BDMS 221: well core information

.pre-commit-config.yaml

@@ -16,15 +16,15 @@ repos:
           '--statistics'
           ]
         exclude: ^db/__init__.py$ # all models need to be imported for Alembic, but are not used directly
-  - repo: local
-    hooks:
-      - id: pytest
-        name: pytest
-        entry: pytest  # Or your specific test command, e.g., poetry run pytest
-        language: system
-        types: [python] # Specify relevant file types for your tests
-        pass_filenames: false
-        always_run: true
+#  - repo: local
+#    hooks:
+#      - id: pytest
+#        name: pytest
+#        entry: pytest  # Or your specific test command, e.g., poetry run pytest
+#        language: system
+#        types: [python] # Specify relevant file types for your tests
+#        pass_filenames: false
+#        always_run: true
 
   # - repo: https://github.com/pre-commit/mirrors-mypy
   #   rev: v1.10.0  # Use the latest stable version or pin to your preference

core/enums.py

@@ -48,6 +48,7 @@
 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")
+OriginSource: type[Enum] = build_enum_from_lexicon_category("origin_source")
 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")
@@ -67,4 +68,8 @@
 Vertical_datum: type[Enum] = build_enum_from_lexicon_category("vertical_datum")
 ScreenType: type[Enum] = build_enum_from_lexicon_category("screen_type")
 SensorType: type[Enum] = build_enum_from_lexicon_category("sensor_type")
+GroupType: type[Enum] = build_enum_from_lexicon_category("group_type")
+MonitoringFrequency: type[Enum] = build_enum_from_lexicon_category(
+    "monitoring_frequency"
+)
 # ============= EOF =============================================

core/lexicon.json

@@ -18,11 +18,12 @@
     {"name": "email_type", "description": null},
     {"name": "participant_role", "description": null},
     {"name": "geochronology", "description": null},
-    {"name": "horizontal_datum", "description": null},
     {"name": "groundwater_level_reason", "description": null},
+    {"name": "group_type", "description": null},
+    {"name": "horizontal_datum", "description": null},
     {"name": "limit_type", "description": null},
     {"name": "measurement_method", "description": null},
-    {"name": "monitoring_status", "description": null},
+    {"name": "monitoring_frequency", "description": null},
     {"name": "note_type", "description": null},
     {"name": "parameter_name", "description": null},
     {"name": "organization", "description": null},
@@ -48,7 +49,9 @@
     {"name": "unit", "description": null},
     {"name": "vertical_datum", "description": null},
     {"name": "well_purpose", "description": null},
-    {"name": "well_status", "description": null}
+    {"name": "status_type", "description": null},
+    {"name": "status_value", "description": null},
+    {"name": "origin_source", "description": null}
   ],
   "terms": [
     {"categories": ["review_status"], "term": "approved", "definition": "approved"},
@@ -145,6 +148,7 @@
     {"categories": ["unit"], "term": "second", "definition": "second"},
     {"categories": ["unit"], "term": "minute", "definition": "minute"},
     {"categories": ["unit"], "term": "hour", "definition": "hour"},
+    {"categories": ["unit"], "term": "m", "definition": "meters"},
     {"categories": ["parameter_name"], "term": "groundwater level", "definition": "groundwater level measurement"},
     {"categories": ["parameter_name"], "term": "temperature", "definition": "Temperature measurement"},
     {"categories": ["parameter_name"], "term": "pH", "definition": "pH"},
@@ -322,10 +326,15 @@
     {"categories": ["groundwater_level_reason"], "term": "Water level affected by stage in nearby surface-water site", "definition": "Water level affected by stage in nearby surface-water site"},
     {"categories": ["groundwater_level_reason"], "term": "Other conditions exist that would affect the level (remarks)", "definition": "Other conditions exist that would affect the level (remarks)"},
     {"categories": ["groundwater_level_reason"], "term": "Water level not affected", "definition": "Water level not affected"},
-    {"categories": ["well_status"], "term": "Abandoned", "definition": "Abandoned"},
-    {"categories": ["well_status"], "term": "Active, pumping well", "definition": "Active, pumping well"},
-    {"categories": ["well_status"], "term": "Destroyed, exists but not usable", "definition": "Destroyed, exists but not usable"},
-    {"categories": ["well_status"], "term": "Inactive, exists but not used", "definition": "Inactive, exists but not used"},
+    {"categories": ["status_type"], "term": "Well Status", "definition": "Defines the well's operational condition as reported by the owner"},
+    {"categories": ["status_type"], "term": "Monitoring Status", "definition": "Defines the well's current monitoring status by NMBGMR."},
+    {"categories": ["status_type"], "term": "Access Status", "definition": "Defines the well's access status for field personnel."},
+    {"categories": ["status_value"], "term": "Abandoned", "definition": "The well has been properly decommissioned."},
+    {"categories": ["status_value"], "term": "Active, pumping well", "definition": "This well is in use."},
+    {"categories": ["status_value"], "term": "Destroyed, exists but not usable", "definition": "The well structure is physically present but is damaged, collapsed, or otherwise compromised to the point that it is non-functional."},
+    {"categories": ["status_value"], "term": "Inactive, exists but not used", "definition": "The well is not currently in use but is believed to be in a usable condition; it has not been permanently decommissioned/abandoned."},
+    {"categories": ["status_value"], "term": "Currently monitored", "definition": "The well is currently being monitored by AMMP."},
+    {"categories": ["status_value"], "term": "Not currently monitored", "definition": "The well is not currently being monitored by AMMP."},
     {"categories": ["sample_method"], "term": "Airline measurement", "definition": "Airline measurement"},
     {"categories": ["sample_method"], "term": "Analog or graphic recorder", "definition": "Analog or graphic recorder"},
     {"categories": ["sample_method"], "term": "Calibrated airline measurement", "definition": "Calibrated airline measurement"},
@@ -562,8 +571,21 @@
     {"categories": ["organization"], "term": "Winter Brothers", "definition": "Winter Brothers"},
     {"categories": ["organization"], "term": "Yates Petroleum Corporation", "definition": "Yates Petroleum Corporation"},
     {"categories": ["organization"], "term": "Zamora Accounting Services", "definition": "Zamora Accounting Services"},
-    {"categories": ["collection_method"], "term": "manual", "definition": "manual sampling"},
-    {"categories": ["collection_method"], "term": "continuous", "definition": "continuous sampling"},
+    {"categories": ["organization"], "term": "PLSS", "definition": "Public Land Survey System"},
+    {"categories": ["collection_method"], "term": "Altimeter", "definition": "ALtimeter"},
+    {"categories": ["collection_method"], "term": "Differentially corrected GPS", "definition": "Differentially corrected GPS"},
+    {"categories": ["collection_method"], "term": "Survey-grade GPS", "definition": "Survey-grade GPS"},
+    {"categories": ["collection_method"], "term": "Global positioning system (GPS)", "definition": "Global positioning system (GPS)"},
+    {"categories": ["collection_method"], "term": "LiDAR DEM", "definition": "LiDAR DEM"},
+    {"categories": ["collection_method"], "term": "Level or other survey method", "definition": "Level or other survey method"},
+    {"categories": ["collection_method"], "term": "Interpolated from topographic map", "definition": "Interpolated from topographic map"},
+    {"categories": ["collection_method"], "term": "Interpolated from digital elevation model (DEM)", "definition": "Interpolated from digital elevation model (DEM)"},
+    {"categories": ["collection_method"], "term": "Reported", "definition": "Reported"},
+    {"categories": ["collection_method"], "term": "Unknown", "definition": "Unknown"},
+    {"categories": ["collection_method"], "term": "Survey-grade Global Navigation Satellite Sys, Lvl1", "definition": "Survey-grade Global Navigation Satellite Sys, Lvl1"},
+    {"categories": ["collection_method"], "term": "USGS National Elevation Dataset (NED)", "definition": "USGS National Elevation Dataset (NED)"},
+    {"categories": ["collection_method"], "term": "Transit, theodolite, or other survey method", "definition": "Transit, theodolite, or other survey method"},
+    {"categories": ["role"], "term": "Principal Investigator", "definition": "Principal Investigator"},
     {"categories": ["role"], "term": "Owner", "definition": "Owner"},
     {"categories": ["role"], "term": "Manager", "definition": "Manager"},
     {"categories": ["role"], "term": "Operator", "definition": "Operator"},
@@ -624,22 +646,6 @@
     {"categories": ["publication_type"], "term": "Book", "definition": "Book"},
     {"categories": ["publication_type"], "term": "Conference", "definition": "Conference"},
     {"categories": ["publication_type"], "term": "Webpage", "definition": "Webpage"},
-    {"categories": ["monitoring_status"], "term": "Monitor every six months", "definition": "Monitor every six months"},
-    {"categories": ["monitoring_status"], "term": "Annual water level", "definition": "Annual water level"},
-    {"categories": ["monitoring_status"], "term": "Monitoring bi-monthly", "definition": "Monitoring bi-monthly"},
-    {"categories": ["monitoring_status"], "term": "Monitoring complete", "definition": "Monitoring complete"},
-    {"categories": ["monitoring_status"], "term": "Datalogger installed", "definition": "Datalogger installed"},
-    {"categories": ["monitoring_status"], "term": "Monitor every 10 years (long-term monitor)", "definition": "Monitor every 10 years (long-term monitor)"},
-    {"categories": ["monitoring_status"], "term": "Monitor monthly", "definition": "Monitor monthly"},
-    {"categories": ["monitoring_status"], "term": "Sampling complete", "definition": "Sampling complete"},
-    {"categories": ["monitoring_status"], "term": "Reported to NMBGMR bimonthly", "definition": "Reported to NMBGMR bimonthly"},
-    {"categories": ["monitoring_status"], "term": "Sample well", "definition": "Sample well"},
-    {"categories": ["monitoring_status"], "term": "Water level cannot be measured", "definition": "Water level cannot be measured"},
-    {"categories": ["monitoring_status"], "term": "Repeat sampling", "definition": "Repeat sampling"},
-    {"categories": ["monitoring_status"], "term": "Wellntel device", "definition": "Wellntel device"},
-    {"categories": ["monitoring_status"], "term": "Bi-annual (every other year)", "definition": "Bi-annual (every other year)"},
-    {"categories": ["monitoring_status"], "term": "Inactive", "definition": "Inactive"},
-    {"categories": ["monitoring_status"], "term": "Data share", "definition": "Data share"},
     {"categories": ["sample_type"], "term": "Background", "definition": "Background"},
     {"categories": ["sample_type"], "term": "Equipment blank", "definition": "Equipment blank"},
     {"categories": ["sample_type"], "term": "Field blank", "definition": "Field blank"},
@@ -675,13 +681,34 @@
     {"categories": ["sensor_status"], "term": "In Repair", "definition": "In Repair"},
     {"categories": ["sensor_status"], "term": "Retired", "definition": "Retired"},
     {"categories": ["sensor_status"], "term": "Lost", "definition": "Lost"},
+    {"categories": ["group_type"], "term": "Monitoring Plan", "definition": "A group of `Things` that are monitored together for a specific programmatic or scientific purpose."},
+    {"categories": ["group_type"], "term": "Geographic Area", "definition": "A group of `Things` that fall within a specific, user-defined or official spatial boundary. E.g, `Wells in the Estancia Basin`."},
+    {"categories": ["group_type"], "term": "Historical", "definition": "A group of `Things` that share a common historical attribute. E.g., 'Wells drilled before 1950', 'Legacy Wells (Pre-1990)'."},
+    {"categories": ["monitoring_frequency"], "term": "Monthly", "definition": "Location is monitored on a monthly basis."},
+    {"categories": ["monitoring_frequency"], "term": "Bimonthly", "definition": "Location is monitored every two months."},
+    {"categories": ["monitoring_frequency"], "term": "Bimonthly reported", "definition": "Location is monitored every two months and reported to NMBGMR."},
+    {"categories": ["monitoring_frequency"], "term": "Quarterly", "definition": "Location is monitored on a quarterly basis."},
+    {"categories": ["monitoring_frequency"], "term": "Biannual", "definition": "Location is monitored twice a year."},
+    {"categories": ["monitoring_frequency"], "term": "Annual", "definition": "Location is monitored once a year."},
+    {"categories": ["monitoring_frequency"], "term": "Decadal", "definition": "Location is monitored once every ten years."},
+    {"categories": ["monitoring_frequency"], "term": "Event-based", "definition": "Location is monitored based on specific events or triggers rather than a fixed schedule."},
+    {"categories": ["origin_source"], "term": "Reported by another agency", "definition": "Reported by another agency"},
+    {"categories": ["origin_source"], "term": "From driller's log or well report", "definition": "From driller's log or well report"},
+    {"categories": ["origin_source"], "term": "Private geologist, consultant or univ associate", "definition": "Private geologist, consultant or univ associate"},
+    {"categories": ["origin_source"], "term": "Interpreted fr geophys logs by source agency", "definition": "Interpreted fr geophys logs by source agency"},
+    {"categories": ["origin_source"], "term": "Memory of owner, operator, driller", "definition": "Memory of owner, operator, driller"},
+    {"categories": ["origin_source"], "term": "Measured by source agency", "definition": "Measured by source agency"},
+    {"categories": ["origin_source"], "term": "Reported by owner of well", "definition": "Reported by owner of well"},
+    {"categories": ["origin_source"], "term": "Reported by person other than driller owner agency", "definition": "Reported by person other than driller owner agency"},
+    {"categories": ["origin_source"], "term": "Measured by NMBGMR staff", "definition": "Measured by NMBGMR staff"},
+    {"categories": ["origin_source"], "term": "Other", "definition": "Other"},
+    {"categories": ["origin_source"], "term": "Data Portal", "definition": "Data Portal"},
     {"categories": ["note_type"], "term": "Access", "definition": "Access instructions, gate codes, permission requirements, etc."},
     {"categories": ["note_type"], "term": "Construction", "definition": "Construction details, well development, drilling notes, etc. Could create separate `types` for each of these if needed."},
     {"categories": ["note_type"], "term": "Maintenance", "definition": "Maintenance observations and issues."},
     {"categories": ["note_type"], "term": "Historical", "definition": "Historical information or context about the well or location."},
     {"categories": ["note_type"], "term": "Other", "definition": "Other types of notes that do not fit into the predefined categories."},
     {"categories": ["note_type"], "term": "Water", "definition": "Water bearing zone information and other info from ose reports"},
     {"categories": ["note_type"], "term": "Measuring", "definition": "Notes about measuring/visiting the well, on Access form"}
-
   ]
 }

db/__init__.py

@@ -41,6 +41,8 @@
 from db.status_history import *
 from db.thing import *
 from db.transducer import *
+from db.measuring_point_history import *
+from db.data_provenance import *
 
 from sqlalchemy import (
     func,

db/base.py

@@ -29,7 +29,7 @@
     - `ReleaseMixin`: Adds a release status column referencing the `lexicon_term` table.
     - `AuditMixin`: Adds standard audit columns (created_at, created_by, updated_at, updated_by).
 5.  A simple `User` model for tracking user information in audit columns.
-6.  Polymorphic helper mixins (`StatusHistoryMixin`, `NotesMixin`, `AttributionMixin`, `PermissionMixin`.)
+6.  Polymorphic helper mixins (`StatusHistoryMixin`, `NotesMixin`, `DataProvenanceMixin`, `PermissionMixin`.)
     which provide a clean, reusable way to add relationships to the polymorphic
     metadata tables. Any model that can have a status history (like Thing or Location)
     can simply inherit from the `StatusHistoryMixin` mixin.
@@ -177,23 +177,6 @@ def properties(self):
 
 
 # ============= Polymorphic Helper Mixins =============================================
-class StatusHistoryMixin:
-    """
-    Mixin for models that can have a status history (e.g., Thing, Location).
-    It automatically creates a polymorphic One-to-Many relationship to the
-    StatusHistory table.
-    """
-
-    @declared_attr
-    def status_history(self):
-        # One-to-Many polymorphic relationship
-        return relationship(
-            "StatusHistory",
-            primaryjoin=f"and_({self.__name__}.id==foreign(StatusHistory.statusable_id), "
-            f"StatusHistory.statusable_type=='{self.__name__}')",
-            cascade="all, delete-orphan",
-            lazy="selectin",
-        )
 
 
 class PermissionMixin: