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NO TICKET: move level_status from observation to field_activity & rename | make observation value non-nullable #169

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NO TICKET: move level_status from observation to field_activity & rename | make observation value non-nullable #169

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4e2998c
refactor: move level_status from obs to activity_status in field_acti…
jacob-a-brown Oct 1, 2025
be73b41
refactor: update water chem activity status term
jacob-a-brown Oct 1, 2025
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49 changes: 25 additions & 24 deletions core/lexicon.json
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
{"name": "field_contact_role", "description": null},
{"name": "geochronology", "description": null},
{"name": "horizontal_datum", "description": null},
{"name": "level_status", "description": null},
{"name": "activity_status", "description": null},
{"name": "measurement_method", "description": null},
{"name": "monitoring_status", "description": null},
{"name": "observed_property", "description": null},
Expand Down Expand Up @@ -284,29 +284,30 @@
{"categories": ["thing_type"], "term": "perennial stream", "definition": "that has a continuous flow of water throughout the year, even during drier periods."},
{"categories": ["thing_type"], "term": "ephemeral stream", "definition": "a stream that flows only briefly during and after precipitation events"},
{"categories": ["thing_type"], "term": "meteorological station", "definition": "a station that measures the weather conditions at a particular location"},
{"categories": ["level_status"], "term": "Water level affected by atmospheric pressure", "definition": "Water level affected by atmospheric pressure"},
{"categories": ["level_status"], "term": "Water level was frozen (no level recorded).", "definition": "Water level was frozen (no level recorded)."},
{"categories": ["level_status"], "term": "Site was dry", "definition": "Site was dry"},
{"categories": ["level_status"], "term": "Site was flowing recently.", "definition": "Site was flowing recently."},
{"categories": ["level_status"], "term": "Site was flowing. Water level or head couldn't be measured w/out additional equipment.", "definition": "Site was flowing. Water level or head couldn't be measured w/out additional equipment."},
{"categories": ["level_status"], "term": "Nearby site that taps the same aquifer was flowing.", "definition": "Nearby site that taps the same aquifer was flowing."},
{"categories": ["level_status"], "term": "Nearby site that taps the same aquifer had been flowing recently.", "definition": "Nearby site that taps the same aquifer had been flowing recently."},
{"categories": ["level_status"], "term": "Recharge water was being injected into the aquifer at this site.", "definition": "Recharge water was being injected into the aquifer at this site."},
{"categories": ["level_status"], "term": "Recharge water was being injected into nearby site that taps the same aquifer.", "definition": "Recharge water was being injected into nearby site that taps the same aquifer."},
{"categories": ["level_status"], "term": "Water was cascading down the inside of the well.", "definition": "Water was cascading down the inside of the well."},
{"categories": ["level_status"], "term": "Water level was affected by brackish or saline water.", "definition": "Water level was affected by brackish or saline water."},
{"categories": ["level_status"], "term": "Well was not in hydraulic contact w/formation (from source other than defined in USGS C714 or C93).", "definition": "Well was not in hydraulic contact w/formation (from source other than defined in USGS C714 or C93)."},
{"categories": ["level_status"], "term": "Measurement was discontinued (no level recorded).", "definition": "Measurement was discontinued (no level recorded)."},
{"categories": ["level_status"], "term": "Obstruction was encountered in the well (no level recorded)", "definition": "Obstruction was encountered in the well (no level recorded)"},
{"categories": ["level_status"], "term": "Site was being pumped", "definition": "Site was being pumped"},
{"categories": ["level_status"], "term": "Site was pumped recently", "definition": "Site was pumped recently"},
{"categories": ["level_status"], "term": "Nearby site that taps the same aquifer was being pumped", "definition": "Nearby site that taps the same aquifer was being pumped"},
{"categories": ["level_status"], "term": "Nearby site that taps the same aquifer was pumped recently", "definition": "Nearby site that taps the same aquifer was pumped recently"},
{"categories": ["level_status"], "term": "Foreign substance present on the water surface", "definition": "Foreign substance present on the water surface"},
{"categories": ["level_status"], "term": "Well was destroyed (no subsequent water levels should be recorded)", "definition": "Well was destroyed (no subsequent water levels should be recorded)"},
{"categories": ["level_status"], "term": "Water level affected by stage in nearby surface-water site", "definition": "Water level affected by stage in nearby surface-water site"},
{"categories": ["level_status"], "term": "Other conditions exist that would affect the level (remarks)", "definition": "Other conditions exist that would affect the level (remarks)"},
{"categories": ["level_status"], "term": "Water level not affected by status", "definition": "Water level not affected by status"},
{"categories": ["activity_status"], "term": "Water level affected by atmospheric pressure", "definition": "Water level affected by atmospheric pressure"},
{"categories": ["activity_status"], "term": "Water level was frozen (no level recorded).", "definition": "Water level was frozen (no level recorded)."},
{"categories": ["activity_status"], "term": "Site was dry", "definition": "Site was dry"},
{"categories": ["activity_status"], "term": "Site was flowing recently.", "definition": "Site was flowing recently."},
{"categories": ["activity_status"], "term": "Site was flowing. Water level or head couldn't be measured w/out additional equipment.", "definition": "Site was flowing. Water level or head couldn't be measured w/out additional equipment."},
{"categories": ["activity_status"], "term": "Nearby site that taps the same aquifer was flowing.", "definition": "Nearby site that taps the same aquifer was flowing."},
{"categories": ["activity_status"], "term": "Nearby site that taps the same aquifer had been flowing recently.", "definition": "Nearby site that taps the same aquifer had been flowing recently."},
{"categories": ["activity_status"], "term": "Recharge water was being injected into the aquifer at this site.", "definition": "Recharge water was being injected into the aquifer at this site."},
{"categories": ["activity_status"], "term": "Recharge water was being injected into nearby site that taps the same aquifer.", "definition": "Recharge water was being injected into nearby site that taps the same aquifer."},
{"categories": ["activity_status"], "term": "Water was cascading down the inside of the well.", "definition": "Water was cascading down the inside of the well."},
{"categories": ["activity_status"], "term": "Water level was affected by brackish or saline water.", "definition": "Water level was affected by brackish or saline water."},
{"categories": ["activity_status"], "term": "Well was not in hydraulic contact w/formation (from source other than defined in USGS C714 or C93).", "definition": "Well was not in hydraulic contact w/formation (from source other than defined in USGS C714 or C93)."},
{"categories": ["activity_status"], "term": "Measurement was discontinued (no level recorded).", "definition": "Measurement was discontinued (no level recorded)."},
{"categories": ["activity_status"], "term": "Obstruction was encountered in the well (no level recorded)", "definition": "Obstruction was encountered in the well (no level recorded)"},
{"categories": ["activity_status"], "term": "Site was being pumped", "definition": "Site was being pumped"},
{"categories": ["activity_status"], "term": "Site was pumped recently", "definition": "Site was pumped recently"},
{"categories": ["activity_status"], "term": "Nearby site that taps the same aquifer was being pumped", "definition": "Nearby site that taps the same aquifer was being pumped"},
{"categories": ["activity_status"], "term": "Nearby site that taps the same aquifer was pumped recently", "definition": "Nearby site that taps the same aquifer was pumped recently"},
{"categories": ["activity_status"], "term": "Foreign substance present on the water surface", "definition": "Foreign substance present on the water surface"},
{"categories": ["activity_status"], "term": "Well was destroyed (no subsequent water levels should be recorded)", "definition": "Well was destroyed (no subsequent water levels should be recorded)"},
{"categories": ["activity_status"], "term": "Water level affected by stage in nearby surface-water site", "definition": "Water level affected by stage in nearby surface-water site"},
{"categories": ["activity_status"], "term": "Other conditions exist that would affect the level (remarks)", "definition": "Other conditions exist that would affect the level (remarks)"},
{"categories": ["activity_status"], "term": "Water level not affected by status", "definition": "Water level not affected by status"},
{"categories": ["activity_status"], "term": "Sample not affected by status", "definition": "Sample not affected by status"},
{"categories": ["status"], "term": "Abandoned", "definition": "Abandoned"},
{"categories": ["status"], "term": "Active, pumping well", "definition": "Active, pumping well"},
{"categories": ["status"], "term": "Destroyed, exists but not usable", "definition": "Destroyed, exists but not usable"},
Expand Down
4 changes: 4 additions & 0 deletions db/field.py
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Expand Up @@ -129,6 +129,10 @@ class FieldActivity(Base, AutoBaseMixin, ReleaseMixin):
nullable=False,
comment="The type of activity performed during the field event (e.g., 'groundwater level', 'water chemistry', 'geothermal').",
)
activity_status: Mapped[str] = lexicon_term(
nullable=False,
comment="The status of the activity, whether normal or impacted by external factors like roving bovine, dry well, or equipment failure.",
)
notes: Mapped[str] = mapped_column(
nullable=True,
comment="Notes or comments about the field activity.",
Expand Down
5 changes: 2 additions & 3 deletions db/observation.py
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Expand Up @@ -56,7 +56,8 @@ class Observation(Base, AutoBaseMixin, ReleaseMixin):
)
observed_property: Mapped[str] = lexicon_term(nullable=False)
value: Mapped[float] = mapped_column(
nullable=True,
nullable=False,
comment="The value of the observation. If a value could not be retrieved then an observation could not be made. The reason for the missing value should be documented in the correct table, like field_activity.",
Comment on lines +59 to +60

@ksmuczynski ksmuczynski Oct 1, 2025

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Thinking more about lab data and value being nullable or not, I think it SHOULD be nullable. It's very common for labs to analyze samples, but the chemical is not present at a high enough concentration to be quantified. In these situations, the value is null, but there are lab qualifiers and reporting limits to provide further context.

I agree NULL values can be a pain to work with sometimes, but no result is a result and the Observation table has additional fields to explain why.

)
unit: Mapped[str] = lexicon_term(nullable=False)

Expand All @@ -67,8 +68,6 @@ class Observation(Base, AutoBaseMixin, ReleaseMixin):
info={"unit": "ft"},
)

level_status: Mapped[str] = lexicon_term(nullable=True)

# geothermal
observation_depth: Mapped[float] = mapped_column(
nullable=True,
Expand Down
1 change: 1 addition & 0 deletions schemas/field.py
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Expand Up @@ -9,6 +9,7 @@
class FieldActivityResponse(BaseResponseModel):
field_event_id: int
activity_type: str
activity_status: str


class FieldEventResponse(BaseResponseModel):
Expand Down
3 changes: 0 additions & 3 deletions schemas/observation.py
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Expand Up @@ -68,7 +68,6 @@ class CreateBaseObservation(BaseCreateModel, ValidateObservation):

class CreateGroundwaterLevelObservation(CreateBaseObservation):
measuring_point_height: float
level_status: str


class CreateWaterChemistryObservation(CreateBaseObservation):
Expand All @@ -94,7 +93,6 @@ class UpdateBaseObservation(BaseUpdateModel, ValidateObservation):

class UpdateGroundwaterLevelObservation(UpdateBaseObservation):
measuring_point_height: float | None = None
level_status: str | None = None


class UpdateWaterChemistryObservation(UpdateBaseObservation):
Expand All @@ -119,7 +117,6 @@ class BaseObservationResponse(BaseResponseModel):
class GroundwaterLevelObservationResponse(BaseObservationResponse):
depth_to_water_bgs: float | None
measuring_point_height: float | None
level_status: str | None

@model_validator(mode="before")
def calculate_depth_to_water_bgs(self: Self) -> Self:
Expand Down
3 changes: 2 additions & 1 deletion tests/conftest.py
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Expand Up @@ -511,6 +511,7 @@ def groundwater_level_field_activity(field_event):
field_activity = FieldActivity(
field_event_id=field_event.id,
activity_type="groundwater level",
activity_status="Water level not affected by status",
notes="field activity fixture notes",
release_status="draft",
)
Expand All @@ -525,6 +526,7 @@ def water_chemistry_field_activity(field_event):
field_activity = FieldActivity(
field_event_id=field_event.id,
activity_type="water chemistry",
activity_status="Sample not affected by status",
notes="field activity fixture notes",
release_status="draft",
)
Expand Down Expand Up @@ -610,7 +612,6 @@ def groundwater_level_observation(sensor, groundwater_level_sample):
value=10.0,
unit="ft",
measuring_point_height=5.0,
level_status="Water level not affected by status",
)
session.add(observation)
session.commit()
Expand Down
10 changes: 0 additions & 10 deletions tests/test_observation.py
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Expand Up @@ -81,7 +81,6 @@ def test_add_groundwater_level_observation(groundwater_level_sample, sensor):
"measuring_point_height": 53,
"sample_id": groundwater_level_sample.id,
"sensor_id": sensor.id,
"level_status": "Water level not affected by status",
"observed_property": "groundwater level",
"unit": "ft",
}
Expand All @@ -96,7 +95,6 @@ def test_add_groundwater_level_observation(groundwater_level_sample, sensor):
assert data["value"] == payload["value"]
assert data["measuring_point_height"] == payload["measuring_point_height"]
assert data["sensor_id"] == payload["sensor_id"]
assert data["level_status"] == payload["level_status"]
assert data["observed_property"] == payload["observed_property"]
assert (
data["depth_to_water_bgs"]
Expand Down Expand Up @@ -343,9 +341,6 @@ def test_get_groundwater_level_observations(groundwater_level_observation):
data["items"][0]["release_status"]
== groundwater_level_observation.release_status
)
assert (
data["items"][0]["level_status"] == groundwater_level_observation.level_status
)
assert data["items"][0]["value"] == groundwater_level_observation.value
assert data["items"][0]["unit"] == groundwater_level_observation.unit
assert (
Expand All @@ -357,9 +352,6 @@ def test_get_groundwater_level_observations(groundwater_level_observation):
data["items"][0]["measuring_point_height"]
== groundwater_level_observation.measuring_point_height
)
assert (
data["items"][0]["level_status"] == groundwater_level_observation.level_status
)


def test_get_groundwater_level_observation_by_id(groundwater_level_observation):
Expand All @@ -384,7 +376,6 @@ def test_get_groundwater_level_observation_by_id(groundwater_level_observation):
== groundwater_level_observation.observed_property[colon_index + 1 :]
)
assert data["release_status"] == groundwater_level_observation.release_status
assert data["level_status"] == groundwater_level_observation.level_status
assert data["value"] == groundwater_level_observation.value
assert data["unit"] == groundwater_level_observation.unit
assert (
Expand All @@ -396,7 +387,6 @@ def test_get_groundwater_level_observation_by_id(groundwater_level_observation):
data["measuring_point_height"]
== groundwater_level_observation.measuring_point_height
)
assert data["level_status"] == groundwater_level_observation.level_status


def test_get_groundwater_level_observation_by_id_404_not_found(
Expand Down
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