairy vegetables,0.0,distribution,91789,PROC,0101000020E61000006F6D3C339C755DC0B735D88A6C014140,POINT (-117.8376587 34.01112495),34.01112495,-117.8376587 +11600 Riverside Dr,0,Mira Loma,Costco Depot,0.0,misc,CA,misc,0.0,distributor,91752,PROC,0101000020E6100000FAFD518A8C625DC07BC9B557D5014140,POINT (-117.5398279 34.0143232),34.0143232,-117.5398279 +3450 Dulles Dr,0,Mira Loma,Nestle Prepared Foods,0.0,misc,CA,food beverage,0.0,distributor,91752,PROC,0101000020E6100000F45723160C615DC0180F4AF322034140,POINT (-117.5163627 34.0245041),34.0245041,-117.5163627 +640 S 6th Ave,0,City of Industry,Golden State Foods,0.0,misc,CA,meat dairy vegetables,0.0,distribution,91746,PROC,0101000020E6100000DDBCCC0B0B7F5DC039E53C29B4034140,POINT (-117.9850492 34.02893558),34.02893558,-117.9850492 +5650 E Santa Ana St,0,Ontario,GEODIS distribution,0.0,misc,CA,misc,0.0,shipping,91761,PROC,0101000020E61000002E156580D5615DC0C0A78306AC064140,POINT (-117.5286561 34.0521248),34.0521248,-117.5286561 +3392 N Mike Daley Dr,0,San Bernardino,heinz,0.0,misc,CA,misc dairy meat bakery,0.0,distributor,92407,PROC,0101000020E6100000B53286DE07555DC01F752ACF72134140,POINT (-117.3286053 34.1519412),34.1519412,-117.3286053 +950 Mountain View Ave,0,Oxnard,pacific coast produce,0.0,misc,CA,misc fruit meat dairy,0.0,distribution,93030,PROC,0101000020E6100000FE2B2B4DCACA5DC00A4F43AF9A184140,POINT (-119.1685975 34.1922206),34.1922206,-119.1685975 +21101 Bear Mountain Blvd,0,Bakersfield,J G Boswell Co,0.0,misc,CA,onion tomato wheat cotton alfalfa,0.0,farm,93311,PROC,0101000020E6100000628CA3CDCCCC5DC0D3E2E71AC19A4140,POINT (-119.2000002 35.2090181),35.2090181,-119.2000002 +Ashe Rd,0,Bakersfield,J G Boswell Co,0.0,misc,CA,onion tomato wheat cotton alfalfa,0.0,farm,93313,PROC,0101000020E6100000A33CF372D8C35DC03048FAB48AA04140,POINT (-119.060086 35.254233),35.254233,-119.060086 +36889 CA 58,0,Buttonwillow,J G Boswell Tomato Co,0.0,misc,CA,onion tomato wheat cotton alfalfa,0.0,misc,93206,PROC,0101000020E6100000CB0EF10F5BDC5DC04015376E31B34140,POINT (-119.443058 35.399946),35.399946,-119.443058 +7835 Estrella Rd,0,San Miguel,Star Farms,0.0,misc,CA,misc,0.0,farm,93451,PROC,0101000020E6100000D7F03ED8F3295EC06A73524E6ADC4140,POINT (-120.6555081 35.7219942),35.7219942,-120.6555081 +28001 Dairy Ave,0,Corcoran,J G Boswell Co,0.0,misc,CA,onion tomato wheat cotton alfalfa,0.0,misc,93212,PROC,0101000020E610000005508C2C99E45DC007BCC43F09064240,POINT (-119.571849 36.04715726),36.04715726,-119.571849 +710 Bainum Ave,0,Corcoran,J G Boswell Co,0.0,misc,CA,onion tomato wheat cotton alfalfa,0.0,misc,93212,PROC,0101000020E61000008E0244C18CE35DC045CFD2BAB20B4240,POINT (-119.555466 36.0913919),36.0913919,-119.555466 +18900 Gayle Ave,0,Huron,Woolf Enterprises,0.0,misc,CA,almond pistachio wheat garlic hay onion tomato grape walnut,0.0,farm,93234,PROC,0101000020E61000002C2CB81FF0055EC03B6D8D08C6174240,POINT (-120.092781 36.185731),36.185731,-120.092781 +2494 S Orange Ave,0,Fresno,kraft,0.0,misc,CA,misc dairy meat bakery,0.0,misc,93725,PROC,0101000020E6100000D136A38BF2F05DC06878B306EF5A4240,POINT (-119.7648038 36.7104195),36.7104195,-119.7648038 +6205 Engle Way E,0,Gilroy,Nestle Prepared Foods,0.0,misc,CA,misc,0.0,misc,95020,PROC,0101000020E610000070FD05CC8D635EC0BFE0890FA27E4240,POINT (-121.5555296 36.9893207),36.9893207,-121.5555296 +1125 Paulson Rd,0,Turlock,Land O Lakes Purina Feed,0.0,misc,CA,misc,0.0,misc,95380,PROC,0101000020E6100000E89491C45C355EC0ED5FBC930DBE4240,POINT (-120.8337871 37.48478934),37.48478934,-120.8337871 +16900 W Schulte Rd,0,Tracy,Safeway Distribution,0.0,misc,CA,misc,0.0,distributor,95377,PROC,0101000020E61000007BF3C06C27615EC032DDB1F9B4DB4240,POINT (-121.5180313 37.71646043),37.71646043,-121.5180313 +25862 S Schulte Ct,0,Tracy,Costco Depot,0.0,misc,CA,misc,0.0,distributor,95377,PROC,0101000020E61000001C977153035D5EC0F88903E8F7DB4240,POINT (-121.453328 37.718503),37.718503,-121.453328 +3000 Executive Pkwy,0,San Ramon,The Kraft Heinz Co,0.0,misc,CA,misc dairy meat bakery,0.0,distributor,94583,PROC,0101000020E6100000A4B38295F97D5EC03F24326255E24240,POINT (-121.9683584 37.7682307),37.7682307,-121.9683584 +2603 Camino Ramon 180,0,San Ramon,hj heinz co,0.0,misc,CA,misc dairy meat bakery,0.0,distributor,94583,PROC,0101000020E610000025F37E92717D5EC0C580579172E24240,POINT (-121.9600569 37.76912133),37.76912133,-121.9600569 +12667 Alcosta Blvd,0,San Ramon,kraft,0.0,misc,CA,misc dairy meat bakery,0.0,distributor,94583,PROC,0101000020E610000042542B5D8B7D5EC0AA549ADE0FE34240,POINT (-121.9616311 37.7739218),37.7739218,-121.9616311 +3656 Perlman Dr,0,Stockton,Hormel Foods Corp,0.0,misc,CA,misc meat,0.0,distributor,95206,PROC,0101000020E6100000F42675B80C515EC034C65E5A1AF54240,POINT (-121.2664014 37.91486673),37.91486673,-121.2664014 +7770 Rd 33,0,Madera,ENZO Olive Oil,0.0,olive,CA,olive,0.0,olive oil,93638,PROC,0101000020E6100000382394089EFC5DC05C6D8B53296E4240,POINT (-119.9471456 36.86063618),36.86063618,-119.9471456 +13950 Thornton Rd,0,Lodi,Calivirgin coldani olive ranch,0.0,olive,CA,olive,0.0,olive oil,95242,PROC,0101000020E610000032906797EF585EC0AA1EBCB8850D4340,POINT (-121.3896235 38.10564336),38.10564336,-121.3896235 +455 Harter Ave,0,Woodland,Boundary Bend Olives,0.0,olive,CA,olive,0.0,olive oil,95776,PROC,0101000020E6100000657506A197705EC092D332ADA8584340,POINT (-121.7592547 38.6926476),38.6926476,-121.7592547 +2675 Lone Tree Rd,0,Oroville,California Olive Ranch,0.0,olive,CA,olive,0.0,olive oil,95965,PROC,0101000020E6100000B81E85EBD1645EC058201F99B3AE4340,POINT (-121.5753125 39.36485590000001),39.36485590000001,-121.5753125 +5945 Co Rd 35,0,Artois,California Olive Ranch,0.0,olive,CA,olive,0.0,olive oil,95913,PROC,0101000020E6100000FDDAFAE93F895EC0B247A81952DD4340,POINT (-122.144526 39.729068),39.729068,-122.144526 +717 Tehama St,0,Orland,west coast products,0.0,olive,CA,olives,0.0,cannery oil,95963,PROC,0101000020E6100000DB9145F5B18C5EC085D726FCEFDF4340,POINT (-122.1983617 39.74951126),39.74951126,-122.1983617 +1367 E Lassen Ave,0,Chico,California Olive Ranch,0.0,olive,CA,olive,0.0,olive oil,95973,PROC,0101000020E6100000301004C8D0755EC01471DF0FE4E24340,POINT (-121.840868 39.7725849),39.7725849,-121.840868 +23377 South Ave,0,Corning,California Olive Ranch,0.0,olive,CA,olive,0.0,olive oil,96021,PROC,0101000020E61000000E187F364D8A5EC092AFE343F9F34340,POINT (-122.1609627 39.90604447),39.90604447,-122.1609627 +770 N Plano St,0,Porterville,Foster Farms,0.0,poultrymeat,CA,poultry,0.0,poultry,93257,PROC,0101000020E610000081DA5EC16CC05DC0ABAE4335250A4240,POINT (-119.0066379 36.0792605),36.0792605,-119.0066379 +2960 S Cherry Ave,0,Fresno,Foster Farms,0.0,poultrymeat,CA,poultry,0.0,poultry,93706,PROC,0101000020E6100000D01154E817F35DC004B5CEAE31594240,POINT (-119.7983342 36.6968287),36.6968287,-119.7983342 +5763 E Shields Ave,0,Fresno,Foster Farms Turkey Hatchery,0.0,poultrymeat,CA,turkey,0.0,poultry,93727,PROC,0101000020E61000002738503B57EC5DC0A98999D8D7634240,POINT (-119.6928242 36.7800246),36.7800246,-119.6928242 +18305 1st Ave,0,Stevinson,Foster Farms,0.0,poultrymeat,CA,poultry,0.0,poultry,95374,PROC,0101000020E6100000EE073C3080345EC079FB9C50C2AB4240,POINT (-120.820324 37.34186752),37.34186752,-120.820324 +1033 S Center St,0,Turlock,Foster Farms,0.0,poultrymeat,CA,poultry,0.0,poultry,95380,PROC,0101000020E61000007BE4C57883355EC0F65C2A5F65BE4240,POINT (-120.8361494 37.48746862),37.48746862,-120.8361494 +17880 W Schulte Rd,0,Tracy,Costco Meat Factory,0.0,poultrymeat,CA,poultry,0.0,poultry,95377,PROC,0101000020E6100000D4997B48F8615EC08513C93E65DC4240,POINT (-121.530779 37.72183976),37.72183976,-121.530779 +1500 Cader Ln,0,Petaluma,Petaluma poultry processors,0.0,poultrymeat,CA,chicken,0.0,poultry,94954,PROC,0101000020E6100000CE8536A5E1A55EC0A4062EEAEE1D4340,POINT (-122.5918973 38.2338536),38.2338536,-122.5918973 +4816 Long Beach Ave,0,Los Angeles,Los Angeles Poultry Co,0.0,poultrymeat,CA,poultry,0.0,processor,90058,PROC,0101000020E6100000C627AE74888F5DC0EE7043A5F4FF4040,POINT (-118.2427036 33.99965349),33.99965349,-118.2427036 +57 Shank Rd,0,Brawley,National Beef LP,0.0,redmeat,CA,beef,0.0,distributer,92227,PROC,0101000020E610000047681547AFE15CC09DC520EA1D804040,POINT (-115.5263231 33.00091292),33.00091292,-115.5263231 +2 Venture 250,0,Irvine,Hormel Foods Corp,0.0,redmeat,CA,misc meat,0.0,meat,92618,PROC,0101000020E6100000D68D774746705DC0D559B1E86BD44040,POINT (-117.7542895 33.65954312),33.65954312,-117.7542895 +3163 E Vernon Ave,0,Vernon,Clougherty Packing LLC Hormel Foods Corp farmer john,0.0,redmeat,CA,pork,0.0,distributor,90058,PROC,0101000020E6100000FB7B84F5DA8D5DC0B2BAD573D2004140,POINT (-118.2164892 34.0064225),34.0064225,-118.2164892 +145 S Hill Dr,0,Brisbane,Del Monte meat co,0.0,redmeat,CA,meat misc,0.0,meat,94005,PROC,0101000020E6100000325871AAB59A5EC0D58BCA1B1AD84240,POINT (-122.417338 37.68829677),37.68829677,-122.417338 +401 Jackson St,0,Oakland,Del Monte meat co,0.0,redmeat,CA,meat misc,0.0,meat,94607,PROC,0101000020E61000006740626042915EC08F464FDBD0E54240,POINT (-122.2696763 37.7954363),37.7954363,-122.2696763 +251 D'Arcy Pkwy,0,Lathrop,Swiss American Sausage Co,0.0,redmeat,CA,meat,0.0,distributor,95330,PROC,0101000020E610000032112510E5525EC0F66758EFE4E64240,POINT (-121.2952309 37.80386154),37.80386154,-121.2952309 +1000 Davis St,0,Livingston,Foster Farms Inc,0.0,redmeat,CA,meat,0.0,processor,95334,PROC,0101000020E6100000BAD4AD435A2E5EC0E714CBCA02B24240,POINT (-120.7242593 37.39071021),37.39071021,-120.7242593 +1210 66th St,0,Sacramento,Reeds Gormet Meat Co,0.0,redmeat,CA,meat,0.0,processor,95819,PROC,0101000020E6100000EB5EDD674B5B5EC0EDABBC2E0D474340,POINT (-121.4264774 38.5550898),38.5550898,-121.4264774 +12136 California Route 2,0,Los Angeles,Star Kosher Meat Market,0.0,redmeat,CA,meat,0.0,processor,90025,PROC,0101000020E6100000795D1A1AAA9D5DC0853A93D32A054140,POINT (-118.4635072 34.04036946),34.04036946,-118.4635072 +1219 N Carpenter Rd,0,Modesto,Ziadeh Meat Market,0.0,redmeat,CA,meat,0.0,processor,95351,PROC,0101000020E610000002EA72EF06425EC02D61E95379D34240,POINT (-121.0316733 37.65214013),37.65214013,-121.0316733 +1220 South Ave,0,Turlock,Sanders Meat Services,0.0,redmeat,CA,meat,0.0,distributer,95380,PROC,0101000020E610000000091E3A18375EC0DEEF48A31FBE4240,POINT (-120.8608537 37.48534051),37.48534051,-120.8608537 +12210 Michigan St #13,0,Grand Terrace,Exotic meat Market,0.0,redmeat,CA,meat,0.0,processor,92313,PROC,0101000020E6100000BB3E181DB5545DC06ED4546012044140,POINT (-117.3235543 34.0318108),34.0318108,-117.3235543 +1301 Rocky Point Dr,0,Oceanside,Olli Salumeria,0.0,redmeat,CA,meat,0.0,processor,92056,PROC,0101000020E6100000B62A2E3391525DC07A56D28A6F9B4040,POINT (-117.2901123 33.2143415),33.2143415,-117.2901123 +140 E Palm St,0,Exeter,Exeter Meats,0.0,redmeat,CA,meat,0.0,processor,93221,PROC,0101000020E6100000A4C8B5FC1BC95DC00F9BC8CC05264240,POINT (-119.1423332 36.297052),36.297052,-119.1423332 +1411 E Baseline St,0,San Bernardino,Nagle Veal and Quality Meats Inc,0.0,redmeat,CA,meat,0.0,distribution,92410,PROC,0101000020E6100000BC653D6B6D505DC0E67D7786840F4140,POINT (-117.2566784 34.12123185),34.12123185,-117.2566784 +1420 S Myrtle Ave,0,Monrovia,Burnett and Son Meat Co Inc,0.0,redmeat,CA,meat,0.0,processor,91016,PROC,0101000020E610000006AFA7670B805DC0540FC1067E114140,POINT (-118.0006961 34.13665852),34.13665852,-118.0006961 +14250 Lomitas Ave,0,City of Industry,Pocino Foods Co,0.0,redmeat,CA,meat,0.0,processor,91746,PROC,0101000020E6100000D718CFFB5A7F5DC086032159C0034140,POINT (-117.9899282 34.0293075),34.0293075,-117.9899282 +1471 Atteberry Ln,0,San Jose,Jims Wholesale Meats,0.0,redmeat,CA,meat,0.0,distribution,95131,PROC,0101000020E610000085D8F4FBD9795EC03F7F901B34B34240,POINT (-121.9039297 37.4000277),37.4000277,-121.9039297 +1480 Drew Ave,0,Davis,Superior Farms Inc,0.0,redmeat,CA,meat,0.0,processor,95618,PROC,0101000020E6100000FAA4C97B8B6E5EC07C03BC9A76454340,POINT (-121.7272634 38.54268202),38.54268202,-121.7272634 +1660 Old Bayshore Hwy,0,San Jose,Mohawk Packing Co,0.0,redmeat,CA,meat,0.0,distributer,95112,PROC,0101000020E6100000CA59338D017A5EC02306B2853DAF4240,POINT (-121.9063447 37.36906501000001),37.36906501000001,-121.9063447 +16691 Hale Ave,0,Irvine,sysco newport meat co,0.0,redmeat,CA,meat,0.0,processor,92606,PROC,0101000020E6100000CEC133A149755DC059F6A8E8DDD84040,POINT (-117.832619 33.69427212),33.69427212,-117.832619 +18256 CA-108,0,Jamestown,Raw Hide Meats,0.0,redmeat,CA,meat,0.0,processor,95327,PROC,0101000020E61000001EA4A7C8211C5EC0029D499BAAF54240,POINT (-120.439562 37.919269),37.919269,-120.439562 +1828 E Hedges Ave,0,Fresno,Valley Protein Inc,0.0,redmeat,CA,red meat poultry,0.0,processor,93703,PROC,0101000020E610000032207BBD7BF25DC0E3E423CE2F614240,POINT (-119.7888025 36.75927140000001),36.75927140000001,-119.7888025 +19455 E Clausen Rd,0,Turlock,Clausen Meat Co,0.0,redmeat,CA,meat,0.0,distribution,95380,PROC,0101000020E610000042EFE8DA72355EC027CBFF9A62BA4240,POINT (-120.8351352 37.4561342),37.4561342,-120.8351352 +2102 W Chestnut Ave,0,Santa Ana,California Sausage Inc,0.0,redmeat,CA,meat,0.0,distributer,92703,PROC,0101000020E6100000122E895869795DC00F234A9C11DF4040,POINT (-117.8970548 33.74272493),33.74272493,-117.8970548 +2300 Hoover Ave,0,Modesto,California Meat Distributing,0.0,redmeat,CA,meat,0.0,processor,95354,PROC,0101000020E610000023CED435243D5EC0EA6D3B862AD14240,POINT (-120.9553351 37.63411024),37.63411024,-120.9553351 +2316 S Fruit Ave,0,Fresno,Ortegas Meat Distribution Inc,0.0,redmeat,CA,meat,0.0,processor,93706,PROC,0101000020E6100000FBDAE9BD67F45DC0461850B9D35B4240,POINT (-119.8188319 36.7173988),36.7173988,-119.8188319 +2443 E 27th St,0,Los Angeles,K and M Food Service,0.0,redmeat,CA,meat,0.0,distributer,90058,PROC,0101000020E6100000201219B1AA8E5DC0D0C8CE78AE014140,POINT (-118.2291682 34.01313696),34.01313696,-118.2291682 +2533 Folex Way,0,Spring Valley,Seaport Meat Co,0.0,redmeat,CA,meat,0.0,distribution,91978,PROC,0101000020E6100000955FABA9D13D5DC079BB140D085D4040,POINT (-116.9659218 32.7268082),32.7268082,-116.9659218 +2550 Britannia Blvd #101,0,San Diego,Jensen Meat Co,0.0,redmeat,CA,meat,0.0,distributer,92154,PROC,0101000020E610000043BD2A61B73E5DC07834A359B8464040,POINT (-116.9799426 32.55250092),32.55250092,-116.9799426 +2900 Ayers Ave,0,Vernon,Harvest Meat Co Inc,0.0,redmeat,CA,meat,0.0,warehouse,90058,PROC,0101000020E610000045AD7A0ACA8B5DC03D15CB88E6FF4040,POINT (-118.1842066 33.99922285),33.99922285,-118.1842066 +299 W Main St,0,Brawley,Brandt Beef LLC,0.0,redmeat,CA,meat,0.0,processor,92227,PROC,0101000020E610000080B74082E2E25CC03BB79E5B477D4040,POINT (-115.545075 32.97874017),32.97874017,-115.545075 +30248 Santucci Ct,0,Hayward,Bay Area Seafood Inc,0.0,redmeat,CA,meat,0.0,processor,94544,PROC,0101000020E6100000820B68D85E835EC005F86EF3C6CF4240,POINT (-122.0526639 37.623259),37.623259,-122.0526639 +3049 E Vernon Ave,0,Los Angeles,Farmer John,0.0,redmeat,CA,meat,0.0,distributer,90058,PROC,0101000020E61000001146FD3F188E5DC01497A1F9B5004140,POINT (-118.2202301 34.00555344),34.00555344,-118.2202301 +3189 W Dakota Ave,0,Fresno,Golden California Meat Packers,0.0,redmeat,CA,beef,0.0,distributer,93722,PROC,0101000020E6100000F2947ABB4AF65DC0B73C7BD399644240,POINT (-119.8483113 36.7859444),36.7859444,-119.8483113 +3196 Bird St,0,Livingston,Mayars Halal Meat,0.0,redmeat,CA,meat,0.0,processor,95334,PROC,0101000020E610000082035ABA822E5EC02BC0779B37B04240,POINT (-120.726729 37.376697),37.376697,-120.726729 +333 Clay St,0,Oakland,Allied Pringle Food Sales,0.0,redmeat,CA,meat,0.0,distributer,94607,PROC,0101000020E610000042DAB573D0915EC025B07B2321E64240,POINT (-122.2783479 37.79788631),37.79788631,-122.2783479 +3336 Fruitland Ave,0,Vernon,Jobbers Meat Packing Co,0.0,redmeat,CA,meat,0.0,distribution,90058,PROC,0101000020E61000004C0EE9013D8D5DC07C3D88328EFF4040,POINT (-118.2068486 33.99652702),33.99652702,-118.2068486 +3421 Guerneville Rd,0,Santa Rosa,Willowside Meats Inc,0.0,redmeat,CA,meat,0.0,processor,95401,PROC,0101000020E6100000AAA6DA5D56B35EC01421753BFB394340,POINT (-122.8021464 38.4529795),38.4529795,-122.8021464 +344 Cliffwood Park St,0,Brea,West Coast Prime Meats,0.0,redmeat,CA,meat,0.0,processor,92821,PROC,0101000020E6100000BB7372D0EF785DC0ACC79EB95EF64040,POINT (-117.8896371 33.92476578),33.92476578,-117.8896371 +3450 Riverside Ave,0,Paso Robles,J and R natural meat and sausage,0.0,redmeat,CA,meat,0.0,processor,93446,PROC,0101000020E610000066DB696B442C5EC0290989B48DD14140,POINT (-120.691676 35.637137),35.637137,-120.691676 +3461 Main St,0,Chula Vista,Heartland Meat Co,0.0,redmeat,CA,meat,0.0,processor,91911,PROC,0101000020E6100000B97768B3C5435DC074B8F3501D4C4040,POINT (-117.0589417 32.59464466),32.59464466,-117.0589417 +3530 Arden Rd,0,Hayward,Grand Food Meat Wholesale,0.0,redmeat,CA,meat,0.0,distribution,94545,PROC,0101000020E6100000AB5736188F875EC0A3F034F4AACF4240,POINT (-122.1181088 37.6224046),37.6224046,-122.1181088 +4215 Exchange Ave,0,Vernon,King Meat Service Inc,0.0,redmeat,CA,meat,0.0,processor,90058,PROC,0101000020E61000003E4ADBAE068D5DC0C02FC3B965004140,POINT (-118.2035329 34.00310442),34.00310442,-118.2035329 +4276 N Tracy Blvd,0,Tracy,American Custom Meats,0.0,redmeat,CA,meat,0.0,processor,95304,PROC,0101000020E61000007392F7BBC15B5EC0DCC9F15451E24240,POINT (-121.4336996 37.76810705),37.76810705,-121.4336996 +4586 E Commerce Ave,0,Fresno,Certified Meat Products,0.0,redmeat,CA,meat,0.0,distribution,93725,PROC,0101000020E6100000E4DDEC6ACDEF5DC01953550D67594240,POINT (-119.7469127 36.6984574),36.6984574,-119.7469127 +5030 Gifford Ave,0,Vernon,Premier Meat Co,0.0,redmeat,CA,meat,0.0,processor,90058,PROC,0101000020E6100000046D173F328C5DC01448C30865FF4040,POINT (-118.1905668 33.99527082),33.99527082,-118.1905668 +511 W North Ave,0,Fresno,Fresno Grind,0.0,redmeat,CA,meat,0.0,processor,93706,PROC,0101000020E6100000BF092A4F45F35DC07613211A82584240,POINT (-119.8011053 36.6914704),36.6914704,-119.8011053 +5151 Alcoa Ave,0,Vernon,Rose and Shore Inc,0.0,redmeat,CA,meat,0.0,processor,90058,PROC,0101000020E6100000F6F873C0648D5DC0A2A476757DFF4040,POINT (-118.2092744 33.9960162),33.9960162,-118.2092744 +5217 Industry Ave,0,Pico Rivera,Daniels Western Meat Packers,0.0,redmeat,CA,meat,0.0,distributer,90660,PROC,0101000020E6100000FF64428218865DC09DAB9CAC87004140,POINT (-118.0952459 34.00414045),34.00414045,-118.0952459 +601 Zeff Rd,0,Modesto,Yosemite Meat Co Inc,0.0,redmeat,CA,meat,0.0,distribution,95351,PROC,0101000020E6100000437B50ABC33F5EC0E87981A3AECF4240,POINT (-120.9963177 37.62251705),37.62251705,-120.9963177 +6114 Scott Way,0,Commerce,Sterling Pacific Meat Co,0.0,redmeat,CA,meat,0.0,distribution,90040,PROC,0101000020E6100000D2510E6693895DC0A4C0F16B5AFD4040,POINT (-118.1496215 33.97932195000001),33.97932195000001,-118.1496215 +6621 Midway Rd,0,Dixon,Superior Farms,0.0,redmeat,CA,meat,0.0,processor,95620,PROC,0101000020E61000002705CC327A745EC0BED32A1B52354340,POINT (-121.8199584 38.41656818),38.41656818,-121.8199584 +6969 Clark Ave,0,Newark,Harvest Meat Co,0.0,redmeat,CA,meat,0.0,distribution,94560,PROC,0101000020E61000001BA6118EB47B5DC0DB93B875D4104140,POINT (-117.9328952 34.13148376),34.13148376,-117.9328952 +730 Spreckels Ave,0,Manteca,Cargill Food Distribution,0.0,redmeat,CA,meat,0.0,processor,95336,PROC,0101000020E6100000F401DC87974C5EC0A94F517964E54240,POINT (-121.1967487 37.79212872),37.79212872,-121.1967487 +7310 Pine Ave,0,Chino,Lizze Custom Processing,0.0,redmeat,CA,meat,0.0,distribution,91708,PROC,0101000020E61000009B6736D950695DC053509B8246FA4040,POINT (-117.6455596 33.9552768),33.9552768,-117.6455596 +769 Caudill St,0,San Luis Obispo,Cattaneo Brothers Inc,0.0,redmeat,CA,meat,0.0,processor,93401,PROC,0101000020E61000003E2C8A0DCC295EC06BDF92D222A24140,POINT (-120.6530794 35.2666877),35.2666877,-120.6530794 +7750 Petaluma Hill Rd,0,Penngrove,Buds Custom Meats,0.0,redmeat,CA,meat,0.0,processor,94951,PROC,0101000020E6100000150AC7E26DAA5EC08A856BFF14294340,POINT (-122.6629569 38.3209533),38.3209533,-122.6629569 +850 E Bidwell St,0,Folsom,Adams Meat Shop,0.0,redmeat,CA,meat,0.0,processor,95630,PROC,0101000020E610000026BD14C3FA495EC08529A99708564340,POINT (-121.1559303 38.67213722),38.67213722,-121.1559303 +9531 Beverly Rd,0,Pico Rivera,Manning Beef LLC,0.0,redmeat,CA,meat,0.0,processor,90660,PROC,0101000020E61000009AFE36D5A4845DC0A0F2F972B0004140,POINT (-118.0725606 34.0053848),34.0053848,-118.0725606 +960 S Sanborn Rd,0,Salinas,Monterey Fish Co,0.0,redmeat,CA,meat,0.0,distribution,93901,PROC,0101000020E6100000D8F0F44A59765EC0FAEDEBC0394B4240,POINT (-121.8492 36.5877),36.5877,-121.8492 +970 E Sandy Mush Rd,0,Merced,Yosemite Valley Beef,0.0,redmeat,CA,meat,0.0,processor,95341,PROC,0101000020E6100000C5BA021BA11E5EC0D4BBF406CA974240,POINT (-120.4785831 37.18585288),37.18585288,-120.4785831 +,0,Commerce,AA Meat Products Inc,0.0,redmeat,CA,beef,0.0,processor,90040,PROC,0101000020E6100000AA9A20EA3E885DC04C6C3EAE0DFD4040,POINT (-118.12884 33.97698),33.97698,-118.12884 +160 Municipal Wharf 2,0,Monterey,Monterey Fish Co,0.0,seafood,CA,seafood,0.0,distribution,93940,PROC,0101000020E6100000D8F0F44A59765EC0FAEDEBC0394B4240,POINT (-121.8492 36.5877),36.5877,-121.8492 +2500 Francisco Blvd,0,Pacifica,Stuckeys Sustainable,0.0,seafood,CA,seafood,0.0,processor,94044,PROC,0101000020E610000036012B2C5D9F5EC02D635CD49BD04240,POINT (-122.4900618 37.62975554),37.62975554,-122.4900618 +6520 Irwindale Ave,0,Irwindale,Harvest Meat Co,0.0,seafood,CA,seafood,0.0,warehouse,91702,PROC,0101000020E61000001BA6118EB47B5DC0DB93B875D4104140,POINT (-117.9328952 34.13148376),34.13148376,-117.9328952 +395 W Keystone Rd,0,Brawley,spreckels sugar co,0.0,sugarbeat,CA,sugar beet,0.0,sugar,92227,PROC,0101000020E61000006227614B34E45CC038718B5CE4734040,POINT (-115.5656918 32.90540654),32.90540654,-115.5656918 +29400 W Whitesbridge Ave,0,Mendota,spreckels sugar co,0.0,sugarbeat,CA,sugar beet,0.0,sugar,93640,PROC,0101000020E6100000B62110F9F8145EC0C8F54AB43F5E4240,POINT (-120.3276961 36.7363191),36.7363191,-120.3276961 +16150 Stephens St,0,City of Industry,Snak King Corp,0.0,tortilla,CA,tortilla,0.0,bakery,91745,PROC,0101000020E61000001C936A44D57C5DC071C4FFC297014140,POINT (-117.9505168 34.0124439),34.0124439,-117.9505168 +11559 Jersey Blvd,0,Rancho Cucamonga,GrumaMissions Food Corp,0.0,tortilla,CA,tortilla,0.0,bakery,91730,PROC,0101000020E6100000245A97BF67635DC0A2BB7F87FD0B4140,POINT (-117.5532073 34.0936746),34.0936746,-117.5532073 +14200 Arminta St,0,Panorama City,Mission Foods,0.0,tortilla,CA,tortilla,0.0,bakery,91402,PROC,0101000020E610000020D4A0C3579C5DC0EA74C531371B4140,POINT (-118.4428567 34.2126219),34.2126219,-118.4428567 +1153 Madison Ln,0,Salinas,Mission Foods,0.0,tortilla,CA,tortilla,0.0,distributor,93907,PROC,0101000020E6100000E523CE2F6F6B5EC073CCC353D9584240,POINT (-121.6786613 36.6941323),36.6941323,-121.6786613 +2849 E Edgar Ave,0,Fresno,Mission Foods,0.0,tortilla,CA,tortilla,0.0,distributor,93706,PROC,0101000020E6100000F97F7AD8B0F15DC06A1327F73B594240,POINT (-119.7764188 36.6971425),36.6971425,-119.7764188 +410 E Trimble Rd,0,San Jose,Mission Foods,0.0,tortilla,CA,tortilla,0.0,distributor,95131,PROC,0101000020E61000007E891D320A7B5EC02E3D79DCE0B14240,POINT (-121.9224973 37.38967472),37.38967472,-121.9224973 +23415 Cabot Blvd,0,Hayward,Mission Foods,0.0,tortilla,CA,tortilla,0.0,distributor,94545,PROC,0101000020E610000074F112F7B3885EC00E02E1F9FBD14240,POINT (-122.1359842 37.6405022),37.6405022,-122.1359842 +4120 Indian Ave,0,Perris,General Mills,0.0,warehouse,CA,bread,0.0,warehouse,92571,PROC,0101000020E6100000A3DE9DC6074F5DC0385211024DEC4040,POINT (-117.2348496 33.8461001),33.8461001,-117.2348496 +1375 Beachey Pl,0,Carson,General Mills,0.0,warehouse,CA,bread,0.0,warehouse,90746,PROC,0101000020E61000008FADC2C1B98F5DC0EABD8CBD72EE4040,POINT (-118.2457127 33.86287660000001),33.86287660000001,-118.2457127 +14344 Carmenita Rd,0,Norwalk,Mission Foods,0.0,warehouse,CA,tortilla,0.0,warehouse,90650,PROC,0101000020E6100000EC1DC940F9825DC0DE39F7CB65F34040,POINT (-118.0464632 33.90154409),33.90154409,-118.0464632 +14600 Proctor Ave,0,City of Industry,FritoLay,0.0,warehouse,CA,bakery,0.0,warehouse,91746,PROC,0101000020E6100000C30FCEA78E7E5DC0477F8183EA034140,POINT (-117.977457 34.03059429),34.03059429,-117.977457 +13508 Marlay Ave,0,Fontana,CocoCola Fontana Warehouse,0.0,warehouse,CA,beverage,0.0,warehouse,92337,PROC,0101000020E610000012CB1C81AE605DC0680EFF9F79054140,POINT (-117.5106509 34.0427742),34.0427742,-117.5106509 +3971 E Airport Dr,0,Ontario,Kraft Foods Warehouse,0.0,warehouse,CA,misc dairy meat bakery,0.0,warehouse,91761,PROC,0101000020E610000032A0281A35645DC067D1E05BFD074140,POINT (-117.5657411 34.0624194),34.0624194,-117.5657411 +1650 E Central Ave,0,San Bernardino,Pepsi Co,0.0,warehouse,CA,beverage,0.0,warehouse,92408,PROC,0101000020E61000009EA3440111505DC01074B4AA250B4140,POINT (-117.2510379 34.087087),34.087087,-117.2510379 +14069 Balboa Blvd,0,Sylmar,FritoLay,0.0,warehouse,CA,bakery,0.0,warehouse,91342,PROC,0101000020E6100000D22FB6B52A9F5DC0CDC11A0429294140,POINT (-118.4869818 34.32156421),34.32156421,-118.4869818 +1055 E North Ave,0,Fresno,Kraft Foods Distribution Center,0.0,warehouse,CA,misc dairy meat bakery,0.0,warehouse,93725,PROC,0101000020E61000003DF207034FF15DC0DEFD96A542584240,POINT (-119.7704475 36.6895339),36.6895339,-119.7704475 +6300 Cameron Blvd,0,Gilroy,Pepsi Co,0.0,warehouse,CA,beverage,0.0,warehouse,95020,PROC,0101000020E6100000EB94A2F0B4625EC0321180C9D77F4240,POINT (-121.5422937 36.9987728),36.9987728,-121.5422937 +2748 W Winton Ave,0,Hayward,Mission Foods,0.0,warehouse,CA,tortilla,0.0,warehouse,94545,PROC,0101000020E61000006E5B4A4C06895EC0782C1103B8D24240,POINT (-122.1410094 37.6462406),37.6462406,-122.1410094 +4718 Newcastle Rd,0,Stockton,General Mills,0.0,warehouse,CA,bread,0.0,warehouse,95215,PROC,0101000020E6100000AC5791D1014D5EC07B336ABE4AFC4240,POINT (-121.203236 37.971031),37.971031,-121.203236 +2224 Industrial Blvd,0,West Sacramento,Farmers Rice Cooperative,0.0,warehouse,CA,rice,0.0,warehouse,95691,PROC,0101000020E6100000F8AAF0C2B1625EC0BF3D192D51484340,POINT (-121.5420997 38.5649773),38.5649773,-121.5420997 +2700 S Eastern Ave,0,Commerce,E J Gallo Winery,0.0,winery,CA,grape,0.0,winery,90040,PROC,0101000020E61000001576ACAD338A5DC0A0C09E23B0FF4040,POINT (-118.1594042 33.99756284),33.99756284,-118.1594042 +5610 E Olive Ave,0,Fresno,E J Gallo Winery,0.0,winery,CA,grape,0.0,winery,93727,PROC,0101000020E6100000688B10C3B3EC5DC00E164ED2FC604240,POINT (-119.6984718 36.7577155),36.7577155,-119.6984718 +31754 Ave 9,0,Madera,E J Gallo Winery,0.0,winery,CA,grape,0.0,winery,93636,PROC,0101000020E610000057C0F34105FE5DC0012C7624AC704240,POINT (-119.9690709 36.88025337),36.88025337,-119.9690709 +18000 River Rd,0,Livingston,E J Gallo Winery,0.0,winery,CA,grape,0.0,winery,95334,PROC,0101000020E6100000BC69E9C0A8345EC0DF87E6AEE3AF4240,POINT (-120.8227999 37.37413584),37.37413584,-120.8227999 +2612 Crows Landing Rd,0,Modesto,E J Gallo Winery,0.0,winery,CA,grape,0.0,winery,95358,PROC,0101000020E6100000A48D23D6623F5EC07F573EAAE5CB4240,POINT (-120.9904075 37.59294632),37.59294632,-120.9904075 +600 Yosemite Blvd,0,Modesto,E J Gallo Winery,0.0,winery,CA,grape,0.0,winery,95354,PROC,0101000020E61000006B42FFA9DD3E5EC0906B43C538D14240,POINT (-120.9822793 37.634545),37.634545,-120.9822793 +2101 Yosemite Blvd,0,Modesto,E J Gallo Winery,0.0,winery,CA,grape,0.0,winery,95354,PROC,0101000020E610000036F63647673D5EC05DD0CEABB2D14240,POINT (-120.9594286 37.63826511),37.63826511,-120.9594286 +1300 Camino Diablo,0,Byron,E J Gallo Winery,0.0,winery,CA,grape,0.0,winery,94514,PROC,0101000020E61000001EE1B4E045675EC0560E2DB29DEF4240,POINT (-121.61364 37.872),37.872,-121.61364 +21280 N Kennefick Rd,0,Acampo,E J Gallo Winery,0.0,winery,CA,grape,0.0,winery,95220,PROC,0101000020E6100000D20957F6934F5EC0363D4936AE164340,POINT (-121.2434059 38.17719153),38.17719153,-121.2434059 +1165 Rutherford Rd,0,Rutherford,Elizabeth spencer winery,0.0,winery,CA,grape,0.0,winery,94573,PROC,0101000020E610000037EE83E2FD9A5EC06483F9E9C73A4340,POINT (-122.4217459 38.45922589),38.45922589,-122.4217459 +1266 N Bethel Rd,0,Templeton,Bethel Rd Distillery,0.0,winery,CA,pomace,0.0,winery,93465,PROC,0101000020E6100000D30F8F69122E5EC0FEDA1387E0C94140,POINT (-120.7198738 35.57716454),35.57716454,-120.7198738 +14679 Summers Ln,0,Sonora,Indigeny Reserve,0.0,winery,CA,distillers grain,0.0,winery,95370,PROC,0101000020E6100000025B6FE5B6145EC00A6AD708ED014340,POINT (-120.3236631 38.01504622),38.01504622,-120.3236631 +18912 MacArthur Blvd,0,Irvine,Z Mario,0.0,winery,CA,pomace,0.0,winery,92612,PROC,0101000020E6100000B76E940648775DC046EC555C03D64040,POINT (-117.8637711 33.67197756),33.67197756,-117.8637711 +2174 CA-46,0,Paso Robles,Grey Wolf Cellars,0.0,winery,CA,pomace,0.0,winery,93446,PROC,0101000020E610000066DB696B442C5EC0290989B48DD14140,POINT (-120.691676 35.637137),35.637137,-120.691676 +22750 Hawthorne Blvd # 205,0,Torrance,Takara Sake USA Inc,0.0,winery,CA,pomace,0.0,winery,90505,PROC,0101000020E61000003B78DCA62E935EC0887A66EEC6EE4240,POINT (-122.2997224 37.8654459),37.8654459,-122.2997224 +3230 Oakdale Rd,0,Paso Robles,Red Soles Winery,0.0,winery,CA,pomace,0.0,winery,93446,PROC,0101000020E61000005029C0C128305EC0723788D68AC84140,POINT (-120.7524876 35.566737),35.566737,-120.7524876 +5963 Graham Ct D,0,Livermore,Eckert Estate Winery,0.0,winery,CA,pomace,0.0,winery,94550,PROC,0101000020E6100000A2F8E758146E5EC0DCEB4905BAD64240,POINT (-121.7199919 37.6775519),37.6775519,-121.7199919 +708 Addison St,0,Berkeley,Takara Sake USA Inc,0.0,winery,CA,pomace,0.0,winery,94710,PROC,0101000020E61000003B78DCA62E935EC0887A66EEC6EE4240,POINT (-122.2997224 37.8654459),37.8654459,-122.2997224 +9275 Midway,0,Durham,Bertagna Son 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], [ -93.20328499948522, 45.02149399982936 ] ] ] } }, +{ "type": "Feature", "properties": { "OBJECTID": 4311, "Opername": null, "Pipename": null, "Source": null, "Type": null, "Notes": null, "ARTIFICIAL": 2, "MASTER_OID": null, "commodity": "Petroleum Products", "Volume": null, "Capacity": null, "VCR": null, "Shape_Length": 836.75242265370196, "Mode_Type": "pipeline_prod", "Length": 0.51993281060410734 }, "geometry": { "type": "MultiLineString", "coordinates": [ [ [ -93.196716291478708, 45.024094588300535 ], [ -93.196598000173807, 45.016566000305204 ] ] ] } }, +{ "type": "Feature", "properties": { "OBJECTID": 4312, "Opername": null, "Pipename": null, "Source": null, "Type": null, "Notes": null, "ARTIFICIAL": 2, "MASTER_OID": null, "commodity": "Petroleum Products", "Volume": null, "Capacity": null, "VCR": null, "Shape_Length": 7215.0357495548769, "Mode_Type": "pipeline_prod", "Length": 4.4832063993051685 }, "geometry": { "type": "MultiLineString", "coordinates": [ [ [ -93.196716291478708, 45.024094588300535 ], [ -93.263835999690585, 44.979964999645212 ] ] ] } } +] +} diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb index e2bf8007..5834652a 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb @@ -20,15 +20,33 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2026-01-13 16:10:18,800 - INFO - Project root 'C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing' is already in sys.path\n", - "2026-01-13 16:10:18,802 - INFO - Successfully imported all project modules.\n" + "2026-01-14 11:30:02,898 - INFO - Added project root 'C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing' to sys.path\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:19: DeprecationWarning: 'setName' deprecated - use 'set_name'\n", + " token = pp.Word(tchar).setName(\"token\")\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:20: DeprecationWarning: 'leaveWhitespace' deprecated - use 'leave_whitespace'\n", + " token68 = pp.Combine(pp.Word(\"-._~+/\" + pp.nums + pp.alphas) + pp.Optional(pp.Word(\"=\").leaveWhitespace())).setName(\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:20: DeprecationWarning: 'setName' deprecated - use 'set_name'\n", + " token68 = pp.Combine(pp.Word(\"-._~+/\" + pp.nums + pp.alphas) + pp.Optional(pp.Word(\"=\").leaveWhitespace())).setName(\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:24: DeprecationWarning: 'setName' deprecated - use 'set_name'\n", + " quoted_string = pp.dblQuotedString.copy().setName(\"quoted-string\").setParseAction(unquote)\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:24: DeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action'\n", + " quoted_string = pp.dblQuotedString.copy().setName(\"quoted-string\").setParseAction(unquote)\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:25: DeprecationWarning: 'setName' deprecated - use 'set_name'\n", + " auth_param_name = token.copy().setName(\"auth-param-name\").addParseAction(downcaseTokens)\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:25: DeprecationWarning: 'addParseAction' deprecated - use 'add_parse_action'\n", + " auth_param_name = token.copy().setName(\"auth-param-name\").addParseAction(downcaseTokens)\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:27: DeprecationWarning: 'delimitedList' deprecated - use 'DelimitedList'\n", + " params = pp.Dict(pp.delimitedList(pp.Group(auth_param)))\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:33: DeprecationWarning: 'delimitedList' deprecated - use 'DelimitedList'\n", + " www_authenticate = pp.delimitedList(pp.Group(challenge))\n", + "2026-01-14 11:30:52,659 - INFO - Successfully imported all project modules.\n" ] } ], @@ -240,7 +258,7 @@ }, { "cell_type": "code", - "execution_count": 72, + "execution_count": 16, "metadata": {}, "outputs": [], "source": [ @@ -248,6 +266,8 @@ "from pydrive2.auth import GoogleAuth, AuthenticationError\n", "from pydrive2.drive import GoogleDrive\n", "from pydrive2.files import ApiRequestError\n", + "import zipfile\n", + "import geopandas as gpd\n", "\n", "def gdrive_to_df(file_name: str, mime_type: str, credentials_path: str, dataset_folder: str) -> pd.DataFrame:\n", " \"\"\"\n", @@ -257,6 +277,7 @@ " file_name: The name of the requested file.\n", " mime_type: The MIME type - according to https://mime-type.com/\n", " credentials_path: The path to the Google Cloud service account credentials JSON file.\n", + " dataset_folder: the folder where the extracted file is stored.\n", "\n", " Returns:\n", " A pandas DataFrame containing the data from the specified worksheet, or None on error.\n", @@ -286,10 +307,26 @@ " print(f\"An unexpected error occurred: {e}\")\n", " return None\n", "\n", - " # Use the first row as header and the rest as data\n", + " # read csv if file is csv\n", " if mime_type == \"text/csv\":\n", " df = pd.read_csv(dataset_folder + file_name)\n", "\n", + " # extract from zip if file is zip \n", + " # note: THIS CODE ASSUMES THAT THE ZIP ONLY CONTAINS ONE CSV FILE\n", + " elif mime_type == \"application/zip\":\n", + "\n", + " # note: THIS CODE ASSUMES THAT THE CSV FILE HAS THE SAME NAME AS THE ZIP FILE\n", + " csv_name = file_name[:-4] + \".csv\"\n", + " \n", + " with zipfile.ZipFile(dataset_folder + file_name,\"r\") as zip_ref:\n", + " zip_ref.extractall(dataset_folder)\n", + " df = pd.read_csv(dataset_folder + csv_name)\n", + "\n", + " elif mime_type == \"application/geo+json\":\n", + " df = gpd.read_file(dataset_folder + file_name)\n", + " \n", + " \n", + "\n", " # De-duplicate columns, keeping the first occurrence\n", " df = df.loc[:, ~df.columns.duplicated()]\n", "\n", @@ -305,7 +342,7 @@ }, { "cell_type": "code", - "execution_count": 73, + "execution_count": 17, "metadata": {}, "outputs": [], "source": [ @@ -357,28 +394,158 @@ }, { "cell_type": "code", - "execution_count": 74, + "execution_count": 18, + "metadata": {}, + "outputs": [], + "source": [ + "from typing import Optional\n", + "import pandas as pd\n", + "from prefect import task, get_run_logger\n", + "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", + "# from resources.prefect import credentials\n", + "\n", + "@task\n", + "def extract_proc(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", + " \"\"\"\n", + " Extracts raw data from a .zip file.\n", + "\n", + " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", + " to the data source and returns the data as is, without transformation.\n", + "\n", + " Returns:\n", + " A pandas DataFrame containing the raw data, or None if an error occurs.\n", + " \"\"\"\n", + " logger = get_run_logger()\n", + "\n", + " FILE_NAME = \"CA_proc_points.zip\"\n", + " MIME_TYPE = \"application/zip\"\n", + " CREDENTIALS_PATH = \"credentials.json\"\n", + " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", + " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", + "\n", + " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", + " # Otherwise, use the default relative path (for the main pipeline)\n", + " credentials_path = CREDENTIALS_PATH\n", + " dataset_folder = DATASET_FOLDER\n", + " if project_root:\n", + " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", + " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", + "\n", + " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", + " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", + "\n", + " \n", + "\n", + " if raw_df is None:\n", + " logger.error(\"Failed to extract data. Aborting.\")\n", + " return None\n", + "\n", + " logger.info(\"Successfully extracted raw data.\")\n", + " return raw_df\n" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [], + "source": [ + "from typing import Optional\n", + "import pandas as pd\n", + "from prefect import task, get_run_logger\n", + "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", + "# from resources.prefect import credentials\n", + "\n", + "@task\n", + "def extract_petro(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", + " \"\"\"\n", + " Extracts raw data from a .geojson file.\n", + "\n", + " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", + " to the data source and returns the data as is, without transformation.\n", + "\n", + " Returns:\n", + " A pandas DataFrame containing the raw data, or None if an error occurs.\n", + " \"\"\"\n", + " logger = get_run_logger()\n", + "\n", + " FILE_NAME = \"US_Petroleum_Pipelines.geojson\"\n", + " MIME_TYPE = \"application/geo+json\"\n", + " CREDENTIALS_PATH = \"credentials.json\"\n", + " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", + " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", + "\n", + " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", + " # Otherwise, use the default relative path (for the main pipeline)\n", + " credentials_path = CREDENTIALS_PATH\n", + " dataset_folder = DATASET_FOLDER\n", + " if project_root:\n", + " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", + " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", + "\n", + " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", + " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", + "\n", + " \n", + "\n", + " if raw_df is None:\n", + " logger.error(\"Failed to extract data. Aborting.\")\n", + " return None\n", + "\n", + " logger.info(\"Successfully extracted raw data.\")\n", + " return raw_df\n" + ] + }, + { + "cell_type": "code", + "execution_count": 22, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2026-01-13 18:36:20,831 - INFO - Starting data extraction...\n", - "2026-01-13 18:36:20,856 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-13 18:36:20,857 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", - "2026-01-13 18:36:20,866 - INFO - Extracting raw data from 'Biodiesel_Plants.csv'...\n", - "2026-01-13 18:36:20,886 - INFO - Attempting refresh to obtain initial access_token\n", + "2026-01-14 12:32:21,077 - INFO - Starting data extraction...\n", + "2026-01-14 12:32:21,097 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 12:32:21,098 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 12:32:21,106 - INFO - Extracting raw data from 'Biodiesel_Plants.csv'...\n", + "2026-01-14 12:32:21,122 - INFO - Attempting refresh to obtain initial access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", + " return crypto.sign(self._key, message, 'sha256')\n", + "2026-01-14 12:32:21,125 - INFO - Refreshing access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " self.token_expiry = delta + _UTCNOW()\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " now = _UTCNOW()\n", + "2026-01-14 12:32:22,387 - INFO - Successfully extracted raw data.\n", + "2026-01-14 12:32:22,393 - INFO - Finished in state Completed()\n", + "2026-01-14 12:32:22,431 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 12:32:22,434 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 12:32:22,445 - INFO - Extracting raw data from 'CA_proc_points.zip'...\n", + "2026-01-14 12:32:22,483 - INFO - Attempting refresh to obtain initial access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", " return crypto.sign(self._key, message, 'sha256')\n", - "2026-01-13 18:36:20,889 - INFO - Refreshing access_token\n", + "2026-01-14 12:32:22,486 - INFO - Refreshing access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " self.token_expiry = delta + _UTCNOW()\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " now = _UTCNOW()\n", - "2026-01-13 18:36:22,092 - INFO - Successfully extracted raw data.\n", - "2026-01-13 18:36:22,097 - INFO - Finished in state Completed()\n", - "2026-01-13 18:36:22,113 - INFO - Data extraction complete.\n" + "2026-01-14 12:32:23,827 - INFO - Successfully extracted raw data.\n", + "2026-01-14 12:32:23,832 - INFO - Finished in state Completed()\n", + "2026-01-14 12:32:23,877 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 12:32:23,878 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 12:32:23,889 - INFO - Extracting raw data from 'US_Petroleum_Pipelines.geojson'...\n", + "2026-01-14 12:32:23,912 - INFO - Attempting refresh to obtain initial access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", + " return crypto.sign(self._key, message, 'sha256')\n", + "2026-01-14 12:32:23,914 - INFO - Refreshing access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " self.token_expiry = delta + _UTCNOW()\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " now = _UTCNOW()\n", + "2026-01-14 12:32:26,422 - INFO - Successfully extracted raw data.\n", + "2026-01-14 12:32:26,428 - INFO - Finished in state Completed()\n", + "2026-01-14 12:32:26,476 - INFO - Data extraction complete.\n" ] }, { @@ -450,7 +617,124 @@ "76 https://issuu.com/bbiinternational/docs/biodie... \n", "77 https://issuu.com/bbiinternational/docs/biodie... \n", "\n", - "[78 rows x 12 columns]]\n" + "[78 rows x 12 columns], Address COUNTY City \\\n", + "0 327 Daniels Ln Kern Bakersfield \n", + "1 26060 Colusa Road Fresno Coalinga \n", + "2 21490 Ortigalita Rd Merced Los Banos \n", + "3 8800 S Minturn Rd Merced Le Grand \n", + "4 NaN Stanislaus NaN \n", + ".. ... ... ... \n", + "707 3230 Oakdale Rd 0 Paso Robles \n", + "708 5963 Graham Ct D 0 Livermore \n", + "709 708 Addison St 0 Berkeley \n", + "710 9275 Midway 0 Durham \n", + "711 95 Booker Rd 0 Templeton \n", + "\n", + " Company Join_Count MASTERTYPE State Subtype \\\n", + "0 Real Almond Processing 1.0 almond CA almond \n", + "1 Harris Woolf 1.0 almond CA almond \n", + "2 Parreira Almond Processing 1.0 almond CA almond \n", + "3 Minturn Nut Co Inc 1.0 almond CA almond \n", + "4 Tree Nuts LLC 1.0 almond CA almond \n", + ".. ... ... ... ... ... \n", + "707 Red Soles Winery 0.0 winery CA pomace \n", + "708 Eckert Estate Winery 0.0 winery CA pomace \n", + "709 Takara Sake USA Inc 0.0 winery CA pomace \n", + "710 Bertagna Son Kissed Vineyards 0.0 winery CA pomace \n", + "711 Pasoport Wine Company 0.0 winery CA pomace \n", + "\n", + " TARGET_FID Type Zip TYPE \\\n", + "0 0.0 shelling 93307 PROC \n", + "1 1.0 shelling 93210 PROC \n", + "2 2.0 shelling 93635 PROC \n", + "3 3.0 shelling 95333 PROC \n", + "4 4.0 shelling 0 PROC \n", + ".. ... ... ... ... \n", + "707 0.0 winery 93446 PROC \n", + "708 0.0 winery 94550 PROC \n", + "709 0.0 winery 94710 PROC \n", + "710 0.0 winery 95938 PROC \n", + "711 0.0 winery 93465 PROC \n", + "\n", + " wkt_geom \\\n", + "0 0101000020E610000090A6D5EBF1BF5DC0D652E5208DAC... \n", + "1 0101000020E6100000931B45D61A175EC0EC67B114C915... \n", + "2 0101000020E610000008951348E4375EC00937B62ACB7D... \n", + "3 0101000020E6100000E025DD3B8F115EC0B26066C8C694... \n", + "4 0101000020E61000007CD3F4D901365EC07E37DDB243BE... \n", + ".. ... \n", + "707 0101000020E61000005029C0C128305EC0723788D68AC8... \n", + "708 0101000020E6100000A2F8E758146E5EC0DCEB4905BAD6... \n", + "709 0101000020E61000003B78DCA62E935EC0887A66EEC6EE... \n", + "710 0101000020E6100000DAB6DE2527735EC042CAF4F00AD2... \n", + "711 0101000020E610000051700C5C792F5EC030FFB661F3C7... \n", + "\n", + " geom latitude longitude \n", + "0 POINT (-118.9991407 35.3480569) 35.348057 -118.999141 \n", + "1 POINT (-120.361013 36.170199) 36.170199 -120.361013 \n", + "2 POINT (-120.8733082 36.98276266) 36.982763 -120.873308 \n", + "3 POINT (-120.2743673 37.16231637) 37.162316 -120.274367 \n", + "4 POINT (-120.843863 37.486441) 37.486441 -120.843863 \n", + ".. ... ... ... \n", + "707 POINT (-120.7524876 35.566737) 35.566737 -120.752488 \n", + "708 POINT (-121.7199919 37.6775519) 37.677552 -121.719992 \n", + "709 POINT (-122.2997224 37.8654459) 37.865446 -122.299722 \n", + "710 POINT (-121.7992644 39.6409589) 39.640959 -121.799264 \n", + "711 POINT (-120.7417822 35.56211492) 35.562115 -120.741782 \n", + "\n", + "[712 rows x 16 columns], OBJECTID Opername Pipename Source \\\n", + "0 1 NUSTAR ENERGY Valley Pipeline EIA \n", + "1 2 TRANSMONTAIGNE PARTNERS Diamondback Pipeline EIA \n", + "2 3 NUSTAR ENERGY Valley Pipeline EIA \n", + "3 4 TRANSMONTAIGNE PARTNERS Diamondback Pipeline EIA \n", + "4 5 TRANSMONTAIGNE PARTNERS Diamondback Pipeline EIA \n", + "... ... ... ... ... \n", + "4307 4308 None None None \n", + "4308 4309 None None None \n", + "4309 4310 None None None \n", + "4310 4311 None None None \n", + "4311 4312 None None None \n", + "\n", + " Type Notes ARTIFICIAL MASTER_OID commodity \\\n", + "0 Petroleum Product None 0 299.0 Petroleum Products \n", + "1 Petroleum Product None 0 300.0 Petroleum Products \n", + "2 Petroleum Product None 0 301.0 Petroleum Products \n", + "3 Petroleum Product None 0 302.0 Petroleum Products \n", + "4 Petroleum Product None 0 303.0 Petroleum Products \n", + "... ... ... ... ... ... \n", + "4307 None None 2 NaN Petroleum Products \n", + "4308 None None 2 NaN Petroleum Products \n", + "4309 None None 2 NaN Petroleum Products \n", + "4310 None None 2 NaN Petroleum Products \n", + "4311 None None 2 NaN Petroleum Products \n", + "\n", + " Volume Capacity VCR Shape_Length Mode_Type Length \\\n", + "0 None None None 1496.712523 pipeline_prod 0.930012 \n", + "1 None None None 1934.748751 pipeline_prod 1.202195 \n", + "2 None None None 55.870089 pipeline_prod 0.034716 \n", + "3 None None None 2082.004459 pipeline_prod 1.293695 \n", + "4 None None None 9904.740005 pipeline_prod 6.154508 \n", + "... ... ... ... ... ... ... \n", + "4307 None None None 207.259275 pipeline_prod 0.128785 \n", + "4308 None None None 242.718991 pipeline_prod 0.150818 \n", + "4309 None None None 592.947623 pipeline_prod 0.368440 \n", + "4310 None None None 836.752423 pipeline_prod 0.519933 \n", + "4311 None None None 7215.035750 pipeline_prod 4.483206 \n", + "\n", + " geometry \n", + "0 MULTILINESTRING ((-97.38949 25.96387, -97.3921... \n", + "1 MULTILINESTRING ((-97.38299 25.96636, -97.3839... \n", + "2 MULTILINESTRING ((-97.39214 25.97691, -97.3922... \n", + "3 MULTILINESTRING ((-97.38165 25.9667, -97.38265... \n", + "4 MULTILINESTRING ((-97.52187 26.00233, -97.5283... \n", + "... ... \n", + "4307 MULTILINESTRING ((-93.19672 45.02409, -93.1989... \n", + "4308 MULTILINESTRING ((-93.19672 45.02409, -93.1997... \n", + "4309 MULTILINESTRING ((-93.19672 45.02409, -93.2032... \n", + "4310 MULTILINESTRING ((-93.19672 45.02409, -93.1966... \n", + "4311 MULTILINESTRING ((-93.19672 45.02409, -93.2638... \n", + "\n", + "[4312 rows x 16 columns]]\n" ] } ], @@ -459,7 +743,9 @@ "# In a real Prefect flow, each extraction would be a separate task.\n", "logger.info('Starting data extraction...')\n", "biodiesel_plants_df = extract(project_root=project_root)\n", - "dataframes = [biodiesel_plants_df]\n", + "proc_points_df = extract_proc(project_root=project_root)\n", + "petro_pipelines_df = extract_petro(project_root=project_root)\n", + "dataframes = [biodiesel_plants_df, proc_points_df, petro_pipelines_df]\n", "print(dataframes)\n", "logger.info('Data extraction complete.')\n", "\n", diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb index e2bf8007..5834652a 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb @@ -20,15 +20,33 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2026-01-13 16:10:18,800 - INFO - Project root 'C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing' is already in sys.path\n", - "2026-01-13 16:10:18,802 - INFO - Successfully imported all project modules.\n" + "2026-01-14 11:30:02,898 - INFO - Added project root 'C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing' to sys.path\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:19: DeprecationWarning: 'setName' deprecated - use 'set_name'\n", + " token = pp.Word(tchar).setName(\"token\")\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:20: DeprecationWarning: 'leaveWhitespace' deprecated - use 'leave_whitespace'\n", + " token68 = pp.Combine(pp.Word(\"-._~+/\" + pp.nums + pp.alphas) + pp.Optional(pp.Word(\"=\").leaveWhitespace())).setName(\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:20: DeprecationWarning: 'setName' deprecated - use 'set_name'\n", + " token68 = pp.Combine(pp.Word(\"-._~+/\" + pp.nums + pp.alphas) + pp.Optional(pp.Word(\"=\").leaveWhitespace())).setName(\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:24: DeprecationWarning: 'setName' deprecated - use 'set_name'\n", + " quoted_string = pp.dblQuotedString.copy().setName(\"quoted-string\").setParseAction(unquote)\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:24: DeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action'\n", + " quoted_string = pp.dblQuotedString.copy().setName(\"quoted-string\").setParseAction(unquote)\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:25: DeprecationWarning: 'setName' deprecated - use 'set_name'\n", + " auth_param_name = token.copy().setName(\"auth-param-name\").addParseAction(downcaseTokens)\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:25: DeprecationWarning: 'addParseAction' deprecated - use 'add_parse_action'\n", + " auth_param_name = token.copy().setName(\"auth-param-name\").addParseAction(downcaseTokens)\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:27: DeprecationWarning: 'delimitedList' deprecated - use 'DelimitedList'\n", + " params = pp.Dict(pp.delimitedList(pp.Group(auth_param)))\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:33: DeprecationWarning: 'delimitedList' deprecated - use 'DelimitedList'\n", + " www_authenticate = pp.delimitedList(pp.Group(challenge))\n", + "2026-01-14 11:30:52,659 - INFO - Successfully imported all project modules.\n" ] } ], @@ -240,7 +258,7 @@ }, { "cell_type": "code", - "execution_count": 72, + "execution_count": 16, "metadata": {}, "outputs": [], "source": [ @@ -248,6 +266,8 @@ "from pydrive2.auth import GoogleAuth, AuthenticationError\n", "from pydrive2.drive import GoogleDrive\n", "from pydrive2.files import ApiRequestError\n", + "import zipfile\n", + "import geopandas as gpd\n", "\n", "def gdrive_to_df(file_name: str, mime_type: str, credentials_path: str, dataset_folder: str) -> pd.DataFrame:\n", " \"\"\"\n", @@ -257,6 +277,7 @@ " file_name: The name of the requested file.\n", " mime_type: The MIME type - according to https://mime-type.com/\n", " credentials_path: The path to the Google Cloud service account credentials JSON file.\n", + " dataset_folder: the folder where the extracted file is stored.\n", "\n", " Returns:\n", " A pandas DataFrame containing the data from the specified worksheet, or None on error.\n", @@ -286,10 +307,26 @@ " print(f\"An unexpected error occurred: {e}\")\n", " return None\n", "\n", - " # Use the first row as header and the rest as data\n", + " # read csv if file is csv\n", " if mime_type == \"text/csv\":\n", " df = pd.read_csv(dataset_folder + file_name)\n", "\n", + " # extract from zip if file is zip \n", + " # note: THIS CODE ASSUMES THAT THE ZIP ONLY CONTAINS ONE CSV FILE\n", + " elif mime_type == \"application/zip\":\n", + "\n", + " # note: THIS CODE ASSUMES THAT THE CSV FILE HAS THE SAME NAME AS THE ZIP FILE\n", + " csv_name = file_name[:-4] + \".csv\"\n", + " \n", + " with zipfile.ZipFile(dataset_folder + file_name,\"r\") as zip_ref:\n", + " zip_ref.extractall(dataset_folder)\n", + " df = pd.read_csv(dataset_folder + csv_name)\n", + "\n", + " elif mime_type == \"application/geo+json\":\n", + " df = gpd.read_file(dataset_folder + file_name)\n", + " \n", + " \n", + "\n", " # De-duplicate columns, keeping the first occurrence\n", " df = df.loc[:, ~df.columns.duplicated()]\n", "\n", @@ -305,7 +342,7 @@ }, { "cell_type": "code", - "execution_count": 73, + "execution_count": 17, "metadata": {}, "outputs": [], "source": [ @@ -357,28 +394,158 @@ }, { "cell_type": "code", - "execution_count": 74, + "execution_count": 18, + "metadata": {}, + "outputs": [], + "source": [ + "from typing import Optional\n", + "import pandas as pd\n", + "from prefect import task, get_run_logger\n", + "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", + "# from resources.prefect import credentials\n", + "\n", + "@task\n", + "def extract_proc(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", + " \"\"\"\n", + " Extracts raw data from a .zip file.\n", + "\n", + " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", + " to the data source and returns the data as is, without transformation.\n", + "\n", + " Returns:\n", + " A pandas DataFrame containing the raw data, or None if an error occurs.\n", + " \"\"\"\n", + " logger = get_run_logger()\n", + "\n", + " FILE_NAME = \"CA_proc_points.zip\"\n", + " MIME_TYPE = \"application/zip\"\n", + " CREDENTIALS_PATH = \"credentials.json\"\n", + " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", + " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", + "\n", + " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", + " # Otherwise, use the default relative path (for the main pipeline)\n", + " credentials_path = CREDENTIALS_PATH\n", + " dataset_folder = DATASET_FOLDER\n", + " if project_root:\n", + " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", + " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", + "\n", + " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", + " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", + "\n", + " \n", + "\n", + " if raw_df is None:\n", + " logger.error(\"Failed to extract data. Aborting.\")\n", + " return None\n", + "\n", + " logger.info(\"Successfully extracted raw data.\")\n", + " return raw_df\n" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [], + "source": [ + "from typing import Optional\n", + "import pandas as pd\n", + "from prefect import task, get_run_logger\n", + "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", + "# from resources.prefect import credentials\n", + "\n", + "@task\n", + "def extract_petro(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", + " \"\"\"\n", + " Extracts raw data from a .geojson file.\n", + "\n", + " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", + " to the data source and returns the data as is, without transformation.\n", + "\n", + " Returns:\n", + " A pandas DataFrame containing the raw data, or None if an error occurs.\n", + " \"\"\"\n", + " logger = get_run_logger()\n", + "\n", + " FILE_NAME = \"US_Petroleum_Pipelines.geojson\"\n", + " MIME_TYPE = \"application/geo+json\"\n", + " CREDENTIALS_PATH = \"credentials.json\"\n", + " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", + " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", + "\n", + " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", + " # Otherwise, use the default relative path (for the main pipeline)\n", + " credentials_path = CREDENTIALS_PATH\n", + " dataset_folder = DATASET_FOLDER\n", + " if project_root:\n", + " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", + " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", + "\n", + " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", + " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", + "\n", + " \n", + "\n", + " if raw_df is None:\n", + " logger.error(\"Failed to extract data. Aborting.\")\n", + " return None\n", + "\n", + " logger.info(\"Successfully extracted raw data.\")\n", + " return raw_df\n" + ] + }, + { + "cell_type": "code", + "execution_count": 22, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2026-01-13 18:36:20,831 - INFO - Starting data extraction...\n", - "2026-01-13 18:36:20,856 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-13 18:36:20,857 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", - "2026-01-13 18:36:20,866 - INFO - Extracting raw data from 'Biodiesel_Plants.csv'...\n", - "2026-01-13 18:36:20,886 - INFO - Attempting refresh to obtain initial access_token\n", + "2026-01-14 12:32:21,077 - INFO - Starting data extraction...\n", + "2026-01-14 12:32:21,097 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 12:32:21,098 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 12:32:21,106 - INFO - Extracting raw data from 'Biodiesel_Plants.csv'...\n", + "2026-01-14 12:32:21,122 - INFO - Attempting refresh to obtain initial access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", + " return crypto.sign(self._key, message, 'sha256')\n", + "2026-01-14 12:32:21,125 - INFO - Refreshing access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " self.token_expiry = delta + _UTCNOW()\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " now = _UTCNOW()\n", + "2026-01-14 12:32:22,387 - INFO - Successfully extracted raw data.\n", + "2026-01-14 12:32:22,393 - INFO - Finished in state Completed()\n", + "2026-01-14 12:32:22,431 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 12:32:22,434 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 12:32:22,445 - INFO - Extracting raw data from 'CA_proc_points.zip'...\n", + "2026-01-14 12:32:22,483 - INFO - Attempting refresh to obtain initial access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", " return crypto.sign(self._key, message, 'sha256')\n", - "2026-01-13 18:36:20,889 - INFO - Refreshing access_token\n", + "2026-01-14 12:32:22,486 - INFO - Refreshing access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " self.token_expiry = delta + _UTCNOW()\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " now = _UTCNOW()\n", - "2026-01-13 18:36:22,092 - INFO - Successfully extracted raw data.\n", - "2026-01-13 18:36:22,097 - INFO - Finished in state Completed()\n", - "2026-01-13 18:36:22,113 - INFO - Data extraction complete.\n" + "2026-01-14 12:32:23,827 - INFO - Successfully extracted raw data.\n", + "2026-01-14 12:32:23,832 - INFO - Finished in state Completed()\n", + "2026-01-14 12:32:23,877 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 12:32:23,878 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 12:32:23,889 - INFO - Extracting raw data from 'US_Petroleum_Pipelines.geojson'...\n", + "2026-01-14 12:32:23,912 - INFO - Attempting refresh to obtain initial access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", + " return crypto.sign(self._key, message, 'sha256')\n", + "2026-01-14 12:32:23,914 - INFO - Refreshing access_token\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " self.token_expiry = delta + _UTCNOW()\n", + "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", + " now = _UTCNOW()\n", + "2026-01-14 12:32:26,422 - INFO - Successfully extracted raw data.\n", + "2026-01-14 12:32:26,428 - INFO - Finished in state Completed()\n", + "2026-01-14 12:32:26,476 - INFO - Data extraction complete.\n" ] }, { @@ -450,7 +617,124 @@ "76 https://issuu.com/bbiinternational/docs/biodie... \n", "77 https://issuu.com/bbiinternational/docs/biodie... \n", "\n", - "[78 rows x 12 columns]]\n" + "[78 rows x 12 columns], Address COUNTY City \\\n", + "0 327 Daniels Ln Kern Bakersfield \n", + "1 26060 Colusa Road Fresno Coalinga \n", + "2 21490 Ortigalita Rd Merced Los Banos \n", + "3 8800 S Minturn Rd Merced Le Grand \n", + "4 NaN Stanislaus NaN \n", + ".. ... ... ... \n", + "707 3230 Oakdale Rd 0 Paso Robles \n", + "708 5963 Graham Ct D 0 Livermore \n", + "709 708 Addison St 0 Berkeley \n", + "710 9275 Midway 0 Durham \n", + "711 95 Booker Rd 0 Templeton \n", + "\n", + " Company Join_Count MASTERTYPE State Subtype \\\n", + "0 Real Almond Processing 1.0 almond CA almond \n", + "1 Harris Woolf 1.0 almond CA almond \n", + "2 Parreira Almond Processing 1.0 almond CA almond \n", + "3 Minturn Nut Co Inc 1.0 almond CA almond \n", + "4 Tree Nuts LLC 1.0 almond CA almond \n", + ".. ... ... ... ... ... \n", + "707 Red Soles Winery 0.0 winery CA pomace \n", + "708 Eckert Estate Winery 0.0 winery CA pomace \n", + "709 Takara Sake USA Inc 0.0 winery CA pomace \n", + "710 Bertagna Son Kissed Vineyards 0.0 winery CA pomace \n", + "711 Pasoport Wine Company 0.0 winery CA pomace \n", + "\n", + " TARGET_FID Type Zip TYPE \\\n", + "0 0.0 shelling 93307 PROC \n", + "1 1.0 shelling 93210 PROC \n", + "2 2.0 shelling 93635 PROC \n", + "3 3.0 shelling 95333 PROC \n", + "4 4.0 shelling 0 PROC \n", + ".. ... ... ... ... \n", + "707 0.0 winery 93446 PROC \n", + "708 0.0 winery 94550 PROC \n", + "709 0.0 winery 94710 PROC \n", + "710 0.0 winery 95938 PROC \n", + "711 0.0 winery 93465 PROC \n", + "\n", + " wkt_geom \\\n", + "0 0101000020E610000090A6D5EBF1BF5DC0D652E5208DAC... \n", + "1 0101000020E6100000931B45D61A175EC0EC67B114C915... \n", + "2 0101000020E610000008951348E4375EC00937B62ACB7D... \n", + "3 0101000020E6100000E025DD3B8F115EC0B26066C8C694... \n", + "4 0101000020E61000007CD3F4D901365EC07E37DDB243BE... \n", + ".. ... \n", + "707 0101000020E61000005029C0C128305EC0723788D68AC8... \n", + "708 0101000020E6100000A2F8E758146E5EC0DCEB4905BAD6... \n", + "709 0101000020E61000003B78DCA62E935EC0887A66EEC6EE... \n", + "710 0101000020E6100000DAB6DE2527735EC042CAF4F00AD2... \n", + "711 0101000020E610000051700C5C792F5EC030FFB661F3C7... \n", + "\n", + " geom latitude longitude \n", + "0 POINT (-118.9991407 35.3480569) 35.348057 -118.999141 \n", + "1 POINT (-120.361013 36.170199) 36.170199 -120.361013 \n", + "2 POINT (-120.8733082 36.98276266) 36.982763 -120.873308 \n", + "3 POINT (-120.2743673 37.16231637) 37.162316 -120.274367 \n", + "4 POINT (-120.843863 37.486441) 37.486441 -120.843863 \n", + ".. ... ... ... \n", + "707 POINT (-120.7524876 35.566737) 35.566737 -120.752488 \n", + "708 POINT (-121.7199919 37.6775519) 37.677552 -121.719992 \n", + "709 POINT (-122.2997224 37.8654459) 37.865446 -122.299722 \n", + "710 POINT (-121.7992644 39.6409589) 39.640959 -121.799264 \n", + "711 POINT (-120.7417822 35.56211492) 35.562115 -120.741782 \n", + "\n", + "[712 rows x 16 columns], OBJECTID Opername Pipename Source \\\n", + "0 1 NUSTAR ENERGY Valley Pipeline EIA \n", + "1 2 TRANSMONTAIGNE PARTNERS Diamondback Pipeline EIA \n", + "2 3 NUSTAR ENERGY Valley Pipeline EIA \n", + "3 4 TRANSMONTAIGNE PARTNERS Diamondback Pipeline EIA \n", + "4 5 TRANSMONTAIGNE PARTNERS Diamondback Pipeline EIA \n", + "... ... ... ... ... \n", + "4307 4308 None None None \n", + "4308 4309 None None None \n", + "4309 4310 None None None \n", + "4310 4311 None None None \n", + "4311 4312 None None None \n", + "\n", + " Type Notes ARTIFICIAL MASTER_OID commodity \\\n", + "0 Petroleum Product None 0 299.0 Petroleum Products \n", + "1 Petroleum Product None 0 300.0 Petroleum Products \n", + "2 Petroleum Product None 0 301.0 Petroleum Products \n", + "3 Petroleum Product None 0 302.0 Petroleum Products \n", + "4 Petroleum Product None 0 303.0 Petroleum Products \n", + "... ... ... ... ... ... \n", + "4307 None None 2 NaN Petroleum Products \n", + "4308 None None 2 NaN Petroleum Products \n", + "4309 None None 2 NaN Petroleum Products \n", + "4310 None None 2 NaN Petroleum Products \n", + "4311 None None 2 NaN Petroleum Products \n", + "\n", + " Volume Capacity VCR Shape_Length Mode_Type Length \\\n", + "0 None None None 1496.712523 pipeline_prod 0.930012 \n", + "1 None None None 1934.748751 pipeline_prod 1.202195 \n", + "2 None None None 55.870089 pipeline_prod 0.034716 \n", + "3 None None None 2082.004459 pipeline_prod 1.293695 \n", + "4 None None None 9904.740005 pipeline_prod 6.154508 \n", + "... ... ... ... ... ... ... \n", + "4307 None None None 207.259275 pipeline_prod 0.128785 \n", + "4308 None None None 242.718991 pipeline_prod 0.150818 \n", + "4309 None None None 592.947623 pipeline_prod 0.368440 \n", + "4310 None None None 836.752423 pipeline_prod 0.519933 \n", + "4311 None None None 7215.035750 pipeline_prod 4.483206 \n", + "\n", + " geometry \n", + "0 MULTILINESTRING ((-97.38949 25.96387, -97.3921... \n", + "1 MULTILINESTRING ((-97.38299 25.96636, -97.3839... \n", + "2 MULTILINESTRING ((-97.39214 25.97691, -97.3922... \n", + "3 MULTILINESTRING ((-97.38165 25.9667, -97.38265... \n", + "4 MULTILINESTRING ((-97.52187 26.00233, -97.5283... \n", + "... ... \n", + "4307 MULTILINESTRING ((-93.19672 45.02409, -93.1989... \n", + "4308 MULTILINESTRING ((-93.19672 45.02409, -93.1997... \n", + "4309 MULTILINESTRING ((-93.19672 45.02409, -93.2032... \n", + "4310 MULTILINESTRING ((-93.19672 45.02409, -93.1966... \n", + "4311 MULTILINESTRING ((-93.19672 45.02409, -93.2638... \n", + "\n", + "[4312 rows x 16 columns]]\n" ] } ], @@ -459,7 +743,9 @@ "# In a real Prefect flow, each extraction would be a separate task.\n", "logger.info('Starting data extraction...')\n", "biodiesel_plants_df = extract(project_root=project_root)\n", - "dataframes = [biodiesel_plants_df]\n", + "proc_points_df = extract_proc(project_root=project_root)\n", + "petro_pipelines_df = extract_petro(project_root=project_root)\n", + "dataframes = [biodiesel_plants_df, proc_points_df, petro_pipelines_df]\n", "print(dataframes)\n", "logger.info('Data extraction complete.')\n", "\n", From b467d736d28d04c46422d93076dd79440a2b9d8e Mon Sep 17 00:00:00 2001 From: Avi <32148378+avi9664@users.noreply.github.com> Date: Wed, 14 Jan 2026 13:23:50 -0800 Subject: [PATCH 79/81] moved drive extraction scripts to their own files --- .../biodiesel_plants-checkpoint.py | 20 +- .../ca_proc_points-checkpoint.py | 44 + .../petroleum_pipelines-checkpoint.py | 45 + .../pipeline/etl/extract/biodiesel_plants.py | 20 +- .../pipeline/etl/extract/ca_proc_points.py | 44 + .../etl/extract/petroleum_pipelines.py | 45 + .../US_Freight_Terminals-checkpoint.geojson | 13 +- .../US_Petroleum_Pipelines-checkpoint.geojson | 130933 ++++++++++++++- .../US_Freight_Terminals.geojson | 13 +- .../US_Petroleum_Pipelines.geojson | 130933 ++++++++++++++- .../external_etl_notebook-checkpoint.ipynb | 300 +- .../gdrive_to_pandas-checkpoint.py | 55 +- .../utils/external_etl_notebook.ipynb | 300 +- .../pipeline/utils/gdrive_to_pandas.py | 55 +- 14 files changed, 253592 insertions(+), 9228 deletions(-) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ca_proc_points-checkpoint.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/petroleum_pipelines-checkpoint.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ca_proc_points.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/petroleum_pipelines.py diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/biodiesel_plants-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/biodiesel_plants-checkpoint.py index 39941ce8..0f0c41cd 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/biodiesel_plants-checkpoint.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/biodiesel_plants-checkpoint.py @@ -1,11 +1,11 @@ from typing import Optional import pandas as pd from prefect import task, get_run_logger -from ...utils.gdrive_to_pandas import gdrive_to_df -# from resources.prefect import credentials +from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df +import os @task -def extract(csv_path) -> Optional[pd.DataFrame]: +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: """ Extracts raw data from a .csv file. @@ -18,11 +18,21 @@ def extract(csv_path) -> Optional[pd.DataFrame]: logger = get_run_logger() FILE_NAME = "Biodiesel_Plants.csv" + MIME_TYPE = "text/csv" CREDENTIALS_PATH = "credentials.json" + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" logger.info(f"Extracting raw data from '{FILE_NAME}'...") - # The gsheet_to_df function handles authentication, data fetching, and error handling. - raw_df = gdrive_to_pandas(FILE_NAME, CREDENTIALS_PATH) + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + dataset_folder = DATASET_FOLDER + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + dataset_folder = os.path.join(project_root, DATASET_FOLDER) + + # The gdrive_to_df function handles authentication, data fetching, and error handling. + raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ca_proc_points-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ca_proc_points-checkpoint.py new file mode 100644 index 00000000..e880b47a --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ca_proc_points-checkpoint.py @@ -0,0 +1,44 @@ +from typing import Optional +import pandas as pd +from prefect import task, get_run_logger +from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df +import os + +@task +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: + """ + Extracts raw data from a .zip file. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + + FILE_NAME = "CA_proc_points.zip" + MIME_TYPE = "application/zip" + CREDENTIALS_PATH = "credentials.json" + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" + logger.info(f"Extracting raw data from '{FILE_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + dataset_folder = DATASET_FOLDER + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + dataset_folder = os.path.join(project_root, DATASET_FOLDER) + + # The gdrive_to_df function handles authentication, data fetching, and error handling. + raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) + + + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df \ No newline at end of file diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/petroleum_pipelines-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/petroleum_pipelines-checkpoint.py new file mode 100644 index 00000000..a345dbbf --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/petroleum_pipelines-checkpoint.py @@ -0,0 +1,45 @@ +from typing import Optional +import pandas as pd +from prefect import task, get_run_logger +from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df +import geopandas as gpd +import os + +@task +def extract(project_root: Optional[str] = None) -> Optional[gpd.GeoDataFrame]: + """ + Extracts raw data from a .geojson file. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + + FILE_NAME = "US_Petroleum_Pipelines.geojson" + MIME_TYPE = "application/geo+json" + CREDENTIALS_PATH = "credentials.json" + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" + logger.info(f"Extracting raw data from '{FILE_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + dataset_folder = DATASET_FOLDER + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + dataset_folder = os.path.join(project_root, DATASET_FOLDER) + + # The gdrive_to_df function handles authentication, data fetching, and error handling. + raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) + + + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py index 39941ce8..0f0c41cd 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/biodiesel_plants.py @@ -1,11 +1,11 @@ from typing import Optional import pandas as pd from prefect import task, get_run_logger -from ...utils.gdrive_to_pandas import gdrive_to_df -# from resources.prefect import credentials +from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df +import os @task -def extract(csv_path) -> Optional[pd.DataFrame]: +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: """ Extracts raw data from a .csv file. @@ -18,11 +18,21 @@ def extract(csv_path) -> Optional[pd.DataFrame]: logger = get_run_logger() FILE_NAME = "Biodiesel_Plants.csv" + MIME_TYPE = "text/csv" CREDENTIALS_PATH = "credentials.json" + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" logger.info(f"Extracting raw data from '{FILE_NAME}'...") - # The gsheet_to_df function handles authentication, data fetching, and error handling. - raw_df = gdrive_to_pandas(FILE_NAME, CREDENTIALS_PATH) + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + dataset_folder = DATASET_FOLDER + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + dataset_folder = os.path.join(project_root, DATASET_FOLDER) + + # The gdrive_to_df function handles authentication, data fetching, and error handling. + raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ca_proc_points.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ca_proc_points.py new file mode 100644 index 00000000..e880b47a --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ca_proc_points.py @@ -0,0 +1,44 @@ +from typing import Optional +import pandas as pd +from prefect import task, get_run_logger +from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df +import os + +@task +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: + """ + Extracts raw data from a .zip file. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + + FILE_NAME = "CA_proc_points.zip" + MIME_TYPE = "application/zip" + CREDENTIALS_PATH = "credentials.json" + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" + logger.info(f"Extracting raw data from '{FILE_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + dataset_folder = DATASET_FOLDER + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + dataset_folder = os.path.join(project_root, DATASET_FOLDER) + + # The gdrive_to_df function handles authentication, data fetching, and error handling. + raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) + + + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df \ No newline at end of file diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/petroleum_pipelines.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/petroleum_pipelines.py new file mode 100644 index 00000000..a345dbbf --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/petroleum_pipelines.py @@ -0,0 +1,45 @@ +from typing import Optional +import pandas as pd +from prefect import task, get_run_logger +from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df +import geopandas as gpd +import os + +@task +def extract(project_root: Optional[str] = None) -> Optional[gpd.GeoDataFrame]: + """ + Extracts raw data from a .geojson file. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + + FILE_NAME = "US_Petroleum_Pipelines.geojson" + MIME_TYPE = "application/geo+json" + CREDENTIALS_PATH = "credentials.json" + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" + logger.info(f"Extracting raw data from '{FILE_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + credentials_path = CREDENTIALS_PATH + dataset_folder = DATASET_FOLDER + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + dataset_folder = os.path.join(project_root, DATASET_FOLDER) + + # The gdrive_to_df function handles authentication, data fetching, and error handling. + raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) + + + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/US_Freight_Terminals-checkpoint.geojson b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/US_Freight_Terminals-checkpoint.geojson index d11b8ef0..22064337 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/US_Freight_Terminals-checkpoint.geojson +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/US_Freight_Terminals-checkpoint.geojson @@ -1,8 +1,9 @@ { -"type": "FeatureCollection", -"name": "us_freight_terminals_ftot", -"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } }, -"features": [ - -] + "type": "FeatureCollection", + "name": "us_freight_terminals_ftot", + "crs": { + "type": "name", + "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } + }, + "features": [] } diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/US_Petroleum_Pipelines-checkpoint.geojson b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/US_Petroleum_Pipelines-checkpoint.geojson index f5a41665..9cc9ad00 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/US_Petroleum_Pipelines-checkpoint.geojson +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/.ipynb_checkpoints/US_Petroleum_Pipelines-checkpoint.geojson @@ -1,4319 +1,126618 @@ { -"type": "FeatureCollection", -"name": "petrol_prod_pipelines_ftot", -"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } }, -"features": [ -{ "type": "Feature", "properties": { "OBJECTID": 1, "Opername": "NUSTAR ENERGY", "Pipename": "Valley Pipeline", "Source": "EIA", "Type": "Petroleum Product", 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b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb index 5834652a..5e3b36b9 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/external_etl_notebook-checkpoint.ipynb @@ -27,7 +27,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2026-01-14 11:30:02,898 - INFO - Added project root 'C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing' to sys.path\n", + "2026-01-14 13:20:42,179 - INFO - Added project root 'C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing' to sys.path\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:19: DeprecationWarning: 'setName' deprecated - use 'set_name'\n", " token = pp.Word(tchar).setName(\"token\")\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:20: DeprecationWarning: 'leaveWhitespace' deprecated - use 'leave_whitespace'\n", @@ -46,7 +46,7 @@ " params = pp.Dict(pp.delimitedList(pp.Group(auth_param)))\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:33: DeprecationWarning: 'delimitedList' deprecated - use 'DelimitedList'\n", " www_authenticate = pp.delimitedList(pp.Group(challenge))\n", - "2026-01-14 11:30:52,659 - INFO - Successfully imported all project modules.\n" + "2026-01-14 13:21:10,726 - INFO - Successfully imported all project modules.\n" ] } ], @@ -93,6 +93,8 @@ " from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import replace_name_with_id_df\n", " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import biodiesel_plants\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import ca_proc_points\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import petroleum_pipelines\n", " logger.info('Successfully imported all project modules.')\n", "except ImportError as e:\n", " logger.error(f'Failed to import project modules: {e}', exc_info=True)" @@ -258,294 +260,54 @@ }, { "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [], - "source": [ - "import pandas as pd\n", - "from pydrive2.auth import GoogleAuth, AuthenticationError\n", - "from pydrive2.drive import GoogleDrive\n", - "from pydrive2.files import ApiRequestError\n", - "import zipfile\n", - "import geopandas as gpd\n", - "\n", - "def gdrive_to_df(file_name: str, mime_type: str, credentials_path: str, dataset_folder: str) -> pd.DataFrame:\n", - " \"\"\"\n", - " Extracts data from a CSV, ZIP, or GEOJSON file into a pandas DataFrame.\n", - "\n", - " Args:\n", - " file_name: The name of the requested file.\n", - " mime_type: The MIME type - according to https://mime-type.com/\n", - " credentials_path: The path to the Google Cloud service account credentials JSON file.\n", - " dataset_folder: the folder where the extracted file is stored.\n", - "\n", - " Returns:\n", - " A pandas DataFrame containing the data from the specified worksheet, or None on error.\n", - " \"\"\"\n", - " try:\n", - " settings = {\n", - " \"client_config_backend\": \"service\",\n", - " \"service_config\": {\n", - " \"client_json_file_path\": credentials_path,\n", - " }\n", - " }\n", - " # Create instance of GoogleAuth\n", - " gauth = GoogleAuth(settings=settings)\n", - " gauth.ServiceAuth()\n", - " drive = GoogleDrive(gauth)\n", - "\n", - " try:\n", - " file_entries = drive.ListFile({\"q\": f\"title = '{file_name}' and mimeType= '{mime_type}'\"}).GetList()\n", - " if len(file_entries) == 0: \n", - " raise FileNotFoundError(f\"Error: File '{file_name}' not found. \\n Please make sure the spreadsheet name is correct and that you have shared it with the service account email.\")\n", - " return None\n", - " else:\n", - " file_entry = file_entries[0]\n", - " file = drive.CreateFile({'id': file_entry['id']})\n", - " file.GetContentFile(dataset_folder + file_name) # Download file\n", - " except ApiRequestError:\n", - " print(f\"An unexpected error occurred: {e}\")\n", - " return None\n", - "\n", - " # read csv if file is csv\n", - " if mime_type == \"text/csv\":\n", - " df = pd.read_csv(dataset_folder + file_name)\n", - "\n", - " # extract from zip if file is zip \n", - " # note: THIS CODE ASSUMES THAT THE ZIP ONLY CONTAINS ONE CSV FILE\n", - " elif mime_type == \"application/zip\":\n", - "\n", - " # note: THIS CODE ASSUMES THAT THE CSV FILE HAS THE SAME NAME AS THE ZIP FILE\n", - " csv_name = file_name[:-4] + \".csv\"\n", - " \n", - " with zipfile.ZipFile(dataset_folder + file_name,\"r\") as zip_ref:\n", - " zip_ref.extractall(dataset_folder)\n", - " df = pd.read_csv(dataset_folder + csv_name)\n", - "\n", - " elif mime_type == \"application/geo+json\":\n", - " df = gpd.read_file(dataset_folder + file_name)\n", - " \n", - " \n", - "\n", - " # De-duplicate columns, keeping the first occurrence\n", - " df = df.loc[:, ~df.columns.duplicated()]\n", - "\n", - " return df\n", - "\n", - " except AuthenticationError as e:\n", - " print(f\"Google Authentication Error: {e}\")\n", - " return None\n", - " except Exception as e:\n", - " print(f\"An unexpected error occurred: {e}\")\n", - " return None\n" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [], - "source": [ - "from typing import Optional\n", - "import pandas as pd\n", - "from prefect import task, get_run_logger\n", - "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", - "# from resources.prefect import credentials\n", - "\n", - "@task\n", - "def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", - " \"\"\"\n", - " Extracts raw data from a .csv file.\n", - "\n", - " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", - " to the data source and returns the data as is, without transformation.\n", - "\n", - " Returns:\n", - " A pandas DataFrame containing the raw data, or None if an error occurs.\n", - " \"\"\"\n", - " logger = get_run_logger()\n", - "\n", - " FILE_NAME = \"Biodiesel_Plants.csv\"\n", - " MIME_TYPE = \"text/csv\"\n", - " CREDENTIALS_PATH = \"credentials.json\"\n", - " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", - " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", - "\n", - " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", - " # Otherwise, use the default relative path (for the main pipeline)\n", - " credentials_path = CREDENTIALS_PATH\n", - " dataset_folder = DATASET_FOLDER\n", - " if project_root:\n", - " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", - " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", - "\n", - " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", - " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", - "\n", - " \n", - "\n", - " if raw_df is None:\n", - " logger.error(\"Failed to extract data. Aborting.\")\n", - " return None\n", - "\n", - " logger.info(\"Successfully extracted raw data.\")\n", - " return raw_df\n" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [], - "source": [ - "from typing import Optional\n", - "import pandas as pd\n", - "from prefect import task, get_run_logger\n", - "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", - "# from resources.prefect import credentials\n", - "\n", - "@task\n", - "def extract_proc(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", - " \"\"\"\n", - " Extracts raw data from a .zip file.\n", - "\n", - " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", - " to the data source and returns the data as is, without transformation.\n", - "\n", - " Returns:\n", - " A pandas DataFrame containing the raw data, or None if an error occurs.\n", - " \"\"\"\n", - " logger = get_run_logger()\n", - "\n", - " FILE_NAME = \"CA_proc_points.zip\"\n", - " MIME_TYPE = \"application/zip\"\n", - " CREDENTIALS_PATH = \"credentials.json\"\n", - " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", - " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", - "\n", - " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", - " # Otherwise, use the default relative path (for the main pipeline)\n", - " credentials_path = CREDENTIALS_PATH\n", - " dataset_folder = DATASET_FOLDER\n", - " if project_root:\n", - " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", - " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", - "\n", - " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", - " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", - "\n", - " \n", - "\n", - " if raw_df is None:\n", - " logger.error(\"Failed to extract data. Aborting.\")\n", - " return None\n", - "\n", - " logger.info(\"Successfully extracted raw data.\")\n", - " return raw_df\n" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": {}, - "outputs": [], - "source": [ - "from typing import Optional\n", - "import pandas as pd\n", - "from prefect import task, get_run_logger\n", - "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", - "# from resources.prefect import credentials\n", - "\n", - "@task\n", - "def extract_petro(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", - " \"\"\"\n", - " Extracts raw data from a .geojson file.\n", - "\n", - " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", - " to the data source and returns the data as is, without transformation.\n", - "\n", - " Returns:\n", - " A pandas DataFrame containing the raw data, or None if an error occurs.\n", - " \"\"\"\n", - " logger = get_run_logger()\n", - "\n", - " FILE_NAME = \"US_Petroleum_Pipelines.geojson\"\n", - " MIME_TYPE = \"application/geo+json\"\n", - " CREDENTIALS_PATH = \"credentials.json\"\n", - " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", - " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", - "\n", - " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", - " # Otherwise, use the default relative path (for the main pipeline)\n", - " credentials_path = CREDENTIALS_PATH\n", - " dataset_folder = DATASET_FOLDER\n", - " if project_root:\n", - " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", - " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", - "\n", - " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", - " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", - "\n", - " \n", - "\n", - " if raw_df is None:\n", - " logger.error(\"Failed to extract data. Aborting.\")\n", - " return None\n", - "\n", - " logger.info(\"Successfully extracted raw data.\")\n", - " return raw_df\n" - ] - }, - { - "cell_type": "code", - "execution_count": 22, + "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2026-01-14 12:32:21,077 - INFO - Starting data extraction...\n", - "2026-01-14 12:32:21,097 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-14 12:32:21,098 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", - "2026-01-14 12:32:21,106 - INFO - Extracting raw data from 'Biodiesel_Plants.csv'...\n", - "2026-01-14 12:32:21,122 - INFO - Attempting refresh to obtain initial access_token\n", + "2026-01-14 13:21:19,648 - INFO - Starting data extraction...\n", + "2026-01-14 13:21:19,691 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 13:21:19,692 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 13:21:19,706 - INFO - Extracting raw data from 'Biodiesel_Plants.csv'...\n", + "2026-01-14 13:21:19,729 - INFO - Attempting refresh to obtain initial access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", " return crypto.sign(self._key, message, 'sha256')\n", - "2026-01-14 12:32:21,125 - INFO - Refreshing access_token\n", + "2026-01-14 13:21:19,733 - INFO - Refreshing access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " self.token_expiry = delta + _UTCNOW()\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " now = _UTCNOW()\n", - "2026-01-14 12:32:22,387 - INFO - Successfully extracted raw data.\n", - "2026-01-14 12:32:22,393 - INFO - Finished in state Completed()\n", - "2026-01-14 12:32:22,431 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-14 12:32:22,434 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", - "2026-01-14 12:32:22,445 - INFO - Extracting raw data from 'CA_proc_points.zip'...\n", - "2026-01-14 12:32:22,483 - INFO - Attempting refresh to obtain initial access_token\n", + "2026-01-14 13:21:20,805 - INFO - Successfully extracted raw data.\n", + "2026-01-14 13:21:20,810 - INFO - Finished in state Completed()\n", + "2026-01-14 13:21:20,841 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 13:21:20,842 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 13:21:20,851 - INFO - Extracting raw data from 'CA_proc_points.zip'...\n", + "2026-01-14 13:21:20,871 - INFO - Attempting refresh to obtain initial access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", " return crypto.sign(self._key, message, 'sha256')\n", - "2026-01-14 12:32:22,486 - INFO - Refreshing access_token\n", + "2026-01-14 13:21:20,873 - INFO - Refreshing access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " self.token_expiry = delta + _UTCNOW()\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " now = _UTCNOW()\n", - "2026-01-14 12:32:23,827 - INFO - Successfully extracted raw data.\n", - "2026-01-14 12:32:23,832 - INFO - Finished in state Completed()\n", - "2026-01-14 12:32:23,877 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-14 12:32:23,878 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", - "2026-01-14 12:32:23,889 - INFO - Extracting raw data from 'US_Petroleum_Pipelines.geojson'...\n", - "2026-01-14 12:32:23,912 - INFO - Attempting refresh to obtain initial access_token\n", + "2026-01-14 13:21:22,027 - INFO - Successfully extracted raw data.\n", + "2026-01-14 13:21:22,034 - INFO - Finished in state Completed()\n", + "2026-01-14 13:21:22,069 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 13:21:22,070 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 13:21:22,082 - INFO - Extracting raw data from 'US_Petroleum_Pipelines.geojson'...\n", + "2026-01-14 13:21:22,105 - INFO - Attempting refresh to obtain initial access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", " return crypto.sign(self._key, message, 'sha256')\n", - "2026-01-14 12:32:23,914 - INFO - Refreshing access_token\n", + "2026-01-14 13:21:22,108 - INFO - Refreshing access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " self.token_expiry = delta + _UTCNOW()\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " now = _UTCNOW()\n", - "2026-01-14 12:32:26,422 - INFO - Successfully extracted raw data.\n", - "2026-01-14 12:32:26,428 - INFO - Finished in state Completed()\n", - "2026-01-14 12:32:26,476 - INFO - Data extraction complete.\n" + "2026-01-14 13:21:23,976 - INFO - Successfully extracted raw data.\n", + "2026-01-14 13:21:23,981 - INFO - Finished in state Completed()\n", + "2026-01-14 13:21:24,019 - INFO - Data extraction complete.\n" ] }, { @@ -742,9 +504,9 @@ "# --- 1. Extraction ---\n", "# In a real Prefect flow, each extraction would be a separate task.\n", "logger.info('Starting data extraction...')\n", - "biodiesel_plants_df = extract(project_root=project_root)\n", - "proc_points_df = extract_proc(project_root=project_root)\n", - "petro_pipelines_df = extract_petro(project_root=project_root)\n", + "biodiesel_plants_df = biodiesel_plants.extract(project_root=project_root)\n", + "proc_points_df = ca_proc_points.extract(project_root=project_root)\n", + "petro_pipelines_df = petroleum_pipelines.extract(project_root=project_root)\n", "dataframes = [biodiesel_plants_df, proc_points_df, petro_pipelines_df]\n", "print(dataframes)\n", "logger.info('Data extraction complete.')\n", diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gdrive_to_pandas-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gdrive_to_pandas-checkpoint.py index 8b083a0c..e3c2ea85 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gdrive_to_pandas-checkpoint.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/.ipynb_checkpoints/gdrive_to_pandas-checkpoint.py @@ -1,14 +1,20 @@ import pandas as pd -from pydrive2.auth import GoogleAuth +from pydrive2.auth import GoogleAuth, AuthenticationError from pydrive2.drive import GoogleDrive +from pydrive2.files import ApiRequestError +import zipfile +import geopandas as gpd +import os -def gdrive_to_df(file_name: str, credentials_path: str) -> pd.DataFrame: +def gdrive_to_df(file_name: str, mime_type: str, credentials_path: str, dataset_folder: str) -> pd.DataFrame | gpd.GeoDataFrame: """ - Extracts data from a CSV or GEOJSON into a pandas DataFrame. + Extracts data from a CSV, ZIP, or GEOJSON file into a pandas DataFrame. Args: file_name: The name of the requested file. + mime_type: The MIME type - according to https://mime-type.com/ credentials_path: The path to the Google Cloud service account credentials JSON file. + dataset_folder: the folder where the extracted file is stored. Returns: A pandas DataFrame containing the data from the specified worksheet, or None on error. @@ -26,30 +32,45 @@ def gdrive_to_df(file_name: str, credentials_path: str) -> pd.DataFrame: drive = GoogleDrive(gauth) try: - file_list = drive.ListFile().GetList() - print(file_list) - except SpreadsheetNotFound: - print(f"Error: Spreadsheet '{gsheet_name}' not found.") - print("Please make sure the spreadsheet name is correct and that you have shared it with the service account email.") + file_entries = drive.ListFile({"q": f"title = '{file_name}' and mimeType= '{mime_type}'"}).GetList() + if len(file_entries) == 0: + raise FileNotFoundError(f"Error: File '{file_name}' not found. \n Please make sure the name and mimeType is correct and that you have shared it with the service account email.") + return None + else: + file_entry = file_entries[0] + file = drive.CreateFile({'id': file_entry['id']}) + file.GetContentFile(dataset_folder + file_name) # Download file + except ApiRequestError: + print(f"An unexpected error occurred: {e}") return None + # read csv if file is csv + if mime_type == "text/csv": + df = pd.read_csv(dataset_folder + file_name) - # Get values directly to ensure we get calculated values, not formulas. - # 'FORMATTED_VALUE' gets the value as you see it in the sheet. - all_values = worksheet.get_all_values(value_render_option='FORMATTED_VALUE') - if not all_values: - return pd.DataFrame() # Return empty DataFrame if sheet is empty + # extract from zip if file is zip + # note: THIS CODE ASSUMES THAT THE ZIP ONLY CONTAINS ONE CSV FILE + elif mime_type == "application/zip": - # Use the first row as header and the rest as data - df = pd.DataFrame(all_values[1:], columns=all_values[0]) + # note: THIS CODE ASSUMES THAT THE CSV FILE HAS THE SAME NAME AS THE ZIP FILE + csv_name = file_name[:-4] + ".csv" + + with zipfile.ZipFile(dataset_folder + file_name,"r") as zip_ref: + zip_ref.extractall(dataset_folder) + df = pd.read_csv(dataset_folder + csv_name) + + elif mime_type == "application/geo+json": + df = gpd.read_file(dataset_folder + file_name) + else: + raise Exception("Can't handle this MIME type. Sorry.") # De-duplicate columns, keeping the first occurrence df = df.loc[:, ~df.columns.duplicated()] return df - except APIError as e: - print(f"Google API Error: {e}") + except AuthenticationError as e: + print(f"Google Authentication Error: {e}") return None except Exception as e: print(f"An unexpected error occurred: {e}") diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb index 5834652a..5e3b36b9 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/external_etl_notebook.ipynb @@ -27,7 +27,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "2026-01-14 11:30:02,898 - INFO - Added project root 'C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing' to sys.path\n", + "2026-01-14 13:20:42,179 - INFO - Added project root 'C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing' to sys.path\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:19: DeprecationWarning: 'setName' deprecated - use 'set_name'\n", " token = pp.Word(tchar).setName(\"token\")\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:20: DeprecationWarning: 'leaveWhitespace' deprecated - use 'leave_whitespace'\n", @@ -46,7 +46,7 @@ " params = pp.Dict(pp.delimitedList(pp.Group(auth_param)))\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\httplib2\\auth.py:33: DeprecationWarning: 'delimitedList' deprecated - use 'DelimitedList'\n", " www_authenticate = pp.delimitedList(pp.Group(challenge))\n", - "2026-01-14 11:30:52,659 - INFO - Successfully imported all project modules.\n" + "2026-01-14 13:21:10,726 - INFO - Successfully imported all project modules.\n" ] } ], @@ -93,6 +93,8 @@ " from src.ca_biositing.datamodels.ca_biositing.datamodels.schemas.generated.ca_biositing import *\n", " from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.name_id_swap import replace_name_with_id_df\n", " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import biodiesel_plants\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import ca_proc_points\n", + " from src.ca_biositing.pipeline.ca_biositing.pipeline.etl.extract import petroleum_pipelines\n", " logger.info('Successfully imported all project modules.')\n", "except ImportError as e:\n", " logger.error(f'Failed to import project modules: {e}', exc_info=True)" @@ -258,294 +260,54 @@ }, { "cell_type": "code", - "execution_count": 16, - "metadata": {}, - "outputs": [], - "source": [ - "import pandas as pd\n", - "from pydrive2.auth import GoogleAuth, AuthenticationError\n", - "from pydrive2.drive import GoogleDrive\n", - "from pydrive2.files import ApiRequestError\n", - "import zipfile\n", - "import geopandas as gpd\n", - "\n", - "def gdrive_to_df(file_name: str, mime_type: str, credentials_path: str, dataset_folder: str) -> pd.DataFrame:\n", - " \"\"\"\n", - " Extracts data from a CSV, ZIP, or GEOJSON file into a pandas DataFrame.\n", - "\n", - " Args:\n", - " file_name: The name of the requested file.\n", - " mime_type: The MIME type - according to https://mime-type.com/\n", - " credentials_path: The path to the Google Cloud service account credentials JSON file.\n", - " dataset_folder: the folder where the extracted file is stored.\n", - "\n", - " Returns:\n", - " A pandas DataFrame containing the data from the specified worksheet, or None on error.\n", - " \"\"\"\n", - " try:\n", - " settings = {\n", - " \"client_config_backend\": \"service\",\n", - " \"service_config\": {\n", - " \"client_json_file_path\": credentials_path,\n", - " }\n", - " }\n", - " # Create instance of GoogleAuth\n", - " gauth = GoogleAuth(settings=settings)\n", - " gauth.ServiceAuth()\n", - " drive = GoogleDrive(gauth)\n", - "\n", - " try:\n", - " file_entries = drive.ListFile({\"q\": f\"title = '{file_name}' and mimeType= '{mime_type}'\"}).GetList()\n", - " if len(file_entries) == 0: \n", - " raise FileNotFoundError(f\"Error: File '{file_name}' not found. \\n Please make sure the spreadsheet name is correct and that you have shared it with the service account email.\")\n", - " return None\n", - " else:\n", - " file_entry = file_entries[0]\n", - " file = drive.CreateFile({'id': file_entry['id']})\n", - " file.GetContentFile(dataset_folder + file_name) # Download file\n", - " except ApiRequestError:\n", - " print(f\"An unexpected error occurred: {e}\")\n", - " return None\n", - "\n", - " # read csv if file is csv\n", - " if mime_type == \"text/csv\":\n", - " df = pd.read_csv(dataset_folder + file_name)\n", - "\n", - " # extract from zip if file is zip \n", - " # note: THIS CODE ASSUMES THAT THE ZIP ONLY CONTAINS ONE CSV FILE\n", - " elif mime_type == \"application/zip\":\n", - "\n", - " # note: THIS CODE ASSUMES THAT THE CSV FILE HAS THE SAME NAME AS THE ZIP FILE\n", - " csv_name = file_name[:-4] + \".csv\"\n", - " \n", - " with zipfile.ZipFile(dataset_folder + file_name,\"r\") as zip_ref:\n", - " zip_ref.extractall(dataset_folder)\n", - " df = pd.read_csv(dataset_folder + csv_name)\n", - "\n", - " elif mime_type == \"application/geo+json\":\n", - " df = gpd.read_file(dataset_folder + file_name)\n", - " \n", - " \n", - "\n", - " # De-duplicate columns, keeping the first occurrence\n", - " df = df.loc[:, ~df.columns.duplicated()]\n", - "\n", - " return df\n", - "\n", - " except AuthenticationError as e:\n", - " print(f\"Google Authentication Error: {e}\")\n", - " return None\n", - " except Exception as e:\n", - " print(f\"An unexpected error occurred: {e}\")\n", - " return None\n" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": {}, - "outputs": [], - "source": [ - "from typing import Optional\n", - "import pandas as pd\n", - "from prefect import task, get_run_logger\n", - "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", - "# from resources.prefect import credentials\n", - "\n", - "@task\n", - "def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", - " \"\"\"\n", - " Extracts raw data from a .csv file.\n", - "\n", - " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", - " to the data source and returns the data as is, without transformation.\n", - "\n", - " Returns:\n", - " A pandas DataFrame containing the raw data, or None if an error occurs.\n", - " \"\"\"\n", - " logger = get_run_logger()\n", - "\n", - " FILE_NAME = \"Biodiesel_Plants.csv\"\n", - " MIME_TYPE = \"text/csv\"\n", - " CREDENTIALS_PATH = \"credentials.json\"\n", - " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", - " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", - "\n", - " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", - " # Otherwise, use the default relative path (for the main pipeline)\n", - " credentials_path = CREDENTIALS_PATH\n", - " dataset_folder = DATASET_FOLDER\n", - " if project_root:\n", - " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", - " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", - "\n", - " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", - " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", - "\n", - " \n", - "\n", - " if raw_df is None:\n", - " logger.error(\"Failed to extract data. Aborting.\")\n", - " return None\n", - "\n", - " logger.info(\"Successfully extracted raw data.\")\n", - " return raw_df\n" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": {}, - "outputs": [], - "source": [ - "from typing import Optional\n", - "import pandas as pd\n", - "from prefect import task, get_run_logger\n", - "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", - "# from resources.prefect import credentials\n", - "\n", - "@task\n", - "def extract_proc(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", - " \"\"\"\n", - " Extracts raw data from a .zip file.\n", - "\n", - " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", - " to the data source and returns the data as is, without transformation.\n", - "\n", - " Returns:\n", - " A pandas DataFrame containing the raw data, or None if an error occurs.\n", - " \"\"\"\n", - " logger = get_run_logger()\n", - "\n", - " FILE_NAME = \"CA_proc_points.zip\"\n", - " MIME_TYPE = \"application/zip\"\n", - " CREDENTIALS_PATH = \"credentials.json\"\n", - " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", - " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", - "\n", - " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", - " # Otherwise, use the default relative path (for the main pipeline)\n", - " credentials_path = CREDENTIALS_PATH\n", - " dataset_folder = DATASET_FOLDER\n", - " if project_root:\n", - " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", - " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", - "\n", - " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", - " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", - "\n", - " \n", - "\n", - " if raw_df is None:\n", - " logger.error(\"Failed to extract data. Aborting.\")\n", - " return None\n", - "\n", - " logger.info(\"Successfully extracted raw data.\")\n", - " return raw_df\n" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": {}, - "outputs": [], - "source": [ - "from typing import Optional\n", - "import pandas as pd\n", - "from prefect import task, get_run_logger\n", - "# from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df\n", - "# from resources.prefect import credentials\n", - "\n", - "@task\n", - "def extract_petro(project_root: Optional[str] = None) -> Optional[pd.DataFrame]:\n", - " \"\"\"\n", - " Extracts raw data from a .geojson file.\n", - "\n", - " This function serves as the 'Extract' step in an ETL pipeline. It connects\n", - " to the data source and returns the data as is, without transformation.\n", - "\n", - " Returns:\n", - " A pandas DataFrame containing the raw data, or None if an error occurs.\n", - " \"\"\"\n", - " logger = get_run_logger()\n", - "\n", - " FILE_NAME = \"US_Petroleum_Pipelines.geojson\"\n", - " MIME_TYPE = \"application/geo+json\"\n", - " CREDENTIALS_PATH = \"credentials.json\"\n", - " DATASET_FOLDER = \"src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/\" \n", - " logger.info(f\"Extracting raw data from '{FILE_NAME}'...\")\n", - "\n", - " # If project_root is provided (e.g., from a notebook), construct an absolute path\n", - " # Otherwise, use the default relative path (for the main pipeline)\n", - " credentials_path = CREDENTIALS_PATH\n", - " dataset_folder = DATASET_FOLDER\n", - " if project_root:\n", - " credentials_path = os.path.join(project_root, CREDENTIALS_PATH)\n", - " dataset_folder = os.path.join(project_root, DATASET_FOLDER)\n", - "\n", - " # The gsheet_to_df function handles authentication, data fetching, and error handling.\n", - " raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder)\n", - "\n", - " \n", - "\n", - " if raw_df is None:\n", - " logger.error(\"Failed to extract data. Aborting.\")\n", - " return None\n", - "\n", - " logger.info(\"Successfully extracted raw data.\")\n", - " return raw_df\n" - ] - }, - { - "cell_type": "code", - "execution_count": 22, + "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "2026-01-14 12:32:21,077 - INFO - Starting data extraction...\n", - "2026-01-14 12:32:21,097 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-14 12:32:21,098 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", - "2026-01-14 12:32:21,106 - INFO - Extracting raw data from 'Biodiesel_Plants.csv'...\n", - "2026-01-14 12:32:21,122 - INFO - Attempting refresh to obtain initial access_token\n", + "2026-01-14 13:21:19,648 - INFO - Starting data extraction...\n", + "2026-01-14 13:21:19,691 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 13:21:19,692 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 13:21:19,706 - INFO - Extracting raw data from 'Biodiesel_Plants.csv'...\n", + "2026-01-14 13:21:19,729 - INFO - Attempting refresh to obtain initial access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", " return crypto.sign(self._key, message, 'sha256')\n", - "2026-01-14 12:32:21,125 - INFO - Refreshing access_token\n", + "2026-01-14 13:21:19,733 - INFO - Refreshing access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " self.token_expiry = delta + _UTCNOW()\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " now = _UTCNOW()\n", - "2026-01-14 12:32:22,387 - INFO - Successfully extracted raw data.\n", - "2026-01-14 12:32:22,393 - INFO - Finished in state Completed()\n", - "2026-01-14 12:32:22,431 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-14 12:32:22,434 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", - "2026-01-14 12:32:22,445 - INFO - Extracting raw data from 'CA_proc_points.zip'...\n", - "2026-01-14 12:32:22,483 - INFO - Attempting refresh to obtain initial access_token\n", + "2026-01-14 13:21:20,805 - INFO - Successfully extracted raw data.\n", + "2026-01-14 13:21:20,810 - INFO - Finished in state Completed()\n", + "2026-01-14 13:21:20,841 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 13:21:20,842 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 13:21:20,851 - INFO - Extracting raw data from 'CA_proc_points.zip'...\n", + "2026-01-14 13:21:20,871 - INFO - Attempting refresh to obtain initial access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", " return crypto.sign(self._key, message, 'sha256')\n", - "2026-01-14 12:32:22,486 - INFO - Refreshing access_token\n", + "2026-01-14 13:21:20,873 - INFO - Refreshing access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " self.token_expiry = delta + _UTCNOW()\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " now = _UTCNOW()\n", - "2026-01-14 12:32:23,827 - INFO - Successfully extracted raw data.\n", - "2026-01-14 12:32:23,832 - INFO - Finished in state Completed()\n", - "2026-01-14 12:32:23,877 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", - "2026-01-14 12:32:23,878 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", - "2026-01-14 12:32:23,889 - INFO - Extracting raw data from 'US_Petroleum_Pipelines.geojson'...\n", - "2026-01-14 12:32:23,912 - INFO - Attempting refresh to obtain initial access_token\n", + "2026-01-14 13:21:22,027 - INFO - Successfully extracted raw data.\n", + "2026-01-14 13:21:22,034 - INFO - Finished in state Completed()\n", + "2026-01-14 13:21:22,069 - INFO - HTTP Request: GET http://localhost:4200/api/admin/version \"HTTP/1.1 200 OK\"\n", + "2026-01-14 13:21:22,070 - WARNING - Your Prefect server is running an older version of Prefect than your client which may result in unexpected behavior. Please upgrade your Prefect server from version 3.5.0 to version 3.6.7 or higher.\n", + "2026-01-14 13:21:22,082 - INFO - Extracting raw data from 'US_Petroleum_Pipelines.geojson'...\n", + "2026-01-14 13:21:22,105 - INFO - Attempting refresh to obtain initial access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\_openssl_crypt.py:97: DeprecationWarning: sign() is deprecated. Use the equivalent APIs in cryptography.\n", " return crypto.sign(self._key, message, 'sha256')\n", - "2026-01-14 12:32:23,914 - INFO - Refreshing access_token\n", + "2026-01-14 13:21:22,108 - INFO - Refreshing access_token\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:789: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " self.token_expiry = delta + _UTCNOW()\n", "C:\\Users\\Abigail\\OneDrive\\Documents\\GitHub\\ca-biositing\\.pixi\\envs\\default\\Lib\\site-packages\\oauth2client\\client.py:647: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC).\n", " now = _UTCNOW()\n", - "2026-01-14 12:32:26,422 - INFO - Successfully extracted raw data.\n", - "2026-01-14 12:32:26,428 - INFO - Finished in state Completed()\n", - "2026-01-14 12:32:26,476 - INFO - Data extraction complete.\n" + "2026-01-14 13:21:23,976 - INFO - Successfully extracted raw data.\n", + "2026-01-14 13:21:23,981 - INFO - Finished in state Completed()\n", + "2026-01-14 13:21:24,019 - INFO - Data extraction complete.\n" ] }, { @@ -742,9 +504,9 @@ "# --- 1. Extraction ---\n", "# In a real Prefect flow, each extraction would be a separate task.\n", "logger.info('Starting data extraction...')\n", - "biodiesel_plants_df = extract(project_root=project_root)\n", - "proc_points_df = extract_proc(project_root=project_root)\n", - "petro_pipelines_df = extract_petro(project_root=project_root)\n", + "biodiesel_plants_df = biodiesel_plants.extract(project_root=project_root)\n", + "proc_points_df = ca_proc_points.extract(project_root=project_root)\n", + "petro_pipelines_df = petroleum_pipelines.extract(project_root=project_root)\n", "dataframes = [biodiesel_plants_df, proc_points_df, petro_pipelines_df]\n", "print(dataframes)\n", "logger.info('Data extraction complete.')\n", diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gdrive_to_pandas.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gdrive_to_pandas.py index 8b083a0c..e3c2ea85 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gdrive_to_pandas.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/utils/gdrive_to_pandas.py @@ -1,14 +1,20 @@ import pandas as pd -from pydrive2.auth import GoogleAuth +from pydrive2.auth import GoogleAuth, AuthenticationError from pydrive2.drive import GoogleDrive +from pydrive2.files import ApiRequestError +import zipfile +import geopandas as gpd +import os -def gdrive_to_df(file_name: str, credentials_path: str) -> pd.DataFrame: +def gdrive_to_df(file_name: str, mime_type: str, credentials_path: str, dataset_folder: str) -> pd.DataFrame | gpd.GeoDataFrame: """ - Extracts data from a CSV or GEOJSON into a pandas DataFrame. + Extracts data from a CSV, ZIP, or GEOJSON file into a pandas DataFrame. Args: file_name: The name of the requested file. + mime_type: The MIME type - according to https://mime-type.com/ credentials_path: The path to the Google Cloud service account credentials JSON file. + dataset_folder: the folder where the extracted file is stored. Returns: A pandas DataFrame containing the data from the specified worksheet, or None on error. @@ -26,30 +32,45 @@ def gdrive_to_df(file_name: str, credentials_path: str) -> pd.DataFrame: drive = GoogleDrive(gauth) try: - file_list = drive.ListFile().GetList() - print(file_list) - except SpreadsheetNotFound: - print(f"Error: Spreadsheet '{gsheet_name}' not found.") - print("Please make sure the spreadsheet name is correct and that you have shared it with the service account email.") + file_entries = drive.ListFile({"q": f"title = '{file_name}' and mimeType= '{mime_type}'"}).GetList() + if len(file_entries) == 0: + raise FileNotFoundError(f"Error: File '{file_name}' not found. \n Please make sure the name and mimeType is correct and that you have shared it with the service account email.") + return None + else: + file_entry = file_entries[0] + file = drive.CreateFile({'id': file_entry['id']}) + file.GetContentFile(dataset_folder + file_name) # Download file + except ApiRequestError: + print(f"An unexpected error occurred: {e}") return None + # read csv if file is csv + if mime_type == "text/csv": + df = pd.read_csv(dataset_folder + file_name) - # Get values directly to ensure we get calculated values, not formulas. - # 'FORMATTED_VALUE' gets the value as you see it in the sheet. - all_values = worksheet.get_all_values(value_render_option='FORMATTED_VALUE') - if not all_values: - return pd.DataFrame() # Return empty DataFrame if sheet is empty + # extract from zip if file is zip + # note: THIS CODE ASSUMES THAT THE ZIP ONLY CONTAINS ONE CSV FILE + elif mime_type == "application/zip": - # Use the first row as header and the rest as data - df = pd.DataFrame(all_values[1:], columns=all_values[0]) + # note: THIS CODE ASSUMES THAT THE CSV FILE HAS THE SAME NAME AS THE ZIP FILE + csv_name = file_name[:-4] + ".csv" + + with zipfile.ZipFile(dataset_folder + file_name,"r") as zip_ref: + zip_ref.extractall(dataset_folder) + df = pd.read_csv(dataset_folder + csv_name) + + elif mime_type == "application/geo+json": + df = gpd.read_file(dataset_folder + file_name) + else: + raise Exception("Can't handle this MIME type. Sorry.") # De-duplicate columns, keeping the first occurrence df = df.loc[:, ~df.columns.duplicated()] return df - except APIError as e: - print(f"Google API Error: {e}") + except AuthenticationError as e: + print(f"Google Authentication Error: {e}") return None except Exception as e: print(f"An unexpected error occurred: {e}") From e063399b84df0229f4ca544d40cc45e5a66a4ff3 Mon Sep 17 00:00:00 2001 From: Avi <32148378+avi9664@users.noreply.github.com> Date: Thu, 15 Jan 2026 14:11:45 -0800 Subject: [PATCH 80/81] added template scripts for extracting from gdrive --- alembic/env.py | 11 ---- .../ca_proc_points-checkpoint.py | 6 +-- .../petroleum_pipelines-checkpoint.py | 4 +- .../pipeline/etl/extract/ca_proc_points.py | 6 +-- .../etl/extract/petroleum_pipelines.py | 4 +- .../templates/extract_gdrive_csv_template.py | 51 +++++++++++++++++++ .../extract_gdrive_geojson_template.py | 51 +++++++++++++++++++ ...template.py => extract_gsheet_template.py} | 0 8 files changed, 112 insertions(+), 21 deletions(-) create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_csv_template.py create mode 100644 src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_geojson_template.py rename src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/{extract_template.py => extract_gsheet_template.py} (100%) diff --git a/alembic/env.py b/alembic/env.py index 8df293e1..585d4550 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -13,17 +13,6 @@ load_dotenv(dotenv_path=PROJECT_ROOT / ".env") # Looks for .env in the project root by default # --- Import your models so Alembic knows about them --- -# from ca_biositing.datamodels.biomass import * -# from ca_biositing.datamodels.data_and_references import * -# from ca_biositing.datamodels.experiments_analysis import * -# from ca_biositing.datamodels.external_datasets import * -# from ca_biositing.datamodels.geographic_locations import * -# from ca_biositing.datamodels.metadata_samples import * -# from ca_biositing.datamodels.organizations import * -# from ca_biositing.datamodels.people_contacts import * -# from ca_biositing.datamodels.sample_preprocessing import * -# from ca_biositing.datamodels.specific_aalysis_results import * -# from ca_biositing.datamodels.user import * from ca_biositing.datamodels.schemas.generated import ca_biositing from ca_biositing.datamodels.schemas.generated.ca_biositing import * # from ca_biositing.datamodels.database import Base diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ca_proc_points-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ca_proc_points-checkpoint.py index e880b47a..cc5edf4a 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ca_proc_points-checkpoint.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/ca_proc_points-checkpoint.py @@ -20,7 +20,7 @@ def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: FILE_NAME = "CA_proc_points.zip" MIME_TYPE = "application/zip" CREDENTIALS_PATH = "credentials.json" - DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" logger.info(f"Extracting raw data from '{FILE_NAME}'...") # If project_root is provided (e.g., from a notebook), construct an absolute path @@ -34,11 +34,11 @@ def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: # The gdrive_to_df function handles authentication, data fetching, and error handling. raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) - + if raw_df is None: logger.error("Failed to extract data. Aborting.") return None logger.info("Successfully extracted raw data.") - return raw_df \ No newline at end of file + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/petroleum_pipelines-checkpoint.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/petroleum_pipelines-checkpoint.py index a345dbbf..b1d90c76 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/petroleum_pipelines-checkpoint.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/.ipynb_checkpoints/petroleum_pipelines-checkpoint.py @@ -21,7 +21,7 @@ def extract(project_root: Optional[str] = None) -> Optional[gpd.GeoDataFrame]: FILE_NAME = "US_Petroleum_Pipelines.geojson" MIME_TYPE = "application/geo+json" CREDENTIALS_PATH = "credentials.json" - DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" logger.info(f"Extracting raw data from '{FILE_NAME}'...") # If project_root is provided (e.g., from a notebook), construct an absolute path @@ -35,7 +35,7 @@ def extract(project_root: Optional[str] = None) -> Optional[gpd.GeoDataFrame]: # The gdrive_to_df function handles authentication, data fetching, and error handling. raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) - + if raw_df is None: logger.error("Failed to extract data. Aborting.") diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ca_proc_points.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ca_proc_points.py index e880b47a..cc5edf4a 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ca_proc_points.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/ca_proc_points.py @@ -20,7 +20,7 @@ def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: FILE_NAME = "CA_proc_points.zip" MIME_TYPE = "application/zip" CREDENTIALS_PATH = "credentials.json" - DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" logger.info(f"Extracting raw data from '{FILE_NAME}'...") # If project_root is provided (e.g., from a notebook), construct an absolute path @@ -34,11 +34,11 @@ def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: # The gdrive_to_df function handles authentication, data fetching, and error handling. raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) - + if raw_df is None: logger.error("Failed to extract data. Aborting.") return None logger.info("Successfully extracted raw data.") - return raw_df \ No newline at end of file + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/petroleum_pipelines.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/petroleum_pipelines.py index a345dbbf..b1d90c76 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/petroleum_pipelines.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/extract/petroleum_pipelines.py @@ -21,7 +21,7 @@ def extract(project_root: Optional[str] = None) -> Optional[gpd.GeoDataFrame]: FILE_NAME = "US_Petroleum_Pipelines.geojson" MIME_TYPE = "application/geo+json" CREDENTIALS_PATH = "credentials.json" - DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" logger.info(f"Extracting raw data from '{FILE_NAME}'...") # If project_root is provided (e.g., from a notebook), construct an absolute path @@ -35,7 +35,7 @@ def extract(project_root: Optional[str] = None) -> Optional[gpd.GeoDataFrame]: # The gdrive_to_df function handles authentication, data fetching, and error handling. raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) - + if raw_df is None: logger.error("Failed to extract data. Aborting.") diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_csv_template.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_csv_template.py new file mode 100644 index 00000000..d080e3eb --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_csv_template.py @@ -0,0 +1,51 @@ +from typing import Optional +import pandas as pd +from prefect import task, get_run_logger +from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df +import os + +@task +def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: + """ + Extracts raw data from a .csv or .zip file. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A pandas DataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + + # replace with the name & MIME type of your file. + # you can find the latter here: https://mime-type.com/ + FILE_NAME = "FILE_NAME.csv" + MIME_TYPE = "text/csv" # or "application/zip" + + CREDENTIALS_PATH = "credentials.json" + + # directory for dumping dataset from gdrive to convert to a Pandas DataFrame + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" + logger.info(f"Extracting raw data from '{FILE_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + + # make sure that these work + credentials_path = CREDENTIALS_PATH + dataset_folder = DATASET_FOLDER + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + dataset_folder = os.path.join(project_root, DATASET_FOLDER) + + # The gdrive_to_df function handles authentication, data fetching, and error handling. + raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) + + + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_geojson_template.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_geojson_template.py new file mode 100644 index 00000000..07ca93ed --- /dev/null +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_geojson_template.py @@ -0,0 +1,51 @@ +from typing import Optional +import pandas as pd +from prefect import task, get_run_logger +from src.ca_biositing.pipeline.ca_biositing.pipeline.utils.gdrive_to_pandas import gdrive_to_df +import geopandas as gpd +import os + +@task +def extract(project_root: Optional[str] = None) -> Optional[gpd.GeoDataFrame]: + """ + Extracts raw data from a .geojson file. + + This function serves as the 'Extract' step in an ETL pipeline. It connects + to the data source and returns the data as is, without transformation. + + Returns: + A geopandas GeoDataFrame containing the raw data, or None if an error occurs. + """ + logger = get_run_logger() + + # replace with the name of your file. + FILE_NAME = "US_Petroleum_Pipelines.geojson" + MIME_TYPE = "application/geo+json" + + CREDENTIALS_PATH = "credentials.json" + + # directory for dumping dataset from gdrive to convert to a GeoPandas GeoDataFrame + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" + logger.info(f"Extracting raw data from '{FILE_NAME}'...") + + # If project_root is provided (e.g., from a notebook), construct an absolute path + # Otherwise, use the default relative path (for the main pipeline) + + # make sure that these work + credentials_path = CREDENTIALS_PATH + dataset_folder = DATASET_FOLDER + if project_root: + credentials_path = os.path.join(project_root, CREDENTIALS_PATH) + dataset_folder = os.path.join(project_root, DATASET_FOLDER) + + # The gdrive_to_df function handles authentication, data fetching, and error handling. + raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) + + + + if raw_df is None: + logger.error("Failed to extract data. Aborting.") + return None + + logger.info("Successfully extracted raw data.") + return raw_df diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_template.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gsheet_template.py similarity index 100% rename from src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_template.py rename to src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gsheet_template.py From bb28100d19ce42a5ccd91065a65d19ad8b6589e7 Mon Sep 17 00:00:00 2001 From: Avi <32148378+avi9664@users.noreply.github.com> Date: Thu, 15 Jan 2026 14:58:17 -0800 Subject: [PATCH 81/81] docs: add style guide --- .../templates/extract_gdrive_csv_template.py | 6 ++--- .../extract_gdrive_geojson_template.py | 4 ++-- src/ca_biositing/pipeline/docs/STYLE_GUIDE.md | 22 +++++++++++++++++++ 3 files changed, 27 insertions(+), 5 deletions(-) create mode 100644 src/ca_biositing/pipeline/docs/STYLE_GUIDE.md diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_csv_template.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_csv_template.py index d080e3eb..6d9b4803 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_csv_template.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_csv_template.py @@ -17,11 +17,11 @@ def extract(project_root: Optional[str] = None) -> Optional[pd.DataFrame]: """ logger = get_run_logger() - # replace with the name & MIME type of your file. - # you can find the latter here: https://mime-type.com/ + # replace with the name & MIME type of your file. + # you can find the latter here: https://mime-type.com/ FILE_NAME = "FILE_NAME.csv" MIME_TYPE = "text/csv" # or "application/zip" - + CREDENTIALS_PATH = "credentials.json" # directory for dumping dataset from gdrive to convert to a Pandas DataFrame diff --git a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_geojson_template.py b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_geojson_template.py index 07ca93ed..999b7e1e 100644 --- a/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_geojson_template.py +++ b/src/ca_biositing/pipeline/ca_biositing/pipeline/etl/templates/extract_gdrive_geojson_template.py @@ -25,7 +25,7 @@ def extract(project_root: Optional[str] = None) -> Optional[gpd.GeoDataFrame]: CREDENTIALS_PATH = "credentials.json" # directory for dumping dataset from gdrive to convert to a GeoPandas GeoDataFrame - DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" + DATASET_FOLDER = "src/ca_biositing/pipeline/ca_biositing/pipeline/temp_external_datasets/" logger.info(f"Extracting raw data from '{FILE_NAME}'...") # If project_root is provided (e.g., from a notebook), construct an absolute path @@ -41,7 +41,7 @@ def extract(project_root: Optional[str] = None) -> Optional[gpd.GeoDataFrame]: # The gdrive_to_df function handles authentication, data fetching, and error handling. raw_df = gdrive_to_df(FILE_NAME, MIME_TYPE, credentials_path, dataset_folder) - + if raw_df is None: logger.error("Failed to extract data. Aborting.") diff --git a/src/ca_biositing/pipeline/docs/STYLE_GUIDE.md b/src/ca_biositing/pipeline/docs/STYLE_GUIDE.md new file mode 100644 index 00000000..b860d85f --- /dev/null +++ b/src/ca_biositing/pipeline/docs/STYLE_GUIDE.md @@ -0,0 +1,22 @@ +# Style Guide + +Contains data formatting conventions for the database that will be standardized throughout **`ca_biositing.datamodels`** and **`ca_biositing.pipeline`**. + +## Text Conventions + +- All column names should be **lowercase** and in **snake case**. For example: + - TARGET_FID -> target_fid + - Join Count -> join_count + +## Date Conventions +- All dates must be in **?????** format. For example: + - 2024 Jan 28 +- Do times matter?? + +## Geospatial Data +- Latitude and longitude should be stored as floats in two separate columns. + +add more... + + +