WIP: Feature/fix infra spatialite (#79)

Introduces changes to fix spatialite extension loading issue to support
data fields in sqlachemy model type `POINT`. This change directly
supports the work in #26
- Fixes spatialite extension as loadable with the updated dockerfile
setup and correct implementation using aiosqlite compatibility
- Temporary disables integration test. The repository return type needs
to be refactored and return type changed to list dto facilities results

<!-- Generated by sourcery-ai[bot]: start summary -->

Fix SpatiaLite extension loading issue to support spatial data fields in
SQLAlchemy models. Introduce a new `PointType` for handling geopoint
data. Refactor test database setup and temporarily disable integration
tests pending refactoring. Update build scripts and Makefile for
improved Docker handling.

New Features:
- Introduce a new `PointType` class to handle geopoint data types in
SQLAlchemy models, enabling support for spatial data fields like
`POINT`.

Bug Fixes:
- Fix the loading of the SpatiaLite extension in the database setup to
support spatial data operations.

Enhancements:
- Refactor the test database setup to use a new `SetUpTestDatabase`
class, improving the management of test database lifecycle and session
handling.

Build:
- Update the Makefile to include a new `set-docker` target and modify
the `docker-run-server` target to remove orphan containers.

Tests:
- Temporarily disable integration tests due to the need for refactoring
repository return types and changing return types to list DTO facilities
results.

Chores:
- Update the `run.sh` script to include additional logging for file
listing and database removal.

<!-- Generated by sourcery-ai[bot]: end summary -->

---------

Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>

xcov19/app/database.py

@@ -49,45 +49,43 @@ def __call__(self) -> async_sessionmaker[AsyncSessionWrapper]:
         )
 
 
-async def setup_database(engine: AsyncEngine) -> None:
-    """Sets up tables for database."""
+async def _load_spatialite(dbapi_conn: AsyncAdapt_aiosqlite_connection) -> None:
+    """Loads spatialite sqlite extension."""
+    conn: aiosqlite.Connection = dbapi_conn.driver_connection
+    await conn.enable_load_extension(True)
+    await conn.load_extension("mod_spatialite")
+    db_logger.info("======= PRAGMA load_extension successful =======")
+    try:
+        async with conn.execute("SELECT spatialite_version() as version") as cursor:
+            result = await cursor.fetchone()
+            db_logger.info(f"==== Spatialite Version: {result} ====")
+            db_logger.info("===== mod_spatialite loaded =====")
+    except (AttributeError, aiosqlite.OperationalError) as e:
+        db_logger.error(e)
+        raise (e)
+
+
+def setup_spatialite(engine: AsyncEngine) -> None:
+    """An event listener hook to setup spatialite using aiosqlite."""
 
     @event.listens_for(engine.sync_engine, "connect")
     def load_spatialite(
         dbapi_conn: AsyncAdapt_aiosqlite_connection, _connection_record
     ):
         loop = asyncio.get_running_loop()
+        # Schedule the coroutine in the existing event loop
+        loop.create_task(_load_spatialite(dbapi_conn))
 
-        async def load_async_extension():
-            conn: aiosqlite.Connection = dbapi_conn.driver_connection
-            await conn.enable_load_extension(True)
-            await conn.load_extension("mod_spatialite")
-            db_logger.info("======= PRAGMA load_extension successful =======")
-            try:
-                async with conn.execute(
-                    "SELECT spatialite_version() as version"
-                ) as cursor:
-                    result = await cursor.fetchone()
-                    db_logger.info(f"==== Spatialite Version: {result} ====")
-                    db_logger.info("===== mod_spatialite loaded =====")
-            except (AttributeError, aiosqlite.OperationalError) as e:
-                db_logger.error(e)
-                raise (e)
 
-        # Schedule the coroutine in the existing event loop
-        loop.create_task(load_async_extension())
+async def setup_database(engine: AsyncEngine) -> None:
+    """Sets up tables for database."""
 
+    setup_spatialite(engine)
     async with engine.begin() as conn:
         # Enable extension loading
         await conn.execute(text("PRAGMA load_extension = 1"))
-        # db_logger.info("SQLAlchemy setup to load the SpatiaLite extension.")
-        # await conn.execute(text("SELECT load_extension('/opt/homebrew/Cellar/libspatialite/5.1.0_1/lib/mod_spatialite.dylib')"))
-        # await conn.execute(text("SELECT load_extension('mod_spatialite')"))
         # see: https://sqlmodel.tiangolo.com/tutorial/relationship-attributes/cascade-delete-relationships/#enable-foreign-key-support-in-sqlite
         await conn.execute(text("PRAGMA foreign_keys=ON"))
-        # test_result = await conn.execute(text("SELECT spatialite_version() as version;"))
-        # print(f"==== Spatialite Version: {test_result.fetchone()} ====")
-
         await conn.run_sync(SQLModel.metadata.create_all)
         await conn.commit()
         db_logger.info("===== Database tables setup. =====")

xcov19/infra/models.py

@@ -90,12 +90,14 @@ def pydantic_adapter(cls) -> TypeAdapter:
         return TypeAdapter(cls)
 
 
+def generate_uuid() -> str:
+    return str(uuid.uuid4())
+
+
 ### These tables map to the domain models for Patient
 class Patient(SQLModel, table=True):
     patient_id: str = Field(
-        sa_column=Column(
-            TEXT, unique=True, primary_key=True, default=str(uuid.uuid4())
-        ),
+        sa_column=Column(TEXT, unique=True, primary_key=True, default=generate_uuid),
         allow_mutation=False,
     )
     queries: Mapped[List["Query"]] = Relationship(
@@ -109,9 +111,7 @@ class Query(SQLModel, table=True):
     """Every Query must have both a Patient and a Location."""
 
     query_id: str = Field(
-        sa_column=Column(
-            TEXT, unique=True, primary_key=True, default=str(uuid.uuid4())
-        ),
+        sa_column=Column(TEXT, unique=True, primary_key=True, default=generate_uuid),
         allow_mutation=False,
     )
     query: str = Field(allow_mutation=False, sa_column=Column(Text))
@@ -128,9 +128,7 @@ class Location(SQLModel, table=True):
         Index("ix_location_composite_lat_lng", "latitude", "longitude", unique=True),
     )
     location_id: str = Field(
-        sa_column=Column(
-            TEXT, unique=True, primary_key=True, default=str(uuid.uuid4())
-        ),
+        sa_column=Column(TEXT, unique=True, primary_key=True, default=generate_uuid),
         allow_mutation=False,
     )
     latitude: float = Field(sa_column=Column(Float))
@@ -148,9 +146,7 @@ class Location(SQLModel, table=True):
 ### These tables map to the domain models for Provider
 class Provider(SQLModel, table=True):
     provider_id: str = Field(
-        sa_column=Column(
-            TEXT, unique=True, primary_key=True, default=str(uuid.uuid4())
-        ),
+        sa_column=Column(TEXT, unique=True, primary_key=True, default=generate_uuid),
         allow_mutation=False,
     )
     name: str = Field(
@@ -160,7 +156,7 @@ class Provider(SQLModel, table=True):
     geopoint: Annotated[
         tuple, lambda geom: PointType.pydantic_adapter().validate_python(geom)
     ] = Field(sa_column=Column(PointType, nullable=False), allow_mutation=False)
-    contact: str = Field(sa_column=Column(NUMERIC, nullable=False))
+    contact: int = Field(sa_column=Column(NUMERIC, nullable=False))
     facility_type: str = Field(sa_column=Column(TEXT, nullable=False))
     ownership_type: str = Field(sa_column=Column(TEXT, nullable=False))
     specialties: List[str] = Field(sa_column=Column(JSON, nullable=False))

xcov19/tests/data/seed_db.py

@@ -9,7 +9,8 @@
 
 
 async def seed_data(session: AsyncSessionWrapper):
-    """
+    """Seeds database with initial data.
+
     dummy GeoLocation:
     lat=0
     lng=0