feat: add normalized chemistry results materialized view and update related configurations

[jirhiker]

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.

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[Copilot]

Pull request overview

Adds a new pygeoapi-exposed OGC collection backed by a PostgreSQL materialized view that pivots “major chemistry” results into normalized/static analyte columns, and wires it into refresh tooling and local dev config.

Changes:

• Add Alembic migration creating ogc_normalized_chemistry_results materialized view + unique index for refresh support.
• Register the new collection in core/pygeoapi-config.yml and include it in the CLI refresh list.
• Update tests and local Docker/dev startup configuration to account for the new view/collection.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/test_ogc.py	Ensures the new normalized_chemistry_results collection appears and its items endpoint works.
tests/test_cli_commands.py	Updates refresh-matview command expectations to include the new matview and updated count.
entrypoint.sh	Makes DB readiness check configurable via env, and updates log message.
docker-compose.yml	Splits DB into db_dev and db_test, updates app wiring to db_dev, and renames volumes.
core/pygeoapi-config.yml	Registers normalized_chemistry_results OGC resource pointing at ogc_normalized_chemistry_results.
cli/cli.py	Adds ogc_normalized_chemistry_results to default refresh list.
alembic/versions/b6f7a8b9c0d1_add_normalized_chemistry_results_materialized_view.py	New migration creating the normalized chemistry results materialized view + index.

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[Copilot]

Pull request overview

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

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[Copilot]

Pull request overview

Copilot reviewed 11 out of 11 changed files in this pull request and generated 4 comments.

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