BDMS 22+: implement sample model | some pytest cleanup | pre-commit hooks

.pre-commit-config.yaml

@@ -14,6 +14,7 @@ repos:
           '--show-source',
           '--statistics'
           ]
+        exclude: ^db/__init__.py$ # all models need to be imported for Alembic, but are not used directly
 
   # - repo: https://github.com/pre-commit/mirrors-mypy
   #   rev: v1.10.0  # Use the latest stable version or pin to your preference

alembic/env.py

@@ -46,7 +46,7 @@
 
 def include_object(object, name, type_, reflected, compare_to):
     # only include tables in sql alchemy model, not auto-generated tables from PostGIS or TIGER
-    if type_ == "table":
+    if type_ == "table" or name.endswith("_version") or name == "transaction":
         return name in model_tables
     return True
 

alembic/versions/66ac1af4ba69_initial_migration.py

@@ -8,10 +8,7 @@
 
 from typing import Sequence, Union
 
-from alembic import op
-import geoalchemy2
-import sqlalchemy as sa
-import sqlalchemy_utils
+# from alembic import op
 from sqlalchemy.orm import configure_mappers
 
 # revision identifiers, used by Alembic.
@@ -39,6 +36,23 @@ def upgrade() -> None:
     # It is here as a record of the initial database state.
     # Actual initial database creation should be done through the Base.metadata.create_all(engine) call above.
 
+    """
+    TODO
+    The following code will need to be regenerated by Alembic since configure_mappers() is now called 
+    in db/__init__.py to ensure all models are loaded before creating the database schema. This is 
+    require for SQL Alchemy continuum. 
+
+    The following code will also need to be added:
+
+    - op.drop_index("idx_location_version_point", table_name="location_version", if_exists=True)
+        - before calling op.create_index("idx_location_version_point", "location_version", ["point"], unique=False, postgresql_using="gist",)
+    - op.drop_index("idx_location_point", table_name="location", if_exists=True)
+        - before calling op.create_index("idx_location_point", "location", ["point"], unique=False, postgresql_using="gist",)
+
+    We will also need to figure out how to handle the SQL Alchemy searchable columns in the models, as they are not currently handled by Alembic.
+    There is some documentation about sync_triggers, but that has not yet been tested.
+    """
+
     # ### commands auto generated by Alembic - please adjust! ###
     # op.create_table('asset',
     # sa.Column('name', sa.String(), nullable=False),

api/sample.py

@@ -14,20 +14,19 @@
 # limitations under the License.
 # ===============================================================================
 
-from fastapi import APIRouter, Depends
+from fastapi import APIRouter, Depends, HTTPException
 from sqlalchemy.orm import Session
-from starlette.status import HTTP_201_CREATED
+from starlette.status import HTTP_201_CREATED, HTTP_404_NOT_FOUND
 
 from api.pagination import CustomPage
 from core.dependencies import session_dependency
 from db import adder
 from db.engine import get_db_session
 from db.sample import Sample
-from schemas_v2.sample import (
-    SampleResponse,
-    CreateSample,
-)
+from schemas_v2 import ResourceNotFoundResponse
+from schemas_v2.sample import SampleResponse, CreateSample, UpdateSample
 from services.query_helper import paginated_all_getter
+from services.crud_helper import model_patcher
 
 router = APIRouter(
     prefix="/sample",
@@ -36,7 +35,7 @@
 
 # ============= Post =============================================
 @router.post("", status_code=HTTP_201_CREATED)
-def add_sample(sample_data: CreateSample, session: Session = Depends(get_db_session)):
+def add_sample(sample_data: CreateSample, session: session_dependency):
     """
     Endpoint to add a sample.
     """
@@ -69,6 +68,33 @@ def add_sample(sample_data: CreateSample, session: Session = Depends(get_db_sess
 #     return adder(session, GeothermalSample, sample_data)
 
 
+# ============= Update =============================================
+@router.patch("/{sample_id}", summary="Update Sample")
+def update_sample(
+    sample_id: int,
+    sample_data: UpdateSample,
+    session: Session = Depends(get_db_session),
+) -> SampleResponse | ResourceNotFoundResponse:
+    """
+    Endpoint to update a sample.
+    """
+
+    """
+    Development notes:
+
+    What do we do if the field is nullable and the schema defaults to None?
+    If that occurs, then we update the field to None, which may not have 
+    been the intension of the user. We could set some string to indicate
+    DO NOT UPDATE. Perhaps coordination between the front and backends?
+    """
+    if session.get(Sample, sample_id) is None:
+        raise HTTPException(
+            status_code=HTTP_404_NOT_FOUND,
+            detail=f"Sample with ID {sample_id} not found.",
+        )
+    return model_patcher(session, Sample, sample_id, sample_data)
+
+
 # ============= Get =============================================
 @router.get("", summary="Get Samples")
 def get_samples(session: session_dependency) -> CustomPage[SampleResponse]:
@@ -102,11 +128,20 @@ def get_samples(session: session_dependency) -> CustomPage[SampleResponse]:
 
 # ============= Get by ID =============================================
 @router.get("/{sample_id}", summary="Get Sample by ID")
-def get_sample_by_id(sample_id: int, session: session_dependency) -> SampleResponse:
+def get_sample_by_id(
+    sample_id: int, session: session_dependency
+) -> SampleResponse | ResourceNotFoundResponse:
     """
     Endpoint to retrieve a sample by its ID.
     """
-    return session.get(Sample, sample_id)
+    sample = session.get(Sample, sample_id)
+    if sample is None:
+        raise HTTPException(
+            status_code=HTTP_404_NOT_FOUND,
+            detail=f"Sample with ID {sample_id} not found.",
+        )
+    else:
+        return sample
 
 
 # @router.get("/{sample_id}", summary="Get Geochemical Sample by ID")

db/__init__.py

@@ -14,20 +14,25 @@
 # limitations under the License.
 # ===============================================================================
 
-from db.asset import *
+# import all models from db package so that Alembic can discover them
+
+from db.base import *
 from db.base import Base
+
+from db.asset import *
 from db.collabnet import *
+from db.contact import *
 from db.geochronology import *
+from db.geothermal import *
+from db.group import *
 from db.lexicon import *
 from db.location import *
 from db.observation import *
 from db.publication import *
 from db.sample import *
-from db.sensor import *
+from db.sensor.groundwaterlevel import *
+from db.sensor.sensor import *
 from db.thing import *
-from db.contact import *
-from db.group import *
-
 
 from sqlalchemy import (
     func,
@@ -40,6 +45,9 @@
     inspect_search_vectors,
     search_manager,
 )
+from sqlalchemy.orm import configure_mappers
+
+configure_mappers()
 
 
 def adder(session, table, model, **kwargs):

schemas_v2/__init__.py

@@ -13,5 +13,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 # ===============================================================================
+from pydantic import BaseModel
+
+
+class ResourceNotFoundResponse(BaseModel):
+    detail: str
+
 
 # ============= EOF =============================================

schemas_v2/sample.py

@@ -13,9 +13,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 # ===============================================================================
-from datetime import datetime
+from datetime import datetime, timezone
+from pydantic import BaseModel, field_validator
 
-from pydantic import BaseModel
+from db.engine import get_db_session
+from db import Thing
 
 
 # -------- CREATE ----------
@@ -47,8 +49,39 @@ class CreateGeothermalSample(BaseModel):
 # -------- RESPONSE ----------
 class SampleResponse(BaseModel):
     id: int
+    collection_timestamp: datetime
+    collection_method: str
+    thing_id: int
 
 
 # -------- UPDATE ----------
+class UpdateSample(BaseModel):
+    collection_timestamp: datetime | None = None
+    collection_method: str | None = None
+    thing_id: int | None = None
+
+    @field_validator("thing_id")
+    def validate_thing_id_exists(cls, thing_id: int) -> int:
+        """
+        Validate that the thing_id exists in the database.
+        """
+        with next(get_db_session()) as session:
+            thing = session.get(Thing, thing_id)
+            if not thing:
+                raise ValueError(f"Thing with ID {thing_id} does not exist.")
+        return thing_id
+
+    @field_validator("collection_timestamp")
+    def validate_collection_timestamp(cls, collection_timestamp: datetime) -> datetime:
+        """
+        Validate that the collection_timestamp is not in the future.
+        """
+        if collection_timestamp:
+            if collection_timestamp > datetime.now(tz=timezone.utc):
+                raise ValueError(
+                    f"Collection timestamp {collection_timestamp} cannot be in the future."
+                )
+        return collection_timestamp
+
 
 # ============= EOF =============================================

services/query_helper.py

@@ -18,7 +18,7 @@
 
 from fastapi import HTTPException
 from fastapi_pagination.ext.sqlalchemy import paginate
-from sqlalchemy import select, Float, Integer, Column, Select, func
+from sqlalchemy import select, Float, Integer, Column, Select
 from sqlalchemy.orm import DeclarativeBase
 from sqlalchemy.sql.elements import OperatorExpression
 
@@ -100,6 +100,12 @@ def simple_get_by_id(session, table, item_id) -> object | None:
     """
     Helper function to get a record by ID from the database.
     """
+    """
+    REFACTOR NOTE/TODO: this function replicates the functionality of
+    session.get(table, item_id), which is a SQL Alchemy method to retrieve
+    a record by its primary key. This function can be replaced with
+    session.get(table, item_id).
+    """
     sql = select(table).where(table.id == item_id)
     result = session.execute(sql)
     return result.scalar_one_or_none()

tests/__init__.py

@@ -13,22 +13,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 # ===============================================================================
-import uuid
-
-import pytest
 from fastapi.testclient import TestClient
-from sqlalchemy.orm import configure_mappers
 
-from core.app import init_lexicon, init_hypertables
-from db.location import Location
-from db.base import Base
-from db.sample import Sample
-from db.sensor import Sensor
+from core.app import init_lexicon
+from db import Base
+from db.engine import engine
 from main import app
-from db.engine import engine, session_ctx
-from services.thing_helper import add_thing
 
-configure_mappers()
 
 Base.metadata.drop_all(engine)
 Base.metadata.create_all(engine)
@@ -38,66 +29,4 @@
 client = TestClient(app)
 
 
-@pytest.fixture(scope="session")
-def location():
-    with session_ctx() as session:
-        loc = Location(point="SRID=4326;POINT(0 0)")
-        session.add(loc)
-        session.commit()
-        session.refresh(loc)
-        yield loc
-
-        session.close()
-
-
-@pytest.fixture(scope="session")
-def thing(location):
-    with session_ctx() as session:
-        # loc = Location(point='SRID=4326;POINT(0 0)')
-        # session.add(loc)
-        # session.commit()
-        # session.refresh(loc)
-
-        wt = add_thing(
-            session,
-            {
-                "location_id": location.id,
-                "name": "Test Well",
-            },
-            "water well",
-        )
-
-        yield wt
-
-        session.close()
-
-
-@pytest.fixture(scope="session")
-def sample(thing):
-    with session_ctx() as session:
-        sample = Sample(
-            collection_timestamp="2025-01-01T00:00:00Z",
-            collection_method="manual",
-            thing_id=thing.id,
-            sample_type="groundwater",
-            sampler="Test Sampler",
-        )
-        session.add(sample)
-        session.commit()
-        yield sample
-
-        session.close()
-
-
-@pytest.fixture(scope="session")
-def sensor():
-    with session_ctx() as session:
-        sensor = Sensor(name=f"Test Sensor {uuid.uuid4()}")
-        session.add(sensor)
-        session.commit()
-        yield sensor
-
-        session.close()
-
-
 # ============= EOF =============================================