BDMS 113 & 114: sample & observation updates & revisions | other updates and revisions

api/observation.py

@@ -21,33 +21,38 @@
 from core.dependencies import (
     session_dependency,
     amp_admin_dependency,
-    admin_dependency,
     amp_viewer_dependency,
-    viewer_dependency,
 )
 from db import Observation
 from schemas.observation import (
     CreateGroundwaterLevelObservation,
     GroundwaterLevelObservationResponse,
     CreateWaterChemistryObservation,
     WaterChemistryObservationResponse,
-    CreateGeothermalObservation,
-    GeothermalObservationResponse,
+    # CreateGeothermalObservation,
+    # GeothermalObservationResponse,
     ObservationResponse,
     UpdateGroundwaterLevelObservation,
     UpdateWaterChemistryObservation,
-    UpdateGeothermalObservation,
+    # UpdateGeothermalObservation,
 )
 from services.crud_helper import model_deleter, model_adder
 from services.query_helper import simple_get_by_id
 from services.observation_helper import (
     get_observations,
     observation_model_patcher,
-    get_observation_of_an_observation_class_by_id,
+    get_observation_of_an_activity_type_by_id,
 )
 
 router = APIRouter(prefix="/observation", tags=["observation"])
 
+"""
+TODO
+
+- add validation that the sample_id exists in the database before creating observation
+- add validation that the activity_type of the sample corresponds with the endpoint where the observation is posted/patched
+"""
+
 
 # ============= Post =============================================
 @router.post("/groundwater-level", status_code=HTTP_201_CREATED)
@@ -75,17 +80,17 @@ async def add_water_chemistry_observation(
     return model_adder(session, Observation, obs_data, user=user)
 
 
-@router.post("/geothermal", status_code=HTTP_201_CREATED)
-async def add_geothermal_observation(
-    obs_data: CreateGeothermalObservation,
-    session: session_dependency,
-    user: admin_dependency,
-) -> GeothermalObservationResponse:
-    """
-    Add a new geothermal observation to the database.
-    This endpoint is currently a placeholder and does not implement any functionality.
-    """
-    return model_adder(session, Observation, obs_data, user=user)
+# @router.post("/geothermal", status_code=HTTP_201_CREATED)
+# async def add_geothermal_observation(
+#     obs_data: CreateGeothermalObservation,
+#     session: session_dependency,
+#     user: admin_dependency,
+# ) -> GeothermalObservationResponse:
+#     """
+#     Add a new geothermal observation to the database.
+#     This endpoint is currently a placeholder and does not implement any functionality.
+#     """
+#     return model_adder(session, Observation, obs_data, user=user)
 
 
 # PATCH ========================================================================
@@ -119,18 +124,18 @@ async def update_water_chemistry_observation(
     return observation_model_patcher(session, request, observation_id, obs_data, user)
 
 
-@router.patch("/geothermal/{observation_id}", status_code=HTTP_200_OK)
-async def update_geothermal_observation(
-    observation_id: int,
-    obs_data: UpdateGeothermalObservation,
-    session: session_dependency,
-    user: admin_dependency,
-    request: Request,
-) -> GeothermalObservationResponse:
-    """
-    Update an existing geothermal observation in the database.
-    """
-    return observation_model_patcher(session, request, observation_id, obs_data, user)
+# @router.patch("/geothermal/{observation_id}", status_code=HTTP_200_OK)
+# async def update_geothermal_observation(
+#     observation_id: int,
+#     obs_data: UpdateGeothermalObservation,
+#     session: session_dependency,
+#     user: admin_dependency,
+#     request: Request,
+# ) -> GeothermalObservationResponse:
+#     """
+#     Update an existing geothermal observation in the database.
+#     """
+#     return observation_model_patcher(session, request, observation_id, obs_data, user)
 
 
 # ============= Get ==============================================
@@ -177,7 +182,7 @@ async def get_groundwater_level_observation_by_id(
     user: amp_viewer_dependency,
     observation_id: int,
 ) -> GroundwaterLevelObservationResponse:
-    return get_observation_of_an_observation_class_by_id(
+    return get_observation_of_an_activity_type_by_id(
         session=session,
         request=request,
         observation_id=observation_id,
@@ -224,54 +229,54 @@ async def get_water_chemistry_observation_by_id(
     user: amp_viewer_dependency,
     observation_id: int,
 ) -> WaterChemistryObservationResponse:
-    return get_observation_of_an_observation_class_by_id(
+    return get_observation_of_an_activity_type_by_id(
         session=session,
         request=request,
         observation_id=observation_id,
     )
 
 
-@router.get("/geothermal", summary="Get geothermal observations")
-async def get_geothermal_observations(
-    request: Request,
-    session: session_dependency,
-    user: viewer_dependency,
-    thing_id: int | None = None,
-    sensor_id: int | None = None,
-    sample_id: int | None = None,
-    start_time: datetime | None = None,
-    end_time: datetime | None = None,
-    sort: str | None = None,
-    order: str | None = None,
-    filter_: str = Query(alias="filter", default=None),
-) -> CustomPage[GeothermalObservationResponse]:
-    """
-    Retrieve all geothermal observations from the database.
-    """
-    return get_observations(
-        request=request,
-        session=session,
-        thing_id=thing_id,
-        sensor_id=sensor_id,
-        sample_id=sample_id,
-        start_time=start_time,
-        end_time=end_time,
-        sort=sort,
-        order=order,
-        filter_=filter_,
-    )
-
-
-@router.get("/geothermal/{observation_id}", summary="Get geothermal observation by ID")
-async def get_geothermal_observation_by_id(
-    session: session_dependency,
-    request: Request,
-    user: amp_viewer_dependency,
-    observation_id: int,
-) -> GeothermalObservationResponse:
-    return get_observation_of_an_observation_class_by_id(
-        session=session, request=request, observation_id=observation_id
-    )
+# @router.get("/geothermal", summary="Get geothermal observations")
+# async def get_geothermal_observations(
+#     request: Request,
+#     session: session_dependency,
+#     user: viewer_dependency,
+#     thing_id: int | None = None,
+#     sensor_id: int | None = None,
+#     sample_id: int | None = None,
+#     start_time: datetime | None = None,
+#     end_time: datetime | None = None,
+#     sort: str | None = None,
+#     order: str | None = None,
+#     filter_: str = Query(alias="filter", default=None),
+# ) -> CustomPage[GeothermalObservationResponse]:
+#     """
+#     Retrieve all geothermal observations from the database.
+#     """
+#     return get_observations(
+#         request=request,
+#         session=session,
+#         thing_id=thing_id,
+#         sensor_id=sensor_id,
+#         sample_id=sample_id,
+#         start_time=start_time,
+#         end_time=end_time,
+#         sort=sort,
+#         order=order,
+#         filter_=filter_,
+#     )
+
+
+# @router.get("/geothermal/{observation_id}", summary="Get geothermal observation by ID")
+# async def get_geothermal_observation_by_id(
+#     session: session_dependency,
+#     request: Request,
+#     user: amp_viewer_dependency,
+#     observation_id: int,
+# ) -> GeothermalObservationResponse:
+#     return get_observation_of_an_activity_type_by_id(
+#         session=session, request=request, observation_id=observation_id
+#     )
 
 
 @router.get("", summary="Get all observations")

api/sample.py

@@ -28,16 +28,23 @@
 from db.sample import Sample
 from schemas import ResourceNotFoundResponse
 from schemas.sample import SampleResponse, CreateSample, UpdateSample
-from services.query_helper import paginated_all_getter, simple_get_by_id
+from services.query_helper import simple_get_by_id
 from services.crud_helper import model_patcher, model_deleter, model_adder
 from services.exceptions_helper import PydanticStyleException
+from services.sample_helper import get_db_samples
 
 router = APIRouter(
     prefix="/sample",
     tags=["sample"],
 )
 
 
+# TODO: add the following database validation handlers
+# invalid sample_id
+# invalid lexicon terms
+# sample_date of the Sample model cannot be before the event_date of the FieldEvent model
+
+
 def database_error_handler(
     payload: CreateSample | UpdateSample, error: IntegrityError | ProgrammingError
 ) -> None:
@@ -47,23 +54,23 @@ def database_error_handler(
     error_message = error.orig.args[0]["M"]
     if (
         error_message
-        == 'duplicate key value violates unique constraint "sample_field_sample_id_key"'
+        == 'duplicate key value violates unique constraint "sample_sample_name_key"'
     ):
         detail = {
-            "loc": ["body", "field_sample_id"],
-            "msg": f"Sample with field_sample_id {payload.field_sample_id} already exists.",
+            "loc": ["body", "sample_name"],
+            "msg": f"Sample with sample_name {payload.sample_name} already exists.",
             "type": "value_error",
-            "input": {"field_sample_id": payload.field_sample_id},
+            "input": {"sample_name": payload.sample_name},
         }
     elif (
         error_message
-        == 'insert or update on table "sample" violates foreign key constraint "sample_thing_id_fkey"'
+        == 'insert or update on table "sample" violates foreign key constraint "sample_field_activity_id_fkey"'
     ):
         detail = {
-            "loc": ["body", "thing_id"],
-            "msg": f"Thing with ID {payload.thing_id} does not exist.",
+            "loc": ["body", "field_activity_id"],
+            "msg": f"FieldActivity with ID {payload.field_activity_id} does not exist.",
             "type": "value_error",
-            "input": {"thing_id": payload.thing_id},
+            "input": {"field_activity_id": payload.field_activity_id},
         }
 
     raise PydanticStyleException(status_code=HTTP_409_CONFLICT, detail=[detail])
@@ -78,6 +85,8 @@ async def add_sample(
     Endpoint to add a sample.
     """
     try:
+        # since this is only one instance N+1 is not a concern for
+        # FieldActivity, FieldEvent, and Thing
         return model_adder(session, Sample, sample_data, user=user)
     except (IntegrityError, ProgrammingError) as e:
         database_error_handler(sample_data, e)
@@ -94,20 +103,9 @@ async def update_sample(
     """
     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?
-
-
-    This is handled by the `model_patcher` function, which excludes unset fields from 
-    the update.
-    """
     try:
+        # since this is only one instance N+1 is not a concern for
+        # FieldActivity, FieldEvent, and Thing
         return model_patcher(session, Sample, sample_id, sample_data, user=user)
     except (IntegrityError, ProgrammingError) as e:
         database_error_handler(sample_data, e)
@@ -125,10 +123,7 @@ async def get_samples(
     """
     Endpoint to retrieve samples.
     """
-
-    return paginated_all_getter(
-        session, Sample, sort=sort, order=order, filter_=filter_
-    )
+    return get_db_samples(session, sort=sort, order=order, filter_=filter_)
 
 
 @router.get("/{sample_id}", summary="Get Sample by ID")
@@ -138,6 +133,8 @@ async def get_sample_by_id(
     """
     Endpoint to retrieve a sample by its ID.
     """
+    # since this is only one instance N+1 is not a concern
+    # FieldActivity, FieldEvent, and Thing
     return simple_get_by_id(session, Sample, sample_id)