From bb461d702d3350830917cfcb85c29b1da4929689 Mon Sep 17 00:00:00 2001 From: Christos Hadjinikolis Date: Mon, 4 Aug 2025 12:35:01 +0300 Subject: [PATCH 1/7] fix: Read --- dynamicio/mixins/with_postgres.py | 10 +- poetry.lock | 2054 ++++++++++--------- pyproject.toml | 37 +- tests/resources/definitions/test_input.yaml | 12 + tests/resources/schemas/vessels6.yaml | 186 ++ tests/test_mixins/test_postgres_mixins.py | 27 +- 6 files changed, 1300 insertions(+), 1026 deletions(-) create mode 100644 tests/resources/schemas/vessels6.yaml diff --git a/dynamicio/mixins/with_postgres.py b/dynamicio/mixins/with_postgres.py index 1bc7c3a..165e35b 100644 --- a/dynamicio/mixins/with_postgres.py +++ b/dynamicio/mixins/with_postgres.py @@ -9,13 +9,14 @@ import pandas as pd # type: ignore from magic_logger import logger -from sqlalchemy import BigInteger, Boolean, Column, create_engine, Date, DateTime, Float, Integer, String # type: ignore +from sqlalchemy import BigInteger, Boolean, Column, Date, DateTime, Float, Integer, String, create_engine # type: ignore from sqlalchemy.ext.declarative import declarative_base # type: ignore from sqlalchemy.orm import Query # type: ignore from sqlalchemy.orm.decl_api import DeclarativeMeta # type: ignore from sqlalchemy.orm.session import Session as SqlAlchemySession # type: ignore from sqlalchemy.orm.session import sessionmaker # type: ignore +# Application Imports from dynamicio.config.pydantic import DataframeSchema, PostgresDataEnvironment from dynamicio.mixins import utils @@ -141,6 +142,13 @@ def _read_database(session: SqlAlchemySession, query: Union[str, Query], **optio """ if isinstance(query, Query): query = query.with_session(session).statement + + if hasattr(query, "compile"): + # Required for compatibility with pandas >= 2.0 + from sqlalchemy import text + + query = text(str(query.compile(compile_kwargs={"literal_binds": True}))) + return pd.read_sql(sql=query, con=session.get_bind(), **options) def _write_to_postgres(self, df: pd.DataFrame): diff --git a/poetry.lock b/poetry.lock index 34f58fa..013ef09 100644 --- a/poetry.lock +++ b/poetry.lock @@ -65,22 +65,22 @@ tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"] [[package]] name = "awscli" -version = "1.38.29" +version = "1.42.1" description = "Universal Command Line Environment for AWS." optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - 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[package.dependencies] @@ -3416,13 +3474,13 @@ setuptools = "*" [[package]] name = "zipp" -version = "3.21.0" +version = "3.23.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.9" files = [ - {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"}, - {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"}, + {file = "zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e"}, + {file = "zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166"}, ] [package.extras] @@ -3430,10 +3488,10 @@ check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] enabler 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flake8-import-order = "*" flake8-print = "*" flake8-tidy-imports = "*" -flake8 = "^7.2.0" -gitlint = "==0.17.0" -mock = "==4.0.3" -pandas-stubs = "==2.0.3.230814" -pre-commit = "==2.20.0" -pydocstyle = "==6.1.1" -pylint = "==2.15.5" -pytest-asyncio = "==0.20.2" -pytest-cov = "==4.0.0" -pytest = "==7.2.0" -tox = "==3.27.1" -types-PyYAML = "==6.0.12.2" -types-setuptools = "==65.5.0.3" -types-simplejson = "==3.17.7.2" -yamllint = "==1.28.0" +flake8 = "*" +gitlint = "*" +mock = "*" +pandas-stubs = "*" +pre-commit = "*" +pydocstyle = "*" +pylint = "*" +pytest-asyncio = "*" +pytest-cov = "*" +pytest = "*" +tox = "*" +types-PyYAML = "*" +types-setuptools = "*" +types-simplejson = "*" +yamllint = "*" [tool.poetry.group.docs.dependencies] -pdoc3 = "==0.10.0" +pdoc3 = "*" [tool.poetry.group.build.dependencies] setuptools = "==70.0.0" diff --git a/tests/resources/definitions/test_input.yaml b/tests/resources/definitions/test_input.yaml index 8ad2428..b0370be 100644 --- a/tests/resources/definitions/test_input.yaml +++ b/tests/resources/definitions/test_input.yaml @@ -127,3 +127,15 @@ REPLACE_SCHEMA_WITH_DYN_VARS: file_type: "parquet" schema: file_path: "[[ TEST_RESOURCES ]]/schemas/bar.yaml" + +VESSELS6: + CLOUD: + type: "postgres" + postgres: + db_host: "dm84db.ch8fsfzkebul.eu-west-1.rds.amazonaws.com" + db_port: "5432" + db_name: "backend" + db_user: "pskgfe2016" + db_password: "pskgfe2016" + schema: + file_path: "[[ TEST_RESOURCES ]]/schemas/vessels6.yaml" diff --git a/tests/resources/schemas/vessels6.yaml b/tests/resources/schemas/vessels6.yaml new file mode 100644 index 0000000..46add37 --- /dev/null +++ b/tests/resources/schemas/vessels6.yaml @@ -0,0 +1,186 @@ +name: vessels6 +columns: + id: + metrics: [] + type: object + validations: {} + name: + metrics: [] + type: object + validations: {} + imo: + metrics: [] + type: float64 + validations: {} + mmsi: + metrics: [] + type: int64 + validations: {} + call_sign: + metrics: [] + type: object + validations: {} + flag: + metrics: [] + type: object + validations: {} + gross_ton: + metrics: [] + type: float64 + validations: {} + dead_weight: + metrics: [] + type: int64 + validations: {} + year: + metrics: [] + type: float64 + validations: {} + type: + metrics: [] + type: object + validations: {} + length: + metrics: [] + type: float64 + validations: {} + width: + metrics: [] + type: float64 + validations: {} + a: + metrics: [] + type: float64 + validations: {} + b: + metrics: [] + type: float64 + validations: {} + c: + metrics: [] + type: float64 + validations: {} + d: + metrics: [] + type: float64 + validations: {} + ais_type: + metrics: [] + type: float64 + validations: {} + owner: + metrics: [] + type: object + validations: {} + vessel_type: + metrics: [] + type: object + validations: {} + owner_id: + metrics: [] + type: object + validations: {} + revision: + metrics: [] + type: int64 + validations: {} + avoid: + metrics: [] + type: object + validations: {} + computed_dwt: + metrics: [] + type: bool + validations: {} + signal_imo: + metrics: [] + type: float64 + validations: {} + short_id: + metrics: [] + type: int64 + validations: {} + blacklisted: + metrics: [] + type: bool + validations: {} + vessel_class: + metrics: [] + type: object + validations: {} + eni: + metrics: [] + type: object + validations: {} + liquid_cubic_98_percent: + metrics: [] + type: float64 + validations: {} + refrigeration: + metrics: [] + type: object + validations: {} + cubic_capacity_source: + metrics: [] + type: object + validations: {} + source_refrigeration_type: + metrics: [] + type: object + validations: {} + ice_class: + metrics: [] + type: object + validations: {} + propulsion_type: + metrics: [] + type: object + validations: {} + ice_classed: + metrics: [] + type: bool + validations: {} + source_ice_class: + metrics: [] + type: object + validations: {} + source_ice_classed: + metrics: [] + type: object + validations: {} + source_propulsion_type: + metrics: [] + type: object + validations: {} + source_dead_weight: + metrics: [] + type: object + validations: {} + source_flag: + metrics: [] + type: object + validations: {} + coated: + metrics: [] + type: bool + validations: {} + source_coated: + metrics: [] + type: object + validations: {} + ethane_capable: + metrics: [] + type: bool + validations: {} + vessel_class_group: + metrics: [] + type: object + validations: {} + vessel_class_coarse: + metrics: [] + type: object + validations: {} + vessel_class_granular: + metrics: [] + type: object + validations: {} diff --git a/tests/test_mixins/test_postgres_mixins.py b/tests/test_mixins/test_postgres_mixins.py index 62447db..73cc67d 100644 --- a/tests/test_mixins/test_postgres_mixins.py +++ b/tests/test_mixins/test_postgres_mixins.py @@ -1,19 +1,16 @@ # pylint: disable=no-member, missing-module-docstring, missing-class-docstring, missing-function-docstring, too-many-public-methods, too-few-public-methods, protected-access, C0103, C0302, R0801 import os -from unittest.mock import ANY, patch +from unittest.mock import ANY, MagicMock, patch import pandas as pd import pytest -from sqlalchemy.sql.base import ImmutableColumnCollection +from sqlalchemy.sql.base import ReadOnlyColumnCollection +# Application Imports from dynamicio import WithPostgres from dynamicio.config import IOConfig from tests import constants -from tests.mocking.io import ( - ReadPostgresIO, - WriteExtendedPostgresIO, - WritePostgresIO, -) +from tests.mocking.io import ReadMockS3CsvIO, ReadPostgresIO, WriteExtendedPostgresIO, WritePostgresIO from tests.mocking.models import ERModel, PgModel @@ -185,7 +182,7 @@ def test_get_table_columns_from_generated_model_returns_valid_list_of_columns(se columns = ReadPostgresIO(source_config=pg_cloud_config)._get_table_columns(model) # pylint: disable=protected-access # Then - assert isinstance(model.__table__.columns, ImmutableColumnCollection) + assert isinstance(model.__table__.columns, ReadOnlyColumnCollection) for x, y in zip(columns, [PgModel.id, PgModel.foo, PgModel.bar, PgModel.baz]): assert str(x) == str(y) @@ -212,3 +209,17 @@ def test_to_check_if_dataframe_has_valid_data_types(self): # Then assert is_valid is True + + @pytest.mark.unit + def test_actual_read(self): + postgres_cloud_config = IOConfig( + path_to_source_yaml=(os.path.join(constants.TEST_RESOURCES, "definitions/test_input.yaml")), + env_identifier="CLOUD", + dynamic_vars=constants, + ).get(source_key="VESSELS6") + + v6 = ReadMockS3CsvIO(source_config=postgres_cloud_config).read() + + print(v6.head().to_string()) + + ReadMockS3CsvIO(source_config=postgres_cloud_config).write(v6) From 81ab96a84616843244421b61183c7f281d7a8408 Mon Sep 17 00:00:00 2001 From: Christos Hadjinikolis Date: Mon, 4 Aug 2025 13:25:13 +0300 Subject: [PATCH 2/7] one step at a time --- dynamicio/mixins/with_postgres.py | 30 +- poetry.lock | 534 ++++++++++++------------------ 2 files changed, 227 insertions(+), 337 deletions(-) diff --git a/dynamicio/mixins/with_postgres.py b/dynamicio/mixins/with_postgres.py index 165e35b..5ea4f34 100644 --- a/dynamicio/mixins/with_postgres.py +++ b/dynamicio/mixins/with_postgres.py @@ -7,18 +7,17 @@ from contextlib import contextmanager from typing import Any, Dict, Generator, MutableMapping, Union -import pandas as pd # type: ignore -from magic_logger import logger -from sqlalchemy import BigInteger, Boolean, Column, Date, DateTime, Float, Integer, String, create_engine # type: ignore -from sqlalchemy.ext.declarative import declarative_base # type: ignore -from sqlalchemy.orm import Query # type: ignore -from sqlalchemy.orm.decl_api import DeclarativeMeta # type: ignore -from sqlalchemy.orm.session import Session as SqlAlchemySession # type: ignore -from sqlalchemy.orm.session import sessionmaker # type: ignore - +import pandas as pd # Application Imports from dynamicio.config.pydantic import DataframeSchema, PostgresDataEnvironment from dynamicio.mixins import utils +from magic_logger import logger +from sqlalchemy import BigInteger, Boolean, Column, create_engine, Date, DateTime, Float, Integer, String, text +from sqlalchemy.ext.declarative import declarative_base +from sqlalchemy.orm import Query +from sqlalchemy.orm.decl_api import DeclarativeMeta +from sqlalchemy.orm.session import Session as SqlAlchemySession +from sqlalchemy.orm.session import sessionmaker Session = sessionmaker(autoflush=True) @@ -114,7 +113,8 @@ def _generate_model_from_schema(schema: DataframeSchema) -> DeclarativeMeta: class_name = "".join(word.capitalize() or "_" for word in schema.name.split("_")) + "Model" class_dict = {"clsname": class_name, "__tablename__": schema.name, "__table_args__": {"extend_existing": True}} - class_dict.update({column["name"]: Column(column["type"], primary_key=True) if idx == 0 else Column(column["type"]) for idx, column in enumerate(json_cls_schema["columns"])}) + class_dict.update( + {column["name"]: Column(column["type"], primary_key=True) if idx == 0 else Column(column["type"]) for idx, column in enumerate(json_cls_schema["columns"])}) generated_model = type(class_name, (Base,), class_dict) return generated_model @@ -127,9 +127,8 @@ def _get_table_columns(model): tables_colums.append(getattr(model, col.name)) return tables_colums - @staticmethod @utils.allow_options(pd.read_sql) - def _read_database(session: SqlAlchemySession, query: Union[str, Query], **options: Any) -> pd.DataFrame: + def _read_database(self, session: SqlAlchemySession, query: Union[str, Query], **options: Any) -> pd.DataFrame: """Run `query` against active `session` and returns the result as a `DataFrame`. Args: @@ -140,15 +139,18 @@ def _read_database(session: SqlAlchemySession, query: Union[str, Query], **optio Returns: DataFrame """ + postgres_config = self.sources_config.postgres + db_host = postgres_config.db_host + db_name = postgres_config.db_name + if isinstance(query, Query): query = query.with_session(session).statement if hasattr(query, "compile"): # Required for compatibility with pandas >= 2.0 - from sqlalchemy import text - query = text(str(query.compile(compile_kwargs={"literal_binds": True}))) + logger.info(f"[postgres] Started downloading table: {self.sources_config.dynamicio_schema.name} from: {db_host}:{db_name}") return pd.read_sql(sql=query, con=session.get_bind(), **options) def _write_to_postgres(self, df: pd.DataFrame): diff --git a/poetry.lock b/poetry.lock index 013ef09..c37430e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -13,13 +13,13 @@ files = [ [[package]] name = "arrow" -version = "1.2.1" +version = "1.2.3" description = "Better dates & times for Python" 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description = "A linter for YAML files." optional = false -python-versions = ">=3.6" +python-versions = ">=3.9" files = [ - {file = "yamllint-1.28.0-py2.py3-none-any.whl", hash = "sha256:89bb5b5ac33b1ade059743cf227de73daa34d5e5a474b06a5e17fc16583b0cf2"}, - {file = "yamllint-1.28.0.tar.gz", hash = "sha256:9e3d8ddd16d0583214c5fdffe806c9344086721f107435f68bad990e5a88826b"}, + {file = "yamllint-1.37.1-py3-none-any.whl", hash = "sha256:364f0d79e81409f591e323725e6a9f4504c8699ddf2d7263d8d2b539cd66a583"}, + {file = "yamllint-1.37.1.tar.gz", hash = "sha256:81f7c0c5559becc8049470d86046b36e96113637bcbe4753ecef06977c00245d"}, ] [package.dependencies] pathspec = ">=0.5.3" pyyaml = "*" -setuptools = "*" + +[package.extras] +dev = ["doc8", "flake8", "flake8-import-order", "rstcheck[sphinx]", "sphinx"] [[package]] name = "zipp" @@ -3494,4 +3382,4 @@ type = ["pytest-mypy"] [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.13" -content-hash = "9801d720e0716d7b1c9e33e58123d87a43527f36ccd2c64d86586791f0eb61f4" +content-hash = "3927527ee75c86b361afa64b1c309c842fe6d385340610f102282ad1d322e306" From 8e144382d18a5de1dc51178e5911bd5fde1db715 Mon Sep 17 00:00:00 2001 From: Christos Hadjinikolis Date: Mon, 4 Aug 2025 17:14:01 +0300 Subject: [PATCH 3/7] feat: Fix postgres approved type --- .pre-commit-config.yaml | 14 +- Makefile | 1 + dynamicio/mixins/with_postgres.py | 75 ++++---- tests/mocking/io.py | 4 + tests/resources/definitions/test_input.yaml | 12 -- tests/resources/schemas/vessels6.yaml | 186 -------------------- tests/test_mixins/test_postgres_mixins.py | 18 +- 7 files changed, 58 insertions(+), 252 deletions(-) delete mode 100644 tests/resources/schemas/vessels6.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 9f5b00f..4f6bcec 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -19,7 +19,7 @@ repos: entry: bash -c '(isort "$@" && black "$@") || true; git add -u' -- language: system types: [python] - stages: [commit] + stages: [pre-commit] - repo: local hooks: @@ -28,7 +28,7 @@ repos: entry: pylint language: system types: [python] - stages: [commit] + stages: [pre-commit] - repo: local hooks: @@ -37,7 +37,7 @@ repos: exclude: ^(tests/.*|demo/*) language: system entry: pydocstyle - stages: [commit] + stages: [pre-commit] - repo: local hooks: @@ -46,7 +46,7 @@ repos: entry: flake8 language: system types: [python] - stages: [commit] + stages: [pre-commit] - repo: local hooks: @@ -56,7 +56,7 @@ repos: entry: yamllint language: python types: [file, yaml] - stages: [commit] + stages: [pre-commit] - repo: local hooks: @@ -66,7 +66,7 @@ repos: exclude: ^(.github|.circleci|docs|.flake8|.gitlint|.pylintrc|.docs.Dockerfile|README.md|Makefile|setup.py) language: system pass_filenames: false - stages: [commit] + stages: [pre-commit] - repo: local hooks: @@ -76,4 +76,4 @@ repos: exclude: ^(.github|.circleci|docs|.flake8|.gitlint|.pylintrc|.docs.Dockerfile|README.md|Makefile|setup.py) language: system pass_filenames: false - stages: [commit] + stages: [pre-commit] diff --git a/Makefile b/Makefile index d11da46..36f6f31 100644 --- a/Makefile +++ b/Makefile @@ -37,6 +37,7 @@ dev-env-setup: install-poetry install-binary-packages-Darwin @pyenv exec poetry self add poetry-pre-commit-plugin @pyenv exec poetry run pre-commit install @pyenv exec poetry run pre-commit install --hook-type commit-msg + @pyenv exec poetry run pre-commit migrate-config # Checks for local development check-linting: diff --git a/dynamicio/mixins/with_postgres.py b/dynamicio/mixins/with_postgres.py index 5ea4f34..6537a90 100644 --- a/dynamicio/mixins/with_postgres.py +++ b/dynamicio/mixins/with_postgres.py @@ -8,30 +8,44 @@ from typing import Any, Dict, Generator, MutableMapping, Union import pandas as pd -# Application Imports -from dynamicio.config.pydantic import DataframeSchema, PostgresDataEnvironment -from dynamicio.mixins import utils from magic_logger import logger -from sqlalchemy import BigInteger, Boolean, Column, create_engine, Date, DateTime, Float, Integer, String, text +from sqlalchemy import BigInteger, Boolean, Column, Date, DateTime, Float, Integer, String, create_engine, text +from sqlalchemy.dialects.postgresql import JSONB from sqlalchemy.ext.declarative import declarative_base from sqlalchemy.orm import Query from sqlalchemy.orm.decl_api import DeclarativeMeta from sqlalchemy.orm.session import Session as SqlAlchemySession from sqlalchemy.orm.session import sessionmaker +# Application Imports +from dynamicio.config.pydantic import DataframeSchema, PostgresDataEnvironment +from dynamicio.mixins import utils + Session = sessionmaker(autoflush=True) Base = declarative_base() + _type_lookup = { - "bool": Boolean, - "boolean": Boolean, - "object": String(64), - "int64": Integer, + # Booleans + "bool": Boolean, # native pandas (non-nullable) + "boolean": Boolean, # pandas nullable boolean dtype + # Strings / objects + "object": String(255), # general fallback for str columns + "string": String(255), # newer pandas string dtype + # Integers (nullable or not) + "int": Integer, # generic int fallback + "int64": BigInteger, # standard numpy int64 + "Int64": BigInteger, # pandas nullable integer + # Floats + "float": Float, # generic float fallback "float64": Float, - "int": Integer, + # Dates and times "date": Date, - "datetime64[ns]": DateTime, - "bigint": BigInteger, + "datetime": DateTime, + "datetime64[ns]": DateTime, # pandas datetime dtype + # Optional extras + "bigint": BigInteger, # explicit large integer support + "json": JSONB, # optional if dealing with structured objects } @@ -59,7 +73,9 @@ class WithPostgres: Args: - options: - - `truncate_and_append: bool`: If set to `True`, truncates the table and then appends the new rows. Otherwise, it drops the table and recreates it with the new rows. + - `truncate_and_append: bool`: If True, truncates the table with CASCADE and appends new rows (faster but destructive). + If False (default), safely deletes all existing rows and then appends new rows. + Use truncate only if you are certain views and FK constraints can be dropped or tolerated. """ sources_config: PostgresDataEnvironment @@ -96,7 +112,6 @@ def _read_from_postgres(self) -> pd.DataFrame: query = Query(self._get_table_columns(model)) if sql_query: query = sql_query - logger.info(f"[postgres] Started downloading table: {self.sources_config.dynamicio_schema.name} from: {db_host}:{db_name}") with session_for(connection_string) as session: return self._read_database(session, query, **self.options) @@ -113,8 +128,7 @@ def _generate_model_from_schema(schema: DataframeSchema) -> DeclarativeMeta: class_name = "".join(word.capitalize() or "_" for word in schema.name.split("_")) + "Model" class_dict = {"clsname": class_name, "__tablename__": schema.name, "__table_args__": {"extend_existing": True}} - class_dict.update( - {column["name"]: Column(column["type"], primary_key=True) if idx == 0 else Column(column["type"]) for idx, column in enumerate(json_cls_schema["columns"])}) + class_dict.update({column["name"]: Column(column["type"], primary_key=True) if idx == 0 else Column(column["type"]) for idx, column in enumerate(json_cls_schema["columns"])}) generated_model = type(class_name, (Base,), class_dict) return generated_model @@ -183,25 +197,24 @@ def _write_to_database(session: SqlAlchemySession, table_name: str, df: pd.DataF Args: session: Generated from a data model and a table name - table_name: The name of the table to read from a DB + table_name: The name of the table to write to df: The dataframe to be written out - is_truncate_and_append: Supply to truncate the table and append new rows to it; otherwise, delete and replace + is_truncate_and_append: If True, truncates the table with CASCADE and appends new rows (faster but destructive). + If False (default), safely deletes all existing rows and then appends new rows. + Use truncate only if you are certain views and FK constraints can be dropped or tolerated. """ if is_truncate_and_append: - session.execute(f"TRUNCATE TABLE {table_name};") - - # Below is a speedup hack in place of `df.to_csv` with the multipart option. As of today, even with - # `method="multi"`, uploading to Postgres is painfully slow. Hence, we're resorting to dumping the file as - # csv and using Postgres's CSV import function. - # https://stackoverflow.com/questions/2987433/how-to-import-csv-file-data-into-a-postgresql-table - with tempfile.NamedTemporaryFile(mode="r+") as temp_file: - df.to_csv(temp_file, index=False, header=False, sep="\t", doublequote=False, escapechar="\\", quoting=csv.QUOTE_NONE) - temp_file.flush() - temp_file.seek(0) - - cur = session.connection().connection.cursor() - cur.copy_from(temp_file, table_name, columns=df.columns, null="") + session.execute(text(f"TRUNCATE TABLE {table_name} CASCADE;")) else: - df.to_sql(name=table_name, con=session.get_bind(), if_exists="replace", index=False) + session.execute(text(f"DELETE FROM {table_name};")) + + # Upload data using PostgreSQL's COPY FROM CSV mechanism for performance + with tempfile.NamedTemporaryFile(mode="r+") as temp_file: + df.to_csv(temp_file, index=False, header=False, sep="\t", doublequote=False, escapechar="\\", quoting=csv.QUOTE_NONE) + temp_file.flush() + temp_file.seek(0) + + cur = session.connection().connection.cursor() + cur.copy_from(temp_file, table_name, columns=df.columns, null="") session.commit() diff --git a/tests/mocking/io.py b/tests/mocking/io.py index 5ec1d41..4e0e633 100644 --- a/tests/mocking/io.py +++ b/tests/mocking/io.py @@ -205,3 +205,7 @@ def validate(df): class ReadAthenaIO(UnifiedIO): schema = {"id": "object", "foo": "object", "bar": "int64"} + + +class GenericIO(UnifiedIO): + schema = SCHEMA_FROM_FILE diff --git a/tests/resources/definitions/test_input.yaml b/tests/resources/definitions/test_input.yaml index b0370be..8ad2428 100644 --- a/tests/resources/definitions/test_input.yaml +++ b/tests/resources/definitions/test_input.yaml @@ -127,15 +127,3 @@ REPLACE_SCHEMA_WITH_DYN_VARS: file_type: "parquet" schema: file_path: "[[ TEST_RESOURCES ]]/schemas/bar.yaml" - -VESSELS6: - CLOUD: - type: "postgres" - postgres: - db_host: "dm84db.ch8fsfzkebul.eu-west-1.rds.amazonaws.com" - db_port: "5432" - db_name: "backend" - db_user: "pskgfe2016" - db_password: "pskgfe2016" - schema: - file_path: "[[ TEST_RESOURCES ]]/schemas/vessels6.yaml" diff --git a/tests/resources/schemas/vessels6.yaml b/tests/resources/schemas/vessels6.yaml deleted file mode 100644 index 46add37..0000000 --- a/tests/resources/schemas/vessels6.yaml +++ /dev/null @@ -1,186 +0,0 @@ -name: vessels6 -columns: - id: - metrics: [] - type: object - validations: {} - name: - metrics: [] - type: object - validations: {} - imo: - metrics: [] - type: float64 - validations: {} - mmsi: - metrics: [] - type: int64 - validations: {} - call_sign: - metrics: [] - type: object - validations: {} - flag: - metrics: [] - type: object - validations: {} - gross_ton: - metrics: [] - type: float64 - validations: {} - dead_weight: - metrics: [] - type: int64 - validations: {} - year: - metrics: [] - type: float64 - validations: {} - type: - metrics: [] - type: object - validations: {} - length: - metrics: [] - type: float64 - validations: {} - width: - metrics: [] - type: float64 - validations: {} - a: - metrics: [] - type: float64 - validations: {} - b: - metrics: [] - type: float64 - validations: {} - c: - metrics: [] - type: float64 - validations: {} - d: - metrics: [] - type: float64 - validations: {} - ais_type: - metrics: [] - type: float64 - validations: {} - owner: - metrics: [] - type: object - validations: {} - vessel_type: - metrics: [] - type: object - validations: {} - owner_id: - metrics: [] - type: object - validations: {} - revision: - metrics: [] - type: int64 - validations: {} - avoid: - metrics: [] - type: object - validations: {} - computed_dwt: - metrics: [] - type: bool - validations: {} - signal_imo: - metrics: [] - type: float64 - validations: {} - short_id: - metrics: [] - type: int64 - validations: {} - blacklisted: - metrics: [] - type: bool - validations: {} - vessel_class: - metrics: [] - type: object - validations: {} - eni: - metrics: [] - type: object - validations: {} - liquid_cubic_98_percent: - metrics: [] - type: float64 - validations: {} - refrigeration: - metrics: [] - type: object - validations: {} - cubic_capacity_source: - metrics: [] - type: object - validations: {} - source_refrigeration_type: - metrics: [] - type: object - validations: {} - ice_class: - metrics: [] - type: object - validations: {} - propulsion_type: - metrics: [] - type: object - validations: {} - ice_classed: - metrics: [] - type: bool - validations: {} - source_ice_class: - metrics: [] - type: object - validations: {} - source_ice_classed: - metrics: [] - type: object - validations: {} - source_propulsion_type: - metrics: [] - type: object - validations: {} - source_dead_weight: - metrics: [] - type: object - validations: {} - source_flag: - metrics: [] - type: object - validations: {} - coated: - metrics: [] - type: bool - validations: {} - source_coated: - metrics: [] - type: object - validations: {} - ethane_capable: - metrics: [] - type: bool - validations: {} - vessel_class_group: - metrics: [] - type: object - validations: {} - vessel_class_coarse: - metrics: [] - type: object - validations: {} - vessel_class_granular: - metrics: [] - type: object - validations: {} diff --git a/tests/test_mixins/test_postgres_mixins.py b/tests/test_mixins/test_postgres_mixins.py index 73cc67d..5e063cc 100644 --- a/tests/test_mixins/test_postgres_mixins.py +++ b/tests/test_mixins/test_postgres_mixins.py @@ -1,6 +1,6 @@ # pylint: disable=no-member, missing-module-docstring, missing-class-docstring, missing-function-docstring, too-many-public-methods, too-few-public-methods, protected-access, C0103, C0302, R0801 import os -from unittest.mock import ANY, MagicMock, patch +from unittest.mock import ANY, patch import pandas as pd import pytest @@ -10,7 +10,7 @@ from dynamicio import WithPostgres from dynamicio.config import IOConfig from tests import constants -from tests.mocking.io import ReadMockS3CsvIO, ReadPostgresIO, WriteExtendedPostgresIO, WritePostgresIO +from tests.mocking.io import ReadPostgresIO, WriteExtendedPostgresIO, WritePostgresIO from tests.mocking.models import ERModel, PgModel @@ -209,17 +209,3 @@ def test_to_check_if_dataframe_has_valid_data_types(self): # Then assert is_valid is True - - @pytest.mark.unit - def test_actual_read(self): - postgres_cloud_config = IOConfig( - path_to_source_yaml=(os.path.join(constants.TEST_RESOURCES, "definitions/test_input.yaml")), - env_identifier="CLOUD", - dynamic_vars=constants, - ).get(source_key="VESSELS6") - - v6 = ReadMockS3CsvIO(source_config=postgres_cloud_config).read() - - print(v6.head().to_string()) - - ReadMockS3CsvIO(source_config=postgres_cloud_config).write(v6) From 89692a369f09de55f6d38ec3c2a2154ea4229631 Mon Sep 17 00:00:00 2001 From: Christos Hadjinikolis Date: Mon, 4 Aug 2025 17:17:16 +0300 Subject: [PATCH 4/7] fix: hooks --- .pre-commit-config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4f6bcec..1e0ea29 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -15,7 +15,7 @@ repos: hooks: - id: formatting name: "isort and black" - exclude: ^(tests/conftest.py) + exclude: ^tests/conftest\.py$ entry: bash -c '(isort "$@" && black "$@") || true; git add -u' -- language: system types: [python] @@ -34,7 +34,7 @@ repos: hooks: - id: pydocstyle name: pydocstyle - exclude: ^(tests/.*|demo/*) + exclude: ^(tests/.*|demo/.*)$ language: system entry: pydocstyle stages: [pre-commit] @@ -63,7 +63,7 @@ repos: - id: pytest-check name: pytest-check-src entry: python -m pytest tests --cov=dynamicio --cov-report=html --cov-report=xml -v - exclude: ^(.github|.circleci|docs|.flake8|.gitlint|.pylintrc|.docs.Dockerfile|README.md|Makefile|setup.py) + exclude: ^(\.github|\.circleci|docs|\.flake8|\.gitlint|\.pylintrc|\.docs\.Dockerfile|README\.md|Makefile|setup\.py)$ language: system pass_filenames: false stages: [pre-commit] @@ -73,7 +73,7 @@ repos: - id: pytest-check name: pytest-check-demo entry: python -m pytest demo/tests - exclude: ^(.github|.circleci|docs|.flake8|.gitlint|.pylintrc|.docs.Dockerfile|README.md|Makefile|setup.py) + exclude: ^(\.github|\.circleci|docs|\.flake8|\.gitlint|\.pylintrc|\.docs\.Dockerfile|README\.md|Makefile|setup\.py)$ language: system pass_filenames: false stages: [pre-commit] From 43c4c8bd18ff1a9298e17ff2b8d20c2fd0bcd462 Mon Sep 17 00:00:00 2001 From: Christos Hadjinikolis Date: Mon, 4 Aug 2025 17:45:23 +0300 Subject: [PATCH 5/7] test: Confirm new behaviour --- dynamicio/mixins/with_postgres.py | 8 +-- tests/test_mixins/test_postgres_mixins.py | 68 +++++++++++++++++++++++ 2 files changed, 72 insertions(+), 4 deletions(-) diff --git a/dynamicio/mixins/with_postgres.py b/dynamicio/mixins/with_postgres.py index 6537a90..6c65d14 100644 --- a/dynamicio/mixins/with_postgres.py +++ b/dynamicio/mixins/with_postgres.py @@ -122,16 +122,16 @@ def _generate_model_from_schema(schema: DataframeSchema) -> DeclarativeMeta: for col in schema.columns.values(): sql_type = _type_lookup.get(col.data_type) - if sql_type: - json_cls_schema["columns"].append({"name": col.name, "type": sql_type}) + if not sql_type: + raise ValueError(f"Unsupported data_type '{col.data_type}' for column '{col.name}' in schema '{schema.name}'") + json_cls_schema["columns"].append({"name": col.name, "type": sql_type}) class_name = "".join(word.capitalize() or "_" for word in schema.name.split("_")) + "Model" class_dict = {"clsname": class_name, "__tablename__": schema.name, "__table_args__": {"extend_existing": True}} class_dict.update({column["name"]: Column(column["type"], primary_key=True) if idx == 0 else Column(column["type"]) for idx, column in enumerate(json_cls_schema["columns"])}) - generated_model = type(class_name, (Base,), class_dict) - return generated_model + return type(class_name, (Base,), class_dict) @staticmethod def _get_table_columns(model): diff --git a/tests/test_mixins/test_postgres_mixins.py b/tests/test_mixins/test_postgres_mixins.py index 5e063cc..c42b540 100644 --- a/tests/test_mixins/test_postgres_mixins.py +++ b/tests/test_mixins/test_postgres_mixins.py @@ -1,5 +1,6 @@ # pylint: disable=no-member, missing-module-docstring, missing-class-docstring, missing-function-docstring, too-many-public-methods, too-few-public-methods, protected-access, C0103, C0302, R0801 import os +import types from unittest.mock import ANY, patch import pandas as pd @@ -186,6 +187,73 @@ def test_get_table_columns_from_generated_model_returns_valid_list_of_columns(se for x, y in zip(columns, [PgModel.id, PgModel.foo, PgModel.bar, PgModel.baz]): assert str(x) == str(y) + @pytest.mark.unit + def test_generate_model_from_schema_raises_on_unknown_type(self): + # Given + pg_cloud_config = IOConfig( + path_to_source_yaml=(os.path.join(constants.TEST_RESOURCES, "definitions/input.yaml")), + env_identifier="CLOUD", + dynamic_vars=constants, + ).get(source_key="READ_FROM_POSTGRES") + + schema = types.SimpleNamespace( + name="bad_schema", + columns={ + "bad_col": types.SimpleNamespace(name="bad_col", data_type="not_a_real_type"), + }, + ) + + # When / Then + with pytest.raises(ValueError, match="Unsupported data_type 'not_a_real_type' for column 'bad_col' in schema 'bad_schema'"): + ReadPostgresIO(source_config=pg_cloud_config)._generate_model_from_schema(schema) # pylint: disable=protected-access + + @pytest.mark.unit + def test_generate_model_sets_primary_key_on_first_column_only(self): + # Given + pg_cloud_config = IOConfig( + path_to_source_yaml=(os.path.join(constants.TEST_RESOURCES, "definitions/input.yaml")), + env_identifier="CLOUD", + dynamic_vars=constants, + ).get(source_key="READ_FROM_POSTGRES") + + schema = types.SimpleNamespace( + name="simple", + columns={ + "id": types.SimpleNamespace(name="id", data_type="int64"), + "value": types.SimpleNamespace(name="value", data_type="float64"), + }, + ) + + # When + model = ReadPostgresIO(source_config=pg_cloud_config)._generate_model_from_schema(schema) # pylint: disable=protected-access + + # Then + columns = model.__table__.columns + assert columns["id"].primary_key is True + assert columns["value"].primary_key is False + + @pytest.mark.unit + def test_generate_model_classname_generation(self): + # Given + pg_cloud_config = IOConfig( + path_to_source_yaml=(os.path.join(constants.TEST_RESOURCES, "definitions/input.yaml")), + env_identifier="CLOUD", + dynamic_vars=constants, + ).get(source_key="READ_FROM_POSTGRES") + + schema = types.SimpleNamespace( + name="ugly_table_name", + columns={ + "id": types.SimpleNamespace(name="id", data_type="int64"), + }, + ) + + # When + model = ReadPostgresIO(source_config=pg_cloud_config)._generate_model_from_schema(schema) # pylint: disable=protected-access + + # Then + assert model.__name__ == "UglyTableNameModel" + @pytest.mark.unit def test_to_check_if_dataframe_has_valid_data_types(self): # Given From 11190dd5d1c57e58cd88c77135a3efc06d03ee04 Mon Sep 17 00:00:00 2001 From: Christos Hadjinikolis Date: Mon, 4 Aug 2025 17:59:57 +0300 Subject: [PATCH 6/7] style: Fixes --- .pylintrc | 6 +- dynamicio/__init__.py | 1 + dynamicio/__main__.py | 2 + dynamicio/cli.py | 2 + dynamicio/config/io_config.py | 2 + dynamicio/config/pydantic/__init__.py | 3 +- dynamicio/config/pydantic/config.py | 9 ++- dynamicio/config/pydantic/table_schema.py | 9 +-- dynamicio/core.py | 5 +- dynamicio/errors.py | 1 + dynamicio/metrics.py | 1 + dynamicio/mixins/utils.py | 1 + dynamicio/mixins/with_kafka.py | 3 +- dynamicio/validations.py | 2 + pyproject.toml | 4 +- tests/mocking/models.py | 1 + tests/test_cli.py | 10 ++- tests/test_mixins/test_s3_mixins.py | 77 +++++++++++++---------- 18 files changed, 87 insertions(+), 52 deletions(-) diff --git a/.pylintrc b/.pylintrc index b6c6c4f..48390b3 100644 --- a/.pylintrc +++ b/.pylintrc @@ -383,10 +383,8 @@ preferred-modules= [EXCEPTIONS] - -# Exceptions that will emit a warning when caught. -overgeneral-exceptions=BaseException, - Exception +overgeneral-exceptions=builtins.BaseException, + builtins.Exception [REFACTORING] diff --git a/dynamicio/__init__.py b/dynamicio/__init__.py index c1aa90f..702ff2d 100644 --- a/dynamicio/__init__.py +++ b/dynamicio/__init__.py @@ -1,4 +1,5 @@ """A package for wrapping your I/O operations.""" + # pylint: disable=abstract-method import os from contextlib import suppress diff --git a/dynamicio/__main__.py b/dynamicio/__main__.py index ba3addf..61f5dbc 100644 --- a/dynamicio/__main__.py +++ b/dynamicio/__main__.py @@ -1,4 +1,6 @@ """Invokes dynamicio cli.""" + +# Application Imports from dynamicio.cli import run run() diff --git a/dynamicio/cli.py b/dynamicio/cli.py index 9497ee2..7513f49 100644 --- a/dynamicio/cli.py +++ b/dynamicio/cli.py @@ -1,4 +1,5 @@ """Implements the dynamicio Command Line Interface (CLI).""" + import argparse import glob import os @@ -8,6 +9,7 @@ import pandas as pd # type: ignore import yaml +# Application Imports from dynamicio.errors import InvalidDatasetTypeError diff --git a/dynamicio/config/io_config.py b/dynamicio/config/io_config.py index f1f6033..0066e76 100644 --- a/dynamicio/config/io_config.py +++ b/dynamicio/config/io_config.py @@ -52,6 +52,7 @@ } } """ + __all__ = ["IOConfig", "SafeDynamicResourceLoader", "SafeDynamicSchemaLoader"] import re @@ -62,6 +63,7 @@ import yaml from magic_logger import logger +# Application Imports from dynamicio.config.pydantic import BindingsYaml, IOEnvironment diff --git a/dynamicio/config/pydantic/__init__.py b/dynamicio/config/pydantic/__init__.py index 2c4be3a..4ba1a42 100644 --- a/dynamicio/config/pydantic/__init__.py +++ b/dynamicio/config/pydantic/__init__.py @@ -1,7 +1,9 @@ """Pydantic config models.""" +# Application Imports from dynamicio.config.pydantic.config import BindingsYaml from dynamicio.config.pydantic.io_resources import ( + AthenaDataEnvironment, IOEnvironment, KafkaDataEnvironment, LocalBatchDataEnvironment, @@ -9,6 +11,5 @@ PostgresDataEnvironment, S3DataEnvironment, S3PathPrefixEnvironment, - AthenaDataEnvironment ) from dynamicio.config.pydantic.table_schema import DataframeSchema, SchemaColumn diff --git a/dynamicio/config/pydantic/config.py b/dynamicio/config/pydantic/config.py index acc8772..f00c34d 100644 --- a/dynamicio/config/pydantic/config.py +++ b/dynamicio/config/pydantic/config.py @@ -1,10 +1,12 @@ +"""Pydantic schema for YAML files.""" + # pylint: disable=no-member, no-self-argument, unused-argument -"""Pydantic schema for YAML files""" from typing import Mapping, MutableMapping import pydantic +# Application Imports import dynamicio.config.pydantic.io_resources as env_spec @@ -21,14 +23,15 @@ def _validate_bindings(cls, value: Mapping): if not isinstance(value, Mapping): raise ValueError(f"Bindings must be a mapping. (got {value!r} instead).") # Tell each binding its name - for (name, sub_config) in value.items(): + for name, sub_config in value.items(): if not isinstance(sub_config, MutableMapping): raise ValueError(f"Each element for the name binding must be a dict. (got {sub_config!r} instead)") sub_config["__binding_name__"] = name return value def update_config_refs(self) -> "BindingsYaml": - """Updates dynamic parts of the config: + """Updates dynamic parts of the config. + - Configure _parent for all `IOEnvironment`s - Replace all IOSchemaRef with actual schema objects """ diff --git a/dynamicio/config/pydantic/table_schema.py b/dynamicio/config/pydantic/table_schema.py index 05bdce0..2a24889 100644 --- a/dynamicio/config/pydantic/table_schema.py +++ b/dynamicio/config/pydantic/table_schema.py @@ -1,6 +1,7 @@ +"""This module defines Config schema for data source (pandas dataframe).""" + # pylint: disable=no-member, no-self-argument, unused-argument -"""This module defines Config schema for data source (pandas dataframe)""" import enum from typing import Mapping, Sequence @@ -51,11 +52,11 @@ def is_valid_pandas_type(cls, info): @pydantic.validator("validations", pre=True) def remap_validations(cls, info): - """Remap the yaml structure of {validation_type: } to a list with validation_type as a key""" + """Remap the yaml structure of {validation_type: } to a list with validation_type as a key.""" if not isinstance(info, dict): raise ValueError(f"{info!r} should be a dict") out = [] - for (key, params) in info.items(): + for key, params in info.items(): new_el = params.copy() new_el.update({"name": key}) out.append(new_el) @@ -79,7 +80,7 @@ class DataframeSchema(pydantic.BaseModel): @pydantic.validator("columns", pre=True) def supply_column_names(cls, info): - """Tell each column its name (the key it is listed under)""" + """Tell each column its name (the key it is listed under).""" if not isinstance(info, Mapping): raise ValueError(f"{info!r} shoudl be a dict.") diff --git a/dynamicio/core.py b/dynamicio/core.py index e263d18..3980647 100644 --- a/dynamicio/core.py +++ b/dynamicio/core.py @@ -1,5 +1,6 @@ """Implements the DynamicDataIO class which provides functionality for data: loading; sinking, and; schema validation.""" -# pylint: disable=no-member + +# pylint: disable=too-many-positional-arguments, disable=no-member __all__ = ["DynamicDataIO", "SCHEMA_FROM_FILE", "CASTING_WARNING_MSG"] import asyncio @@ -100,7 +101,7 @@ def _schema_from_obj(target) -> DataframeSchema: - CAN have `schema_validations` and `schema_metrics` attributes """ col_info = {} - for (col_name, dtype) in target.schema.items(): + for col_name, dtype in target.schema.items(): col_validations = {} col_metrics = [] try: diff --git a/dynamicio/errors.py b/dynamicio/errors.py index 7c41fe8..ed3d02c 100644 --- a/dynamicio/errors.py +++ b/dynamicio/errors.py @@ -1,4 +1,5 @@ """Hosts exception implementations for different errors.""" + # pylint: disable=missing-module-docstring, missing-class-docstring, missing-function-docstring, super-init-not-called __all__ = [ "DynamicIOError", diff --git a/dynamicio/metrics.py b/dynamicio/metrics.py index 109b112..cc1dbc9 100644 --- a/dynamicio/metrics.py +++ b/dynamicio/metrics.py @@ -1,4 +1,5 @@ """A module responsible for metrics generation and logging.""" + # pylint: disable=missing-function-docstring,missing-class-docstring import json import logging diff --git a/dynamicio/mixins/utils.py b/dynamicio/mixins/utils.py index 3076222..816dd43 100644 --- a/dynamicio/mixins/utils.py +++ b/dynamicio/mixins/utils.py @@ -1,4 +1,5 @@ """Mixin utility functions.""" + # pylint: disable=no-member, protected-access, too-few-public-methods import inspect diff --git a/dynamicio/mixins/with_kafka.py b/dynamicio/mixins/with_kafka.py index 0583459..fab3b3a 100644 --- a/dynamicio/mixins/with_kafka.py +++ b/dynamicio/mixins/with_kafka.py @@ -1,5 +1,6 @@ """This module provides mixins that are providing Kafka I/O support.""" -# pylint: disable=no-member, protected-access, too-few-public-methods + +# pylint: disable=no-member, protected-access, too-few-public-methods, broad-exception-raised from typing import Any, Callable, Mapping, MutableMapping, Optional diff --git a/dynamicio/validations.py b/dynamicio/validations.py index 7650571..4ef1306 100644 --- a/dynamicio/validations.py +++ b/dynamicio/validations.py @@ -1,4 +1,6 @@ """Implements the Validator class responsible for various generic data validations and metrics generation.""" + +# pylint: disable=too-many-positional-arguments import operator from typing import Callable, NamedTuple, Set diff --git a/pyproject.toml b/pyproject.toml index 87e6ac4..314daad 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -88,9 +88,9 @@ style = "pep440" fix-shallow-repository = true [tool.black] -py38 = true +target-version = ['py310'] line-length = 185 -include = '\\.(pyi?)$' +include = '\.pyi?$' exclude = ''' ( /( diff --git a/tests/mocking/models.py b/tests/mocking/models.py index 849ee2e..020b03b 100644 --- a/tests/mocking/models.py +++ b/tests/mocking/models.py @@ -1,4 +1,5 @@ """A module for defining sql_alchemy models.""" + # pylint: disable=too-few-public-methods, R0801, C0104 __all__ = ["ERModel", "PgModel"] diff --git a/tests/test_cli.py b/tests/test_cli.py index f31ba90..d789498 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -6,6 +6,7 @@ import pandas as pd import pytest +# Application Imports import dynamicio from dynamicio import cli from dynamicio.cli import parse_args @@ -80,9 +81,12 @@ def test_parse_args_raises_system_exit_with_approved_flag_without_path_and_outpu @pytest.mark.unit def test_when_single_flag_is_used__generate_schema_for__is_called_once(self): - with patch.object(cli.argparse.ArgumentParser, "parse_args") as mocked__parse_args, patch.object(cli, "generate_schema_for") as mocked__generate_schema_for, patch.object( - cli, "open" - ) as mocked__open, patch.object(cli.yaml, "safe_dump") as mocked__dump: + with ( + patch.object(cli.argparse.ArgumentParser, "parse_args") as mocked__parse_args, + patch.object(cli, "generate_schema_for") as mocked__generate_schema_for, + patch.object(cli, "open") as mocked__open, + patch.object(cli.yaml, "safe_dump") as mocked__dump, + ): # Given mocked__parse_args.return_value = argparse.Namespace(batch=False, single=True, path="the_one.parquet", output=".") mocked__generate_schema_for.return_value = {"name": "the_one", "columns": {}} diff --git a/tests/test_mixins/test_s3_mixins.py b/tests/test_mixins/test_s3_mixins.py index 32c3ee5..e7baa8f 100644 --- a/tests/test_mixins/test_s3_mixins.py +++ b/tests/test_mixins/test_s3_mixins.py @@ -10,6 +10,7 @@ import pytest import yaml +# Application Imports import dynamicio.mixins.with_local import dynamicio.mixins.with_s3 from dynamicio.config import IOConfig @@ -46,9 +47,10 @@ def test_read_resolves_file_path_if_templated(self): file_path = f"{constants.TEST_RESOURCES}/data/input/some_csv_to_read.csv" # When - with patch.object(dynamicio.mixins.with_local.WithLocal, "_read_csv_file") as mock__read_csv_file, patch.object( - dynamicio.mixins.with_s3.WithS3File, "_s3_named_file_reader" - ) as mock_s3_reader: + with ( + patch.object(dynamicio.mixins.with_local.WithLocal, "_read_csv_file") as mock__read_csv_file, + patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_named_file_reader") as mock_s3_reader, + ): with open(file_path, "r") as file: # pylint: disable=unspecified-encoding mock_s3_reader.return_value = file io_obj = TemplatedFile(source_config=config, file_name_to_replace="some_csv_to_read") @@ -105,9 +107,10 @@ def test_s3_reader_is_not_called_for_loading_a_parquet_with_env_as_cloud_s3_and_ file_path = f"{constants.TEST_RESOURCES}/data/input/some_csv_to_read.csv" # When - with patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_reader") as mock_s3_reader, patch.object( - dynamicio.mixins.with_s3.WithS3File, "_read_parquet_file" - ) as mock_read_parquet_file: + with ( + patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_reader") as mock_s3_reader, + patch.object(dynamicio.mixins.with_s3.WithS3File, "_read_parquet_file") as mock_read_parquet_file, + ): with open(file_path, "r") as file: # pylint: disable=unspecified-encoding mock_s3_reader.return_value = file ReadS3ParquetIO(source_config=s3_parquet_cloud_config, no_disk_space=True).read() @@ -148,9 +151,10 @@ def test_s3_reader_is_not_called_for_loading_a_json_with_env_as_cloud_s3_and_typ ).get(source_key="READ_FROM_S3_JSON") # When - with patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_reader") as mock__s3_reader, patch.object( - dynamicio.mixins.with_s3.WithS3File, "_read_json_file" - ) as mock__read_json_file: + with ( + patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_reader") as mock__s3_reader, + patch.object(dynamicio.mixins.with_s3.WithS3File, "_read_json_file") as mock__read_json_file, + ): ReadS3JsonIO(source_config=s3_json_cloud_config, no_disk_space=True).read() # Then @@ -167,9 +171,10 @@ def test_s3_reader_is_not_called_for_loading_a_csv_with_env_as_cloud_s3_and_type ).get(source_key="READ_FROM_S3_CSV") # When - with patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_reader") as mock__s3_reader, patch.object( - dynamicio.mixins.with_s3.WithS3File, "_read_csv_file" - ) as mock__read_csv_file: + with ( + patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_reader") as mock__s3_reader, + patch.object(dynamicio.mixins.with_s3.WithS3File, "_read_csv_file") as mock__read_csv_file, + ): ReadS3CsvIO(source_config=s3_csv_cloud_config, no_disk_space=True).read() # Then @@ -225,9 +230,11 @@ def test_s3_writers_only_validate_schema_prior_writing_out_the_dataframe(self): # @staticmethod # def validate(df: pd.DataFrame): # pass - with patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_writer") as mock__s3_writer, patch.object(WriteS3ParquetIO, "_apply_schema") as mock__apply_schema, patch.object( - WriteS3ParquetIO, "_write_parquet_file" - ) as mock__write_parquet_file: + with ( + patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_writer") as mock__s3_writer, + patch.object(WriteS3ParquetIO, "_apply_schema") as mock__apply_schema, + patch.object(WriteS3ParquetIO, "_write_parquet_file") as mock__write_parquet_file, + ): with NamedTemporaryFile(delete=False) as temp_file: mock__s3_writer.return_value = temp_file WriteS3ParquetIO(source_config=s3_parquet_cloud_config).write(input_df) @@ -246,8 +253,9 @@ def test_columns_data_type_error_exception_is_not_generated_if_column_dtypes_can ).get(source_key="READ_FROM_S3_PARQUET") # When - with patch.object(dynamicio.mixins.with_s3.WithS3File, "_read_parquet_file") as mock__read_parquet_file, patch.object( - dynamicio.mixins.with_s3.WithS3File, "_s3_named_file_reader" + with ( + patch.object(dynamicio.mixins.with_s3.WithS3File, "_read_parquet_file") as mock__read_parquet_file, + patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_named_file_reader"), ): mock__read_parquet_file.return_value = expected_s3_parquet_df ReadS3ParquetWithDifferentCastableDTypeIO(source_config=s3_parquet_cloud_config).read() @@ -299,9 +307,10 @@ def test_read_parquet_file_is_called_while_s3_reader_is_not_for_loading_a_parque ).get(source_key="READ_FROM_S3_PARQUET") # When - with patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_reader") as mock__s3_reader, patch.object( - dynamicio.mixins.with_local.WithLocal, "_read_parquet_file" - ) as mock__read_parquet_file: + with ( + patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_reader") as mock__s3_reader, + patch.object(dynamicio.mixins.with_local.WithLocal, "_read_parquet_file") as mock__read_parquet_file, + ): ReadS3ParquetIO(source_config=s3_parquet_cloud_config, no_disk_space=True).read() # Then @@ -338,9 +347,10 @@ def test_write_parquet_file_is_called_for_writing_a_parquet_with_env_as_cloud_s3 ).get(source_key="WRITE_TO_S3_PARQUET") # When - with patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_writer") as mock__s3_writer, patch.object( - dynamicio.mixins.with_local.WithLocal, "_write_parquet_file" - ) as mock__write_parquet_file: + with ( + patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_writer") as mock__s3_writer, + patch.object(dynamicio.mixins.with_local.WithLocal, "_write_parquet_file") as mock__write_parquet_file, + ): with NamedTemporaryFile(delete=False) as temp_file: mock__s3_writer.return_value = temp_file WriteS3ParquetIO(source_config=s3_parquet_local_config).write(df) @@ -360,9 +370,10 @@ def test_write_csv_file_is_called_for_writing_a_parquet_with_env_as_cloud_s3_and ).get(source_key="WRITE_TO_S3_CSV") # When - with patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_writer") as mock__s3_writer, patch.object( - dynamicio.mixins.with_local.WithLocal, "_write_csv_file" - ) as mock__write_csv_file: + with ( + patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_writer") as mock__s3_writer, + patch.object(dynamicio.mixins.with_local.WithLocal, "_write_csv_file") as mock__write_csv_file, + ): with NamedTemporaryFile(delete=False) as temp_file: mock__s3_writer.return_value = temp_file WriteS3CsvIO(source_config=s3_csv_local_config).write(df) @@ -382,9 +393,10 @@ def test_write_json_file_is_called_for_writing_a_parquet_with_env_as_cloud_s3_an ).get(source_key="WRITE_TO_S3_JSON") # When - with patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_writer") as mock__s3_writer, patch.object( - dynamicio.mixins.with_local.WithLocal, "_write_json_file" - ) as mock__write_json_file: + with ( + patch.object(dynamicio.mixins.with_s3.WithS3File, "_s3_writer") as mock__s3_writer, + patch.object(dynamicio.mixins.with_local.WithLocal, "_write_json_file") as mock__write_json_file, + ): with NamedTemporaryFile(delete=False) as temp_file: mock__s3_writer.return_value = temp_file WriteS3JsonIO(source_config=s3_json_local_config).write(df) @@ -632,9 +644,10 @@ def test_read_parquet_file_is_called_while_awscli_runner_is_not_for_loading_a_pa ).get(source_key="READ_FROM_S3_PATH_PREFIX_PARQUET") # When - with patch.object(dynamicio.mixins.with_s3, "awscli_runner") as mock__awscli_runner, patch.object( - dynamicio.mixins.with_local.WithLocal, "_read_parquet_file" - ) as mock__read_parquet_file: + with ( + patch.object(dynamicio.mixins.with_s3, "awscli_runner") as mock__awscli_runner, + patch.object(dynamicio.mixins.with_local.WithLocal, "_read_parquet_file") as mock__read_parquet_file, + ): ReadS3ParquetIO(source_config=s3_parquet_cloud_config, no_disk_space=True).read() # Then From 4bc566fd48682f4424e41369c7810da83589bd9e Mon Sep 17 00:00:00 2001 From: Christos Hadjinikolis Date: Mon, 4 Aug 2025 18:06:34 +0300 Subject: [PATCH 7/7] style: Fixes --- dynamicio/config/pydantic/io_resources.py | 4 ++-- tests/test_mixins/test_kafka_mixins.py | 9 +++++---- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/dynamicio/config/pydantic/io_resources.py b/dynamicio/config/pydantic/io_resources.py index 209474a..aeca020 100644 --- a/dynamicio/config/pydantic/io_resources.py +++ b/dynamicio/config/pydantic/io_resources.py @@ -1,7 +1,7 @@ -# pylint: disable=no-member, no-self-argument, unused-argument - """This module contains pylint models for physical data sources (places the bytes are being read from).""" +# pylint: disable=no-member, no-self-argument, unused-argument, broad-exception-raised + import enum import posixpath from typing import Mapping, Optional, Union diff --git a/tests/test_mixins/test_kafka_mixins.py b/tests/test_mixins/test_kafka_mixins.py index 4455d5d..7cbe4a2 100644 --- a/tests/test_mixins/test_kafka_mixins.py +++ b/tests/test_mixins/test_kafka_mixins.py @@ -1,4 +1,4 @@ -# pylint: disable=no-member, missing-module-docstring, missing-class-docstring, missing-function-docstring, too-many-public-methods, too-few-public-methods, protected-access, C0103, C0302, R0801 +# pylint: disable=no-member, missing-module-docstring, missing-class-docstring, missing-function-docstring, too-many-public-methods, too-few-public-methods, protected-access, C0103, C0302, R0801, broad-exception-raised import os from unittest.mock import patch @@ -68,7 +68,7 @@ def rows_generator(_df, chunk_size): # When with patch("dynamicio.mixins.with_kafka.Producer", return_value=mock_kafka_producer_instance): - write_kafka_io = WriteKafkaIO(kafka_cloud_config, document_transformer=lambda v: dict(**v, worked=True)) + write_kafka_io = WriteKafkaIO(kafka_cloud_config, document_transformer=lambda v: {"worked": True, **v}) for chunk in rows_generator(_df=df, chunk_size=2): write_kafka_io.write(chunk) @@ -78,7 +78,7 @@ def rows_generator(_df, chunk_size): # Then for i in range(len(df)): assert len(mock_kafka_producer_instance.my_stream) > 0, "No messages were produced" - assert mock_kafka_producer_instance.my_stream[i]["value"] == simplejson.dumps(dict(**df.iloc[i].to_dict(), worked=True), ignore_nan=True).encode("utf-8") + assert mock_kafka_producer_instance.my_stream[i]["value"] == simplejson.dumps({"worked": True, **df.iloc[i].to_dict()}, ignore_nan=True).encode("utf-8") @pytest.mark.unit def test_kafka_producer_default_value_serialiser_is_used_unless_alternative_is_given(self, test_df): @@ -391,7 +391,8 @@ def rows_generator(_df, chunk_size): def mock_produce(*args, **kwargs): # pylint: disable=unused-argument if mock_kafka_producer_instance.produce_call_count == 1: - raise Exception("Mock message delivery failure") + raise RuntimeError("Mock message delivery failure") + mock_kafka_producer_instance.produce_call_count += 1 # When