jir-transducer-data

.env.example

@@ -8,6 +8,11 @@ POSTGRES_DB=
 GCS_BUCKET_NAME=
 GOOGLE_APPLICATION_CREDENTIALS=/path/to/gcs_credentials.json
 
+
+
+# disable authentication (for development only)
+AUTHENTIK_DISABLE_AUTHENTICATION=1
+
 # authentik
 AUTHENTIK_URL=
 AUTHENTIK_CLIENT_ID=

.github/workflows/CD_staging.yml

@@ -90,4 +90,4 @@ jobs:
         - name: Tag commit
           run: |
             git tag -a "staging-deploy-$(date -u +%Y-%m-%d)T$(date -u +%H-%M-%S%z)" -m "staging gcloud deployment: $(date -u +%Y-%m-%d)T$(date -u +%H:%M:%S%z)"
-            git push origin --tags
+            git push origin --tags

.github/workflows/tests.yml

@@ -65,6 +65,23 @@ jobs:
 
       run: uv run pytest -vv --durations=20 --cov --cov-report=xml --junitxml=junit.xml
 
+#    - name: Checkout BDD repo (features only)
+#      uses: actions/checkout@v4
+#      with:
+#        repository: DataIntegrationGroup/OcotilloBDD
+#        path: bdd
+#
+#    - name: Copy BDD features into backend test directory
+#      run: |
+#        mkdir -p tests/features
+#        cp -r bdd/features/backend/* tests/features/
+#
+#    - name: Run BDD tests
+#      env:
+#        BASE_URL: ${{ secrets.BACKEND_URL }}
+#      run: |
+#        uv run behave tests/features --tags=@backend,@approved --no-capture
+
     - name: Upload results to Codecov
       uses: codecov/codecov-action@v4
       with:

.gitignore

@@ -26,6 +26,7 @@ gcs_credentials.json
 transfers/data/assets*
 transfers/transfer*.log
 transfer*.log
+tests/features/*.feature
 
 # deployment files
 app.yaml

api/observation.py

@@ -14,6 +14,7 @@
 # limitations under the License.
 # ===============================================================================
 from datetime import datetime
+
 from fastapi import APIRouter, Query, Request
 from starlette.status import HTTP_200_OK, HTTP_201_CREATED, HTTP_204_NO_CONTENT
 
@@ -34,13 +35,15 @@
     UpdateGroundwaterLevelObservation,
     UpdateWaterChemistryObservation,
 )
+from schemas.transducer import TransducerObservationWithBlockResponse
 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_activity_type_by_id,
+    get_transducer_observations,
 )
+from services.query_helper import simple_get_by_id
 
 router = APIRouter(prefix="/observation", tags=["observation"])
 
@@ -112,6 +115,24 @@ async def update_water_chemistry_observation(
 # ============= Get ==============================================
 
 
+@router.get(
+    "/transducer-groundwater-level",
+    summary="Get transducer groundwater level observations",
+)
+async def get_transducer_groundwater_level_observations(
+    request: Request,
+    session: session_dependency,
+    user: amp_viewer_dependency,
+    thing_id: int | None = None,
+    parameter_id: int | None = None,
+    start_time: datetime | None = None,
+    end_time: datetime | None = None,
+) -> CustomPage[TransducerObservationWithBlockResponse]:
+    return get_transducer_observations(
+        session, thing_id, parameter_id, start_time, end_time
+    )
+
+
 @router.get("/groundwater-level", summary="Get groundwater level observations")
 async def get_groundwater_level_observations(
     request: Request,

api/search.py

@@ -14,12 +14,12 @@
 # limitations under the License.
 # ===============================================================================
 from fastapi import APIRouter
-from sqlalchemy import select, func, text
-from sqlalchemy.orm import Session
-from api.pagination import CustomPage
 from fastapi_pagination import paginate
 from fastapi_pagination.utils import disable_installed_extensions_check
+from sqlalchemy import select, func, text
+from sqlalchemy.orm import Session
 
+from api.pagination import CustomPage
 from core.dependencies import session_dependency, viewer_dependency
 from db import (
     Contact,
@@ -34,7 +34,6 @@
     search,
 )
 
-
 disable_installed_extensions_check()
 router = APIRouter(prefix="/search", tags=["search"])
 

api/thing.py

@@ -50,6 +50,7 @@
 )
 from services.crud_helper import model_patcher, model_adder, model_deleter
 from services.exceptions_helper import PydanticStyleException
+from services.lexicon_helper import get_terms_by_category
 from services.query_helper import (
     simple_get_by_id,
     paginated_all_getter,
@@ -64,7 +65,6 @@
     modify_well_descriptor_tables,
     WELL_DESCRIPTOR_MODEL_MAP,
 )
-from services.lexicon_helper import get_terms_by_category
 
 router = APIRouter(prefix="/thing", tags=["thing"])
 

core/app.py

@@ -23,8 +23,9 @@
     get_swagger_ui_oauth2_redirect_html,
 )
 from fastapi.openapi.utils import get_openapi
+from fastapi_pagination import add_pagination
 
-from .initializers import init_db, init_lexicon, init_parameter
+from .initializers import init_db, init_lexicon, init_parameter, register_routes
 from .settings import settings
 
 
@@ -37,6 +38,9 @@ async def lifespan(app: FastAPI) -> AsyncGenerator[None, None]:
         init_db()
         init_lexicon()
         init_parameter()
+
+    register_routes(app)
+    add_pagination(app)
     yield
 
 

core/dependencies.py

@@ -21,7 +21,7 @@
 from core.permissions import authenticated
 from db.engine import get_db_session
 
-session_dependency = Annotated[Session, Depends(get_db_session)]
+session_dependency: type[Session] = Annotated[Session, Depends(get_db_session)]
 
 """
 Developer Notes
@@ -61,16 +61,18 @@
 
 
 # Permissions Dependencies -----------------------------------------------------
-admin_dependency = Annotated[dict, Depends(admin_function)]
-editor_dependency = Annotated[dict, Depends(editor_function)]
-viewer_dependency = Annotated[dict, Depends(viewer_function)]
+admin_dependency: type[dict] = Annotated[dict, Depends(admin_function)]
+editor_dependency: type[dict] = Annotated[dict, Depends(editor_function)]
+viewer_dependency: type[dict] = Annotated[dict, Depends(viewer_function)]
 
-lexicon_admin_dependency = Annotated[dict, Depends(lexicon_admin_function)]
-lexicon_editor_dependency = Annotated[dict, Depends(lexicon_editor_function)]
+lexicon_admin_dependency: type[dict] = Annotated[dict, Depends(lexicon_admin_function)]
+lexicon_editor_dependency: type[dict] = Annotated[
+    dict, Depends(lexicon_editor_function)
+]
 
-amp_admin_dependency = Annotated[dict, Depends(amp_admin_function)]
-amp_editor_dependency = Annotated[dict, Depends(amp_editor_function)]
-amp_viewer_dependency = Annotated[dict, Depends(amp_viewer_function)]
+amp_admin_dependency: type[dict] = Annotated[dict, Depends(amp_admin_function)]
+amp_editor_dependency: type[dict] = Annotated[dict, Depends(amp_editor_function)]
+amp_viewer_dependency: type[dict] = Annotated[dict, Depends(amp_viewer_function)]
 
-no_permission_dependency = Annotated[dict, Depends(no_permission_function)]
+no_permission_dependency: type[dict] = Annotated[dict, Depends(no_permission_function)]
 # ============= EOF =============================================

core/enums.py

@@ -0,0 +1,69 @@
+# ===============================================================================
+# Copyright 2025 ross
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ===============================================================================
+from enum import Enum
+
+from services.lexicon_helper import build_enum_from_lexicon_category
+
+ActivityType: type[Enum] = build_enum_from_lexicon_category("activity_type")
+AddressType: type[Enum] = build_enum_from_lexicon_category("address_type")
+AnalysisMethodType: type[Enum] = build_enum_from_lexicon_category(
+    "analysis_method_type"
+)
+CasingMaterial: type[Enum] = build_enum_from_lexicon_category("casing_material")
+CollectionMethod: type[Enum] = build_enum_from_lexicon_category("collection_method")
+ConstructionMethod: type[Enum] = build_enum_from_lexicon_category("construction_method")
+ContactType: type[Enum] = build_enum_from_lexicon_category("contact_type")
+CoordinateMethod: type[Enum] = build_enum_from_lexicon_category("coordinate_method")
+WellPurpose: type[Enum] = build_enum_from_lexicon_category("well_purpose")
+DataQuality: type[Enum] = build_enum_from_lexicon_category("data_quality")
+DataSource: type[Enum] = build_enum_from_lexicon_category("data_source")
+DepthCompletionSource: type[Enum] = build_enum_from_lexicon_category(
+    "depth_completion_source"
+)
+DischargeSource: type[Enum] = build_enum_from_lexicon_category("discharge_source")
+DrillingFluid: type[Enum] = build_enum_from_lexicon_category("drilling_fluid")
+ElevationMethod: type[Enum] = build_enum_from_lexicon_category("elevation_method")
+EmailType: type[Enum] = build_enum_from_lexicon_category("email_type")
+ParticipantRole: type[Enum] = build_enum_from_lexicon_category("participant_role")
+Geochronology: type[Enum] = build_enum_from_lexicon_category("geochronology")
+HorizontalDatum: type[Enum] = build_enum_from_lexicon_category("horizontal_datum")
+GroundwaterLevelReason: type[Enum] = build_enum_from_lexicon_category(
+    "groundwater_level_reason"
+)
+LimitType: type[Enum] = build_enum_from_lexicon_category("limit_type")
+MeasurementMethod: type[Enum] = build_enum_from_lexicon_category("measurement_method")
+MonitoringStatus: type[Enum] = build_enum_from_lexicon_category("monitoring_status")
+ParameterName: type[Enum] = build_enum_from_lexicon_category("parameter_name")
+Organization: type[Enum] = build_enum_from_lexicon_category("organization")
+ParameterType: type[Enum] = build_enum_from_lexicon_category("parameter_type")
+PhoneType: type[Enum] = build_enum_from_lexicon_category("phone_type")
+PublicationType: type[Enum] = build_enum_from_lexicon_category("publication_type")
+SampleQcType: type[Enum] = build_enum_from_lexicon_category("qc_type")
+QualityFlag: type[Enum] = build_enum_from_lexicon_category("quality_flag")
+Relation: type[Enum] = build_enum_from_lexicon_category("relation")
+ReleaseStatus: type[Enum] = build_enum_from_lexicon_category("release_status")
+ReviewStatus: type[Enum] = build_enum_from_lexicon_category("review_status")
+Role: type[Enum] = build_enum_from_lexicon_category("role")
+SampleMatrix: type[Enum] = build_enum_from_lexicon_category("sample_matrix")
+SampleMethod: type[Enum] = build_enum_from_lexicon_category("sample_method")
+SampleType: type[Enum] = build_enum_from_lexicon_category("sample_type")
+SpringType: type[Enum] = build_enum_from_lexicon_category("spring_type")
+Status: type[Enum] = build_enum_from_lexicon_category("status")
+ThingType: type[Enum] = build_enum_from_lexicon_category("thing_type")
+Unit: type[Enum] = build_enum_from_lexicon_category("unit")
+Vertical_datum: type[Enum] = build_enum_from_lexicon_category("vertical_datum")
+ScreenType: type[Enum] = build_enum_from_lexicon_category("screen_type")
+# ============= EOF =============================================

core/initializers.py

@@ -31,8 +31,16 @@ def init_db():
     This function is called during application startup.
     """
 
-    Base.metadata.drop_all(bind=engine)
-    Base.metadata.create_all(bind=engine)
+    from sqlalchemy import text
+
+    with engine.connect() as conn:
+        conn.execute(text("DROP SCHEMA public CASCADE"))
+        conn.execute(text("CREATE SCHEMA public"))
+        conn.execute(text("CREATE EXTENSION IF NOT EXISTS postgis"))
+        conn.commit()
+
+    Base.metadata.drop_all(engine)
+    Base.metadata.create_all(engine)
 
 
 def init_hypertables():
@@ -117,3 +125,36 @@ def init_lexicon(path: str = None) -> None:
                 )
 
                 session.rollback()
+
+
+def register_routes(app):
+    from api.group import router as group_router
+    from api.contact import router as contact_router
+    from api.location import router as location_router
+    from api.thing import router as thing_router
+    from api.sensor import router as sensor_router
+
+    from api.sample import router as sample_router
+    from api.observation import router as observation_router
+
+    from api.lexicon import router as lexicon_router
+
+    from api.publication import router as publication_router
+    from api.author import router as author_router
+    from api.asset import router as asset_router
+    from api.search import router as search_router
+    from api.geospatial import router as geospatial_router
+
+    app.include_router(asset_router)
+    app.include_router(author_router)
+    app.include_router(contact_router)
+    app.include_router(geospatial_router)
+    app.include_router(group_router)
+    app.include_router(lexicon_router)
+    app.include_router(location_router)
+    app.include_router(observation_router)
+    app.include_router(publication_router)
+    app.include_router(sample_router)
+    app.include_router(sensor_router)
+    app.include_router(search_router)
+    app.include_router(thing_router)

core/lexicon.json

@@ -32,10 +32,12 @@
     {"name": "quality_flag", "description": null},
     {"name": "relation", "description": null},
     {"name": "release_status", "description": null},
+    {"name": "review_status", "description": null},
     {"name": "role", "description": null},
     {"name": "sample_matrix", "description": null},
     {"name": "sample_method", "description": null},
     {"name": "sample_type", "description": null},
+    {"name": "screen_type", "description": null},
     {"name": "sensor_type", "description": null},
     {"name": "sensor_status", "description": null},
     {"name": "spring_type", "description": null},
@@ -48,6 +50,8 @@
     {"name": "well_status", "description": null}
   ],
   "terms": [
+    {"categories": ["review_status"], "term": "approved", "definition": "approved"},
+    {"categories": ["review_status"], "term": "not reviewed", "definition": "raw"},
     {"categories": ["qc_type"], "term": "Normal", "definition": "The primary environmental sample collected from the well, spring, or soil boring."},
     {"categories": ["qc_type"], "term": "Duplicate", "definition": "A second, independent sample collected at the same location, at the same time, and in the same manner as the normal sample. This sample is sent to the primary laboratory."},
     {"categories": ["qc_type"], "term": "Split", "definition": "A subsample of a primary environmental sample that is sent to a separate, independent laboratory for analysis."},
@@ -448,9 +452,9 @@
     {"categories": ["spring_type"], "term": "Perennial", "definition": "perennial spring"},
     {"categories": ["spring_type"], "term": "Thermal", "definition": "thermal spring"},
     {"categories": ["spring_type"], "term": "Mineral", "definition": "mineral spring"},
-    {"categories": ["casing_material"], "term": "PVC", "definition": "Polyvinyl Chloride"},
-    {"categories": ["casing_material"], "term": "Steel", "definition": "Steel"},
-    {"categories": ["casing_material"], "term": "Concrete", "definition": "Concrete"},
+    {"categories": ["casing_material", "screen_type"], "term": "PVC", "definition": "Polyvinyl Chloride"},
+    {"categories": ["casing_material", "screen_type"], "term": "Steel", "definition": "Steel"},
+    {"categories": ["casing_material", "screen_type"], "term": "Concrete", "definition": "Concrete"},
     {"categories": ["quality_flag"], "term": "Good", "definition": "The measurement was collected and analyzed according to standard procedures and passed all QA/QC checks."},
     {"categories": ["quality_flag"], "term": "Questionable", "definition": "The measurement is suspect due to a known issue during collection or analysis, but it may still be usable."},
     {"categories": ["quality_flag"], "term": "Estimated", "definition": "The value is not a direct measurement but an estimate derived from other data or models."},