refactor: rename sample_type to activity_type

Author: jacob-a-brown

api/observation.py

@@ -43,7 +43,7 @@
 from services.observation_helper import (
     get_observations,
     observation_model_patcher,
-    get_observation_of_a_sample_type_by_id,
+    get_observation_of_an_activity_type_by_id,
 )
 
 router = APIRouter(prefix="/observation", tags=["observation"])
@@ -184,7 +184,7 @@ async def get_groundwater_level_observation_by_id(
     user: amp_viewer_dependency,
     observation_id: int,
 ) -> GroundwaterLevelObservationResponse:
-    return get_observation_of_a_sample_type_by_id(
+    return get_observation_of_an_activity_type_by_id(
         session=session,
         request=request,
         observation_id=observation_id,
@@ -231,7 +231,7 @@ async def get_water_chemistry_observation_by_id(
     user: amp_viewer_dependency,
     observation_id: int,
 ) -> WaterChemistryObservationResponse:
-    return get_observation_of_a_sample_type_by_id(
+    return get_observation_of_an_activity_type_by_id(
         session=session,
         request=request,
         observation_id=observation_id,
@@ -276,7 +276,7 @@ async def get_geothermal_observation_by_id(
     user: amp_viewer_dependency,
     observation_id: int,
 ) -> GeothermalObservationResponse:
-    return get_observation_of_a_sample_type_by_id(
+    return get_observation_of_an_activity_type_by_id(
         session=session, request=request, observation_id=observation_id
     )
 

core/lexicon.json

@@ -251,9 +251,9 @@
   {"categories": [{"name": "relation", "description": null}], "term": "OSEPOD", "definition": "NM OSE 'Point of Diversion' ID"},
   {"categories": [{"name": "relation", "description": null}], "term": "PLSS", "definition": "Public Land Survey System ID"},
 
-  {"categories": [{"name": "sample_type", "description": null}], "term": "groundwater level", "definition": "groundwater level"},
-  {"categories": [{"name": "sample_type", "description": null}], "term": "water chemistry", "definition": "water chemistry"},
-  {"categories": [{"name": "sample_type", "description": null}], "term": "geothermal", "definition": "geothermal"},
+  {"categories": [{"name": "activity_type", "description": null}], "term": "groundwater level", "definition": "groundwater level"},
+  {"categories": [{"name": "activity_type", "description": null}], "term": "water chemistry", "definition": "water chemistry"},
+  {"categories": [{"name": "activity_type", "description": null}], "term": "geothermal", "definition": "geothermal"},
 
   {"categories": [{"name": "sample_matrix", "description": null}], "term": "groundwater", "definition": "groundwater"},
 

db/sample.py

@@ -79,9 +79,9 @@ class Sample(Base, AutoBaseMixin, ReleaseMixin):
         default=0,
         comment="Identifier for duplicate samples (0 = original sample, not a duplicate, 1 = dup no.1, 2 = dup no.2, etc.).",
     )
-    sample_type: Mapped[str] = lexicon_term(
+    activity_type: Mapped[str] = lexicon_term(
         nullable=False,
-        comment="The type of sample (e.g., 'geochemical', 'geothermal', 'groundwater').",
+        comment="The type of sampling activity (e.g., 'geochemical', 'geothermal', 'groundwater level', 'water chemistry').",
     )
 
     # --- Relationship Definitions ---

schemas/sample.py

@@ -87,7 +87,7 @@ def convert_sample_date_to_utc(sample_date: AwareDatetime) -> AwareDatetime:
 # -------- CREATE ----------
 class CreateSample(BaseCreateModel, ValidateSample):
     thing_id: int
-    sample_type: str
+    activity_type: str
     field_sample_id: str
     sample_date: Annotated[AwareDatetime, PastDatetime()]
     sampler_name: str  # REFACTOR TODO: update with enum/restricted values
@@ -118,7 +118,7 @@ class UpdateSample(BaseUpdateModel, ValidateSample):
     """
 
     thing_id: int | None = None  # REFACTOR TODO: should users be able to change this?
-    sample_type: str | None = None
+    activity_type: str | None = None
     field_sample_id: str | None = None
     sample_date: Annotated[AwareDatetime, PastDatetime()] | None = None
     sampler_name: str | None = None  # REFACTOR TODO: update with enum/restricted values
@@ -143,7 +143,7 @@ class UpdateSample(BaseUpdateModel, ValidateSample):
 # -------- RESPONSE ----------
 class SampleResponse(BaseResponseModel):
     thing: ThingResponse
-    sample_type: str
+    activity_type: str
     field_sample_id: str
     sample_date: AwareDatetime
     release_status: str

services/observation_helper.py

@@ -19,18 +19,18 @@
 from services.query_helper import simple_get_by_id, order_sort_filter
 
 
-def get_sample_type_from_request(request: Request) -> str:
+def get_activity_type_from_request(request: Request) -> str:
     path = request.url.path
     path_components = path.split("/")
     if len(path_components) == 2:
         # no sample type specified in path
-        sample_type_in_path = path_components[1]
+        activity_type_in_path = path_components[1]
     if len(path_components) >= 3:
         # sample type specified in path
-        sample_type_in_path = path_components[2]
+        activity_type_in_path = path_components[2]
 
-    sample_type = sample_type_in_path.replace("-", " ")
-    return sample_type
+    activity_type = activity_type_in_path.replace("-", " ")
+    return activity_type
 
 
 def get_observations(
@@ -54,7 +54,7 @@ def get_observations(
     Retrieve all observations
     """
     sample_table_is_joined = False
-    sample_type = get_sample_type_from_request(request)
+    activity_type = get_activity_type_from_request(request)
 
     sql = select(Observation)
     if thing_id is not None:
@@ -72,10 +72,10 @@ def get_observations(
         sql = sql.where(Observation.observation_datetime <= end_time)
 
     # root of path is /observation
-    if sample_type != "observation":
+    if activity_type != "observation":
         if sample_table_is_joined is False:
             sql = sql.join(Sample, Sample.id == Observation.sample_id)
-        sql = sql.where(Sample.sample_type == sample_type)
+        sql = sql.where(Sample.activity_type == activity_type)
 
     sql = order_sort_filter(sql, Observation, sort, order, filter_)
 
@@ -85,35 +85,35 @@ def get_observations(
     return paginate(query=sql, conn=session)
 
 
-def verify_observed_property_corresponds_with_sample_type(
+def verify_observed_property_corresponds_with_activity_type(
     observation: Observation, request: Request
 ):
-    requested_sample_type = get_sample_type_from_request(request)
-    actual_sample_type = observation.sample.sample_type
+    requested_activity_type = get_activity_type_from_request(request)
+    actual_activity_type = observation.sample.activity_type
 
-    if actual_sample_type != requested_sample_type:
+    if actual_activity_type != requested_activity_type:
         raise PydanticStyleException(
             status_code=HTTP_404_NOT_FOUND,
             detail=[
                 {
                     "loc": ["path", "observation_id"],
                     "type": "value_error",
                     "input": {"observation_id": observation.id},
-                    "msg": f"Observation with ID {observation.id} is not a {requested_sample_type} observation. It is a {actual_sample_type} observation.",
+                    "msg": f"Observation with ID {observation.id} is not a {requested_activity_type} observation. It is a {actual_activity_type} observation.",
                 }
             ],
         )
 
 
-def get_observation_of_a_sample_type_by_id(
+def get_observation_of_an_activity_type_by_id(
     session: Session, request: Request, observation_id: int
 ) -> Observation:
     """
     Retrieve an observation by its ID.
     """
     observation = simple_get_by_id(session, Observation, observation_id)
 
-    verify_observed_property_corresponds_with_sample_type(observation, request)
+    verify_observed_property_corresponds_with_activity_type(observation, request)
 
     return observation
 
@@ -131,7 +131,7 @@ def observation_model_patcher(
     # simple_get_by_id raises HTTP_404_NOT_FOUND if the item is not found
     observation = simple_get_by_id(session, Observation, observation_id)
 
-    verify_observed_property_corresponds_with_sample_type(observation, request)
+    verify_observed_property_corresponds_with_activity_type(observation, request)
 
     for key, value in payload.model_dump(exclude_unset=True).items():
         setattr(observation, key, value)

tests/conftest.py

@@ -464,7 +464,7 @@ def groundwater_level_sample(water_well_thing, sensor):
         sample = Sample(
             sample_date="2025-01-01T00:00:00Z",
             thing_id=water_well_thing.id,
-            sample_type="groundwater level",
+            activity_type="groundwater level",
             sampler_name="Test Sampler",
             release_status="draft",
             field_sample_id=f"FS-{uuid.uuid4()}",
@@ -487,7 +487,7 @@ def water_chemistry_sample(water_well_thing, sensor):
         sample = Sample(
             sample_date="2025-01-01T00:00:00Z",
             thing_id=water_well_thing.id,
-            sample_type="water chemistry",
+            activity_type="water chemistry",
             sampler_name="Test Sampler",
             release_status="draft",
             field_sample_id=f"FS-{uuid.uuid4()}",
@@ -510,7 +510,7 @@ def geothermal_sample(water_well_thing, sensor):
         sample = Sample(
             sample_date="2025-01-01T00:00:00Z",
             thing_id=water_well_thing.id,
-            sample_type="geothermal",
+            activity_type="geothermal",
             sampler_name="Test Sampler",
             release_status="draft",
             field_sample_id=f"FS-{uuid.uuid4()}",
@@ -532,7 +532,7 @@ def second_sample(water_well_thing, sensor):
     with session_ctx() as session:
         sample = Sample(
             thing_id=water_well_thing.id,
-            sample_type="groundwater level",
+            activity_type="groundwater level",
             field_sample_id="FS-9999999",
             sample_date="2025-01-01T00:00:00Z",
             release_status="draft",

tests/test_observation.py

@@ -160,7 +160,7 @@ def test_patch_groundwater_level_observation_404_not_found(
     assert data["detail"] == f"Observation with ID {bad_id} not found."
 
 
-def test_patch_groundwater_level_observation_404_wrong_sample_type(
+def test_patch_groundwater_level_observation_404_wrong_activity_type(
     water_chemistry_observation, geothermal_observation
 ):
     for obs in water_chemistry_observation, geothermal_observation:
@@ -172,13 +172,13 @@ def test_patch_groundwater_level_observation_404_wrong_sample_type(
         data = response.json()
 
         if obs.observed_property == "temperature":
-            sample_type = "geothermal"
+            activity_type = "geothermal"
         else:
-            sample_type = "water chemistry"
+            activity_type = "water chemistry"
 
         assert (
             data["detail"][0]["msg"]
-            == f"Observation with ID {obs.id} is not a groundwater level observation. It is a {sample_type} observation."
+            == f"Observation with ID {obs.id} is not a groundwater level observation. It is a {activity_type} observation."
         )
 
 
@@ -206,7 +206,7 @@ def test_patch_water_chemistry_observation_404_not_found(water_chemistry_observa
     assert data["detail"] == f"Observation with ID {bad_id} not found."
 
 
-def test_patch_water_chemistry_observation_404_wrong_sample_type(
+def test_patch_water_chemistry_observation_404_wrong_activity_type(
     groundwater_level_observation, geothermal_observation
 ):
     for obs in groundwater_level_observation, geothermal_observation:
@@ -216,13 +216,13 @@ def test_patch_water_chemistry_observation_404_wrong_sample_type(
         data = response.json()
 
         if obs.observed_property == "temperature":
-            sample_type = "geothermal"
+            activity_type = "geothermal"
         else:
-            sample_type = "groundwater level"
+            activity_type = "groundwater level"
 
         assert (
             data["detail"][0]["msg"]
-            == f"Observation with ID {obs.id} is not a water chemistry observation. It is a {sample_type} observation."
+            == f"Observation with ID {obs.id} is not a water chemistry observation. It is a {activity_type} observation."
         )
 
 
@@ -248,7 +248,7 @@ def test_patch_geothermal_observation_404_not_found(geothermal_observation):
     assert data["detail"] == f"Observation with ID {bad_id} not found."
 
 
-def test_patch_geothermal_observation_404_wrong_sample_type(
+def test_patch_geothermal_observation_404_wrong_activity_type(
     groundwater_level_observation, water_chemistry_observation
 ):
     for obs in groundwater_level_observation, water_chemistry_observation:
@@ -258,13 +258,13 @@ def test_patch_geothermal_observation_404_wrong_sample_type(
         data = response.json()
 
         if obs.observed_property == "groundwater level":
-            sample_type = "groundwater level"
+            activity_type = "groundwater level"
         else:
-            sample_type = "water chemistry"
+            activity_type = "water chemistry"
 
         assert (
             data["detail"][0]["msg"]
-            == f"Observation with ID {obs.id} is not a geothermal observation. It is a {sample_type} observation."
+            == f"Observation with ID {obs.id} is not a geothermal observation. It is a {activity_type} observation."
         )
 
 
@@ -412,7 +412,7 @@ def test_get_groundwater_level_observation_by_id_404_not_found(
     assert data["detail"] == f"Observation with ID {bad_id} not found."
 
 
-def test_get_groundwater_level_observation_by_id_404_wrong_sample_type(
+def test_get_groundwater_level_observation_by_id_404_wrong_activity_type(
     water_chemistry_observation, geothermal_observation
 ):
     for obs in water_chemistry_observation, geothermal_observation:
@@ -421,13 +421,13 @@ def test_get_groundwater_level_observation_by_id_404_wrong_sample_type(
         data = response.json()
 
         if obs.observed_property == "temperature":
-            actual_sample_type = "geothermal"
+            actual_activity_type = "geothermal"
         else:
-            actual_sample_type = "water chemistry"
+            actual_activity_type = "water chemistry"
 
         assert (
             data["detail"][0]["msg"]
-            == f"Observation with ID {obs.id} is not a groundwater level observation. It is a {actual_sample_type} observation."
+            == f"Observation with ID {obs.id} is not a groundwater level observation. It is a {actual_activity_type} observation."
         )
         assert data["detail"][0]["type"] == "value_error"
         assert data["detail"][0]["input"] == {"observation_id": obs.id}
@@ -569,7 +569,7 @@ def test_get_water_chemistry_observation_by_id_404_not_found(
     assert data["detail"] == f"Observation with ID {bad_id} not found."
 
 
-def test_get_water_chemistry_observation_by_id_404_wrong_sample_type(
+def test_get_water_chemistry_observation_by_id_404_wrong_activity_type(
     groundwater_level_observation, geothermal_observation
 ):
     for obs in groundwater_level_observation, geothermal_observation:
@@ -578,13 +578,13 @@ def test_get_water_chemistry_observation_by_id_404_wrong_sample_type(
         data = response.json()
 
         if obs.observed_property == "groundwater level":
-            actual_sample_type = "groundwater level"
+            actual_activity_type = "groundwater level"
         else:
-            actual_sample_type = "geothermal"
+            actual_activity_type = "geothermal"
 
         assert (
             data["detail"][0]["msg"]
-            == f"Observation with ID {obs.id} is not a water chemistry observation. It is a {actual_sample_type} observation."
+            == f"Observation with ID {obs.id} is not a water chemistry observation. It is a {actual_activity_type} observation."
         )
         assert data["detail"][0]["type"] == "value_error"
         assert data["detail"][0]["input"] == {"observation_id": obs.id}
@@ -650,7 +650,7 @@ def test_get_geothermal_observation_by_id_404_not_found(geothermal_observation):
     assert data["detail"] == f"Observation with ID {bad_id} not found."
 
 
-def test_get_geothermal_observation_by_id_404_wrong_sample_type(
+def test_get_geothermal_observation_by_id_404_wrong_activity_type(
     water_chemistry_observation, groundwater_level_observation
 ):
     for obs in water_chemistry_observation, groundwater_level_observation:
@@ -659,13 +659,13 @@ def test_get_geothermal_observation_by_id_404_wrong_sample_type(
         data = response.json()
 
         if obs.observed_property == "groundwater level":
-            actual_sample_type = "groundwater level"
+            actual_activity_type = "groundwater level"
         else:
-            actual_sample_type = "water chemistry"
+            actual_activity_type = "water chemistry"
 
         assert (
             data["detail"][0]["msg"]
-            == f"Observation with ID {obs.id} is not a geothermal observation. It is a {actual_sample_type} observation."
+            == f"Observation with ID {obs.id} is not a geothermal observation. It is a {actual_activity_type} observation."
         )
         assert data["detail"][0]["type"] == "value_error"
         assert data["detail"][0]["input"] == {"observation_id": obs.id}