🤖 cli-water-levels

api/location.py

@@ -13,12 +13,14 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 # ===============================================================================
+from fastapi import APIRouter
 from fastapi import Query, Response
 from fastapi_pagination.ext.sqlalchemy import paginate
 from sqlalchemy import select, func
 from starlette import status
+
 from api.pagination import CustomPage
-from constants import SRID_WGS84
+from core.constants import SRID_WGS84
 from core.dependencies import (
     session_dependency,
     admin_dependency,
@@ -27,12 +29,10 @@
 )
 from db.location import Location
 from schemas.location import CreateLocation, LocationResponse, UpdateLocation
-from services.geospatial_helper import make_within_wkt
-from services.query_helper import make_query, order_sort_filter, simple_get_by_id
 from services.crud_helper import model_patcher, model_deleter, model_adder
+from services.geospatial_helper import make_within_wkt
 from services.location_helper import set_geographic_attributes
-
-from fastapi import APIRouter
+from services.query_helper import make_query, order_sort_filter, simple_get_by_id
 
 router = APIRouter(prefix="/location", tags=["location"])
 

cli/cli.py

@@ -59,10 +59,19 @@ def well_inventory_csv(file_path: str):
     well_inventory_csv(file_path)
 
 
-@cli.command()
-@click.argument(
+@cli.group()
+def water_levels():
+    """Water-level utilities"""
+    pass
+
+
+@water_levels.command("bulk-upload")
+@click.option(
+    "--file",
     "file_path",
     type=click.Path(exists=True, file_okay=True, dir_okay=False, readable=True),
+    required=True,
+    help="Path to CSV file containing water level rows",
 )
 @click.option(
     "--output",
@@ -71,7 +80,7 @@ def well_inventory_csv(file_path: str):
     default=None,
     help="Optional output format",
 )
-def water_levels_csv(file_path: str, output_format: str | None):
+def water_levels_bulk_upload(file_path: str, output_format: str | None):
     """
     parse and upload a csv
     """

cli/service_adapter.py

@@ -39,7 +39,6 @@ def water_levels_csv(source_file: Path | str, *, pretty_json: bool = False):
         source_file = Path(source_file)
 
     result = bulk_upload_water_levels(source_file, pretty_json=pretty_json)
-    print(result.stdout)
     if result.stderr:
         print(result.stderr, file=sys.stderr)
     return result.exit_code

db/aquifer_system.py

@@ -6,16 +6,15 @@
 
 from typing import List, TYPE_CHECKING
 
+from geoalchemy2 import Geometry
 from sqlalchemy import Text, Index
-from sqlalchemy.orm import relationship, Mapped, mapped_column
 from sqlalchemy.ext.associationproxy import association_proxy, AssociationProxy
-from geoalchemy2 import Geometry
+from sqlalchemy.orm import relationship, Mapped, mapped_column
 
+from core.constants import SRID_WGS84
 from db.base import Base, AutoBaseMixin, ReleaseMixin
 from db.lexicon import lexicon_term
 
-from constants import SRID_WGS84
-
 if TYPE_CHECKING:
     from db.thing import WellScreen, ThingAquiferAssociation, Thing
     from db.aquifer_type import AquiferType

db/geologic_formation.py

@@ -7,16 +7,15 @@
 
 from typing import List, TYPE_CHECKING
 
+from geoalchemy2 import Geometry
 from sqlalchemy import Text, Index
-from sqlalchemy.orm import relationship, Mapped, mapped_column
 from sqlalchemy.ext.associationproxy import association_proxy, AssociationProxy
-from geoalchemy2 import Geometry
+from sqlalchemy.orm import relationship, Mapped, mapped_column
 
+from core.constants import SRID_WGS84
 from db.base import Base, AutoBaseMixin, ReleaseMixin
 from db.lexicon import lexicon_term
 
-from constants import SRID_WGS84
-
 if TYPE_CHECKING:
     from db.thing import Thing, WellScreen
     from db.thing_geologic_formation_association import (

db/group.py

@@ -17,11 +17,11 @@
 
 from geoalchemy2 import Geometry, WKBElement
 from sqlalchemy import String, Integer, ForeignKey
+from sqlalchemy.ext.associationproxy import association_proxy, AssociationProxy
 from sqlalchemy.orm import relationship, Mapped
 from sqlalchemy.testing.schema import mapped_column
-from sqlalchemy.ext.associationproxy import association_proxy, AssociationProxy
 
-from constants import SRID_WGS84
+from core.constants import SRID_WGS84
 from db.base import Base, AutoBaseMixin, ReleaseMixin, lexicon_term
 
 if TYPE_CHECKING:

db/location.py

@@ -30,7 +30,7 @@
 from sqlalchemy.ext.associationproxy import association_proxy, AssociationProxy
 from sqlalchemy.orm import relationship, Mapped, mapped_column
 
-from constants import SRID_WGS84
+from core.constants import SRID_WGS84
 from db.base import Base, AutoBaseMixin, ReleaseMixin
 from db.data_provenance import DataProvenanceMixin
 from db.notes import NotesMixin

pyproject.toml

@@ -100,6 +100,12 @@ dependencies = [
   "yarl==1.20.1",
 ]
 
+[tool.uv]
+package = true
+
+[tool.setuptools]
+packages = ["alembic", "cli", "core", "db", "schemas", "services"]
+
 [project.scripts]
 oco = "cli.cli:cli"
 

schemas/location.py

@@ -14,19 +14,19 @@
 # limitations under the License.
 # ===============================================================================
 from datetime import date
+from typing import Any
 from typing import List
 
 from geoalchemy2 import WKBElement
 from geoalchemy2.shape import to_shape
 from pydantic import BaseModel, model_validator, field_validator, Field, ConfigDict
-from typing import Any
 
-from constants import SRID_WGS84, SRID_UTM_ZONE_13N
+from core.constants import SRID_WGS84, SRID_UTM_ZONE_13N
 from core.enums import ElevationMethod, CoordinateMethod
 from schemas import BaseCreateModel, BaseUpdateModel, BaseResponseModel
 from schemas.notes import NoteResponse, CreateNote, UpdateNote
-from services.validation.geospatial import validate_wkt_geometry
 from services.util import convert_m_to_ft, transform_srid
+from services.validation.geospatial import validate_wkt_geometry
 
 
 # -------- VALIDATE --------

services/geospatial_helper.py

@@ -14,19 +14,19 @@
 # limitations under the License.
 # ===============================================================================
 import shapefile
-from shapely.errors import GEOSException
-from shapely.io import from_geojson
-
-import constants
-from db.thing import Thing
-from db.group import GroupThingAssociation, Group
-from db.location import Location, LocationThingAssociation
 from geoalchemy2.functions import ST_GeomFromText, ST_Within, ST_AsGeoJSON
 from geoalchemy2.shape import to_shape
+from shapely.errors import GEOSException
+from shapely.io import from_geojson
 from shapely.wkt import loads as wkt_loads
 from sqlalchemy import Select, select
-from sqlalchemy.orm import aliased
 from sqlalchemy import func
+from sqlalchemy.orm import aliased
+
+from core import constants
+from db.group import GroupThingAssociation, Group
+from db.location import Location, LocationThingAssociation
+from db.thing import Thing
 
 
 def get_thing_features(

services/util.py

@@ -6,7 +6,7 @@
 from shapely.ops import transform
 from sqlalchemy.orm import DeclarativeBase
 
-from constants import SRID_WGS84
+from core.constants import SRID_WGS84
 
 TRANSFORMERS = {}
 METERS_TO_FEET = 3.28084

tests/features/data/water-levels.csv

@@ -0,0 +1,3 @@
+field_staff,well_name_point_id,field_event_date_time,measurement_date_time,sampler,sample_method,mp_height,level_status,depth_to_water_ft,data_quality,water_level_notes
+Alice Lopez,AR0001,2025-02-15T08:00:00-07:00,2025-02-15T10:30:00-07:00,Groundwater Team,electric tape,1.5,stable,45.2,approved,Initial measurement after irrigation shutdown
+Bernardo Chen,AR0002,2025-03-05T09:15:00-07:00,2025-03-05T11:10:00-07:00,Consultant,steel tape,1.8,rising,47.0,provisional,Follow-up visit; pump was off for 24h

tests/features/environment.py

@@ -46,6 +46,7 @@
     ThingGeologicFormationAssociation,
     Base,
     Asset,
+    Sample,
 )
 from db.engine import session_ctx
 
@@ -687,12 +688,16 @@ def before_all(context):
 
 def after_all(context):
     with session_ctx() as session:
-        for table in context.objects.values():
-            for record in table:
-                obj = session.get(record.__class__, record.id)
-                if obj:
-                    session.delete(obj)
+        for table in reversed(Base.metadata.sorted_tables):
+            if table.name in ("alembic_version", "parameter"):
+                continue
+            elif table.name.startswith("lexicon"):
+                continue
+            elif table.name == "sample":
+                continue
+            session.execute(table.delete())
         session.commit()
+    context.objects.clear()
 
 
 def before_scenario(context, scenario):
@@ -714,6 +719,13 @@ def after_scenario(context, scenario):
                 asset = session.scalars(sql).one()
                 session.delete(asset)
             session.commit()
+    elif "cleanup_samples" in scenario.tags:
+        # delete all samples created during happy path tests
+        with session_ctx() as session:
+            samples = session.query(Sample).all()
+            for sample in samples:
+                session.delete(sample)
+            session.commit()
 
 
 # ============= EOF =============================================

tests/features/steps/well-core-information.py

@@ -1,13 +1,13 @@
-from constants import SRID_WGS84, SRID_UTM_ZONE_13N
+from behave import then
+from geoalchemy2.shape import to_shape
+
+from core.constants import SRID_WGS84, SRID_UTM_ZONE_13N
 from services.util import (
     transform_srid,
     convert_m_to_ft,
     retrieve_latest_polymorphic_history_table_record,
 )
 
-from behave import then
-from geoalchemy2.shape import to_shape
-
 
 @then("the response should be in JSON format")
 def step_impl(context):

tests/features/water-level-csv.feature

@@ -1,6 +1,5 @@
 # features/cli/bulk_upload_water_levels.feature
 
-@skip
 @cli
 @backend
 @BDMS-TBD
@@ -20,7 +19,7 @@ Feature: Bulk upload water level entries from CSV via CLI
 #      | level_status     |
 #      | data_quality     |
 
-  @positive @happy_path @BDMS-TBD
+  @positive @happy_path @BDMS-TBD @cleanup_samples
   Scenario: Uploading a valid water level entry CSV containing required and optional fields
     Given a valid CSV file for bulk water level entry upload
     And my CSV file is encoded in UTF-8 and uses commas as separators
@@ -56,7 +55,7 @@ Feature: Bulk upload water level entries from CSV via CLI
     And stdout includes an array of created water level entry objects
     And stderr should be empty
 
-  @positive @validation @column_order @BDMS-TBD
+  @positive @validation @column_order @BDMS-TBD @cleanup_samples
   Scenario: Upload succeeds when required columns are present but in a different order
     Given my CSV file contains all required headers but in a different column order
     And the CSV includes required fields:
@@ -77,7 +76,7 @@ Feature: Bulk upload water level entries from CSV via CLI
     And all water level entries are imported
     And stderr should be empty
 
-  @positive @validation @extra_columns @BDMS-TBD
+  @positive @validation @extra_columns @BDMS-TBD @cleanup_samples
   Scenario: Upload succeeds when CSV contains extra, unknown columns
     Given my CSV file contains extra columns but is otherwise valid
     When I run the CLI command: