adding database.py and config.py to datamodels folder. modifying ca_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 ###

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()

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

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

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:

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},)"
 
 
 

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},)"