Jir feature collections

[jirhiker]

Summary

Adds new OGC/pygeoapi well analytics views and updates existing OGC support views/config, including:

• Latest TDS and Average TDS well outputs (with date-based fields/fallback behavior)
• Depth-to-water trend classification view
• Water well summary view
• OGC view schema cleanup and metadata alignment
• pygeoapi OpenAPI generation fixes and refresh CLI updates

What Changed

1. New/updated Alembic OGC views

• Updated existing pygeoapi supporting views migration:

  • alembic/versions/d5e6f7a8b9c0_create_pygeoapi_supporting_views.py
  • Added location.elevation to Thing collection views
  • Removed spring_type and thing_type from Thing collection projections
  • Updated avg TDS columns to use _date naming (first_tds_observation_date, last_tds_observation_date)

• Added latest/avg TDS migration:

  • alembic/versions/i2b3c4d5e6f7_add_latest_tds_pygeoapi_materialized_view.py
  • ogc_latest_tds_wells is a view (not materialized)
  • ogc_avg_tds_wells remains a materialized view
  • Uses COALESCE(AnalysisDate, CollectionDate) for TDS observation date logic
  • Latest column renamed to latest_tds_observation_date

• Added depth-to-water trend materialized view:

  • alembic/versions/k4d5e6f7a8b9_add_depth_to_water_trend_materialized_view.py
  • ogc_depth_to_water_trend_wells
  • Classification rules:
    • eligibility: >=10 records OR (>=4 records AND span >=2 years)
    • slope > 0.25 ft/yr: increasing
    • slope < -0.25 ft/yr: decreasing
    • otherwise: stable
    • else: not enough data

• Added water well summary materialized view:

  • alembic/versions/l5e6f7a8b9c0_add_water_well_summary_materialized_view.py
  • ogc_water_well_summary includes:
    • thing.name
    • well_depth
    • elevation
    • elevation_method
    • formation_zone
    • total_water_levels
    • last_water_level
    • last_water_level_datetime
    • min_water_level
    • max_water_level
    • water_level_trend_ft_per_year
  • Excludes wells with total_water_levels = 0

2. pygeoapi config updates

• core/pygeoapi-config.yml
  • Added/updated collections:
    • latest_tds_wells
    • depth_to_water_trend_wells
    • water_well_summary
  • Renamed title:
    • Latest Depth to Water (Wells) -> Latest Depth to Water (Water Wells)

3. pygeoapi runtime OpenAPI generation fix

• core/pygeoapi.py
  • Switched from placeholder OpenAPI content to pygeoapi-generated OpenAPI
  • Added safer generation behavior for invalid collections during startup
  • Improved DB env fallback (PYGEOAPI_POSTGRES_* -> POSTGRES_*)

4. CLI refresh defaults and tests

• cli/cli.py

  • refresh-pygeoapi-materialized-views default set now includes:
    • ogc_latest_depth_to_water_wells
    • ogc_avg_tds_wells
    • ogc_depth_to_water_trend_wells
    • ogc_water_well_summary
  • ogc_latest_tds_wells removed from refresh defaults (it is a regular view)

• Tests updated:

  • tests/test_cli_commands.py
  • tests/test_ogc.py

Notes / Compatibility

• ogc_latest_tds_wells is intentionally a non-materialized view.
• TDS observation field naming moved to _date (not _datetime) for TDS date outputs.
• Consumers should update any references to old TDS datetime column names.

Verification

• Python compile checks passed for changed migration/CLI/test files.
• Alembic head at: l5e6f7a8b9c0.

[Copilot]

Pull request overview

This PR expands the OGC/pygeoapi feature collections for well analytics by adding new SQL views/materialized views, wiring them into the pygeoapi config, and improving runtime OpenAPI generation and CLI refresh behavior.

Changes:

• Add new OGC views/materialized views for latest/avg TDS, depth-to-water trend classification, and water well summary metrics.
• Update pygeoapi runtime/config to expose the new collections and generate OpenAPI via pygeoapi at startup.
• Update CLI refresh defaults and add/adjust tests for OpenAPI and TDS date fallback logic.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
alembic/versions/d5e6f7a8b9c0_create_pygeoapi_supporting_views.py	Updates existing pygeoapi supporting views (schema cleanup + avg TDS date fields).
alembic/versions/i2b3c4d5e6f7_add_latest_tds_pygeoapi_materialized_view.py	Adds ogc_latest_tds_wells (view) and redefines ogc_avg_tds_wells (matview).
alembic/versions/k4d5e6f7a8b9_add_depth_to_water_trend_materialized_view.py	Adds depth-to-water trend classification materialized view.
alembic/versions/l5e6f7a8b9c0_add_water_well_summary_materialized_view.py	Adds water well summary materialized view.
core/pygeoapi-config.yml	Registers new OGC collections/providers in pygeoapi config.
core/pygeoapi.py	Uses pygeoapi to generate OpenAPI and improves DB env var fallback.
cli/cli.py	Expands default list of materialized views to refresh.
tests/test_cli_commands.py	Updates CLI refresh default expectations/count.
tests/test_ogc.py	Adds OpenAPI presence test + TDS observation date fallback integration test.

Comments suppressed due to low confidence (1)

alembic/versions/i2b3c4d5e6f7_add_latest_tds_pygeoapi_materialized_view.py:6

• The migration module docstring and filename say “materialized view”, but upgrade() creates ogc_latest_tds_wells as a regular CREATE VIEW (and explicitly drops any prior materialized view). This is misleading for future maintainers/operators who may expect it to be refreshable/handled like a matview. Update the docstring (and ideally the migration filename if feasible) to reflect that ogc_latest_tds_wells is intentionally a non-materialized view.

"""add latest tds pygeoapi materialized view

Revision ID: i2b3c4d5e6f7
Revises: d5e6f7a8b9c0
Create Date: 2026-03-02 11:00:00.000000
"""

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[Copilot]

Pull request overview

Copilot reviewed 10 out of 10 changed files in this pull request and generated 3 comments.

Comments suppressed due to low confidence (1)

alembic/versions/i2b3c4d5e6f7_add_latest_tds_pygeoapi_materialized_view.py:5

• The migration docstring/file name says "materialized view", but this migration creates ogc_latest_tds_wells as a regular VIEW (only ogc_avg_tds_wells is materialized). Please rename/update the docstring (and ideally the filename) to match what’s actually created so future operators don’t refresh/maintain the wrong object type.

"""add latest tds pygeoapi materialized view

Revision ID: i2b3c4d5e6f7
Revises: d5e6f7a8b9c0
Create Date: 2026-03-02 11:00:00.000000

[Copilot]

Pull request overview

Copilot reviewed 10 out of 10 changed files in this pull request and generated 2 comments.

Comments suppressed due to low confidence (1)

core/pygeoapi.py:296

• The PR description mentions a PYGEOAPI_POSTGRES_* → POSTGRES_* fallback for DB env vars, but _pygeoapi_db_settings() still requires PYGEOAPI_POSTGRES_PASSWORD specifically and does not fall back to POSTGRES_PASSWORD. If a deployment only sets POSTGRES_PASSWORD, pygeoapi config generation will still fail.

Consider either (a) adding a password fallback to POSTGRES_PASSWORD and choosing the corresponding placeholder (${POSTGRES_PASSWORD} vs ${PYGEOAPI_POSTGRES_PASSWORD}), or (b) updating the PR description/docs to clarify that only host/port/db/user fall back.

    if os.environ.get("PYGEOAPI_POSTGRES_PASSWORD") is None:
        raise RuntimeError(
            "PYGEOAPI_POSTGRES_PASSWORD must be set to "
            "generate the pygeoapi configuration."
        )
    return host, port, dbname, user, "${PYGEOAPI_POSTGRES_PASSWORD}"