Summary

This PR adds normalized chemistry materialized views for water wells, exposes them as pygeoapi collections, hardens startup/CI behavior, and aligns docs/config for Docker/ENV usage.

Primary changes

1. Major chemistry normalized view (water wells)

Updated existing migration:

• b6f7a8b9c0d1_add_normalized_chemistry_results_materialized_view.py

What it now does:

• Sources major chemistry only
• Restricts rows to thing_type = 'water well'
• One row per current location/thing
• Uses most recent result per analyte (analysis_date fallback to collection_date)
• Static analyte columns (not JSON)
• Matching *_units static columns
• Single date column: latest_chemistry_date
• Expanded analyte alias mapping to match current DB codes (Ca, Ca(total), SO4, IONBAL, TAn, TCat, Na+K, etc.)

2. New minor chemistry normalized view (water wells)

Added migration:

• c7f8a9b0d1e2_add_minor_chemistry_wells_materialized_view.py

Creates:

• ogc_minor_chemistry_wells materialized view with:
  • water-well-only filter
  • one row per current location/thing
  • latest-per-analyte selection
  • static analyte value columns
  • matching *_units columns
  • latest_chemistry_date
  • analyte_count
  • unique index for concurrent-safe refresh patterns

pygeoapi collection changes

Updated:

• core/pygeoapi-config.yml

Changes:

• Renamed collection title:
  • normalized_chemistry_results -> Major Chemistry (Water Wells)
• Added new collection:
  • minor_chemistry_wells -> Minor Chemistry (Water Wells)

CLI refresh defaults

Updated:

• cli/cli.py

Added to default refresh set:

• ogc_normalized_chemistry_results
• ogc_minor_chemistry_wells

Test expectation updates:

• tests/test_cli_commands.py

OGC test updates

Updated collection assertions/endpoints:

• tests/test_ogc.py

Startup/Compose/CI improvements

Fail-fast entrypoint

Updated:

• entrypoint.sh
• Added set -eu so migration failures stop startup before Uvicorn launches.

Compose service/profile adjustments

Updated:

• docker-compose.yml

Changes:

• db_test is now opt-in (profiles: ["test"])
• Kept hardcoded DB names:
  • dev: ocotilloapi_dev
  • test: ocotilloapi_test

CI service name fix

Updated:

• .github/workflows/tests.yml

Changes:

• docker compose build db -> docker compose build db_dev
• docker compose up -d db -> docker compose up -d db_dev

Documentation/env alignment (Option B)

Updated:

• .env.example
• README.md

Changes:

• .env.example now aligns with Compose dev DB name (POSTGRES_DB=ocotilloapi_dev)
• README now documents:
  • required/optional env vars
  • Compose service names (db_dev, db_test profile)
  • hardcoded dev/test DB names

Validation highlights

• Verified major view now includes only water wells and populates non-TDS analytes after alias mapping fixes.
• Verified minor view creation and population in current DB; no non-water-well rows.
• CLI refresh test updates are in place; local targeted run currently blocked by missing local ocotilloapi_test DB in this environment.