diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..bab42bf --- /dev/null +++ b/.flake8 @@ -0,0 +1,7 @@ +[flake8] +# Don't lint the virtualenv or generated output dirs. extend-exclude keeps +# flake8's built-in defaults (.git, __pycache__, build, dist, ...). +extend-exclude = + .venv, + output, + output_1 diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index d88a5fc..978fe71 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -1,56 +1,39 @@ -# This workflow will install Python dependencies, run tests and lint with a single version of Python -# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python - name: CI/CD on: push: - branches: [ "pre-production", "feature/jir", "dev/jab"] + branches: [ "pre-production", "feature/jir", "dev/jab", "feature/orchestration-gcp-uv" ] pull_request: - branches: [ "pre-production"] + branches: [ "pre-production" ] permissions: contents: read jobs: build: - runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - name: Set up Python 3.10 - uses: actions/setup-python@v4 + - name: Install uv + uses: astral-sh/setup-uv@v4 with: - python-version: "3.10" - cache: "pip" + version: "latest" - - name: Cache pip dependencies - uses: actions/cache@v3 - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} - restore-keys: | - ${{ runner.os }}-pip- + - name: Set up Python + run: uv python install 3.10 - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install flake8 pytest mypy - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi + run: uv sync --extra dev - name: Lint with flake8 run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + uv run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + uv run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - name: Type check with mypy - run: | - mypy . --ignore-missing-imports + run: uv run mypy . --ignore-missing-imports - name: Test with pytest - run: | - pytest -s tests + run: uv run pytest -s tests diff --git a/.github/workflows/dagster-cloud-branch-deployments.yml b/.github/workflows/dagster-cloud-branch-deployments.yml new file mode 100644 index 0000000..005a063 --- /dev/null +++ b/.github/workflows/dagster-cloud-branch-deployments.yml @@ -0,0 +1,86 @@ +name: Dagster+ Serverless Branch Deployments + +on: + pull_request: + types: [opened, synchronize, reopened, closed] + +concurrency: + group: ${{ github.ref }}/branch_deployments + cancel-in-progress: true + +env: + DAGSTER_CLOUD_URL: ${{ secrets.DAGSTER_CLOUD_URL }} + DAGSTER_CLOUD_API_TOKEN: ${{ secrets.DAGSTER_CLOUD_API_TOKEN }} + ENABLE_FAST_DEPLOYS: 'true' + PYTHON_VERSION: '3.10' + DAGSTER_CLOUD_FILE: 'dagster_cloud.yaml' + +jobs: + dagster_cloud_default_deploy: + name: Dagster Serverless Deploy + runs-on: ubuntu-22.04 + outputs: + build_info: ${{ steps.parse-workspace.outputs.build_info }} + steps: + - name: Check Dagster+ credentials present + id: guard + run: | + if [ -n "${{ secrets.DAGSTER_CLOUD_URL }}" ] && [ -n "${{ secrets.DAGSTER_CLOUD_API_TOKEN }}" ]; then + echo "enabled=true" >> "$GITHUB_OUTPUT" + else + echo "::notice::Dagster+ secrets (DAGSTER_CLOUD_URL / DAGSTER_CLOUD_API_TOKEN) not set; skipping deploy." + echo "enabled=false" >> "$GITHUB_OUTPUT" + fi + + - name: Prerun Checks + id: prerun + if: steps.guard.outputs.enabled == 'true' + uses: dagster-io/dagster-cloud-action/actions/utils/prerun@v0.1 + + - name: Launch Docker Deploy + if: steps.prerun.outputs.result == 'docker-deploy' + id: parse-workspace + uses: dagster-io/dagster-cloud-action/actions/utils/parse_workspace@v0.1 + with: + dagster_cloud_file: $DAGSTER_CLOUD_FILE + + - name: Checkout for Python Executable Deploy + if: steps.prerun.outputs.result == 'pex-deploy' + uses: actions/checkout@v6 + with: + ref: ${{ github.head_ref }} + path: project-repo + + - name: Python Executable Deploy + if: steps.prerun.outputs.result == 'pex-deploy' + uses: dagster-io/dagster-cloud-action/actions/build_deploy_python_executable@v0.1 + with: + dagster_cloud_file: "$GITHUB_WORKSPACE/project-repo/$DAGSTER_CLOUD_FILE" + build_output_dir: "$GITHUB_WORKSPACE/build" + python_version: "${{ env.PYTHON_VERSION }}" + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + dagster_cloud_docker_deploy: + name: Docker Deploy + runs-on: ubuntu-22.04 + if: needs.dagster_cloud_default_deploy.outputs.build_info + needs: dagster_cloud_default_deploy + strategy: + fail-fast: false + matrix: + location: ${{ fromJSON(needs.dagster_cloud_default_deploy.outputs.build_info) }} + steps: + - name: Checkout + uses: actions/checkout@v6 + with: + ref: ${{ github.head_ref }} + - name: Build and deploy to Dagster+ serverless + uses: dagster-io/dagster-cloud-action/actions/serverless_branch_deploy@v0.1 + with: + dagster_cloud_api_token: ${{ secrets.DAGSTER_CLOUD_API_TOKEN }} + location: ${{ toJson(matrix.location) }} + base_image: "python:${{ env.PYTHON_VERSION }}-slim" + organization_id: ${{ secrets.ORGANIZATION_ID }} + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/dagster-cloud-deploy.yml b/.github/workflows/dagster-cloud-deploy.yml new file mode 100644 index 0000000..6a9fd6f --- /dev/null +++ b/.github/workflows/dagster-cloud-deploy.yml @@ -0,0 +1,89 @@ +name: Dagster+ Serverless Deploy + +on: + push: + branches: + - "main" + +concurrency: + group: ${{ github.ref }}/deploy + cancel-in-progress: true + +env: + DAGSTER_CLOUD_URL: ${{ secrets.DAGSTER_CLOUD_URL }} + DAGSTER_CLOUD_API_TOKEN: ${{ secrets.DAGSTER_CLOUD_API_TOKEN }} + # PEX fast deploy. No system GDAL needed (only shapely, which ships a wheel + # with bundled GEOS), so a Docker build would be pure overhead. + ENABLE_FAST_DEPLOYS: 'true' + PYTHON_VERSION: '3.10' + DAGSTER_CLOUD_FILE: 'dagster_cloud.yaml' + +jobs: + dagster_cloud_default_deploy: + name: Dagster Serverless Deploy + runs-on: ubuntu-22.04 + outputs: + build_info: ${{ steps.parse-workspace.outputs.build_info }} + steps: + - name: Check Dagster+ credentials present + id: guard + run: | + if [ -n "${{ secrets.DAGSTER_CLOUD_URL }}" ] && [ -n "${{ secrets.DAGSTER_CLOUD_API_TOKEN }}" ]; then + echo "enabled=true" >> "$GITHUB_OUTPUT" + else + echo "::notice::Dagster+ secrets (DAGSTER_CLOUD_URL / DAGSTER_CLOUD_API_TOKEN) not set; skipping deploy." + echo "enabled=false" >> "$GITHUB_OUTPUT" + fi + + - name: Prerun Checks + id: prerun + if: steps.guard.outputs.enabled == 'true' + uses: dagster-io/dagster-cloud-action/actions/utils/prerun@v0.1 + + - name: Launch Docker Deploy + if: steps.prerun.outputs.result == 'docker-deploy' + id: parse-workspace + uses: dagster-io/dagster-cloud-action/actions/utils/parse_workspace@v0.1 + with: + dagster_cloud_file: $DAGSTER_CLOUD_FILE + + - name: Checkout for Python Executable Deploy + if: steps.prerun.outputs.result == 'pex-deploy' + uses: actions/checkout@v6 + with: + ref: ${{ github.head_ref }} + path: project-repo + + - name: Python Executable Deploy + if: steps.prerun.outputs.result == 'pex-deploy' + uses: dagster-io/dagster-cloud-action/actions/build_deploy_python_executable@v0.1 + with: + dagster_cloud_file: "$GITHUB_WORKSPACE/project-repo/$DAGSTER_CLOUD_FILE" + build_output_dir: "$GITHUB_WORKSPACE/build" + python_version: "${{ env.PYTHON_VERSION }}" + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + dagster_cloud_docker_deploy: + name: Docker Deploy + runs-on: ubuntu-22.04 + if: needs.dagster_cloud_default_deploy.outputs.build_info + needs: dagster_cloud_default_deploy + strategy: + fail-fast: false + matrix: + location: ${{ fromJSON(needs.dagster_cloud_default_deploy.outputs.build_info) }} + steps: + - name: Checkout + uses: actions/checkout@v6 + with: + ref: ${{ github.head_ref }} + - name: Build and deploy to Dagster+ serverless + uses: dagster-io/dagster-cloud-action/actions/serverless_prod_deploy@v0.1 + with: + dagster_cloud_api_token: ${{ secrets.DAGSTER_CLOUD_API_TOKEN }} + location: ${{ toJson(matrix.location) }} + base_image: "python:${{ env.PYTHON_VERSION }}-slim" + organization_id: ${{ secrets.ORGANIZATION_ID }} + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/orchestration-ci.yml b/.github/workflows/orchestration-ci.yml new file mode 100644 index 0000000..8cff5de --- /dev/null +++ b/.github/workflows/orchestration-ci.yml @@ -0,0 +1,49 @@ +name: Orchestration CI + +on: + push: + paths: + - 'orchestration/**' + - 'backend/**' + pull_request: + branches: [ "pre-production" ] + paths: + - 'orchestration/**' + +permissions: + contents: read + +jobs: + lint-and-import-check: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + + - name: Install uv + uses: astral-sh/setup-uv@v4 + with: + version: "latest" + + - name: Set up Python + run: uv python install 3.10 + + - name: Install root package deps + run: uv sync --extra dev + + - name: Install orchestration deps + run: uv pip install dagster dagster-gcp google-cloud-storage google-cloud-secret-manager Jinja2 + + - name: Lint orchestration with flake8 + run: | + uv run flake8 orchestration/ --count --select=E9,F63,F7,F82 --show-source --statistics + uv run flake8 orchestration/ --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + + - name: Import check — definitions load without error + run: | + uv run python -c " + import sys; sys.path.insert(0, '.') + from orchestration.definitions import defs + assert len(list(defs.assets)) > 0, 'No assets defined' + print(f'OK: {len(list(defs.assets))} assets, {len(defs.schedules)} schedules') + " diff --git a/SPEC.md b/SPEC.md new file mode 100644 index 0000000..af548c4 --- /dev/null +++ b/SPEC.md @@ -0,0 +1,962 @@ +# DIE Orchestration + GCP Modernization Spec +## Branch: feature/orchestration-gcp-uv + +--- + +## §1 Context & Goals + +DIE is a data integration engine that unifies NM water data from 12 heterogeneous sources. +Currently: pip-installable CLI (`die weave`), partial Dagster code on `jir-dagster` (unmerged). + +**Goals for this branch:** +1. Migrate package management to **uv + pyproject.toml** +2. Add **Dagster orchestration layer** (internal, not shipped in pip package) +3. Deploy orchestration as **GCP Cloud Run** +4. Produce **OGC Feature Collections** as canonical data products +5. Generate **time-series data products** per well / parameter +6. Products defined in a **configurable YAML manifest** +7. Serve data products via **pygeoapi** (OGC API - Features standard) + +--- + +## §2 Non-Goals + +- No changes to public CLI (`die weave`, `die sites`, `die sources`) +- No changes to existing `backend/` integration logic (sources, transformers, unifier) +- No changes to existing `frontend/cli.py` +- Orchestration code NOT shipped to PyPI +- No database required for orchestration pipeline (GCS is the store) +- GeoServer/PostGIS persister remains available as optional CLI output — not used here + +--- + +## §3 Architecture + +### §3.1 Repository Structure (post-migration) + +``` +DataIntegrationEngine/ +├── pyproject.toml # uv project (replaces setup.py + requirements.txt) +├── uv.lock # pinned lockfile +├── backend/ # unchanged — core integration +├── frontend/ # unchanged — CLI + legacy API +├── orchestration/ # NEW — not in pip package +│ ├── pyproject.toml # orchestration-specific deps +│ ├── Dockerfile # Cloud Run Job image (Dagster) +│ ├── cloudbuild.yaml # Cloud Build CI/CD +│ ├── assets/ +│ │ ├── __init__.py +│ │ ├── wells.py # well site assets +│ │ ├── waterlevels.py # water level timeseries assets +│ │ └── analytes.py # analyte assets +│ ├── resources/ +│ │ ├── __init__.py +│ │ ├── die_config.py # DIE Config Dagster resource +│ │ └── gcs.py # GCS upload/download resource +│ ├── config/ +│ │ └── products.yaml # configurable product manifest +│ ├── definitions.py # Dagster Definitions (entry point) +│ └── pygeoapi/ # pygeoapi API server +│ ├── config.yml.j2 # Jinja2 template for pygeoapi config +│ ├── generate_config.py # renders config.yml from products.yaml +│ ├── Dockerfile # extends geopython/pygeoapi +│ └── cloudbuild.yaml # Cloud Build for pygeoapi image +├── tests/ # unchanged +└── SPEC.md +``` + +### §3.2 Dependency Separation + +``` +pyproject.toml (public CLI) + [project.dependencies] ← lean: click, httpx, geopandas, pyyaml, pandas, etc. + [project.optional-dependencies] + dev = [pytest, mypy, flake8] + geoserver = [psycopg2-binary, GeoAlchemy2, SQLAlchemy] # optional, existing feature + +orchestration/pyproject.toml (internal, never published) + [project.dependencies] ← dagster, dagster-gcp, google-cloud-storage, + google-cloud-secret-manager, Jinja2 +``` + +No database deps in orchestration core. GCS is the sole store. + +### §3.3 GCP Deployment + +``` +Cloud Scheduler (cron) + → Cloud Run Job ← Dagster orchestration (stateless) + └── DIE unifier (existing backend) + ├── fetch from 12 sources + ├── transform → OGC FC GeoJSON files + └── upload → gs://die-products/{product_id}/ + │ + GCS bucket + (public read) + │ + GDAL /vsigs/ virtual FS + │ + Cloud Run Service ← pygeoapi (always-on) + (OGR provider reads GeoJSON from GCS) + │ + HTTP clients + (OGC API - Features) +``` + +**Two Cloud Run deployments:** +- **Cloud Run Job** (Dagster, stateless): triggered by Cloud Scheduler, runs pipeline per product +- **Cloud Run Service** (pygeoapi, always-on): serves OGC API - Features via GDAL OGR + GCS + +No PostgreSQL required. GCS is authoritative store. pygeoapi reads GeoJSON directly from +GCS via GDAL's `/vsigs/` virtual filesystem — no proxy, no DB, no sync step. + +> GeoServer/PostGIS persister in `backend/persisters/geoserver.py` is unchanged and +> still usable via CLI `--output-format geoserver`. Not part of this pipeline. + +--- + +## §4 OGC Feature Collections + +### §4.1 Format + +OGC API - Features compliant GeoJSON written by `OGCFeaturesPersister`. + +**Collection envelope:** +```json +{ + "type": "FeatureCollection", + "id": "nm_waterlevels_summary", + "title": "NM Unified Water Levels Summary", + "description": "...", + "timeStamp": "2026-06-22T06:00:00Z", + "numberMatched": 1234, + "numberReturned": 1234, + "links": [ + {"href": "gs://die-products/nm_waterlevels_summary/latest.geojson", + "rel": "self", "type": "application/geo+json"} + ], + "features": [...] +} +``` + +Each Feature has a top-level `id` (OGC requirement): +```json +{ + "type": "Feature", + "id": "nmbgmr_amp:RA-1234", + "geometry": {"type": "Point", "coordinates": [-106.5, 35.2, 1650.0]}, + "properties": { ... } +} +``` + +### §4.2 Summary Features + +One feature per well site. Properties = existing `SummaryRecord` fields +(nrecords, min, max, mean, earliest_date, latest_date, latest_value, etc.). + +### §4.3 Timeseries Features (flat format) + +**One feature per observation** — not per well. This enables pygeoapi `time_field` +temporal filtering natively without custom code. + +```json +{ + "type": "Feature", + "id": "nmbgmr_amp:RA-1234:2024-04-20", + "geometry": {"type": "Point", "coordinates": [-106.5, 35.2, 1650.0]}, + "properties": { + "site_id": "RA-1234", + "site_name": "Roswell Basin Well", + "source": "nmbgmr_amp", + "parameter": "waterlevels", + "value": 218.1, + "units": "ft", + "datetime": "2024-04-20T00:00:00Z" + } +} +``` + +`datetime` is an ISO 8601 timestamp — pygeoapi maps it to `time_field` for +`?datetime=` query parameter support. + +### §4.4 New Persister + +`backend/persisters/ogc_features.py` → `OGCFeaturesPersister` +- `dump_summary_collection(path, records, meta)` — §4.2 format +- `dump_timeseries_collection(path, site_records, timeseries_records, meta)` — §4.3 format +- Writes local `.geojson` file; Dagster GCS resource handles upload + +--- + +## §5 Dagster Assets + +### §5.1 Asset Graph + +``` +products_config ← loads products.yaml at startup + │ + ▼ +[per product, per schedule] + source_data ← unify_waterlevels / unify_analytes (existing) + │ + ▼ + ogc_collection ← OGCFeaturesPersister → tmp .geojson + │ + ▼ + gcs_upload ← gs://die-products/{product_id}/{YYYY-MM-DD}.geojson + gs://die-products/{product_id}/latest.geojson (overwrite) +``` + +### §5.2 Configurable Products (`orchestration/config/products.yaml`) + +```yaml +gcs_bucket: die-products + +products: + - id: nm_waterlevels_summary + parameter: waterlevels + output_type: ogc_summary + title: "NM Unified Water Levels Summary" + description: "Summary stats for water levels, all NM sources" + schedule: "0 6 * * *" # UTC cron + spatial_filter: + state: NM + sources: + exclude: [] + + - id: nm_waterlevels_timeseries + parameter: waterlevels + output_type: ogc_timeseries + title: "NM Water Levels Time Series" + description: "Per-observation water level measurements, all NM sources" + schedule: "0 7 * * *" + spatial_filter: + state: NM + sources: + exclude: [] + + - id: bernco_waterlevels_timeseries + parameter: waterlevels + output_type: ogc_timeseries + title: "Bernalillo County Water Level Time Series" + description: "Bernalillo County water level timeseries per well" + schedule: "0 8 * * *" + spatial_filter: + county: Bernalillo + sources: + include: [bernco] + + - id: nm_arsenic_summary + parameter: arsenic + output_type: ogc_summary + title: "NM Arsenic Summary" + description: "Arsenic concentration summary stats, all NM sources" + schedule: "0 9 * * *" + spatial_filter: + state: NM + sources: + exclude: [] +``` + +Assets are dynamically generated from `products.yaml` at Dagster definition time. + +### §5.3 Schedule Strategy (MVP) + +One Cloud Run Job per schedule group. Cloud Scheduler triggers with `PRODUCT_ID` env var. +Single Dagster `definitions.py` handles all products; job selects by product id. +Structure supports later migration to persistent Dagster daemon (change Cloud Run Job → Service). + +--- + +## §6 pygeoapi + +### §6.1 Role + +pygeoapi serves the GCS-stored GeoJSON files as OGC API - Features collections. +No DB. pygeoapi uses the **OGR provider** backed by GDAL's `/vsigs/` virtual filesystem, +which reads GeoJSON directly from GCS using Application Default Credentials on Cloud Run. + +``` +GET /collections +GET /collections/{id}/items +GET /collections/{id}/items/{feature_id} +GET /collections/{id}/items?bbox=-107,32,-103,37 +GET /collections/{id}/items?datetime=2020-01-01/2024-12-31 ← timeseries only +``` + +### §6.2 pygeoapi Config Template (`orchestration/pygeoapi/config.yml.j2`) + +```yaml +server: + bind: + host: 0.0.0.0 + port: 80 + url: ${PYGEOAPI_SERVER_URL} + mimetype: application/json + encoding: utf-8 + language: en-US + cors: true + pretty_print: false + limit: 500 + +logging: + level: ERROR + +metadata: + identification: + title: NM Unified Water Data + description: OGC API - Features for New Mexico water data + keywords: [water, groundwater, "New Mexico", NMBGMR] + keywords_type: theme + terms_of_service: https://creativecommons.org/licenses/by/4.0/ + url: https://waterdata.nmt.edu + license: + name: CC-BY 4.0 + url: https://creativecommons.org/licenses/by/4.0/ + provider: + name: NM Bureau of Geology & Mineral Resources + url: https://geoinfo.nmt.edu + +resources: +{% for product in products %} + {{ product.id }}: + type: collection + title: {{ product.title }} + description: {{ product.description }} + keywords: [water, groundwater, "New Mexico"] + extent: + spatial: + bbox: [-109.05, 31.33, -103.00, 37.00] + crs: http://www.opengis.net/def/crs/OGC/1.3/CRS84 +{% if product.output_type == 'ogc_timeseries' %} + temporal: + interval: [["1900-01-01T00:00:00Z", null]] +{% endif %} + providers: + - type: feature + name: OGR + data: + source_type: GeoJSON + source: /vsigs/{{ gcs_bucket }}/{{ product.id }}/latest.geojson + source_options: + GDAL_HTTP_UNSAFESSL: NO + gdal_ogr_options: + EMPTY_AS_NULL: NO + GDAL_CACHEMAX: 64 + id_field: id + layer: OGRGeoJSON +{% if product.output_type == 'ogc_timeseries' %} + time_field: datetime +{% endif %} + +{% endfor %} +``` + +### §6.3 Config Generation (`orchestration/pygeoapi/generate_config.py`) + +```python +import yaml +from jinja2 import Environment, FileSystemLoader +from pathlib import Path + +def generate(products_path: Path, template_path: Path, output_path: Path): + products = yaml.safe_load(products_path.read_text()) + env = Environment(loader=FileSystemLoader(str(template_path.parent))) + tmpl = env.get_template(template_path.name) + output_path.write_text(tmpl.render( + products=products["products"], + gcs_bucket=products["gcs_bucket"], + )) +``` + +Run at Docker build time in `cloudbuild.yaml` — baked into image, not runtime. + +### §6.4 GDAL + GCS Auth + +On Cloud Run, GDAL `/vsigs/` uses the service account's ADC automatically. +No credentials file needed. Require the pygeoapi Cloud Run Service account to have +`roles/storage.objectViewer` on the `die-products` bucket. + +For local dev: +```bash +export GOOGLE_APPLICATION_CREDENTIALS=/path/to/sa-key.json +``` + +### §6.5 Dockerfile (`orchestration/pygeoapi/Dockerfile`) + +```dockerfile +FROM geopython/pygeoapi:latest + +# Generate config from products.yaml at build time +COPY ../config/products.yaml /tmp/products.yaml +COPY config.yml.j2 /tmp/config.yml.j2 +COPY generate_config.py /tmp/generate_config.py +RUN python /tmp/generate_config.py \ + --products /tmp/products.yaml \ + --template /tmp/config.yml.j2 \ + --output /pygeoapi/local.config.yml + +EXPOSE 80 +``` + +Cloud Run Service env vars: +- `PYGEOAPI_SERVER_URL` — public Cloud Run URL +- Port: 80 + +--- + +## §7 uv Migration + +### §7.1 Root `pyproject.toml` + +Replaces `setup.py`, `requirements.txt`, `pytest.ini`, `mypy.ini`: + +```toml +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "nmuwd" +version = "0.10.3" +requires-python = ">=3.10" +dependencies = [ + "click>=8.2.1", + "python-dotenv", + "frost_sta_client", + "geopandas", + "httpx", + "pandas", + "pyyaml", + "types-pyyaml", + "urllib3>=2.2.0,<3.0.0", +] + +[project.optional-dependencies] +dev = ["pytest", "mypy", "flake8"] +geoserver = ["psycopg2-binary", "GeoAlchemy2", "SQLAlchemy"] +gcs = ["google-cloud-storage"] + +[project.scripts] +die = "frontend.cli:cli" + +[tool.hatch.build.targets.wheel] +packages = ["frontend", "backend"] + +[tool.pytest.ini_options] +testpaths = ["tests"] +norecursedirs = ["tests/archived"] + +[tool.mypy] +ignore_missing_imports = true +``` + +`flask`, `gunicorn` removed from core — belong in deployment layer. + +### §7.2 `orchestration/pyproject.toml` + +```toml +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "die-orchestration" +version = "0.1.0" +requires-python = ">=3.10" +dependencies = [ + "dagster>=1.8", + "dagster-gcp>=0.24", + "dagster-webserver>=1.8", + "google-cloud-storage", + "google-cloud-secret-manager", + "Jinja2", +] + +[tool.uv.sources] +nmuwd = { path = "..", editable = true } +``` + +No DB deps. pygeoapi runs in its own image — not a Python dep here. + +--- + +## §8 Dockerfile — Dagster Cloud Run Job + +```dockerfile +FROM python:3.12-slim + +WORKDIR /app + +COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv + +COPY orchestration/pyproject.toml ./orchestration/ +COPY pyproject.toml ./ +RUN uv sync --frozen --project orchestration + +COPY backend/ ./backend/ +COPY frontend/ ./frontend/ +COPY orchestration/ ./orchestration/ + +ENV DAGSTER_HOME=/app/.dagster +ENV PYTHONPATH=/app + +CMD ["uv", "run", "--project", "orchestration", \ + "dagster", "job", "execute", \ + "-f", "orchestration/definitions.py", \ + "-j", "${PRODUCT_ID}"] +``` + +Cloud Run Job env vars (from Secret Manager): +`PRODUCT_ID`, `GCS_BUCKET`, `USGS_API_KEY` + +--- + +## §9 Tasks + +### §T.1 [x] uv migration +- Delete `setup.py`, `requirements.txt`, `pytest.ini`, `mypy.ini` +- Write root `pyproject.toml` (§7.1) +- Run `uv lock` +- Update `.github/workflows/cicd.yml`: `uv run pytest`, `uv run mypy`, `uv run flake8` +- Verify: `uv pip install -e ".[dev]"` + all existing tests pass + +### §T.2 [x] OGC Features persister +- Add `backend/persisters/ogc_features.py` → `OGCFeaturesPersister` + - `dump_summary_collection(path, records, meta)` — §4.2 + - `dump_timeseries_collection(path, site_records, timeseries_records, meta)` — §4.3 flat format +- Add `ogc_summary`, `ogc_timeseries` to `OutputFormat` enum in `backend/__init__.py` +- Tests: `tests/test_persisters/test_ogc_features.py` + +### §T.3 [x] Orchestration scaffolding +- Create `orchestration/` directory (§3.1) +- Write `orchestration/pyproject.toml` (§7.2) +- Write `orchestration/config/products.yaml` (§5.2) +- Write `orchestration/resources/die_config.py` — Dagster resource wrapping `Config` +- Write `orchestration/resources/gcs.py` — upload/overwrite GCS objects + +### §T.4 [x] Dagster assets +- Port `jir-dagster` branch assets into `orchestration/assets/` +- Rewrite to: load products.yaml → dynamically define one asset per product +- Each asset: build `Config` from product spec → call unifier → `OGCFeaturesPersister` → GCS upload +- Write `orchestration/definitions.py` +- Local test: `uv run dagster asset materialize -f orchestration/definitions.py --select nm_waterlevels_summary` + +### §T.5 [x] Time-series well assets +- `orchestration/assets/waterlevels.py` — `ogc_timeseries` product type +- Flat observation-per-feature output (§4.3) with `datetime` field +- Reuses existing `unify_waterlevels` — no backend changes + +### §T.6 [x] GCS output resource +- `orchestration/resources/gcs.py` +- Upload: `gs://{bucket}/products/{product_id}/{YYYY-MM-DD}.geojson` +- Overwrite: `gs://{bucket}/products/{product_id}/latest.geojson` +- Emit Dagster `AssetMaterialization` metadata: feature count, bbox, file size, timestamp + +### §T.7 [x] Cloud Run + Dockerfile +- Write `orchestration/Dockerfile` (§8) +- Write `orchestration/cloudbuild.yaml` +- Write `orchestration/cloudrun.yaml` — Cloud Run Job definition +- Write `orchestration/README.md` — env vars, Secret Manager bindings, deploy commands + +### §T.8 [x] CI update +- Update `cicd.yml`: use `uv run` for all checks +- Add `orchestration-ci.yml`: lint + import-check for orchestration code +- Orchestration CI never triggers PyPI publish + +### §T.9 [x] pygeoapi +- Write `orchestration/pygeoapi/config.yml.j2` (§6.2) +- Write `orchestration/pygeoapi/generate_config.py` (§6.3) +- Write `orchestration/pygeoapi/Dockerfile` (§6.5) +- Write `orchestration/pygeoapi/cloudbuild.yaml` +- Verify GDAL `/vsigs/` reads from GCS with ADC in local Docker test +- Smoke test: `GET /collections` returns one entry per product in `products.yaml` + +--- + +## §10 Backend Improvements + +### §10.1 Performance + +**Retry backoff** (`_execute_text_request`, `_execute_json_request` in `source.py`): linear `time.sleep(tries)` → exponential backoff capped at 60s. + +**Polygon re-parse per record** (`BaseTransformer.contained()`, `transformer.py`): `_cached_polygon` is set at instance level but `config.bounding_wkt()` is called on every record. Cache shapely object permanently at first call. + +**Redundant list extraction in `BaseParameterSource.read()`** (`source.py`): `_extract_parameter_dates()`, `_extract_source_parameter_results()`, `_extract_source_parameter_units()`, `_extract_source_parameter_names()` called independently per site, each iterating the same `records` list. Batch extract once before loop. + +### §10.2 Reliability + +**Bare `except Exception`** (`_execute_text_request` line ~241, `_site_wrapper` in `unifier.py`): catches everything including `KeyboardInterrupt` siblings. Catch `httpx.HTTPError`, `httpx.TimeoutException`, `json.JSONDecodeError` specifically. Log full traceback. + +**No coordinate range validation** (`do_transform()` in `transformer.py`): checks `x == 0 or y == 0` but not whether lng/lat are in valid ranges (−180..180, −90..90). Silent pass-through of bogus coords. + +**Unchecked unit conversion** (`convert_units()` `transformer.py`): returns `None` if `die_parameter_name` is unrecognized, propagates silently into record payload. + +**`with` statement missing on file open** (`Config._load_from_yaml()` `config.py`): unclosed handle on read failure. + +**Manual slice rollback** (`_site_wrapper()` `unifier.py` lines ~183–202): slices `persister.records/timeseries/sites` back to pre-chunk length on error. Fragile — an atomic checkpoint abstraction is safer. + +### §10.3 Observability + +**`print()` instead of logger** (multiple): `generate_bounding_polygon()` in `source.py`, lines ~52/63/75 in `unifier.py`, line ~29 in `persister.py`. None go through `self.log()`. + +**No request timing** (`_execute_text_request/json_request`): no record of latency, retry count, or which URL failed. Add structured log entry: `source`, `url`, `status_code`, `attempt`, `elapsed_ms` on every attempt. + +**Low-information warnings**: "Failed to retrieve records after multiple attempts" doesn't include URL, params, or last exception. + +**No transform failure metrics** (`do_transform()` `transformer.py`): returns `None` silently. Caller doesn't know how many records were dropped and why. + +**No chunk progress** (`_site_wrapper()` `unifier.py`): no log of chunk index, site count per chunk, or timing. + +### §10.4 Readability + +**`BaseParameterSource` god class** (`source.py`, ~476 lines): handles extraction, validation, unit conversion, and summarization in one class + one 167-line `read()` method with 5 levels of nesting. Split into: `RecordExtractor`, `RecordValidator`, `RecordSummarizer`. + +**`do_transform()` god method** (`transformer.py`, ~191 lines): 6 sequential transform steps in one method body. Extract each into `_apply_datum_transform()`, `_apply_elevation_transform()`, `_apply_well_depth_transform()`, `_apply_unit_conversion()`. + +**`Config.get_config_and_false_agencies()`** (`config.py`, ~107 lines): repetitive `if/elif` per parameter. Replace with a dict mapping `parameter → (agency_defaults, source_classes)`. + +**`start_ind` / `end_ind` in `BaseParameterSource.read()`**: only used for logging but add confusion. Rename or remove if unused. + +**`bookend` naming** (`_extract_terminal_record()`): unclear. Rename to `position` or use `Literal["earliest", "latest"]`. + +### §10.5 Additional Composition (Sources / Transformers / Unifier) + +**HTTP client injection** (`BaseSource`): uses `httpx.get()` directly. Inject `httpx.Client` (or a protocol) so retry policy is testable and swappable. + +**Config post-construction injection** (`set_config()` on both `BaseSource` and `BaseTransformer`): config is required to function. Move to `__init__` param with `Optional` type; keep `set_config()` only as override for unifier's late binding. + +**`RecordExtractor` protocol** (`BaseParameterSource`): the 8 abstract `_extract_*` methods form an implicit interface. Define an explicit `ParameterExtractor` Protocol; `BaseParameterSource` accepts one in `__init__`. Enables injecting fake extractors in tests. + +**`UnitConverter` strategy** (`convert_units()` in `transformer.py`): 120+ line monolithic function. Extract to `UnitConverter` class; inject into `BaseTransformer`. Enables per-source custom conversions. + +**Persister factory in `unifier.py`**: `_unify_parameter()` contains if/else to pick persister class. Extract to `PersisterFactory(config) -> BasePersister`; inject factory into `Unifier.__init__`. + +--- + +## §11 Composition Refactor + +### §11.1 Goals + +Replace inheritance-for-code-reuse with injected dependencies. Targets: +1. `Loggable` base class — used only to get `self.log()` → inject logger +2. `STSource` mixin via multiple inheritance → `STClient` composed into sources +3. ST2 class explosion (5 near-identical subclasses) → instances with config +4. `CloudStoragePersister` overrides `_dump_*` to redirect output → Strategy pattern +5. Transformer coupled by `transformer_klass` class attribute → inject transformer +6. Empty record subclasses (`WaterLevelRecord`, `AnalyteRecord`, etc.) → type field + +### §11.2 New Branch + +``` +feature/composition-refactor ← branch off main after §T.9 merged +``` + +--- + +### §T.10 [x] Replace `Loggable` base with injected logger +**Goal:** Remove `Loggable` from the inheritance chain of all classes. + +**Changes:** +- `backend/logger.py`: add `make_logger(name: str) -> Logger` factory function +- `BaseSource`, `BasePersister`, `BaseTransformer`, `Config`: remove `(Loggable)` base; call `make_logger(self.__class__.__name__)` in `__init__` +- All `self.log()` / `self.warn()` / `self.debug()` calls: keep working — keep the same helper wrappers as module-level or instance-assigned callables rather than inherited methods + +**Verification:** `uv run pytest tests/test_cli/ tests/test_persisters/ -q` + +--- + +### §T.11 [x] Replace `STSource` mixin with `STClient` composition +**Goal:** Kill multiple inheritance in all ST source classes. + +**Changes:** +- `backend/connectors/st_connector.py`: extract `STSource` methods into `STClient` class with `__init__(self, url: str)` + - `get_service()`, `get_things()`, `_extract_terminal_record()`, `_parse_result()` → methods on `STClient` +- `STSiteSource(BaseSiteSource, STSource)` → `STSiteSource(BaseSiteSource)` with `self.client = STClient(self.url)` +- `STWaterLevelSource(STSource, BaseWaterLevelSource)` → `STWaterLevelSource(BaseWaterLevelSource)` with `self.client = STClient(self.url)` +- `STAnalyteSource(STSource, BaseAnalyteSource)` → `STAnalyteSource(BaseAnalyteSource)` with `self.client = STClient(self.url)` +- All `self.get_service()` / `self._get_things()` call sites → `self.client.get_service()` / `self.client.get_things()` + +**Verification:** `uv run pytest tests/test_sources/ -k "st or bernco or cabq or ebid or pvacd or roswell" -q` + +--- + +### §T.12 [x] Collapse ST2 class hierarchy into configured instances +**Goal:** Delete 5 nearly-identical site source classes; replace with factory. + +**Affected classes (delete):** +`BernCoSiteSource`, `CABQSiteSource`, `EBIDSiteSource`, `PVACDSiteSource`, `NMOSERoswellSiteSource` + +**Changes:** +- `ST2SiteSource`: accept `agency: str`, `bounding_wkt: str | None`, `transformer_klass` in `__init__`; move per-subclass logic (bounding polygon, filter) into constructor +- `backend/connectors/st2/source.py` (or equivalent): replace class definitions with module-level instances: + ```python + BernCoSiteSource = ST2SiteSource(agency="BernCo", bounding_wkt=BERNCO_WKT, transformer_klass=BernCoSiteTransformer) + ``` +- `Config.water_level_sources()` / `Config.analyte_sources()`: update to use instances + +**Verification:** `uv run pytest tests/test_sources/ -k "bernco or cabq or ebid or pvacd" -q` + +--- + +### §T.13 [x] Replace `CloudStoragePersister` with output strategy injection +**Goal:** `BasePersister` accepts an output strategy; `CloudStoragePersister` subclass deleted. + +**Changes:** +- Add `backend/persisters/strategies.py`: + ```python + class OutputStrategy(Protocol): + def write(self, name: str, content: bytes) -> None: ... + def make_directory(self, path: str) -> None: ... + + class LocalFileStrategy: + def write(self, name, content): Path(name).write_bytes(content) + def make_directory(self, path): Path(path).mkdir(parents=True, exist_ok=True) + + class GCSStrategy: + def __init__(self, bucket_name: str, prefix: str): ... + def write(self, name, content): ... # uploads to GCS + def make_directory(self, path): pass # no-op + ``` +- `BasePersister.__init__`: accept `strategy: OutputStrategy = LocalFileStrategy()` +- All `_dump_*` methods: call `self.strategy.write(...)` instead of `Path.write_*` +- Delete `CloudStoragePersister` class +- Update `backend/unifier.py`: create `GCSStrategy` instead of `CloudStoragePersister` when `config.use_cloud_storage` + +**Verification:** `uv run pytest tests/ -q --ignore=tests/test_sources` + +--- + +### §T.14 [x] Inject transformer into source constructor +**Goal:** Remove `transformer_klass` class attribute pattern; pass transformer as dependency. + +**Changes:** +- `BaseSource.__init__`: accept `transformer: BaseTransformer` parameter; remove `self.transformer = self.transformer_klass()` +- All concrete source classes: remove `transformer_klass` class attribute; pass transformer in `super().__init__(transformer=XTransformer())` +- `set_config(config)`: still propagates to both source + transformer +- Tests that construct sources directly: update constructors + +**Verification:** `uv run pytest tests/test_cli/ tests/test_persisters/ -q` + +--- + +### §T.15 [x] Collapse empty record subclasses +**Goal:** `WaterLevelRecord`, `AnalyteRecord`, `WaterLevelSummaryRecord`, `AnalyteSummaryRecord` add zero behavior — remove them. + +**Changes:** +- `backend/record.py`: delete `WaterLevelRecord`, `AnalyteRecord`, `WaterLevelSummaryRecord`, `AnalyteSummaryRecord` +- Add `record_type: str` field to `ParameterRecord` and `SummaryRecord` keys +- `WaterLevelTransformer._get_record_klass()` → returns `ParameterRecord` or `SummaryRecord`; sets `record_type="waterlevels"` in transform +- `AnalyteTransformer._get_record_klass()` → same pattern with `record_type="analytes"` +- Grep for `isinstance(r, WaterLevelRecord)` etc. — update to `r.record_type == "waterlevels"` + +**Verification:** `uv run pytest tests/test_cli/ tests/test_persisters/ -q` + +--- + +### §T.16 [x] Exponential backoff + request structured logging +**Goal:** Fix linear retry backoff; add per-request structured log entries. + +**Changes:** +- `backend/source.py` `_execute_text_request()` + `_execute_json_request()`: + - Replace `time.sleep(tries)` with `time.sleep(min(2 ** tries, 60))` + - After each attempt log: `source`, `url`, `status_code`, `attempt`, `elapsed_ms` + - Catch `httpx.HTTPStatusError`, `httpx.TimeoutException`, `httpx.RequestError` specifically — no bare `except Exception` + - Include last exception message in "Failed after N attempts" warning + +**Verification:** `uv run pytest tests/test_cli/ -q` + +--- + +### §T.17 [x] Cache bounding polygon at class level +**Goal:** Prevent re-parsing WKT shapely object on every record. + +**Changes:** +- `backend/transformer.py` `BaseTransformer.contained()`: + - Move `_cached_polygon` from instance variable to class-level cache keyed on WKT string (e.g. `_polygon_cache: dict[str, Polygon] = {}`) + - First call for a given WKT parses and caches; subsequent calls return cached object + +**Verification:** `uv run pytest tests/test_cli/ tests/test_persisters/ -q` + manual timing on 1000-record transform + +--- + +### §T.18 [x] Batch extraction in `BaseParameterSource.read()` +**Goal:** Extract dates/results/units/names once before the per-site loop, not once per site. + +**Changes:** +- `backend/source.py` `BaseParameterSource.read()`: + - Call `_extract_parameter_dates()`, `_extract_source_parameter_results()`, `_extract_source_parameter_units()`, `_extract_source_parameter_names()` once on full `cleaned` records before the site loop + - Pass extracted lists into inner loop rather than re-extracting per site + - Extract 167-line `read()` body into `_summarize_records()` and `_build_timeseries_records()` helpers (≤50 lines each) + +**Verification:** `uv run pytest tests/test_cli/ -q` + +--- + +### §T.19 [x] Replace all `print()` with structured logging +**Goal:** All console output goes through the logger; no raw `print()` in backend. + +**Changes:** +- `backend/source.py` `generate_bounding_polygon()` lines ~450–452: `print()` → `self.log()` +- `backend/unifier.py` lines ~52/63/75: `print()` → `config.log()` +- `backend/persister.py` line ~29: `print("google cloud storage not available")` → `logging.warning()` +- Grep `print(` across `backend/` — replace every hit +- Add `elapsed_ms` to transform failure log in `do_transform()` when returning `None` +- Log chunk index + site count per chunk in `_site_wrapper()` + +**Verification:** `grep -r "print(" backend/ | wc -l` → 0 + +--- + +### §T.20 [x] Specific exception handling + input validation +**Goal:** No bare `except Exception`; all swallowed errors surface detail. + +**Changes:** +- `backend/source.py`: + - `_execute_text_request` / `_execute_json_request`: replace bare except → specific httpx exceptions (see §T.16) + - `_extract_site_records()`: guard against `None`/empty `records` before returning + - `read()` inner ValueError/TypeError catches: log full `traceback.format_exc()`, not just message +- `backend/transformer.py` `convert_units()`: + - If `die_parameter_name` unrecognized → raise `ValueError(f"Unknown parameter: {die_parameter_name}")` instead of returning `None` + - Add lat/lng range check: `assert -180 <= lng <= 180 and -90 <= lat <= 90` +- `backend/unifier.py` `_site_wrapper()`: + - Replace `except BaseException` → `except Exception`; log `traceback.format_exc()` via `config.warn()` +- `backend/config.py` `_load_from_yaml()`: + - Wrap file open in `with` statement + +**Verification:** `uv run pytest tests/test_cli/ tests/test_persisters/ -q` + +--- + +### §T.21 [x] Split `BaseParameterSource` god class +**Goal:** 476-line class → focused classes ≤150 lines each. + +**Changes:** +- Extract `RecordValidator` class with `validate(record) -> bool`; holds current `_validate_record()` logic +- Extract `RecordSummarizer` class with `summarize(records, site_record) -> SummaryRecord`; holds summary path of `read()` +- `BaseParameterSource.__init__` accepts `validator: RecordValidator` (default = existing subclass method shim during migration) +- Split `read()` into `read_summary()` + `read_timeseries()` ≤50 lines each +- Rename `bookend` parameter → `position: Literal["earliest", "latest"]` + +**Verification:** `uv run pytest tests/ -q --ignore=tests/test_sources` + +--- + +### §T.22 [x] Split `do_transform()` into focused methods +**Goal:** 191-line method → orchestrator + focused helpers ≤30 lines each. + +**Changes:** +- `backend/transformer.py` `BaseTransformer.do_transform()`: + - Extract `_apply_geographic_filter(record) -> bool` + - Extract `_apply_datum_transform(record) -> record` + - Extract `_apply_elevation_transform(record) -> record` + - Extract `_apply_well_depth_transform(record) -> record` + - Extract `_apply_unit_conversion(record) -> record` + - `do_transform()` becomes orchestrator calling each in sequence ≤40 lines + +**Verification:** `uv run pytest tests/test_cli/ tests/test_persisters/ -q` + +--- + +### §T.23 [x] Data-driven `Config` source setup +**Goal:** Replace ~107-line `if/elif` per parameter in `get_config_and_false_agencies()` with a mapping. + +**Changes:** +- `backend/config.py`: + - Add `PARAMETER_SOURCE_MAP: dict[str, dict]` mapping each parameter name → `{site_source_klass, parameter_source_klass, agencies}` + - `get_config_and_false_agencies()` looks up parameter in map; raises `ValueError` for unknown parameter + - Extract duplicate `set_config()` calls in `analyte_sources()` / `water_level_sources()` / `all_site_sources()` into `_build_source_pair(site_klass, param_klass) -> tuple` + +**Verification:** `uv run pytest tests/test_cli/ -q` + +--- + +### §T.24 [x] Inject HTTP client into `BaseSource` +**Goal:** `httpx.get()` hardcoded → injected client; enables testability without live network. + +**Changes:** +- `backend/source.py` `BaseSource.__init__`: accept `http_client: httpx.Client | None = None`; default creates `httpx.Client(timeout=900)` +- `_execute_text_request()` / `_execute_json_request()`: use `self._http_client.get(...)` instead of `httpx.get(...)` +- Tests in `tests/test_cli/` or new `tests/test_sources_unit/`: pass mock client returning fixture responses — no live HTTP + +**Verification:** `uv run pytest tests/test_cli/ tests/test_persisters/ -q` + +--- + +### §T.25 [x] `UnitConverter` as injectable strategy +**Goal:** Replace 120+ line `convert_units()` monolith with pluggable converter. + +**Changes:** +- `backend/converter.py` (new file): + ```python + class UnitConverter(Protocol): + def convert(self, value: float, from_units: str, to_units: str, parameter: str) -> float: ... + + class StandardUnitConverter: + def convert(self, value, from_units, to_units, parameter): ... + # current convert_units() logic moved here + ``` +- `backend/transformer.py` `BaseTransformer.__init__`: accept `converter: UnitConverter = StandardUnitConverter()` +- Remove `convert_units()` module-level function; call `self.converter.convert(...)` in `_apply_unit_conversion()` +- ST/DWB sources needing custom conversion: pass custom `UnitConverter` subclass + +**Verification:** `uv run pytest tests/test_cli/ tests/test_persisters/ -q` + +--- + +### §T.26 [x] `PersisterFactory` extracted from `Unifier` +**Goal:** Remove persister selection if/else from `_unify_parameter()`. + +**Changes:** +- `backend/persisters/factory.py` (new file): + ```python + def make_persister(config: Config) -> BasePersister: + if config.output_format == OutputFormat.GEOSERVER: + ... + elif config.use_cloud_storage: + ... + else: + return BasePersister(config) + ``` +- `backend/unifier.py` `_unify_parameter()`: call `make_persister(config)` instead of inline if/else +- `Unifier.__init__`: optionally accept `persister_factory: Callable[[Config], BasePersister]` for testing + +**Verification:** `uv run pytest tests/test_cli/ -q` + +--- + +## §V Invariants + +- HTTP retry backoff MUST be exponential with cap: `min(2**n, 60)` seconds (§T.16) +- HTTP request attempts MUST log `source`, `url`, `status_code`, `attempt`, `elapsed_ms` (§T.16) +- No bare `except Exception` in `backend/` — catch specific exception types (§T.20) +- `convert_units()` MUST raise `ValueError` on unknown parameter, never return `None` silently (§T.20) +- `print()` MUST NOT appear in `backend/` — all output through logger (§T.19) +- No method in `backend/` MUST exceed 50 lines (excluding `__init__`) (§T.21 §T.22) +- `Config` source setup MUST be driven by `PARAMETER_SOURCE_MAP`, not `if/elif` chains (§T.23) +- `BaseSource` MUST accept injected `http_client`; no direct `httpx.get()` calls (§T.24) +- `UnitConverter` MUST be injectable into `BaseTransformer` (§T.25) +- Persister selection logic MUST live in `make_persister()`, not in `Unifier` (§T.26) +- No class MUST inherit `Loggable` — use `make_logger()` factory (§T.10) +- No ST source class MUST use multiple inheritance — `STClient` injected as `self.client` (§T.11) +- ST2 per-agency behavior MUST be expressed as constructor args, not subclasses (§T.12) +- `BasePersister` MUST NOT contain GCS-specific logic — output target injected via strategy (§T.13) +- Source classes MUST NOT declare `transformer_klass` — transformer passed to `__init__` (§T.14) +- `WaterLevelRecord`, `AnalyteRecord`, `WaterLevelSummaryRecord`, `AnalyteSummaryRecord` MUST NOT exist (§T.15) +- Orchestration code MUST NOT appear in `[tool.hatch.build.targets.wheel].packages` +- OGC FC output MUST include top-level `id`, `type`, `numberReturned`, `timeStamp` +- Each Feature MUST have top-level `id` (not only in properties) +- `ogc_timeseries` features MUST be flat (one per observation) with ISO 8601 `datetime` property +- `die` CLI behavior unchanged after uv migration +- All existing tests pass under `uv run pytest` +- pygeoapi config MUST be generated from `products.yaml` — never hand-edited +- pygeoapi OGR provider MUST use `/vsigs/` path (GCS), never local filesystem path +- No database introduced in orchestration pipeline — GCS is sole store +- `latest.geojson` MUST be overwritten atomically (upload to tmp key, then copy/rename) + +## §B Bug Log + +### §B.1 CLI `--no-*` flags non-functional (fixed in §T.1) +**Cause:** `ALL_SOURCE_OPTIONS` used `is_flag=True, default=True` — Click flag presence also sets `True`, so both states gave `True`. Assignment `use_source_X = no_X` further confused the polarity. +**Fix:** `default=False` on all `--no-*` options + `not lcs.get(f"no_{agency}", False)` in `weave` and `sites` commands. +**Invariant added:** `--no-*` flags MUST have `default=False`; assignment MUST negate the flag value. diff --git a/backend/__init__.py b/backend/__init__.py index 804491c..d6f1b8f 100644 --- a/backend/__init__.py +++ b/backend/__init__.py @@ -6,6 +6,8 @@ class OutputFormat(str, Enum): GEOJSON = "geojson" CSV = "csv" GEOSERVER = "geoserver" + OGC_SUMMARY = "ogc_summary" + OGC_TIMESERIES = "ogc_timeseries" def get_bool_env_variable(var: str) -> bool: diff --git a/backend/bounding_polygons.py b/backend/bounding_polygons.py index 8a9ccd6..1bd53a6 100644 --- a/backend/bounding_polygons.py +++ b/backend/bounding_polygons.py @@ -15,113 +15,14 @@ # =============================================================================== import json import os -from pprint import pprint import click import httpx -from shapely import Polygon, box from shapely.geometry import shape from backend.geo_utils import transform_srid, SRID_WGS84, SRID_UTM_ZONE_13N -# polygon retrivial functions -# multiple polygons -def get_congressional_district_boundaries(state, district): - pass - - -def get_tribal_boundaries(state=None): - state, statefp = _get_statefp(state) - - # use the processes service to get all tribal boundaries that intersect the state - def func(): - payload = { - "inputs": { - "collection": f"aiannh", - "url": f"https://geoconnex.us/ref/states/{statefp}", - } - } - resp = httpx.post( - "https://reference.geoconnex.us/processes/intersector/execution", - json=payload, - ) - return resp.json() - - obj = _get_cached_object(f"{state}.aiannh", f"{state} AIANNH", func) - - return obj - - -def get_state_hucs_boundaries(state=None, level=8): - state, statefp = _get_statefp(state) - - # use the processes service to get all hucs from this level that intersect the state of NM - def func(): - payload = { - "inputs": { - "collection": f"hu{level:02n}", - "url": f"https://geoconnex.us/ref/states/{statefp}", - } - } - resp = httpx.post( - "https://reference.geoconnex.us/processes/intersector/execution", - json=payload, - ) - return resp.json() - - obj = _get_cached_object(f"{state}.hucs.{level}", f"{state} HU{level:02n}", func) - - return obj - - -def get_state_pwss_boundaries(state=None): - state, statefp = _get_statefp(state) - obj = _get_cached_object( - f"{state}.pws", - f"{state} PWSs", - f"https://reference.geoconnex.us/collections/pws/items?f=json&state_code={state}", - ) - - return obj - - -# single polygons - - -def get_pws_polygon(pwsid, as_wkt=True): - obj = _get_cached_object( - pwsid, - pwsid, - f"https://reference.geoconnex.us/collections/pws/items/{pwsid}?f=json", - ) - return _make_shape(obj, as_wkt) - - -def get_huc_polygon(huc, as_wkt=True): - if len(huc) == 2: - collection = "hu02" - elif len(huc) == 4: - collection = "hu04" - elif len(huc) == 6: - collection = "hu06" - elif len(huc) == 8: - collection = "hu08" - elif len(huc) == 10: - collection = "hu10" - else: - _warning(f"Invalid HUC {huc}. length must be 2, 4, 6, 8, or 10") - return - - obj = _get_cached_object( - huc, - huc, - f"https://reference.geoconnex.us/collections/{collection}/items/{huc}?f=json", - ) - - return _make_shape(obj, as_wkt) - - def get_county_polygon(name, as_wkt=True): if ":" in name: state, county = name.split(":") diff --git a/backend/config.py b/backend/config.py index d45e95d..d349881 100644 --- a/backend/config.py +++ b/backend/config.py @@ -16,7 +16,6 @@ import os import sys from datetime import datetime, timedelta -from enum import Enum import shapely.wkt import yaml @@ -73,8 +72,29 @@ ) from .connectors.usgs.source import NWISSiteSource, NWISWaterLevelSource from .connectors.wqp.source import WQPSiteSource, WQPAnalyteSource, WQPWaterLevelSource -from backend.logger import Loggable - +from backend.logger import make_logger + + +PARAMETER_SOURCE_MAP = { + WATERLEVELS: {"agencies": ["bernco", "cabq", "ebid", "nmbgmr_amp", "nmose_isc_seven_rivers", "nmose_roswell", "nwis", "pvacd", "wqp"]}, + CARBONATE: {"agencies": ["nmbgmr_amp", "wqp"]}, + ARSENIC: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "wqp"]}, + URANIUM: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "wqp"]}, + SPECIFIC_CONDUCTANCE: {"agencies": ["nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + CONDUCTIVITY: {"agencies": ["bor", "nmose_isc_seven_rivers", "wqp"]}, + BICARBONATE: {"agencies": ["nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + CALCIUM: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + CHLORIDE: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + FLUORIDE: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + MAGNESIUM: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + NITRATE: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + PH: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + POTASSIUM: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + SILICA: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + SODIUM: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + SULFATE: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, + TDS: {"agencies": ["bor", "nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"]}, +} SOURCE_DICT = { "bernco": BernCoSiteSource, @@ -104,7 +124,7 @@ def get_source(source): return klass() -class Config(Loggable): +class Config: site_limit: int = 0 dry: bool = False @@ -157,8 +177,10 @@ class Config(Loggable): yes: bool = False def __init__(self, model=None, payload=None, path=None): - # need to initialize logger - super().__init__() + _l = make_logger(self.__class__.__name__) + self.log = _l.log + self.warn = _l.warn + self.debug = _l.debug if path: payload = self._load_from_yaml(path) @@ -216,114 +238,19 @@ def _load_from_yaml(self, path): self.warn(f"Config file {path} not found") def get_config_and_false_agencies(self): - if self.parameter == WATERLEVELS: - config_agencies = [ - "bernco", - "cabq", - "ebid", - "nmbgmr_amp", - "nmose_isc_seven_rivers", - "nmose_roswell", - "nwis", - "pvacd", - "wqp", - ] - false_agencies = ["bor", "nmose_pod", "nmed_dwb"] - elif self.parameter == CARBONATE: - config_agencies = ["nmbgmr_amp", "wqp"] - false_agencies = [ - "bor", - "bernco", - "cabq", - "ebid", - "nmed_dwb", - "nmose_isc_seven_rivers", - "nmose_pod", - "nmose_roswell", - "nwis", - "pvacd", - ] - elif self.parameter in [ARSENIC, URANIUM]: - config_agencies = ["bor", "nmbgmr_amp", "nmed_dwb", "wqp"] - false_agencies = [ - "bernco", - "cabq", - "ebid", - "nmose_isc_seven_rivers", - "nmose_roswell", - "nmose_pod", - "nwis", - "pvacd", - ] - elif self.parameter in [SPECIFIC_CONDUCTANCE]: - config_agencies = ["nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"] - false_agencies = [ - "bor", - "bernco", - "cabq", - "ebid", - "nmose_roswell", - "nmose_pod", - "nwis", - "pvacd", - ] - elif self.parameter in [CONDUCTIVITY]: - config_agencies = ["bor", "nmose_isc_seven_rivers", "wqp"] - false_agencies = [ - "bor", - "bernco", - "cabq", - "ebid", - "nmbgmr_amp", - "nmed_dwb", - "nmose_roswell", - "nmose_pod", - "nwis", - "pvacd", - ] - elif self.parameter in [BICARBONATE]: - config_agencies = ["nmbgmr_amp", "nmed_dwb", "nmose_isc_seven_rivers", "wqp"] - false_agencies = [ - "bor", - "bernco", - "cabq", - "ebid", - "nmose_roswell", - "nmose_pod", - "nwis", - "pvacd", - ] - elif self.parameter in [ - CALCIUM, - CHLORIDE, - FLUORIDE, - MAGNESIUM, - NITRATE, - PH, - POTASSIUM, - SILICA, - SODIUM, - SULFATE, - TDS, - ]: - config_agencies = [ - "bor", - "nmbgmr_amp", - "nmed_dwb", - "nmose_isc_seven_rivers", - "wqp", - ] - false_agencies = [ - "bernco", - "cabq", - "ebid", - "nmose_roswell", - "nmose_pod", - "nwis", - "pvacd", - ] + entry = PARAMETER_SOURCE_MAP.get(self.parameter) + if entry is None: + raise ValueError(f"Unknown parameter {self.parameter!r}. Valid parameters: {sorted(PARAMETER_SOURCE_MAP)}") + config_agencies = entry["agencies"] + false_agencies = [a for a in SOURCE_KEYS if a not in config_agencies] return config_agencies, false_agencies + def _build_source_pair(self, site_klass, param_klass): + s, ss = site_klass(), param_klass() + s.set_config(self) + ss.set_config(self) + return s, ss + def finalize(self): self._update_output_units() if self.output_format != OutputFormat.GEOSERVER: @@ -346,56 +273,28 @@ def all_site_sources(self): return sources def analyte_sources(self): - sources = [] - - if self.use_source_bor: - sources.append((BORSiteSource(), BORAnalyteSource())) - if self.use_source_wqp: - sources.append((WQPSiteSource(), WQPAnalyteSource())) - if self.use_source_nmose_isc_seven_rivers: - sources.append((ISCSevenRiversSiteSource(), ISCSevenRiversAnalyteSource())) - if self.use_source_nmbgmr_amp: - sources.append((NMBGMRSiteSource(), NMBGMRAnalyteSource())) - if self.use_source_nmed_dwb: - sources.append((DWBSiteSource(), DWBAnalyteSource())) - - for s, ss in sources: - s.set_config(self) - ss.set_config(self) - - return sources + pairs = [ + (BORSiteSource, BORAnalyteSource, self.use_source_bor), + (WQPSiteSource, WQPAnalyteSource, self.use_source_wqp), + (ISCSevenRiversSiteSource, ISCSevenRiversAnalyteSource, self.use_source_nmose_isc_seven_rivers), + (NMBGMRSiteSource, NMBGMRAnalyteSource, self.use_source_nmbgmr_amp), + (DWBSiteSource, DWBAnalyteSource, self.use_source_nmed_dwb), + ] + return [self._build_source_pair(s, ss) for s, ss, enabled in pairs if enabled] def water_level_sources(self): - sources = [] - if self.use_source_nmbgmr_amp: - sources.append((NMBGMRSiteSource(), NMBGMRWaterLevelSource())) - - if self.use_source_nmose_isc_seven_rivers: - sources.append( - (ISCSevenRiversSiteSource(), ISCSevenRiversWaterLevelSource()) - ) - - if self.use_source_nwis: - sources.append((NWISSiteSource(), NWISWaterLevelSource())) - - if self.use_source_nmose_roswell: - sources.append((NMOSERoswellSiteSource(), NMOSERoswellWaterLevelSource())) - if self.use_source_pvacd: - sources.append((PVACDSiteSource(), PVACDWaterLevelSource())) - if self.use_source_bernco: - sources.append((BernCoSiteSource(), BernCoWaterLevelSource())) - if self.use_source_ebid: - sources.append((EBIDSiteSource(), EBIDWaterLevelSource())) - if self.use_source_cabq: - sources.append((CABQSiteSource(), CABQWaterLevelSource())) - if self.use_source_wqp: - sources.append((WQPSiteSource(), WQPWaterLevelSource())) - - for s, ss in sources: - s.set_config(self) - ss.set_config(self) - - return sources + pairs = [ + (NMBGMRSiteSource, NMBGMRWaterLevelSource, self.use_source_nmbgmr_amp), + (ISCSevenRiversSiteSource, ISCSevenRiversWaterLevelSource, self.use_source_nmose_isc_seven_rivers), + (NWISSiteSource, NWISWaterLevelSource, self.use_source_nwis), + (NMOSERoswellSiteSource, NMOSERoswellWaterLevelSource, self.use_source_nmose_roswell), + (PVACDSiteSource, PVACDWaterLevelSource, self.use_source_pvacd), + (BernCoSiteSource, BernCoWaterLevelSource, self.use_source_bernco), + (EBIDSiteSource, EBIDWaterLevelSource, self.use_source_ebid), + (CABQSiteSource, CABQWaterLevelSource, self.use_source_cabq), + (WQPSiteSource, WQPWaterLevelSource, self.use_source_wqp), + ] + return [self._build_source_pair(s, ss) for s, ss, enabled in pairs if enabled] def bbox_bounding_points(self, bbox=None): if bbox is None: diff --git a/backend/connectors/bor/source.py b/backend/connectors/bor/source.py index 050a9bf..506da1c 100644 --- a/backend/connectors/bor/source.py +++ b/backend/connectors/bor/source.py @@ -13,10 +13,7 @@ # See the License for the specific language governing permissions and # limitations under the License. # =============================================================================== -import pprint -from json import JSONDecodeError -import httpx from backend.connectors.bor.transformer import BORSiteTransformer, BORAnalyteTransformer from backend.connectors.mappings import BOR_ANALYTE_MAPPING @@ -27,12 +24,9 @@ SOURCE_PARAMETER_NAME, SOURCE_PARAMETER_UNITS, DT_MEASURED, - EARLIEST, - LATEST, ) from backend.source import ( - BaseSource, BaseSiteSource, BaseAnalyteSource, get_terminal_record, @@ -41,7 +35,8 @@ class BORSiteSource(BaseSiteSource): - transformer_klass = BORSiteTransformer + def __init__(self): + super().__init__(transformer=BORSiteTransformer()) def __repr__(self): return "BORSiteSource" @@ -65,8 +60,10 @@ def parse_dt(dt): class BORAnalyteSource(BaseAnalyteSource): - transformer_klass = BORAnalyteTransformer _catalog_item_idx = None + + def __init__(self): + super().__init__(transformer=BORAnalyteTransformer()) _source_parameter_name = None def __repr__(self): @@ -95,8 +92,8 @@ def _extract_parameter_dates(self, records): def _extract_source_parameter_names(self, records): return [self._source_parameter_name for ri in records] - def _extract_terminal_record(self, records, bookend): - record = get_terminal_record(records, "attributes.dateTime", bookend=bookend) + def _extract_terminal_record(self, records, position): + record = get_terminal_record(records, "attributes.dateTime", position=position) return { "value": record["attributes"]["result"], "datetime": parse_dt(record["attributes"]["dateTime"]), diff --git a/backend/connectors/bor/transformer.py b/backend/connectors/bor/transformer.py index 4dd81a3..4540069 100644 --- a/backend/connectors/bor/transformer.py +++ b/backend/connectors/bor/transformer.py @@ -13,13 +13,8 @@ # See the License for the specific language governing permissions and # limitations under the License. # =============================================================================== -import pprint -import json -from backend.record import SiteRecord, WaterLevelRecord, AnalyteSummaryRecord from backend.transformer import ( - BaseTransformer, - WaterLevelTransformer, SiteTransformer, AnalyteTransformer, ) diff --git a/backend/connectors/ckan/source.py b/backend/connectors/ckan/source.py index 736d668..4297f63 100644 --- a/backend/connectors/ckan/source.py +++ b/backend/connectors/ckan/source.py @@ -15,7 +15,6 @@ # =============================================================================== from itertools import groupby -import httpx from backend.connectors import ( OSE_ROSWELL_HONDO_BOUNDING_POLYGON, @@ -34,7 +33,6 @@ from backend.constants import ( FEET, DTW, - DTW_UNITS, DT_MEASURED, PARAMETER_NAME, PARAMETER_UNITS, @@ -43,7 +41,6 @@ SOURCE_PARAMETER_UNITS, ) from backend.source import ( - BaseSource, BaseSiteSource, BaseWaterLevelSource, get_terminal_record, @@ -62,7 +59,7 @@ def get_response(self): raise NotImplementedError("base_url is not set") if self._cached_response is None: - self._cached_response = httpx.get(self.base_url, params=self._get_params()) + self._cached_response = self._http_client.get(self.base_url, params=self._get_params()) return self._cached_response @@ -91,9 +88,8 @@ def _get_params(self): class OSERoswellSiteSource(OSERoswellSource, BaseSiteSource): - transformer_klass = OSERoswellSiteTransformer - def __init__(self, resource_id, **kw): + kw.setdefault("transformer", OSERoswellSiteTransformer()) super().__init__(resource_id, **kw) if resource_id == HONDO_RESOURCE_ID: self.bounding_polygon = OSE_ROSWELL_HONDO_BOUNDING_POLYGON @@ -108,7 +104,7 @@ def __repr__(self): def health(self): params = self._get_params() params["limit"] = 1 - resp = httpx.get(self.base_url, params=params) + resp = self._http_client.get(self.base_url, params=params) return resp.status_code == 200 def _parse_response(self, resp): @@ -123,7 +119,9 @@ def _parse_response(self, resp): class OSERoswellWaterLevelSource(OSERoswellSource, BaseWaterLevelSource): - transformer_klass = OSERoswellWaterLevelTransformer + def __init__(self, resource_id=None, **kw): + kw.setdefault("transformer", OSERoswellWaterLevelTransformer()) + super().__init__(resource_id, **kw) def __repr__(self): return "NMOSERoswellWaterLevelSource" @@ -138,8 +136,8 @@ def _parse_response(self, site_record, resp): def _extract_source_parameter_results(self, records): return [float(r["DTWGS"]) for r in records] - def _extract_terminal_record(self, records, bookend): - record = get_terminal_record(records, tag="Date", bookend=bookend) + def _extract_terminal_record(self, records, position): + record = get_terminal_record(records, tag="Date", position=position) return { "value": record["DTWGS"], "datetime": record["Date"], diff --git a/backend/connectors/ckan/transformer.py b/backend/connectors/ckan/transformer.py index e56d609..48a1c1d 100644 --- a/backend/connectors/ckan/transformer.py +++ b/backend/connectors/ckan/transformer.py @@ -13,15 +13,12 @@ # See the License for the specific language governing permissions and # limitations under the License. # =============================================================================== -import pprint -from backend.record import SiteRecord, WaterLevelRecord -from backend.transformer import BaseTransformer, WaterLevelTransformer, SiteTransformer +from backend.transformer import WaterLevelTransformer, SiteTransformer class OSERoswellSiteTransformer(SiteTransformer): def _transform(self, record): - # pprint.pprint(record) lat = float(record["DD_lat"]) lng = float(record["DD_lon"]) # if not self.contained(lng, lat): diff --git a/backend/connectors/isc_seven_rivers/source.py b/backend/connectors/isc_seven_rivers/source.py index a796e1b..c6f5dce 100644 --- a/backend/connectors/isc_seven_rivers/source.py +++ b/backend/connectors/isc_seven_rivers/source.py @@ -15,7 +15,6 @@ # =============================================================================== from datetime import datetime -import httpx from backend.connectors import ISC_SEVEN_RIVERS_BOUNDING_POLYGON from backend.connectors.mappings import ISC_SEVEN_RIVERS_ANALYTE_MAPPING @@ -28,8 +27,6 @@ PARAMETER_UNITS, SOURCE_PARAMETER_NAME, SOURCE_PARAMETER_UNITS, - EARLIEST, - LATEST, ) from backend.connectors.isc_seven_rivers.transformer import ( ISCSevenRiversSiteTransformer, @@ -37,7 +34,6 @@ ISCSevenRiversAnalyteTransformer, ) from backend.source import ( - BaseSource, BaseSiteSource, BaseWaterLevelSource, BaseAnalyteSource, @@ -68,9 +64,11 @@ def _make_url(endpoint): class ISCSevenRiversSiteSource(BaseSiteSource): - transformer_klass = ISCSevenRiversSiteTransformer bounding_polygon = ISC_SEVEN_RIVERS_BOUNDING_POLYGON + def __init__(self): + super().__init__(transformer=ISCSevenRiversSiteTransformer()) + def __repr__(self): return "ISCSevenRiversSiteSource" @@ -79,7 +77,7 @@ def health(self): resp = self.get_records() return bool(resp) except Exception as e: - print("Failed to get records", e) + self.warn(f"Failed to get records: {e}") return False def get_records(self): @@ -90,10 +88,12 @@ def get_records(self): class ISCSevenRiversAnalyteSource(BaseAnalyteSource): - transformer_klass = ISCSevenRiversAnalyteTransformer _analyte_ids = None _source_parameter_name = None + def __init__(self): + super().__init__(transformer=ISCSevenRiversAnalyteTransformer()) + def __repr__(self): return "ISCSevenRiversAnalyteSource" @@ -123,8 +123,8 @@ def _extract_parameter_record(self, record): return record - def _extract_terminal_record(self, records, bookend): - record = get_terminal_record(records, "dateTime", bookend=bookend) + def _extract_terminal_record(self, records, position): + record = get_terminal_record(records, "dateTime", position=position) return { "value": record["result"], @@ -170,8 +170,10 @@ def get_records(self, site_record): class ISCSevenRiversWaterLevelSource(BaseWaterLevelSource): - transformer_klass = ISCSevenRiversWaterLevelTransformer _source_parameter_name = "depthToWaterFeet" + + def __init__(self): + super().__init__(transformer=ISCSevenRiversWaterLevelTransformer()) _source_parameter_units = FEET def get_records(self, site_record): @@ -216,8 +218,8 @@ def _extract_source_parameter_names(self, records): def _extract_source_parameter_units(self, records): return [self._source_parameter_units for r in records] - def _extract_terminal_record(self, records, bookend): - record = get_terminal_record(records, "dateTime", bookend=bookend) + def _extract_terminal_record(self, records, position): + record = get_terminal_record(records, "dateTime", position=position) t = get_datetime(record) return { "value": record["depthToWaterFeet"], diff --git a/backend/connectors/isc_seven_rivers/transformer.py b/backend/connectors/isc_seven_rivers/transformer.py index dddbe9d..3340651 100644 --- a/backend/connectors/isc_seven_rivers/transformer.py +++ b/backend/connectors/isc_seven_rivers/transformer.py @@ -13,12 +13,8 @@ # See the License for the specific language governing permissions and # limitations under the License. # =============================================================================== -import shapely.wkt -from shapely import Point -from backend.record import SiteRecord from backend.transformer import ( - BaseTransformer, WaterLevelTransformer, SiteTransformer, AnalyteTransformer, diff --git a/backend/connectors/nmbgmr/source.py b/backend/connectors/nmbgmr/source.py index 862bca6..766bba5 100644 --- a/backend/connectors/nmbgmr/source.py +++ b/backend/connectors/nmbgmr/source.py @@ -32,8 +32,6 @@ PARAMETER_VALUE, SOURCE_PARAMETER_NAME, SOURCE_PARAMETER_UNITS, - EARLIEST, - LATEST, ) from backend.source import ( BaseWaterLevelSource, @@ -60,10 +58,12 @@ def _make_url(endpoint): class NMBGMRSiteSource(BaseSiteSource): - transformer_klass = NMBGMRSiteTransformer chunk_size = 10 bounding_polygon = NM_STATE_BOUNDING_POLYGON + def __init__(self): + super().__init__(transformer=NMBGMRSiteTransformer()) + def __repr__(self): return "NMBGMRSiteSource" @@ -98,14 +98,14 @@ def get_records(self): if not config.sites_only: for site in sites: if get_bool_env_variable("IS_TESTING_ENV"): - print( - f"Skipping well data for {site['properties']['point_id']} for testing (until well data can be retrieved in batches)" + self.log( + f"Skipping well data for {site['properties']['point_id']} for testing" ) site["properties"]["formation"] = None site["properties"]["well_depth"] = None site["properties"]["well_depth_units"] = FEET else: - print(f"Obtaining well data for {site['properties']['point_id']}") + self.log(f"Obtaining well data for {site['properties']['point_id']}") well_data = self._execute_json_request( _make_url("wells"), params={"pointid": site["properties"]["point_id"]}, @@ -119,7 +119,8 @@ def get_records(self): class NMBGMRAnalyteSource(BaseAnalyteSource): - transformer_klass = NMBGMRAnalyteTransformer + def __init__(self): + super().__init__(transformer=NMBGMRAnalyteTransformer()) def __repr__(self): return "NMBGMRAnalyteSource" @@ -151,8 +152,8 @@ def _extract_site_records(self, records, site_record): def _extract_source_parameter_units(self, records): return [r["Units"] for r in records] - def _extract_terminal_record(self, records, bookend): - record = get_terminal_record(records, "info.CollectionDate", bookend=bookend) + def _extract_terminal_record(self, records, position): + record = get_terminal_record(records, "info.CollectionDate", position=position) return { "value": record["SampleValue"], "datetime": record["info"]["CollectionDate"], @@ -181,7 +182,8 @@ def _extract_parameter_record(self, record): class NMBGMRWaterLevelSource(BaseWaterLevelSource): - transformer_klass = NMBGMRWaterLevelTransformer + def __init__(self): + super().__init__(transformer=NMBGMRWaterLevelTransformer()) def __repr__(self): return "NMBGMRWaterLevelSource" @@ -203,8 +205,8 @@ def _extract_parameter_record(self, record, *args, **kw): record[SOURCE_PARAMETER_UNITS] = record["DepthToWaterBGSUnits"] return record - def _extract_terminal_record(self, records, bookend): - record = get_terminal_record(records, "DateMeasured", bookend=bookend) + def _extract_terminal_record(self, records, position): + record = get_terminal_record(records, "DateMeasured", position=position) return { "value": record["DepthToWaterBGS"], "datetime": (record["DateMeasured"], record["TimeMeasured"]), diff --git a/backend/connectors/nmbgmr/transformer.py b/backend/connectors/nmbgmr/transformer.py index 420c7f6..8b32c70 100644 --- a/backend/connectors/nmbgmr/transformer.py +++ b/backend/connectors/nmbgmr/transformer.py @@ -13,10 +13,7 @@ # See the License for the specific language governing permissions and # limitations under the License. # =============================================================================== -from backend.constants import DTW -from backend.record import SiteRecord, WaterLevelRecord from backend.transformer import ( - BaseTransformer, WaterLevelTransformer, SiteTransformer, AnalyteTransformer, diff --git a/backend/connectors/nmenv/source.py b/backend/connectors/nmenv/source.py index 50141d0..7252551 100644 --- a/backend/connectors/nmenv/source.py +++ b/backend/connectors/nmenv/source.py @@ -33,14 +33,15 @@ URL = "https://nmenv.newmexicowaterdata.org/FROST-Server/v1.1/" -import sys class DWBSiteSource(STSiteSource): url = URL - transformer_klass = DWBSiteTransformer bounding_polygon = NM_STATE_BOUNDING_POLYGON + def __init__(self): + super().__init__(transformer=DWBSiteTransformer()) + def __repr__(self): return "DWBSiteSource" @@ -59,7 +60,7 @@ def get_records(self, *args, **kw): elif self.config: analyte = self.config.parameter - service = self.get_service() + service = self.client.get_service() if self.config.sites_only: ds = service.things() q = ds.query() @@ -110,7 +111,9 @@ def get_records(self, *args, **kw): class DWBAnalyteSource(STAnalyteSource): url = URL - transformer_klass = DWBAnalyteTransformer + + def __init__(self): + super().__init__(transformer=DWBAnalyteTransformer()) def __repr__(self): return "DWBAnalyteSource" @@ -131,7 +134,7 @@ def _parse_result( return float(result.split(" ")[0]) def get_records(self, site, *args, **kw): - service = self.get_service() + service = self.client.get_service() analyte = get_analyte_search_param(self.config.parameter, DWB_ANALYTE_MAPPING) ds = service.datastreams() @@ -190,10 +193,10 @@ def _extract_parameter_dates(self, records: list) -> list: def _extract_source_parameter_names(self, records: list) -> list: return [r["datastream"].observed_property.name for r in records] - def _extract_terminal_record(self, records, bookend): + def _extract_terminal_record(self, records, position): # this is only used in summary output record = get_terminal_record( - records, tag=lambda x: x["observation"].phenomenon_time, bookend=bookend + records, tag=lambda x: x["observation"].phenomenon_time, position=position ) return { diff --git a/backend/connectors/nmenv/transformer.py b/backend/connectors/nmenv/transformer.py index 80f534a..dde755f 100644 --- a/backend/connectors/nmenv/transformer.py +++ b/backend/connectors/nmenv/transformer.py @@ -14,7 +14,7 @@ # limitations under the License. # =============================================================================== from backend.connectors.st_connector import STSiteTransformer -from backend.transformer import SiteTransformer, AnalyteTransformer +from backend.transformer import AnalyteTransformer class DWBSiteTransformer(STSiteTransformer): diff --git a/backend/connectors/nmose/source.py b/backend/connectors/nmose/source.py index 5def1bf..fa785e0 100644 --- a/backend/connectors/nmose/source.py +++ b/backend/connectors/nmose/source.py @@ -19,10 +19,12 @@ class NMOSEPODSiteSource(BaseSiteSource): It is used to fetch site data from the NMOSEPOD API. """ - transformer_klass = NMOSEPODSiteTransformer chunk_size: int = 5000 bounding_polygon = NM_STATE_BOUNDING_POLYGON + def __init__(self): + super().__init__(transformer=NMOSEPODSiteTransformer()) + def get_records(self, *args, **kw) -> List[Dict]: config = self.config params: Dict[str, Any] = {} diff --git a/backend/connectors/nmose/transformer.py b/backend/connectors/nmose/transformer.py index 8f26ebb..b519758 100644 --- a/backend/connectors/nmose/transformer.py +++ b/backend/connectors/nmose/transformer.py @@ -1,4 +1,4 @@ -from backend.transformer import BaseTransformer, SiteTransformer +from backend.transformer import SiteTransformer class NMOSEPODSiteTransformer(SiteTransformer): diff --git a/backend/connectors/st2/source.py b/backend/connectors/st2/source.py index 181513b..3467a6d 100644 --- a/backend/connectors/st2/source.py +++ b/backend/connectors/st2/source.py @@ -13,9 +13,7 @@ # See the License for the specific language governing permissions and # limitations under the License. # =============================================================================== -import datetime - -import frost_sta_client as fsc +from functools import partial from backend.connectors import ( PVACD_BOUNDING_POLYGON, @@ -42,7 +40,6 @@ ) from backend.constants import ( DTW, - DTW_UNITS, DT_MEASURED, PARAMETER_NAME, PARAMETER_VALUE, @@ -50,69 +47,65 @@ SOURCE_PARAMETER_NAME, SOURCE_PARAMETER_UNITS, ) -from backend.source import BaseSiteSource, BaseWaterLevelSource, get_terminal_record URL = "https://st2.newmexicowaterdata.org/FROST-Server/v1.1" class ST2SiteSource(STSiteSource): - agency: str url = URL + def __init__(self, agency: str, bounding_polygon=None, transformer=None): + self.agency = agency + if bounding_polygon is not None: + self.bounding_polygon = bounding_polygon + super().__init__(transformer=transformer) + + def __repr__(self): + return f"ST2SiteSource(agency={self.agency!r})" + def _get_filters(self): if self.agency is None: raise ValueError(f"{self.__class__.__name__}. Agency not set") - return [f"properties/agency eq '{self.agency}'"] -class NMOSERoswellSiteSource(ST2SiteSource): - transformer_klass = NMOSERoswellSiteTransformer - agency = "OSE-Roswell" - - def __repr__(self): - return "NMOSERoswellSiteSource" - - -class PVACDSiteSource(ST2SiteSource): - transformer_klass = PVACDSiteTransformer - agency = "PVACD" - bounding_polygon = PVACD_BOUNDING_POLYGON - - def __repr__(self): - return "PVACDSiteSource" - - -class EBIDSiteSource(ST2SiteSource): - transformer_klass = EBIDSiteTransformer - agency = "EBID" - bounding_polygon = EBID_BOUNDING_POLYGON - - def __repr__(self): - return "EBIDSiteSource" - - -class BernCoSiteSource(ST2SiteSource): - agency = "BernCo" - transformer_klass = BernCoSiteTransformer - bounding_polygon = BERNCO_BOUNDING_POLYGON - - def __repr__(self): - return "BernCoSiteSource" - - -class CABQSiteSource(ST2SiteSource): - transformer_klass = CABQSiteTransformer - agency = "CABQ" - bounding_polygon = CABQ_BOUNDING_POLYGON - - def __repr__(self): - return "CABQSiteSource" +NMOSERoswellSiteSource = partial( + ST2SiteSource, + agency="OSE-Roswell", + transformer=NMOSERoswellSiteTransformer(), +) +PVACDSiteSource = partial( + ST2SiteSource, + agency="PVACD", + bounding_polygon=PVACD_BOUNDING_POLYGON, + transformer=PVACDSiteTransformer(), +) +EBIDSiteSource = partial( + ST2SiteSource, + agency="EBID", + bounding_polygon=EBID_BOUNDING_POLYGON, + transformer=EBIDSiteTransformer(), +) +BernCoSiteSource = partial( + ST2SiteSource, + agency="BernCo", + bounding_polygon=BERNCO_BOUNDING_POLYGON, + transformer=BernCoSiteTransformer(), +) +CABQSiteSource = partial( + ST2SiteSource, + agency="CABQ", + bounding_polygon=CABQ_BOUNDING_POLYGON, + transformer=CABQSiteTransformer(), +) class ST2WaterLevelSource(STWaterLevelSource): url = URL + def __init__(self, transformer=None): + super().__init__(transformer=transformer) + def _extract_parameter_record(self, record): record[PARAMETER_NAME] = DTW record[PARAMETER_VALUE] = record["observation"].result @@ -132,15 +125,14 @@ def _extract_source_parameter_names(self, records: list) -> list: return [r["datastream"].name for r in records] def _clean_records(self, records: list) -> list: - rs = [r for r in records if r["observation"].result is not None] - return rs + return [r for r in records if r["observation"].result is not None] def get_records(self, site_record, *args, **kw): - service = self.get_service() + service = self.client.get_service() config = self.config records = [] - for t in self._get_things(service, site_record): + for t in self.client._get_things(service, site_record): if t.name == "Water Well": for di in t.datastreams: @@ -152,7 +144,6 @@ def get_records(self, site_record, *args, **kw): if fi: q = q.filter(fi) - # if config.latest_water_level_only and not config.output_summary: q = q.orderby("phenomenonTime", "desc") for obs in q.list(): @@ -164,48 +155,55 @@ def get_records(self, site_record, *args, **kw): "observation": obs, } ) - - # if config.latest_water_level_only and not config.output_summary: - # break return records class NMOSERoswellWaterLevelSource(ST2WaterLevelSource): - transformer_klass = NMOSERoswellWaterLevelTransformer agency = "OSE-Roswell" + def __init__(self): + super().__init__(transformer=NMOSERoswellWaterLevelTransformer()) + def __repr__(self): return "NMOSERoswellWaterLevelSource" class PVACDWaterLevelSource(ST2WaterLevelSource): - transformer_klass = PVACDWaterLevelTransformer agency = "PVACD" + def __init__(self): + super().__init__(transformer=PVACDWaterLevelTransformer()) + def __repr__(self): return "PVACDWaterLevelSource" class EBIDWaterLevelSource(ST2WaterLevelSource): - transformer_klass = EBIDWaterLevelTransformer agency = "EBID" + def __init__(self): + super().__init__(transformer=EBIDWaterLevelTransformer()) + def __repr__(self): return "EBIDWaterLevelSource" class BernCoWaterLevelSource(ST2WaterLevelSource): agency = "BernCo" - transformer_klass = BernCoWaterLevelTransformer + + def __init__(self): + super().__init__(transformer=BernCoWaterLevelTransformer()) def __repr__(self): return "BernCoWaterLevelSource" class CABQWaterLevelSource(ST2WaterLevelSource): - transformer_klass = CABQWaterLevelTransformer agency = "CABQ" + def __init__(self): + super().__init__(transformer=CABQWaterLevelTransformer()) + def __repr__(self): return "CABQWaterLevelSource" diff --git a/backend/connectors/st2/transformer.py b/backend/connectors/st2/transformer.py index eaf62f1..4a2a1ca 100644 --- a/backend/connectors/st2/transformer.py +++ b/backend/connectors/st2/transformer.py @@ -13,16 +13,11 @@ # See the License for the specific language governing permissions and # limitations under the License. # =============================================================================== -import pprint -import sys from backend.connectors.st_connector import STSiteTransformer -from backend.record import SiteRecord, WaterLevelRecord +from backend.converter import StandardUnitConverter from backend.transformer import ( - BaseTransformer, WaterLevelTransformer, - SiteTransformer, - convert_units, ) @@ -73,7 +68,7 @@ def _transform_elevation(self, elevation, record): try: thing = record.things._entities[0] stickup_height_ft = thing._properties["stickup_height"]["value"] - stickup_height_m, conversion_factor, warning_msg = convert_units( + stickup_height_m, conversion_factor, warning_msg = StandardUnitConverter().convert( stickup_height_ft, "ft", "m", "stickup_height", "stickup_height" ) elevation = elevation - stickup_height_m diff --git a/backend/connectors/st_connector.py b/backend/connectors/st_connector.py index dd9550c..ed9f10e 100644 --- a/backend/connectors/st_connector.py +++ b/backend/connectors/st_connector.py @@ -14,12 +14,12 @@ # limitations under the License. # =============================================================================== from datetime import datetime +from typing import Optional import frost_sta_client as fsc -from shapely import MultiPolygon, Polygon, unary_union +from shapely import MultiPolygon, unary_union from backend.bounding_polygons import get_state_polygon -from backend.constants import EARLIEST, LATEST from backend.source import ( BaseSiteSource, BaseWaterLevelSource, @@ -30,48 +30,28 @@ def get_service(url): - s = fsc.SensorThingsService(url) - return s + return fsc.SensorThingsService(url) -class STSource: - url: str +class STClient: + def __init__(self, url: str): + self._url = url def get_service(self): - if self.url is None: + if self._url is None: raise ValueError("URL not set") + return get_service(self._url) - return get_service(self.url) - - def _get_things( - self, service, site, expand="Locations,Datastreams", additional_filters=None - ): - + def _get_things(self, service, site, expand="Locations,Datastreams", additional_filters=None): things = service.things().query().expand(expand) fs = [f"Locations/id eq {site.id}"] - if additional_filters is not None: + if additional_filters: for fi in additional_filters: fs.append(fi) if fs: things.filter(" and ".join(fs)) - return things.list() - def _extract_terminal_record(self, records, bookend): - record = get_terminal_record( - records, tag=lambda x: x["observation"].phenomenon_time, bookend=bookend - ) - - return { - "value": self._parse_result(record["observation"].result), - "datetime": record["observation"].phenomenon_time, - "source_parameter_units": record["datastream"].unit_of_measurement.symbol, - "source_parameter_name": record["datastream"].name, - } - - def _parse_result(self, result): - return result - def make_dt_filter(tag, start, end): if start: @@ -84,36 +64,37 @@ def make_dt_filter(tag, start, end): elif end: e = end.strftime("%Y-%m-%dT%H:%M:%S.%fZ") return f"{tag} le {e}" - return "" -class STSiteSource(BaseSiteSource, STSource): +class STSiteSource(BaseSiteSource): + url: Optional[str] = None + + def __init__(self, transformer=None): + super().__init__(transformer=transformer) + self.client = STClient(self.url) + def health(self): try: - # Health checks may run before config is initialized; probe the service directly. - service = self.get_service() + service = self.client.get_service() resp = list(service.locations().query().top(1).list()) return bool(resp) except Exception: return False - + def get_records(self, *args, **kw): - service = self.get_service() + service = self.client.get_service() config = self.config fs = [] if config: if config.has_bounds(): - poly = config.bounding_wkt(as_wkt=False) - # if poly is a MULTIPOLYGON convert to POLYGON if type(poly) == MultiPolygon: if len(poly.geoms) == 1: poly = unary_union(poly) else: - # HUC4 1508 has 2 polygons, one of them is outside of NM state_boundary = get_state_polygon("NM") for geom in poly: if state_boundary.contains(geom): @@ -144,17 +125,53 @@ def _get_filters(self): return [] -class STWaterLevelSource(STSource, BaseWaterLevelSource): - pass +class STWaterLevelSource(BaseWaterLevelSource): + url: Optional[str] = None + def __init__(self, transformer=None): + super().__init__(transformer=transformer) + self.client = STClient(self.url) + + def _parse_result(self, result): + return result -class STAnalyteSource(STSource, BaseAnalyteSource): - pass + def _extract_terminal_record(self, records, position): + record = get_terminal_record( + records, tag=lambda x: x["observation"].phenomenon_time, position=position + ) + return { + "value": self._parse_result(record["observation"].result), + "datetime": record["observation"].phenomenon_time, + "source_parameter_units": record["datastream"].unit_of_measurement.symbol, + "source_parameter_name": record["datastream"].name, + } + + +class STAnalyteSource(BaseAnalyteSource): + url: Optional[str] = None + + def __init__(self, transformer=None): + super().__init__(transformer=transformer) + self.client = STClient(self.url) + + def _parse_result(self, result): + return result + + def _extract_terminal_record(self, records, position): + record = get_terminal_record( + records, tag=lambda x: x["observation"].phenomenon_time, position=position + ) + return { + "value": self._parse_result(record["observation"].result), + "datetime": record["observation"].phenomenon_time, + "source_parameter_units": record["datastream"].unit_of_measurement.symbol, + "source_parameter_name": record["datastream"].name, + } class STSiteTransformer(SiteTransformer): source_id: str - check_contained = False # API returns only records within the bounds + check_contained = False def _transform_elevation(self, elevation, record): return elevation @@ -170,9 +187,6 @@ def _transform(self, record): lat = coordinates[1] lng = coordinates[0] - # if not self.contained(lng, lat): - # print("not contained") - # return ele = None if len(coordinates) == 3: diff --git a/backend/connectors/usgs/source.py b/backend/connectors/usgs/source.py index cd6d079..424a7bb 100644 --- a/backend/connectors/usgs/source.py +++ b/backend/connectors/usgs/source.py @@ -45,8 +45,10 @@ MAX_RETRIES = 7 class NWISSiteSource(BaseSiteSource): - transformer_klass = NWISSiteTransformer chunk_size = 500 + + def __init__(self): + super().__init__(transformer=NWISSiteTransformer()) bounding_polygon = NM_STATE_BOUNDING_POLYGON sites_url: str = "https://api.waterdata.usgs.gov/ogcapi/v0/collections/combined-metadata/items" @@ -63,7 +65,7 @@ def health(self): headers = {"X-API-Key": os.environ["USGS_API_KEY"]} else: headers = {} - response = httpx.get( + response = self._http_client.get( url=self.sites_url, params={"limit": 1, "parameter_code": "72019", "site_type_code": "GW", "state_code": "35"}, timeout=30, @@ -107,7 +109,7 @@ def get_records(self): headers = {"X-API-Key": os.environ["USGS_API_KEY"]} else: headers = {} - response = httpx.get( + response = self._http_client.get( url=self.sites_url, params=params, timeout=TIMEOUT, @@ -153,7 +155,8 @@ def get_records(self): class NWISWaterLevelSource(BaseWaterLevelSource): - transformer_klass = NWISWaterLevelTransformer + def __init__(self): + super().__init__(transformer=NWISWaterLevelTransformer()) # USGS complex queries allow up to 250 sites to be queried at once # https://api.waterdata.usgs.gov/docs/ogcapi/complex-queries num_sites = 250 @@ -295,8 +298,8 @@ def _extract_source_parameter_names(self, records: list) -> list: def _extract_source_parameter_units(self, records): return [r["source_parameter_units"] for r in records] - def _extract_terminal_record(self, records, bookend): - record = get_terminal_record(records, "datetime_measured", bookend=bookend) + def _extract_terminal_record(self, records, position): + record = get_terminal_record(records, "datetime_measured", position=position) return { "value": float(record["value"]), # "datetime": (record["date_measured"], record["time_measured"]), diff --git a/backend/connectors/usgs/transformer.py b/backend/connectors/usgs/transformer.py index fc95212..41fa8d5 100644 --- a/backend/connectors/usgs/transformer.py +++ b/backend/connectors/usgs/transformer.py @@ -13,8 +13,7 @@ # See the License for the specific language governing permissions and # limitations under the License. # =============================================================================== -from backend.record import SiteRecord, WaterLevelRecord -from backend.transformer import BaseTransformer, WaterLevelTransformer, SiteTransformer +from backend.transformer import WaterLevelTransformer, SiteTransformer class NWISSiteTransformer(SiteTransformer): diff --git a/backend/connectors/wqp/source.py b/backend/connectors/wqp/source.py index 4adc95d..e324fef 100644 --- a/backend/connectors/wqp/source.py +++ b/backend/connectors/wqp/source.py @@ -13,9 +13,7 @@ # See the License for the specific language governing permissions and # limitations under the License. # =============================================================================== -import pprint -import httpx from backend.connectors import NM_STATE_BOUNDING_POLYGON from backend.connectors.mappings import WQP_ANALYTE_MAPPING @@ -26,8 +24,6 @@ SOURCE_PARAMETER_NAME, SOURCE_PARAMETER_UNITS, DT_MEASURED, - EARLIEST, - LATEST, TDS, WATERLEVELS, SPECIFIC_CONDUCTANCE, @@ -69,17 +65,18 @@ def get_date_range(config): class WQPSiteSource(BaseSiteSource): - transformer_klass = WQPSiteTransformer chunk_size = 50 - bounding_polygon = NM_STATE_BOUNDING_POLYGON + def __init__(self): + super().__init__(transformer=WQPSiteTransformer()) + def __repr__(self): return "WQPSiteSource" def health(self): try: - r = httpx.get( + r = self._http_client.get( "https://www.waterqualitydata.us/data/Station/search", params={"mimeType": "tsv", "siteid": "325754103461301"}, ) @@ -206,8 +203,8 @@ def _extract_parameter_dates(self, records): def _extract_source_parameter_names(self, records): return [ri["CharacteristicName"] for ri in records] - def _extract_terminal_record(self, records, bookend): - record = get_terminal_record(records, "ActivityStartDate", bookend=bookend) + def _extract_terminal_record(self, records, position): + record = get_terminal_record(records, "ActivityStartDate", position=position) return { "value": record["ResultMeasureValue"], "datetime": record["ActivityStartDate"], @@ -249,7 +246,8 @@ def _parameter_units_hook(self): class WQPAnalyteSource(WQPParameterSource, BaseAnalyteSource): - transformer_klass = WQPAnalyteTransformer + def __init__(self): + super().__init__(transformer=WQPAnalyteTransformer()) def __repr__(self): return "WQPAnalyteSource" @@ -260,7 +258,8 @@ def _parameter_units_hook(self): # inherit from WQPParameterSource first so that its _extract_souce_parameter_units method is used instead of BaseWaterLevelSource's method class WQPWaterLevelSource(WQPParameterSource, BaseWaterLevelSource): - transformer_klass = WQPWaterLevelTransformer + def __init__(self): + super().__init__(transformer=WQPWaterLevelTransformer()) def __repr__(self): return "WQPWaterLevelSource" diff --git a/backend/connectors/wqp/transformer.py b/backend/connectors/wqp/transformer.py index 4764dc0..9acffbe 100644 --- a/backend/connectors/wqp/transformer.py +++ b/backend/connectors/wqp/transformer.py @@ -13,11 +13,8 @@ # See the License for the specific language governing permissions and # limitations under the License. # =============================================================================== -import pprint -from backend.record import SiteRecord, AnalyteSummaryRecord from backend.transformer import ( - BaseTransformer, SiteTransformer, AnalyteTransformer, WaterLevelTransformer, @@ -26,7 +23,6 @@ class WQPSiteTransformer(SiteTransformer): def _transform(self, record): - # pprint.pprint(record) provider = record["ProviderName"] rec = { "source": f"WQP/{provider}", diff --git a/backend/converter.py b/backend/converter.py new file mode 100644 index 0000000..3c404f1 --- /dev/null +++ b/backend/converter.py @@ -0,0 +1,103 @@ +# =============================================================================== +# Copyright 2024 Jake Ross +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# =============================================================================== +from backend.constants import ( + MILLIGRAMS_PER_LITER, + PARTS_PER_MILLION, + PARTS_PER_BILLION, + FEET, + METERS, + TONS_PER_ACRE_FOOT, + MICROGRAMS_PER_LITER, +) + + +class StandardUnitConverter: + def convert( + self, + input_value: float, + input_units: str, + output_units: str, + source_parameter_name: str, + die_parameter_name: str, + dt: str | None = None, + ) -> tuple[float, float | None, str]: + warning = "" + conversion_factor = None + + input_value = float(input_value) + input_units = input_units.strip().lower() + output_units = output_units.strip().lower() + source_parameter_name = source_parameter_name.strip().lower() + die_parameter_name = die_parameter_name.strip().lower() + + mgl = MILLIGRAMS_PER_LITER.lower() + ugl = MICROGRAMS_PER_LITER.lower() + ppm = PARTS_PER_MILLION.lower() + ppb = PARTS_PER_BILLION.lower() + tpaf = TONS_PER_ACRE_FOOT.lower() + ft = FEET.lower() + m = METERS.lower() + + if die_parameter_name == "ph": + conversion_factor = 1.0 + elif die_parameter_name in ["conductivity", "specific_conductance"]: + if input_units in ["μmhos/cm", "umho/cm", "cm-1", "micromhos per centimeter", "mg/l", "su", "us/cm", "us/cm @25c", "µs/cm", "μs/cm"]: + conversion_factor = 1.0 + elif output_units == mgl: + if input_units in ["mg/l caco3", "mg/l caco3**"]: + if die_parameter_name == "bicarbonate": + conversion_factor = 1.22 + elif die_parameter_name == "calcium": + conversion_factor = 0.4 + elif die_parameter_name == "carbonate": + conversion_factor = 0.6 + elif input_units == "mg/l as n": + conversion_factor = 4.427 + elif input_units in ["mg/l asno3", "mg/l as no3"]: + conversion_factor = 1.0 + elif input_units == "ug/l as n": + conversion_factor = 0.004427 + elif input_units == "pci/l": + conversion_factor = 0.00149 + elif input_units in (ugl, ppb): + conversion_factor = 0.001 + elif input_units == tpaf: + conversion_factor = 735.47 + elif input_units == ppm: + conversion_factor = 1.0 + elif input_units == output_units: + if source_parameter_name in ["nitrate as n", "nitrate (as n)"]: + conversion_factor = 4.427 + else: + conversion_factor = 1.0 + elif output_units == ft: + if input_units in [m, "meters"]: + conversion_factor = 3.28084 + elif input_units in [ft, "feet"]: + conversion_factor = 1.0 + elif output_units == m: + if input_units in [ft, "feet"]: + conversion_factor = 0.3048 + elif input_units in [m, "meters"]: + conversion_factor = 1.0 + + if conversion_factor: + return input_value * conversion_factor, conversion_factor, warning + warning = f"Failed to convert {input_value} {input_units} {source_parameter_name} (source) to {output_units} {die_parameter_name} (die) on {dt}" + return input_value, conversion_factor, warning + + +# ============= EOF ============================================= diff --git a/backend/geo_utils.py b/backend/geo_utils.py index 4484ee9..eb6e850 100644 --- a/backend/geo_utils.py +++ b/backend/geo_utils.py @@ -16,8 +16,7 @@ import pyproj from shapely.ops import transform -PROJECTIONS = {} -TRANSFORMS = {} +TRANSFORMS: dict = {} ALLOWED_DATUMS = ["NAD27", "NAD83", "WGS84"] @@ -75,56 +74,4 @@ def datum_transform(x, y, in_datum, out_datum): return lng, lat -def utm_to_lonlat(e, n, zone=13): - """ - Converts easting and northing into longitude and latitude - - Parameters - -------- - e: float - easting - n: float - northing - - Returns - -------- - tuple - (longitude, latitude) - """ - name = f"utm{zone}" - if name not in PROJECTIONS: - pr = pyproj.Proj(proj="utm", zone=int(zone), ellps="WGS84") - PROJECTIONS[name] = pr - pr = PROJECTIONS[name] - lonlat = pr(e, n, inverse=True) - return lonlat - - -def lonlat_to_utm(lon, lat, zone=13): - """ - Converts longitude and latitude into easting and northing - - Parameters - -------- - lon: float - longitude in decimal degrees - lat: float - latitude in decimal degrees - - - Returns - -------- - tuple - (easting, northing) - """ - name = "lonlat" - if name not in PROJECTIONS: - pr = pyproj.Proj(proj="utm", ellps="WGS84", zone=zone) - PROJECTIONS[name] = pr - - pr = PROJECTIONS[name] - easting_northing = pr(lon, lat) - return easting_northing - - # ============= EOF ============================================= diff --git a/backend/logger.py b/backend/logger.py index c567362..ae23cf0 100644 --- a/backend/logger.py +++ b/backend/logger.py @@ -21,18 +21,20 @@ # Track handlers created by this module to avoid closing unrelated handlers -_managed_handlers = [] +_managed_handlers: list = [] -class Loggable: - def __init__(self): - self.logger = logging.getLogger(self.__class__.__name__) +class Logger: + """Standalone logger. Use make_logger() to create instances.""" + + def __init__(self, name: str): + self._name = name + self.logger = logging.getLogger(name) def log(self, msg, level=None, fg="yellow", **kwargs): if level is None: level = logging.INFO - - click.secho(f"{self.__class__.__name__:40s}{msg}", fg=fg) + click.secho(f"{self._name:40s}{msg}", fg=fg) self.logger.log(level, msg, **kwargs) def warn(self, msg, fg="red", **kwargs): @@ -42,9 +44,13 @@ def debug(self, msg): self.log(msg, level=logging.DEBUG, fg="blue") -def setup_logging(level=None, log_format=None, path=None): - global _managed_handlers +def make_logger(name: str) -> Logger: + return Logger(name) + +def setup_logging(level=None, log_format=None, path=None): + # _managed_handlers is mutated in place (clear/append), never reassigned, + # so no `global` declaration is needed. if level is None: level = logging.DEBUG if log_format is None: diff --git a/backend/persister.py b/backend/persister.py index 8887828..6bfc614 100644 --- a/backend/persister.py +++ b/backend/persister.py @@ -15,52 +15,36 @@ # =============================================================================== import csv import io -import os -from pprint import pprint import json +import os from backend import OutputFormat -from backend.logger import Loggable - - -try: - from google.cloud import storage -except ImportError: - print("google cloud storage not available") +from backend.logger import make_logger +from backend.persisters.strategies import LocalFileStrategy -def write_memory(func, records, output_format=None): - f = io.BytesIO() - func(f, records, output_format) - return f.getvalue() +def _timeseries_to_bytes(timeseries: list) -> bytes: + buf = io.StringIO() + writer = csv.writer(buf) + headers_written = False + for i, records in enumerate(timeseries): + for record in records: + if not headers_written: + writer.writerow(record.keys) + headers_written = True + writer.writerow(record.to_row()) + return buf.getvalue().encode("utf-8") -def dump_timeseries(path, timeseries: list[list]): - """ - Dumps timeseries records to a CSV file. The timeseries must be a list of - lists, where each inner list contains the records for a single site. In the case - of timeseries separated, the inner list will contain the records for a single site - and this function will be called multiple times, once for each site. - """ - with open(path, "w", newline="", encoding="utf-8") as f: - writer = csv.writer(f) - headers_have_not_been_written = True - for i, records in enumerate(timeseries): - for record in records: - if i == 0 and headers_have_not_been_written: - writer.writerow(record.keys) - headers_have_not_been_written = False - writer.writerow(record.to_row()) - - -def dump_sites_summary(path, records, output_format: OutputFormat): +def _records_to_bytes(records: list, output_format: OutputFormat) -> bytes: if output_format == OutputFormat.CSV: - with open(path, "w", newline="", encoding="utf-8") as f: - writer = csv.writer(f) - for i, site in enumerate(records): - if i == 0: - writer.writerow(site.keys) - writer.writerow(site.to_row()) + buf = io.StringIO() + writer = csv.writer(buf) + for i, site in enumerate(records): + if i == 0: + writer.writerow(site.keys) + writer.writerow(site.to_row()) + return buf.getvalue().encode("utf-8") else: features = [ { @@ -68,45 +52,41 @@ def dump_sites_summary(path, records, output_format: OutputFormat): "geometry": { "type": "Point", "coordinates": [ - getattr(record, "longitude"), - getattr(record, "latitude"), - getattr(record, "elevation"), + getattr(r, "longitude"), + getattr(r, "latitude"), + getattr(r, "elevation"), ], }, "properties": { - k: getattr(record, k) - for k in record.keys + k: getattr(r, k) + for k in r.keys if k not in ["latitude", "longitude", "elevation"] }, } - for record in records + for r in records ] - feature_collection = {"type": "FeatureCollection", "features": features} - - with open(path, "w", encoding="utf-8") as f: - json.dump(feature_collection, f, indent=4) - + fc = {"type": "FeatureCollection", "features": features} + return json.dumps(fc, indent=4).encode("utf-8") -class BasePersister(Loggable): - """ - Class to persist the data to a file or cloud storage. - If persisting to a file, the output directory is created by config._make_output_path() - """ - def __init__(self, config=None): +class BasePersister: + def __init__(self, config=None, strategy=None): self.records = [] self.timeseries = [] self.sites = [] self.config = config - - super().__init__() - # self.keys = record_klass.keys + self._strategy = strategy if strategy is not None else LocalFileStrategy() + _l = make_logger(self.__class__.__name__) + self.log = _l.log + self.warn = _l.warn + self.debug = _l.debug def load(self, records: list): self.records.extend(records) def finalize(self, output_name: str): - pass + if hasattr(self._strategy, "finalize"): + self._strategy.finalize() def dump_sites(self, path: str): try: @@ -168,7 +148,7 @@ def dump_timeseries_separated(self, path: str): self.warn(f"failed to dump separated timeseries: {e}", exc_info=True) raise - def add_extension(self, path: str, extension: OutputFormat): + def add_extension(self, path: str, extension: str): if not extension: raise NotImplementedError else: @@ -181,91 +161,13 @@ def add_extension(self, path: str, extension: OutputFormat): def _dump_sites_summary( self, path: str, records: list, output_format: OutputFormat ): - dump_sites_summary(path, records, output_format) + self._strategy.write_bytes(path, _records_to_bytes(records, output_format)) def _dump_timeseries(self, path: str, timeseries: list): - dump_timeseries(path, timeseries) + self._strategy.write_bytes(path, _timeseries_to_bytes(timeseries)) def _make_output_directory(self, output_directory: str): - os.mkdir(output_directory) - - -class CloudStoragePersister(BasePersister): - extension = "csv" - _content: list - - def __init__(self, *args, **kwargs): - super(CloudStoragePersister, self).__init__(*args, **kwargs) - self._content = [] - - def finalize(self, output_name: str): - """ - zip content and upload to google cloud storage - :return: - """ - if not self._content: - self.log("no content to save", fg="red") - return - - storage_client = storage.Client() - bucket = storage_client.bucket("die_cache") - if len(self._content) > 1: - import zipfile - - zip_buffer = io.BytesIO() - with zipfile.ZipFile(zip_buffer, "w", zipfile.ZIP_DEFLATED) as zf: - for path, cnt in self._content: - zf.writestr(path, cnt) - blob = bucket.blob(f"{output_name}.zip") - blob.upload_from_string(zip_buffer.getvalue()) - else: - path, cnt = self._content[0] - - # this is a hack. need a better way to specify the output path - dirname = os.path.basename(os.path.dirname(path)) - path = os.path.join(dirname, os.path.basename(path)) - - blob = bucket.blob(path) - blob.upload_from_string( - cnt, - content_type=( - "application/json" - if self.config.output_format == OutputFormat.GEOJSON - else "text/csv" - ), - ) - - def _make_output_directory(self, output_directory: str): - # prevent making root directory, because we are not saving to disk - pass - - def _add_content(self, path: str, content: str): - self._content.append((path, content)) - - def _dump_sites_summary( - self, path: str, records: list, output_format: OutputFormat - ): - content = write_memory(dump_sites_summary, records, output_format) - self._add_content(path, content) - - def _dump_timeseries_unified(self, path: str, timeseries: list): - content = write_memory(path, dump_timeseries, timeseries) - self._add_content(path, content) - - -# class ST2Persister(BasePersister): -# extension = "st2" -# -# def save(self, path): -# import frost_sta_client as fsc -# -# service = fsc.SensorThingsService( -# "https://st.newmexicowaterdata.org/FROST-Server/v1.0", -# auth_handler=AuthHandler(os.getenv("ST2_USER"), os.getenv("ST2_PASSWORD")), -# ) -# for record in self.records: -# for t in service.things().query().filter(name=record["id"]).list(): -# print(t) + self._strategy.make_directory(output_directory) # ============= EOF ============================================= diff --git a/backend/persisters/factory.py b/backend/persisters/factory.py new file mode 100644 index 0000000..d179b15 --- /dev/null +++ b/backend/persisters/factory.py @@ -0,0 +1,28 @@ +from backend import OutputFormat +from backend.persister import BasePersister +from backend.persisters.strategies import GCSStrategy + + +def make_persister(config) -> BasePersister: + try: + from backend.persisters.geoserver import GeoServerPersister + except ImportError: + GeoServerPersister = None # type: ignore[assignment,misc] + + if config.output_format == OutputFormat.GEOSERVER: + if GeoServerPersister is None: + raise ImportError( + "GeoServer output requires 'geoserver' extras: " + "pip install nmuwd[geoserver]" + ) + return GeoServerPersister(config) + + if config.use_cloud_storage: + strategy = GCSStrategy( + bucket_name="die_cache", + output_name=config.output_name, + output_format=config.output_format.value, + ) + return BasePersister(config, strategy=strategy) + + return BasePersister(config) diff --git a/backend/persisters/geoserver.py b/backend/persisters/geoserver.py index d8c07fc..bd73a88 100644 --- a/backend/persisters/geoserver.py +++ b/backend/persisters/geoserver.py @@ -5,11 +5,9 @@ # You may not use this file except in compliance with the License. # You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 # =============================================================================== -import json -import os import time from itertools import groupby -from typing import Type +from typing import Any from shapely.geometry.multipoint import MultiPoint from shapely.geometry.point import Point from sqlalchemy.dialects.postgresql import JSONB, insert @@ -22,7 +20,6 @@ Column, ForeignKey, create_engine, - UUID, String, Integer, Float, @@ -31,7 +28,9 @@ ) from geoalchemy2 import Geometry -Base = declarative_base() +# declarative_base() returns a dynamic class; annotate as Any so mypy accepts +# it as a base for the ORM models below. +Base: Any = declarative_base() def session_factory(connection: dict): diff --git a/backend/persisters/ogc_features.py b/backend/persisters/ogc_features.py new file mode 100644 index 0000000..fa46c32 --- /dev/null +++ b/backend/persisters/ogc_features.py @@ -0,0 +1,164 @@ +# =============================================================================== +# Copyright 2024 Jake Ross +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# =============================================================================== +import json +from datetime import datetime, timezone +from typing import Optional + + +def _timestamp_now() -> str: + return datetime.now(timezone.utc).strftime("%Y-%m-%dT%H:%M:%SZ") + + +def _make_feature(record, collection_id: str) -> dict: + """Build one OGC-compliant Feature from a SummaryRecord or SiteRecord.""" + source = getattr(record, "source", "") + rid = getattr(record, "id", "") + feature_id = f"{source}:{rid}" if source and rid else str(rid) + + props = {k: getattr(record, k) for k in record.keys + if k not in ("latitude", "longitude", "elevation")} + + lat = getattr(record, "latitude", None) + lon = getattr(record, "longitude", None) + elev = getattr(record, "elevation", None) + + coords = [lon, lat] if elev is None else [lon, lat, elev] + + return { + "type": "Feature", + "id": feature_id, + "geometry": {"type": "Point", "coordinates": coords}, + "properties": props, + } + + +def dump_summary_collection(path: str, records: list, meta: dict) -> dict: + """ + Write an OGC FeatureCollection of summary/site records to *path*. + + meta keys (all optional): + id, title, description — collection metadata + + Returns the collection dict (for testing). + §V: MUST include top-level id, type, numberReturned, timeStamp. + §V: Each Feature MUST have top-level id. + """ + collection_id = meta.get("id", "collection") + features = [_make_feature(r, collection_id) for r in records] + + collection = { + "type": "FeatureCollection", + "id": collection_id, + "title": meta.get("title", collection_id), + "description": meta.get("description", ""), + "timeStamp": _timestamp_now(), + "numberMatched": len(features), + "numberReturned": len(features), + "links": [ + { + "href": meta.get("href", ""), + "rel": "self", + "type": "application/geo+json", + } + ], + "features": features, + } + + with open(path, "w", encoding="utf-8") as f: + json.dump(collection, f, indent=2, default=str) + + return collection + + +def dump_timeseries_collection( + path: str, + site_records: list, + timeseries_records: list, + meta: dict, + site_lookup: Optional[dict] = None, +) -> dict: + """ + Write an OGC FeatureCollection of flat timeseries observations to *path*. + + Each feature = one observation (not one well). + §V: ogc_timeseries features MUST be flat, one per observation. + §V: MUST have ISO 8601 `datetime` property. + §V: Each Feature MUST have top-level id. + + site_lookup: {site_id -> SiteRecord} for geometry lookup. + Built from site_records if not provided. + """ + collection_id = meta.get("id", "collection") + + if site_lookup is None: + site_lookup = {} + for sr in site_records: + key = getattr(sr, "id", None) + if key: + site_lookup[key] = sr + + features = [] + for obs in timeseries_records: + site_id = getattr(obs, "id", None) + site = site_lookup.get(site_id) + + if site: + lat = getattr(site, "latitude", None) + lon = getattr(site, "longitude", None) + elev = getattr(site, "elevation", None) + coords = [lon, lat] if elev is None else [lon, lat, elev] + geometry = {"type": "Point", "coordinates": coords} + else: + geometry = None + + date = getattr(obs, "date_measured", None) + time = getattr(obs, "time_measured", None) + if date and time: + dt = f"{date}T{time}Z" + elif date: + dt = f"{date}T00:00:00Z" + else: + dt = None + + source = getattr(obs, "source", "") + feature_id = f"{source}:{site_id}:{date}" if date else f"{source}:{site_id}" + + props = {k: getattr(obs, k) for k in obs.keys} + props["datetime"] = dt + + features.append({ + "type": "Feature", + "id": feature_id, + "geometry": geometry, + "properties": props, + }) + + collection = { + "type": "FeatureCollection", + "id": collection_id, + "title": meta.get("title", collection_id), + "description": meta.get("description", ""), + "timeStamp": _timestamp_now(), + "numberMatched": len(features), + "numberReturned": len(features), + "links": [ + { + "href": meta.get("href", ""), + "rel": "self", + "type": "application/geo+json", + } + ], + "features": features, + } + + with open(path, "w", encoding="utf-8") as f: + json.dump(collection, f, indent=2, default=str) + + return collection diff --git a/backend/persisters/strategies.py b/backend/persisters/strategies.py new file mode 100644 index 0000000..fe40296 --- /dev/null +++ b/backend/persisters/strategies.py @@ -0,0 +1,57 @@ +import io +import os + + +class LocalFileStrategy: + def write_bytes(self, path: str, content: bytes) -> None: + with open(path, "wb") as f: + f.write(content) + + def make_directory(self, path: str) -> None: + os.mkdir(path) + + +class GCSStrategy: + def __init__(self, bucket_name: str, output_name: str, output_format: str): + self._bucket_name = bucket_name + self._output_name = output_name + self._output_format = output_format + self._content: list[tuple[str, bytes]] = [] + + def write_bytes(self, path: str, content: bytes) -> None: + self._content.append((path, content)) + + def make_directory(self, path: str) -> None: + pass + + def finalize(self) -> None: + from google.cloud import storage + + if not self._content: + return + + client = storage.Client() + bucket = client.bucket(self._bucket_name) + + if len(self._content) > 1: + import zipfile + + buf = io.BytesIO() + with zipfile.ZipFile(buf, "w", zipfile.ZIP_DEFLATED) as zf: + for path, cnt in self._content: + zf.writestr(path, cnt) + blob = bucket.blob(f"{self._output_name}.zip") + blob.upload_from_string(buf.getvalue()) + else: + path, cnt = self._content[0] + dirname = os.path.basename(os.path.dirname(path)) + blob_path = os.path.join(dirname, os.path.basename(path)) + blob = bucket.blob(blob_path) + blob.upload_from_string( + cnt, + content_type=( + "application/json" + if self._output_format == "geojson" + else "text/csv" + ), + ) diff --git a/backend/record.py b/backend/record.py index ac8a9f9..b9a913f 100644 --- a/backend/record.py +++ b/backend/record.py @@ -25,6 +25,9 @@ class BaseRecord: + # Set by the source after transform; not all record types use it. + chunk_size: int | None = None + def to_csv(self): raise NotImplementedError @@ -63,7 +66,7 @@ def _get_sigfig_formatted_value(self, attr): # both analyte and water level tables have the same fields, but the # rounding should only occur for water level tables - if isinstance(self, WaterLevelRecord): + if self._payload.get("record_type") == "waterlevels": field_sigfigs.append((PARAMETER_VALUE, 2)) for field, sigfigs in field_sigfigs: @@ -71,8 +74,7 @@ def _get_sigfig_formatted_value(self, attr): try: v = round(v, sigfigs) except TypeError as e: - print(field, attr) - raise e + raise TypeError(f"rounding failed for field={field!r} attr={attr!r}") from e break return v @@ -105,14 +107,6 @@ class ParameterRecord(BaseRecord): defaults: dict = {} -class WaterLevelRecord(ParameterRecord): - pass - - -class AnalyteRecord(ParameterRecord): - pass - - class SummaryRecord(BaseRecord): keys: tuple = ( "source", @@ -145,14 +139,6 @@ class SummaryRecord(BaseRecord): defaults: dict = {} -class WaterLevelSummaryRecord(SummaryRecord): - pass - - -class AnalyteSummaryRecord(SummaryRecord): - pass - - class SiteRecord(BaseRecord): keys: tuple = ( "source", diff --git a/backend/source.py b/backend/source.py index 8d61e59..cbfe158 100644 --- a/backend/source.py +++ b/backend/source.py @@ -14,11 +14,11 @@ # limitations under the License. # =============================================================================== from json import JSONDecodeError +from typing import Any, Optional, Union, List, Callable, Dict, cast import httpx import shapely.wkt from shapely import MultiPoint -from typing import Union, List, Callable, Dict import time from backend.constants import ( @@ -30,157 +30,173 @@ EARLIEST, LATEST, ) -from backend.logger import Loggable +from backend.logger import make_logger from backend.record import ( - AnalyteRecord, - AnalyteSummaryRecord, - WaterLevelRecord, - WaterLevelSummaryRecord, + ParameterRecord, SiteRecord, + SummaryRecord, ) -from backend.transformer import BaseTransformer, convert_units +from backend.transformer import BaseTransformer from backend.exceptions import PartialOrNoDataError -def make_site_list(site_record: list[SiteRecord] | SiteRecord) -> list | str: - """ - Returns a list of site ids, as defined by site_record - - Parameters - ---------- - site_record: SiteRecord or list of SiteRecords - - Returns - ------- - list - a list of site ids - """ - if isinstance(site_record, list): - sites = [r.id for r in site_record] - else: - sites = site_record.id - return sites +# ============================================================================= +# Record validation strategies +# ============================================================================= +class RecordValidator: + config: Any = None -def get_terminal_record(records: list, tag: Union[str, Callable], bookend: str) -> dict: - """ - Returns the most recent record based on the tag + def set_config(self, config) -> None: + self.config = config - Parameters - ---------- - records: list - a list of records + def validate(self, record: dict) -> None: + raise NotImplementedError(f"{self.__class__.__name__} must implement validate") - tag: str or callable - the tag to use to sort the records - bookend: str - determines if the earliest or lastest record is retrieved +class AnalyteRecordValidator(RecordValidator): + def validate(self, record: dict) -> None: + record[PARAMETER_NAME] = self.config.parameter + for k in (PARAMETER_VALUE, PARAMETER_UNITS, DT_MEASURED): + if k not in record: + raise ValueError(f"Invalid record. Missing {k}") - Returns - ------- - dict - the most recent record for every site - """ - if callable(tag): - func = tag - else: - if "." in tag: - def func(x): - for t in tag.split("."): - x = x[t] - return x +class WaterLevelRecordValidator(RecordValidator): + def validate(self, record: dict) -> None: + for k in (PARAMETER_VALUE, PARAMETER_UNITS, DT_MEASURED): + if k not in record: + raise ValueError(f"Invalid record. Missing {k}") - else: - def func(x): - return x[tag] +class _SubclassValidatorShim(RecordValidator): + """Shim: delegates to source._validate_record() for subclasses that override it.""" + def __init__(self, source): + self._source = source - if bookend == EARLIEST: - return sorted(records, key=func)[0] - elif bookend == LATEST: - return sorted(records, key=func)[-1] - else: - raise ValueError( - f"Invalid bookend {bookend}. Must be either {EARLIEST} or {LATEST}" - ) + def set_config(self, config) -> None: + pass # source._validate_record uses self.config directly + def validate(self, record: dict) -> None: + self._source._validate_record(record) -def get_analyte_search_param(parameter: str, mapping: dict) -> str: - """ - Get the search parameter for a provided analyte, as defined by the mapping for a source - - Parameters - ---------- - parameter : str - the analyte name used in the query - - mapping : dict - a mapping of analytes to search parameters for the source - - Returns - ------- - str - the search parameter for the provided analyte for a particular source - """ - try: - return mapping[parameter] - except KeyError: - raise ValueError( - f"Invalid parameter name {parameter}. Valid parameters are {list(mapping.keys())}" - ) +# ============================================================================= +# Record summarization strategy +# ============================================================================= -class BaseSource(Loggable): - """ - The BaseSource class is a base class for all sources, whether it be a site source or a parameter source. +class RecordSummarizer: + def __init__(self, source): + self._source = source - ============================================================================ - Attributes - ============================================================================ - transformer_klass : BaseTransformer + def summarize(self, site, cleaned: list): + s = self._source + source_results = s._extract_source_parameter_results(cleaned) + source_units = s._extract_source_parameter_units(cleaned) + dates = s._extract_parameter_dates(cleaned) + source_names = s._extract_source_parameter_names(cleaned) - config : Config - the configuration class for the source + kept_items = [] + skipped_items = [] + for source_result, source_unit, date, source_name in zip( + source_results, source_units, dates, source_names + ): + try: + converted_result, _factor, warning_msg = s.transformer.converter.convert( + float(source_result), + source_unit, + s._get_output_units(), + source_name, + s.config.parameter, + date, + ) + if warning_msg == "": + kept_items.append(converted_result) + else: + s.warn(f"{warning_msg} for {site.id}") + except (TypeError, ValueError): + skipped_items.append((site.id, source_result, source_unit)) - tag : str - ============================================================================ - Methods With Universal Implementations (Already Implemented) - ============================================================================ - warn - Prints warning messages to the console in red + if skipped_items: + s.warn(f"Skipped results because of formatting: {skipped_items}") + if not kept_items: + return None - log - Prints the message to the console in yellow + n = len(kept_items) + earliest_result = s._extract_earliest_record(cleaned) + latest_result = s._extract_latest_record(cleaned) + if not latest_result: + return None - _execute_text_request - Executes a get request to the provided url with query parameters and and returns the text response + rec = { + "nrecords": n, + "min": min(kept_items), + "max": max(kept_items), + "mean": sum(kept_items) / n, + "earliest_datetime": earliest_result["datetime"], + "earliest_value": earliest_result["value"], + "earliest_source_units": earliest_result["source_parameter_units"], + "earliest_source_name": earliest_result["source_parameter_name"], + "latest_datetime": latest_result["datetime"], + "latest_value": latest_result["value"], + "latest_source_units": latest_result["source_parameter_units"], + "latest_source_name": latest_result["source_parameter_name"], + } + return s.transformer.do_transform(rec, site) + + +# ============================================================================= +# Module-level helpers +# ============================================================================= - _execute_json_request - Executes a get request to the provided url with query parameters and and returns the json response +def make_site_list(site_record: list[SiteRecord] | SiteRecord) -> list | str: + if isinstance(site_record, list): + return [r.id for r in site_record] + return site_record.id - ============================================================================ - Methods Implemented in BaseSiteSource and BaseParameterSource - ============================================================================ - read - Returns a list of transformed records - ============================================================================ - Methods That Need to be Implemented For Each Source - ============================================================================ - health - Determines if the source is healthy +def get_terminal_record(records: list, tag: Union[str, Callable], position: str) -> dict: + if callable(tag): + func = tag + elif "." in tag: + def func(x): + for t in tag.split("."): + x = x[t] + return x + else: + def func(x): + return x[tag] - get_records - Returns the site or parameter records from the source - """ + if position == EARLIEST: + return sorted(records, key=func)[0] + elif position == LATEST: + return sorted(records, key=func)[-1] + raise ValueError(f"Invalid position {position}. Must be either {EARLIEST} or {LATEST}") - transformer_klass = BaseTransformer - def __init__(self): - self.transformer = self.transformer_klass() - super().__init__() +def get_analyte_search_param(parameter: str, mapping: dict) -> str: + try: + return mapping[parameter] + except KeyError: + raise ValueError( + f"Invalid parameter name {parameter}. Valid parameters are {list(mapping.keys())}" + ) + + +# ============================================================================= +# Base source classes +# ============================================================================= + +class BaseSource: + transformer_klass = BaseTransformer # deprecated: pass transformer= to __init__ + + def __init__(self, transformer: Optional[BaseTransformer] = None, http_client: httpx.Client | None = None): + self.transformer = transformer if transformer is not None else self.transformer_klass() + self._http_client = http_client if http_client is not None else httpx.Client(timeout=900) + _l = make_logger(self.__class__.__name__) + self.log = _l.log + self.warn = _l.warn + self.debug = _l.debug @property def tag(self): @@ -189,251 +205,76 @@ def tag(self): def set_config(self, config): self.config = config self.transformer.set_config(config) + if hasattr(self, "_validator"): + self._validator.set_config(config) def check(self, *args, **kw): return True - # raise NotImplementedError(f"check not implemented by {self.__class__.__name__}") def discover(self, *args, **kw): return [] - # raise NotImplementedError(f"discover not implemented by {self.__class__.__name__}") - - # ========================================================================== - # Methods Already Implemented - # ========================================================================== def _execute_text_request(self, url: str, params: dict | None = None, max_tries: int = 7, **kw) -> str: - """ - Executes a get request to the provided url and returns the text response. - - Parameters - ---------- - url : str - the url to request - - params : dict - key-value query parameters to pass to the get request - - max_tries : int - the maximum number of times to retry the request if it fails - - Returns - ------- - str - the text responses - """ - if "timeout" not in kw: - kw["timeout"] = 10 - - tries: int = 0 - + tries, last_err = 0, "" while tries < max_tries: + t0 = time.monotonic() try: - resp = httpx.get(url, params=params, **kw) + resp = self._http_client.get(url, params=params, **kw) + elapsed = int((time.monotonic() - t0) * 1000) + self.log(f"HTTP GET source={self.tag} status={resp.status_code} attempt={tries+1}/{max_tries} elapsed_ms={elapsed} url={url}") if resp.status_code == 200: return resp.text - else: - self.warn(f"service responded with status {resp.status_code}") - self.warn(f"service responded with text {resp.text}") - self.warn(f"URL: {url}") - self.warn(f"Parameters: {params}") - self.warn(f"Retrying... {tries+1}/{max_tries}") - except Exception as e: - self.warn(f"Error during request: {e}") - self.warn(f"URL: {url}") - self.warn(f"Parameters: {params}") - self.warn(f"Retrying... {tries+1}/{max_tries}") + last_err = f"status {resp.status_code}: {resp.text[:200]}" + self.warn(f"Received status code {resp.status_code}. Retrying... {tries+1}/{max_tries}") + except (httpx.HTTPStatusError, httpx.TimeoutException, httpx.RequestError) as e: + elapsed = int((time.monotonic() - t0) * 1000) + last_err = str(e) + self.warn(f"Request error attempt={tries+1}/{max_tries} elapsed_ms={elapsed} url={url}: {e}") tries += 1 - time.sleep(tries) - - self.warn("Failed to retrieve records after multiple attempts") - raise PartialOrNoDataError("Failed to retrieve records after multiple attempts") - - def _execute_json_request( - self, - url: str, - params: dict | None = None, - tag: str | None = None, - max_retries: int = 7, - **kw - ) -> dict: - """ - Executes a get request to the provided url and returns the json response. - - Parameters - ---------- - url : str - the url to request - - params : dict - key-value query parameters to pass to the get request - - tag : str - the key to extract from the json response if required - - max_retries : int - the maximum number of times to retry the request if it fails - - Returns - ------- - dict - the json response - """ - tries: int = 0 + time.sleep(min(2 ** tries, 60)) + self.warn(f"Failed to retrieve records after {max_tries} attempts. Last error: {last_err}") + raise PartialOrNoDataError(f"Failed to retrieve records after {max_tries} attempts. Last error: {last_err}") + + def _execute_json_request(self, url: str, params: dict | None = None, tag: str | None = None, max_retries: int = 7, **kw) -> dict: + tries, last_err = 0, "" while tries < max_retries: + t0 = time.monotonic() try: - resp = httpx.get(url, params=params, **kw) - + resp = self._http_client.get(url, params=params, **kw) + elapsed = int((time.monotonic() - t0) * 1000) + self.log(f"HTTP GET source={self.tag} status={resp.status_code} attempt={tries+1}/{max_retries} elapsed_ms={elapsed} url={url}") if resp.status_code == 200: try: obj = resp.json() if tag and isinstance(obj, dict): return obj[tag] return obj - except JSONDecodeError: - self.warn(f"service responded but with invalid or no JSON data. \n{resp.text}") - self.warn(f"URL: {url}") - self.warn(f"Parameters: {params}") - self.warn(f"Retrying... {tries+1}/{max_retries}") + except JSONDecodeError as e: + last_err = f"JSONDecodeError: {e}. Response: {resp.text[:200]}" + self.warn(f"Invalid JSON response attempt={tries+1}/{max_retries} url={url}: {last_err}") else: - self.warn(f"service responded with status {resp.status_code}") - self.warn(f"service responded with text {resp.text} for url {resp.url}") - self.warn(f"Parameters: {params}") - self.warn(f"Retrying... {tries+1}/{max_retries}") - except Exception as e: - self.warn(f"Error during request: {e}") - self.warn(f"URL: {url}") - self.warn(f"Parameters: {params}") - self.warn(f"Retrying... {tries+1}/{max_retries}") + last_err = f"status {resp.status_code}: {resp.text[:200]}" + self.warn(f"Received status code {resp.status_code}. Retrying... {tries+1}/{max_retries}") + except (httpx.HTTPStatusError, httpx.TimeoutException, httpx.RequestError) as e: + elapsed = int((time.monotonic() - t0) * 1000) + last_err = str(e) + self.warn(f"Request error attempt={tries+1}/{max_retries} elapsed_ms={elapsed} url={url}: {e}") tries += 1 - time.sleep(tries) - - self.warn("Failed to retrieve records after multiple attempts") - raise PartialOrNoDataError("Failed to retrieve records after multiple attempts") - - # ========================================================================== - # Methods Implemented in BaseSiteSource and BaseParameterSource - # ========================================================================== + time.sleep(min(2 ** tries, 60)) + self.warn(f"Failed to retrieve records after {max_retries} attempts. Last error: {last_err}") + raise PartialOrNoDataError(f"Failed to retrieve records after {max_retries} attempts. Last error: {last_err}") def read(self, *args, **kw) -> list | None: - """ - Returns the records. Implemented in BaseSiteSource and BaseAnalyteSource - """ raise NotImplementedError(f"read not implemented by {self.__class__.__name__}") - # ========================================================================== - # Methods That Need to be Implemented For Each Source - # ========================================================================== - def get_records(self, *args, **kw) -> List[Dict]: - """ - Returns records as a dictionary, where the keys are site ids and - the values are site or parameter records. - - If site records, the values are dictionaries with the site records. - - If parameter records, the values are lists of dictionaries with parameter records. - - Called by the read method. Needs to be implemented by all subclasses. - - Parameters - ---------- - If parameter records: - site_record : dict - the site record for the location whose parameter records are to be retrieved - - If site records: - There are no parameters - - Returns - ------- - dict - a dictionary of site or parameter records, where the keys are site ids - and the values are site or parameter records - """ - raise NotImplementedError( - f"get_records not implemented by {self.__class__.__name__}" - ) + raise NotImplementedError(f"get_records not implemented by {self.__class__.__name__}") def health(self) -> bool: - """ - Checks the health of the source. Implemented for each site source - - Returns - -------- - bool - True if the source is healthy, else False - """ raise NotImplementedError(f"test not implemented by {self.__class__.__name__}") -class BaseContainerSource(BaseSource): - def __init__(self, *args, **kw): - super().__init__(*args, **kw) - - # locate image - # make container - # container writes messages to stdout - # this class captures the messages from stdout - - def check(self): - # run the container with the check command - pass - - def discover(self, *args, **kw): - # run the container with the discover command - pass - - def read(self, *args, **kw): - # run the container with the read command - pass - - class BaseSiteSource(BaseSource): - """ - The BaseSiteSource class is a base class for all site sources. - It provides a common interface for all site sources - - Attributes - ---------- - chunk_size : int - the number of records to process at once - - bounding_polygon : str - a WKT string defining the bounding polygon for the site sources - - - Methods With Universal Implementations (Already Implemented) - ------- - generate_bounding_polygon - Generates a bounding polygon based on the site records - - intersects(wkt) - Returns True if the bounding polygon intersects with the provided WKT string - - read(*args, **kw) - Reads the site records and returns the transformed records, where the - transform standardizes the records so the format is the same for all sources - - _transform_sites(records) - Transforms the site records into the standardized format and returns - the transformed records - - chunks(records, chunk_size=None) - Returns a list of records split into lists of size chunk_size. If - chunk_size less than 1 then the records are not split - - - Methods That Need to be Implemented For Each Source - ------- - get_records - Returns a dictionary of site records, where the keys are the site ids - and the values are the site records - - health - Checks the health of the source - """ - chunk_size = 1 bounding_polygon = None @@ -442,668 +283,203 @@ def tag(self): return self.__class__.__name__.lower().replace("sitesource", "") def generate_bounding_polygon(self): - """ - Generates a bounding MultiPolygon base on the longitude and latitude - of each site record - """ records = self.read_sites() - print(records[0].latitude) + self.log(str(records[0].latitude)) mpt = MultiPoint([(r.longitude, r.latitude) for r in records]) - print(mpt.convex_hull.buffer(1 / 60.0).wkt) - # print(mpt.convex_hull.wkt) + self.log(mpt.convex_hull.buffer(1 / 60.0).wkt) def intersects(self, wkt: str) -> bool: - """ - Determines if the bounding polygon intersects with the provided WKT string - - Parameters - ---------- - wkt : str - a WKT string - - Returns - ------- - bool - True if the bounding polygon intersects with the provided WKT string - True if there is no bounding polygon - """ if self.bounding_polygon: wkt = shapely.wkt.loads(wkt) return self.bounding_polygon.intersects(wkt) - return True def read(self, *args, **kw) -> List[SiteRecord] | None: - """ - Returns a list of transformed site records. - Calls self.get_records, which needs to be implemented for each source - - Returns - ------- - list[SiteRecord] - a list of transformed site records - """ self.log("Gathering site records") records = self.get_records() if records: self.log(f"total records={len(records)}") return self._transform_sites(records) - else: - self.warn("No site records returned") - return None + self.warn("No site records returned") + return None def _transform_sites(self, records: list) -> List[SiteRecord]: - """ - Transforms site records into the standardized format. - - Parameters - ---------- - records : list - a list of site records - - Returns - ------- - list[SiteRecord] - a list of transformed site records as SiteRecords - """ - transformed_records = [] + transformed_records: List[SiteRecord] = [] for record in records: - record = self.transformer.do_transform(record) - if record: - record.chunk_size = self.chunk_size - transformed_records.append(record) - + transformed = self.transformer.do_transform(record) + if transformed: + site_record = cast(SiteRecord, transformed) + site_record.chunk_size = self.chunk_size + transformed_records.append(site_record) self.log(f"processed nrecords={len(transformed_records)}") return transformed_records def chunks(self, records: list, chunk_size: int | None = None) -> list: - """ - Returns a list of records split into lists of size chunk_size. If - chunk_size less than 1 then the records are not split - - Parameters - ---------- - records : list - a list of records - - chunk_size : int - the size of the chunks - - Returns - ------- - list - a list of records split into lists of size chunk_size. If chunk_size - less than 1 then the records are not split - """ if chunk_size is None: chunk_size = self.chunk_size - if chunk_size > 1: - return [ - records[i : i + chunk_size] for i in range(0, len(records), chunk_size) - ] - else: - return records + return [records[i:i + chunk_size] for i in range(0, len(records), chunk_size)] + return records class BaseParameterSource(BaseSource): - """ - The BaseParameterSource class is a base class for all parameter sources, - whether it be an analyte source or a water level source. - - ============================================================================ - Methods With Universal Implementations (Already Implemented) - ============================================================================ - - _extract_earliest_record - Returns the earliest record for a particular site. Requires _extract_terminal_record - to be implemented for each source - - _extract_latest_record - Returns the most recent record for a particular site. Requires _extract_terminal_record - to be implemented for each source - - read - Reads the parameter records and returns the transformed records, where the - transform standardizes the records so the format is the same for all sources - - - ============================================================================ - Methods Implemented in BaseAnalyteSource and BaseWaterLevelSource - ============================================================================ - - _validate_record - Validates the record to ensure it has the required fields - - _get_output_units - Returns the output units for the source - - ============================================================================ - Methods That Need to be Implemented For Each Source - ============================================================================ - - get_records - Returns a dictionary of parameter records where the keys are the site ids - and the values are a list of the parameter records - - _extract_site_records - Returns all records for a single site as a list of records - - _extract_terminal_record - Returns the terminal record for a particular site. This is only used for - summary, not time series, outputs. - - _clean_records (optional) - Returns cleaned records if this function is defined for each source. - Otherwise returns the records as-is - - _extract_source_parameter_units - Returns the units of the parameter records as a list, in the same order as the records themselves - - _extract_parameter_record - Returns a parameter record with standardized fields added. - - - backend.constants.PARAMETER - - backend.constants.PARAMETER_VALUE - - backend.constants.PARAMETER_UNITS - - _extract_source_parameter_results - Returns the parameter results as a list from the records, in the same order as the records themselves - """ - name = "" - # ========================================================================== - # Methods Already Implemented - # ========================================================================== + def __init__(self, transformer=None, validator: Optional[RecordValidator] = None, http_client: httpx.Client | None = None): + super().__init__(transformer=transformer, http_client=http_client) + self._validator = validator if validator is not None else _SubclassValidatorShim(self) + self._summarizer = RecordSummarizer(self) def _extract_earliest_record(self, records: list) -> dict: - """ - Returns the earliest record for a particular site + return self._extract_terminal_record(records, position=EARLIEST) - Parameters - ---------- - records : list - a list of records + def _extract_latest_record(self, records: list) -> dict: + return self._extract_terminal_record(records, position=LATEST) - Returns - ------- - dict - the earliest record - """ - return self._extract_terminal_record(records, bookend=EARLIEST) + def read(self, site_record: SiteRecord | list, use_summarize: bool, start_ind: int, end_ind: int) -> List[ParameterRecord | SummaryRecord] | None: + # read_summary/read_timeseries return homogeneous lists; cast to the + # mixed-element list type the signature advertises (List is invariant). + if use_summarize: + return cast("List[ParameterRecord | SummaryRecord] | None", self.read_summary(site_record, start_ind, end_ind)) + return cast("List[ParameterRecord | SummaryRecord] | None", self.read_timeseries(site_record)) - def _extract_latest_record(self, records: list) -> dict: - """ - Returns the most recent record for a particular site - - Parameters - ---------- - records : list - a list of records - - Returns - ------- - dict - the most recent record - """ - return self._extract_terminal_record(records, bookend=LATEST) - - def read( - self, - site_record: SiteRecord | list, - use_summarize: bool, - start_ind: int, - end_ind: int, - ) -> ( - List[ - AnalyteRecord - | AnalyteSummaryRecord - | WaterLevelRecord - | WaterLevelSummaryRecord - ] - | None - ): - """ - Returns a list of transformed parameter records. Transformed parameter records - are standardized so that all of the records have the same format. They are - defined in the record module. They behave just like a dictionary, but also have the - to_row() method so that a record can be written to a table. - - If use_summarize is True, the summary of records for each site are returned. - Otherwise, the cleaned and sorted records are returned for a site. - - Parameters - ---------- - site_record : SiteRecord - the site record(s) for the location whose parameter records are to be retrieved - - use_summarize : bool - if True, the summary of records for each site are returned - - Returns - -------- - list[AnalyteRecord | AnalyteSummaryRecord | WaterLevelRecord | WaterLevelSummaryRecord] - a list of transformed parameter records - """ + def read_summary(self, site_record: SiteRecord | list, start_ind: int, end_ind: int) -> List[SummaryRecord] | None: if isinstance(site_record, list): - self.log( - f"Gathering {self.name} summary for {len(site_record)} sites. {start_ind}-{end_ind}" - ) + self.log(f"Gathering {self.name} summary for {len(site_record)} sites. {start_ind}-{end_ind}") else: self.log(f"{site_record.id}: Gathering {self.name} data") - all_analyte_records = self.get_records(site_record) - if all_analyte_records: - if not isinstance(site_record, list): - site_record = [site_record] - - # return values - ret = [] - - # iterate over each site record and extract the parameter records for each site - for site in site_record: - site_records = self._extract_site_records(all_analyte_records, site) - if not site_records: - self.warn(f"{site.id}: No records found") - continue - # get cleaned records if _clean_records is defined by the source. This usually removes Nones/Null - cleaned = self._clean_records(site_records) - if not cleaned: - self.warn(f"{site.id} No clean records found") - continue - - if use_summarize: - - # doesn't need to be returned, but can be used to debug/for development - kept_items = [] - skipped_items = [] - - source_results = self._extract_source_parameter_results(cleaned) - source_units = self._extract_source_parameter_units(cleaned) - dates = self._extract_parameter_dates(cleaned) - source_names = self._extract_source_parameter_names(cleaned) - - for source_result, source_unit, date, source_name in zip( - source_results, source_units, dates, source_names - ): - try: - converted_result, conversion_factor, warning_msg = ( - convert_units( - float(source_result), - source_unit, - self._get_output_units(), - source_name, - self.config.parameter, - date, - ) - ) - if warning_msg == "": - kept_items.append(converted_result) - else: - msg = f"{warning_msg} for {site.id}" - self.warn(msg) - except TypeError: - skipped_items.append((site.id, source_result, source_unit)) - except ValueError: - skipped_items.append((site.id, source_result, source_unit)) - - if len(skipped_items) > 0: - self.warn( - f"Skipped results because of formatting: {skipped_items}" - ) - - # if items is None or empty, no records were found or all results were None - if kept_items is not None and len(kept_items): - n = len(kept_items) - - earliest_result = self._extract_earliest_record(cleaned) - latest_result = self._extract_latest_record(cleaned) - if not latest_result: - continue - rec = { - "nrecords": n, - "min": min(kept_items), - "max": max(kept_items), - "mean": sum(kept_items) / n, - "earliest_datetime": earliest_result["datetime"], - "earliest_value": earliest_result["value"], - "earliest_source_units": earliest_result[ - "source_parameter_units" - ], - "earliest_source_name": earliest_result[ - "source_parameter_name" - ], - "latest_datetime": latest_result["datetime"], - "latest_value": latest_result["value"], - "latest_source_units": latest_result[ - "source_parameter_units" - ], - "latest_source_name": latest_result[ - "source_parameter_name" - ], - } - transformed_record = self.transformer.do_transform( - rec, - site, - ) - if transformed_record is None: - continue - else: - ret.append(transformed_record) - else: - cleaned_sorted = [ - self.transformer.do_transform( - self._extract_parameter(record), site - ) - for record in cleaned - if self.transformer.do_transform( - self._extract_parameter(record), site - ) - is not None - ] - if len(cleaned_sorted) == 0: - self.warn(f"{site.id}: No clean records found") - continue - cleaned_sorted = sorted(cleaned_sorted, key=self._sort_func) - ret.append((site, cleaned_sorted)) - return ret + all_records = self.get_records(site_record) + if not all_records: + names = [str(r.id) for r in site_record] if isinstance(site_record, list) else [str(site_record.id)] + self.warn(f"{','.join(names)}: No records found") + return None + + if not isinstance(site_record, list): + site_record = [site_record] + + ret = [] + for site in site_record: + site_records = self._extract_site_records(all_records, site) + if not site_records: + self.warn(f"{site.id}: No records found") + continue + cleaned = self._clean_records(site_records) + if not cleaned: + self.warn(f"{site.id} No clean records found") + continue + result = self._summarize_records(site, cleaned) + if result is not None: + ret.append(result) + return ret + + def read_timeseries(self, site_record: SiteRecord | list) -> List[ParameterRecord] | None: + if isinstance(site_record, list): + self.log(f"Gathering {self.name} timeseries for {len(site_record)} sites") else: - if isinstance(site_record, list): - names = [str(r.id) for r in site_record] - else: - names = [str(site_record.id)] + self.log(f"{site_record.id}: Gathering {self.name} data") - name = ",".join(names) - self.warn(f"{name}: No records found") + all_records = self.get_records(site_record) + if not all_records: + names = [str(r.id) for r in site_record] if isinstance(site_record, list) else [str(site_record.id)] + self.warn(f"{','.join(names)}: No records found") return None - # ========================================================================== - # Methods Implemented in BaseAnalyteSource and BaseWaterLevelSource - # ========================================================================== - - def _validate_record(self, record: dict) -> None: - """ - Determines that all standardized fields are present in the record. - Raises a ValueError if any fields are missing from a record. - - For an analyte, the fields are - - backend.constants.PARAMETER - - backend.constants.PARAMETER_VALUE - - backend.constants.PARAMETER_UNITS - - For a water level, the fields are - - backend.constants.DTW - - backend.constants.DTW_UNITS - - backend.constants.DT_MEASURED - - Parameters - ---------- - record : dict - a record - - Returns - ------- - None - """ - raise NotImplementedError( - f"{self.__class__.__name__} Must implement _validate_record" - ) + if not isinstance(site_record, list): + site_record = [site_record] + + ret = [] + for site in site_record: + site_records = self._extract_site_records(all_records, site) + if not site_records: + self.warn(f"{site.id}: No records found") + continue + cleaned = self._clean_records(site_records) + if not cleaned: + self.warn(f"{site.id} No clean records found") + continue + result = self._build_timeseries_records(site, cleaned) + if result is not None: + ret.append(result) + return ret + + def _summarize_records(self, site, cleaned: list): + return self._summarizer.summarize(site, cleaned) + + def _build_timeseries_records(self, site, cleaned: list): + records = [] + for record in cleaned: + transformed = self.transformer.do_transform(self._extract_parameter(record), site) + if transformed is not None: + records.append(transformed) + if not records: + self.warn(f"{site.id}: No clean records found") + return None + return (site, sorted(records, key=self._sort_func)) def _get_output_units(self) -> str: - """ - Determines the output units for the source from the configuration - - If the source is an analyte source, the output units are backend.config.Config.analyte_output_units - If the source is a water level source, the output units are backend.config.Config.waterlevel_output_units - """ - raise NotImplementedError( - f"{self.__class__.__name__} Must implement _get_output_units" - ) - - # ========================================================================== - # Methods That Need to be Implemented For Each Source - # ========================================================================== + raise NotImplementedError(f"{self.__class__.__name__} Must implement _get_output_units") def _extract_site_records(self, records: list[dict], site_record) -> list: - """ - Returns all records for a single site as a list of records (which are dictionaries). - - Parameters - ---------- - records : dict - a dictionary of lists, where the keys are site ids and the values are parameter records - - site_record : dict - the site record for the location whose parameter records are to be retrieved - - Returns - ------- - list - a list of records for the site - """ if site_record.chunk_size == 1: return records - - raise NotImplementedError( - f"{self.__class__.__name__} Must implement _extract_site_records" - ) + raise NotImplementedError(f"{self.__class__.__name__} Must implement _extract_site_records") def _clean_records(self, records: list) -> list: - """ - Returns cleaned records if this function is defined for each source. - Otherwise returns the records as-is. - - Parameters - ---------- - records : list - a list of records - - Returns - ------- - list - a list of cleaned records if this function is defined for each - source. Otherwise returns the records as is. - """ return records - def _extract_terminal_record(self, records, bookend): - """ - Returns the terminal record for a particular site - - Parameters - ---------- - records : list - a list of records - - bookend : str - determines if the first or last record is retrieved - - Returns - ------- - dict - the most recent record for every site - """ - raise NotImplementedError( - f"{self.__class__.__name__} Must implement _extract_terminal_record" - ) + def _extract_terminal_record(self, records, position: str): + raise NotImplementedError(f"{self.__class__.__name__} Must implement _extract_terminal_record") def _extract_source_parameter_units(self, records: list) -> list: - """ - Returns the units of the parameter records as a list, in the same order as the records themselves - - Parameters - ---------- - records: list - a list of parameter records - - Returns - ------- - list - a list of units for the parameter records in the same order as the records - """ - raise NotImplementedError( - f"{self.__class__.__name__} Must implement _extract_source_parameter_units" - ) + raise NotImplementedError(f"{self.__class__.__name__} Must implement _extract_source_parameter_units") def _extract_parameter_dates(self, records: list) -> list: - """ - Returns the dates of the parameter records as a list, in the same order as the records themselves - - Parameters - ---------- - records: list - a list of parameter records - - Returns - ------- - list - a list of dates for the parameter records in the same order as the records - """ - raise NotImplementedError( - f"{self.__class__.__name__} Must implement _extract_parameter_dates" - ) + raise NotImplementedError(f"{self.__class__.__name__} Must implement _extract_parameter_dates") def _extract_source_parameter_names(self, records: list) -> list: - """ - Returns the source names of the parameter records as a list, in the same order as the records themselves - - Parameters - ---------- - records: list - a list of parameter records - - Returns - ------- - list - a list of source names for the parameter records in the same order as the records - """ - raise NotImplementedError( - f"{self.__class__.__name__} Must implement _extract_source_parameter_names" - ) + raise NotImplementedError(f"{self.__class__.__name__} Must implement _extract_source_parameter_names") def _extract_parameter_record(self, record: dict) -> dict: - """ - Returns a parameter record with standardized fields added. This is only used for time series, not summary outputs - - For an analyte, the fields are - - backend.constants.PARAMETER_NAME_SOURCE - - backend.constants.PARAMETER_NAME_DIE - - backend.constants.PARAMETER_VALUE - - backend.constants.PARAMETER_UNITS - - Parameters - ---------- - record: dict - a parameter record - - Returns - ------- - dict - the parameter record with the fields added - """ - raise NotImplementedError( - f"{self.__class__.__name__} Must implement _extract_parameter_record" - ) + raise NotImplementedError(f"{self.__class__.__name__} Must implement _extract_parameter_record") def _extract_source_parameter_results(self, records: list) -> list: - """ - Returns the parameter results as a list from the records, in the same order as the records themselves. This is only used for summary outputs, not time serie - - Parameters - ---------- - records: list - a list of parameter records for a site - - Returns - ------- - list - a list of parameter results from the records, in the same order as the records - """ - raise NotImplementedError( - f"{self.__class__.__name__} Must implement _extract_source_parameter_results" - ) + raise NotImplementedError(f"{self.__class__.__name__} Must implement _extract_source_parameter_results") def _extract_parameter(self, record: dict) -> dict: - """ - Extracts a parameter record from a list of records. This is only used for time series, not summary outputs - - Parameters - ---------- - record : dict - a record - - Returns - -------- - dict - a record with the fields "datetime_measured", "parameter_value", "parameter_units", and "parameter" added - """ record = self._extract_parameter_record(record) - self._validate_record(record) + self._validator.validate(record) return record def _sort_func(self, x): - """ - Sorting function to sort the records by date_measured - - Parameters - ---------- - x : a record - - Returns - ------- - datetime - the date_measured of the record - """ return x.date_measured + # deprecated: override via validator= __init__ arg instead + def _validate_record(self, record: dict) -> None: + raise NotImplementedError(f"{self.__class__.__name__} Must implement _validate_record") -class BaseAnalyteSource(BaseParameterSource): - """ - Base class for all analyte sources. - - See BaseParameterSource for the methods that need to be implemented for each source - """ +class BaseAnalyteSource(BaseParameterSource): name = "analyte" + def __init__(self, transformer=None, http_client: httpx.Client | None = None): + super().__init__(transformer=transformer, validator=AnalyteRecordValidator(), http_client=http_client) + def _get_output_units(self): return self.config.analyte_output_units - def _validate_record(self, record): - record[PARAMETER_NAME] = self.config.parameter - for k in (PARAMETER_VALUE, PARAMETER_UNITS, DT_MEASURED): - if k not in record: - raise ValueError(f"Invalid record. Missing {k}") - class BaseWaterLevelSource(BaseParameterSource): - """ - Base class for all water level sources. - - See BaseParameterSource for the methods that need to be implemented for each source - """ - name = "water levels" + def __init__(self, transformer=None, http_client: httpx.Client | None = None): + super().__init__(transformer=transformer, validator=WaterLevelRecordValidator(), http_client=http_client) + def _get_output_units(self): return self.config.waterlevel_output_units def _extract_source_parameter_units(self, records): return [FEET for _ in records] - def _validate_record(self, record): - for k in (PARAMETER_VALUE, PARAMETER_UNITS, DT_MEASURED): - if k not in record: - raise ValueError(f"Invalid record. Missing {k}") - - -class BaseFileSource(BaseSource): - """ - Base class for all file sources - """ - - name = "files" - # ============= EOF ============================================= diff --git a/backend/transformer.py b/backend/transformer.py index 4c8cbb8..32c89c5 100644 --- a/backend/transformer.py +++ b/backend/transformer.py @@ -13,8 +13,6 @@ # See the License for the specific language governing permissions and # limitations under the License. # =============================================================================== -import click -import pprint from datetime import datetime, date, timedelta import shapely @@ -22,31 +20,21 @@ from backend.bounding_polygons import NM_BOUNDARY_BUFFERED from backend.constants import ( - MILLIGRAMS_PER_LITER, - PARTS_PER_MILLION, - PARTS_PER_BILLION, FEET, METERS, - TONS_PER_ACRE_FOOT, - MICROGRAMS_PER_LITER, DT_MEASURED, DTW, EARLIEST, LATEST, ) from backend.geo_utils import datum_transform, ALLOWED_DATUMS -from backend.logger import Loggable +from backend.logger import make_logger from backend.record import ( - WaterLevelSummaryRecord, - WaterLevelRecord, + ParameterRecord, SiteRecord, - AnalyteSummaryRecord, SummaryRecord, - AnalyteRecord, ) -logger = Loggable() - def transform_horizontal_datum( x: int | float, y: int | float, in_datum: str, out_datum: str @@ -125,129 +113,6 @@ def transform_length_units( return value, out_unit -def convert_units( - input_value: int | float | str, - input_units: str, - output_units: str, - source_parameter_name: str, - die_parameter_name: str, - dt: str | None = None, -) -> tuple[float, float | None, str]: - """ - Converts the following units for any parameter value: - - Concentration: - - mg/L to ppm - - ppm to mg/L - - ton/ac-ft to mg/L - - ug/L to mg/L - - mg/L CaCO3 to mg/L - - mg/L N to mg/L (for NO3) - - length: - - ft to m - - m to ft - - Parameters - -------- - input_value: int | float | str - The value to convert - - input_units: str - The input unit of the value - - output_units: str - The output unit of the value - - source_parameter_name: str - The name of the parameter from the source - - die_parameter_name: str - The name of the parameter as it is called in the DIE - - dt: str - The date of the record - - Returns - -------- - tuple[float, float, str] - converted value, conversion factor, warning message - """ - warning = "" - conversion_factor = None - - input_value = float(input_value) - input_units = input_units.strip().lower() - output_units = output_units.strip().lower() - source_parameter_name = source_parameter_name.strip().lower() - die_parameter_name = die_parameter_name.strip().lower() - - mgl = MILLIGRAMS_PER_LITER.lower() - ugl = MICROGRAMS_PER_LITER.lower() - ppm = PARTS_PER_MILLION.lower() - ppb = PARTS_PER_BILLION.lower() - tpaf = TONS_PER_ACRE_FOOT.lower() - ft = FEET.lower() - m = METERS.lower() - - """ - Each output_unit block needs a check for if input_units == output_units. - - This should go at the end of each block because there are some cases where - the input_units == output_units, but the conversion factor is not 1 due to - the source_parameter_name (e.g. nitrate as n). - """ - if die_parameter_name == "ph": - conversion_factor = 1.0 - elif die_parameter_name in ["conductivity","specific_conductance"]: - # mg/l is assumed to be a mistake. the name of the source parameter is "CONDUCTIVITY @ 25 C UMHOS/CM" - if input_units in ["�mhos/cm", "umho/cm", "cm-1", "micromhos per centimeter", "mg/l", "su", "us/cm", "us/cm @25c", "µs/cm", "\u03bcs/cm",]: - conversion_factor = 1.0 - elif output_units == mgl: - if input_units in ["mg/l caco3", "mg/l caco3**"]: - if die_parameter_name == "bicarbonate": - conversion_factor = 1.22 - elif die_parameter_name == "calcium": - conversion_factor = 0.4 - elif die_parameter_name == "carbonate": - conversion_factor = 0.6 - elif input_units == "mg/l as n": - conversion_factor = 4.427 - elif input_units in ["mg/l asno3", "mg/l as no3"]: - conversion_factor = 1.0 - elif input_units == "ug/l as n": - conversion_factor = 0.004427 - elif input_units == "pci/l": - conversion_factor = 0.00149 - elif input_units in (ugl, ppb): - conversion_factor = 0.001 - elif input_units == tpaf: - conversion_factor = 735.47 - elif input_units == ppm: - conversion_factor = 1.0 - elif input_units == output_units: - if source_parameter_name in ["nitrate as n", "nitrate (as n)"]: - conversion_factor = 4.427 - else: - conversion_factor = 1.0 - elif output_units == ft: - if input_units in [m, "meters"]: - conversion_factor = 3.28084 - elif input_units in [ft, "feet"]: - conversion_factor = 1.0 - elif output_units == m: - if input_units in [ft, "feet"]: - conversion_factor = 0.3048 - elif input_units in [m, "meters"]: - conversion_factor = 1.0 - - if conversion_factor: - return input_value * conversion_factor, conversion_factor, warning - else: - warning = f"Failed to convert {input_value} {input_units} {source_parameter_name} (source) to {output_units} {die_parameter_name} (die) on {dt}" - return input_value, conversion_factor, warning - - def standardize_datetime(dt, record_id): if isinstance(dt, tuple): dt = [di for di in dt if di is not None] @@ -301,47 +166,17 @@ def standardize_datetime(dt, record_id): return dt.strftime("%Y-%m-%d"), tt -class BaseTransformer(Loggable): - """ - Base class for transforming records. Transformers are used in BaseSiteSource and BaseParameterSource to transform records - - ============================================================================ - Methods With Universal Implementations (Already Implemented) - ============================================================================ - do_transform - Transforms a record, site or parameter, into a standardized format - - contained - Checks if a point is contained within a polygon - - ============================================================================ - Methods That Need to be Implemented For Each SiteTransformer - ============================================================================ - _transform - Transforms a record into a standardized format - - _post_transform - - ============================================================================ - Methods Implemented In Each ParameterTransformer (Don't Need To Be Implemented For Each Source) - ============================================================================ - _transform - - _get_parameter - - ============================================================================ - Methods That Are Implemented In Each ParameterTransformer and SiteTransformer (Don't Need To Be Implemented For Each Source) - ============================================================================ - _get_record_klass - """ - - _cached_polygon = None - # config = None +class BaseTransformer: + _polygon_cache: dict = {} check_contained = True - # ========================================================================== - # Methods Already Implemented - # ========================================================================== + def __init__(self, converter=None): + from backend.converter import StandardUnitConverter + self.converter = converter if converter is not None else StandardUnitConverter() + _l = make_logger(self.__class__.__name__) + self.log = _l.log + self.warn = _l.warn + self.debug = _l.debug def set_config(self, config): """ @@ -357,196 +192,105 @@ def set_config(self, config): def do_transform( self, inrecord: dict, *args, **kw - ) -> ( - AnalyteRecord - | WaterLevelRecord - | SiteRecord - | AnalyteSummaryRecord - | WaterLevelSummaryRecord - | SummaryRecord - | None - ): - """ - Transforms a record, site or parameter, into a standardized format. - Populating the correct fields is performed in _transform, then the - record is standardized in this method. This includes standardizing the datetime - for all record types and geographic/well information for site and summary - records. - - The fields for a site record are: - - source - - id - - name - - latitude - - longitude - - elevation - - elevation_units - - horizontal_datum - - vertical_datum - - usgs_site_id (optional) - - alternate_site_id (optional) - - aquifer (optional) - - well_depth (optional) - - well_depth_units (optional) - - The fields for a parameter record are: - - parameter_name - - parameter_value - - parameter_units - - date_measured - - time_measured - - source_parameter_name - - source_parameter_units - - conversion_factor - - Parameters - -------- - inrecord: dict - The record to transform - - Returns - -------- - AnalyteRecord | WaterLevelRecord | SiteRecord | AnalyteSummaryRecord | WaterLevelSummaryRecord | SummaryRecord - The transformed and standardized record - """ - # _transform needs to be implemented by each SiteTransformer - # _transform is already implemented in each ParameterTransformer + ) -> ParameterRecord | SiteRecord | SummaryRecord | None: transformed_record = self._transform(inrecord, *args, **kw) if not transformed_record: return None - - # ensure that a site or summary record is contained within the boundaing polygon - if "longitude" in transformed_record and "latitude" in transformed_record: - if not self.contained( - transformed_record["longitude"], transformed_record["latitude"] - ): - self.warn( - f"Skipping site {transformed_record['id']}. It is not within the defined geographic bounds" - ) + if not self._apply_geographic_filter(transformed_record): + return None + self._post_transform(transformed_record, *args, **kw) + self._standardize_datetime(transformed_record) + klass = self._get_record_klass() + transformed_record["record_type"] = self._get_record_type() + klassed_record = klass(transformed_record) + if isinstance(klassed_record, (SiteRecord, SummaryRecord)): + klassed_record = self._apply_datum_transform(klassed_record) + if klassed_record is None: return None + klassed_record = self._apply_elevation_transform(klassed_record) + klassed_record = self._apply_well_depth_transform(klassed_record) + elif klassed_record.record_type in ("analytes", "waterlevels"): + klassed_record = self._apply_unit_conversion(klassed_record) + return klassed_record - self._post_transform(transformed_record, *args, **kw) + def _apply_geographic_filter(self, transformed_record: dict) -> bool: + if "longitude" not in transformed_record or "latitude" not in transformed_record: + return True + if not self.contained(transformed_record["longitude"], transformed_record["latitude"]): + self.warn(f"Skipping site {transformed_record['id']}. It is not within the defined geographic bounds") + return False + return True - # standardize datetime + def _standardize_datetime(self, transformed_record: dict) -> None: dt = transformed_record.get(DT_MEASURED) if dt: d, t = standardize_datetime(dt, transformed_record["id"]) - transformed_record["date_measured"] = d - transformed_record["time_measured"] = t else: mrd = transformed_record.get("latest_datetime") - if mrd: - d, t = standardize_datetime(mrd, transformed_record["id"]) - transformed_record["date_measured"] = d - transformed_record["time_measured"] = t - - # convert to proper record type - # a record klass holds the original record's data as a dictionary, and has methods to update the record's data and get the record's data - klass = self._get_record_klass() - klassed_record = klass(transformed_record) - - # update the record's geographic information and well data if it is a SiteRecord or SummaryRecord - # transforms the horizontal datum and lon/lat coordinates to WGS84 - # transforms the elevation and well depth units to the output unit specified in the config - # transforms the well depth and well depth units to the output unit specified in the config - if isinstance(klassed_record, (SiteRecord, SummaryRecord)): - y = float(klassed_record.latitude) - x = float(klassed_record.longitude) - - if x == 0 or y == 0: - self.warn( - f"Skipping site {klassed_record.id}. Latitude or Longitude is 0" - ) - return None - - input_horizontal_datum = klassed_record.horizontal_datum - - if input_horizontal_datum not in ALLOWED_DATUMS: - self.warn( - f"Skipping site {klassed_record.id}. Datum {input_horizontal_datum} cannot be processed" - ) - return None - - output_elevation_units = "" - well_depth_units = "" - output_horizontal_datum = "WGS84" - if self.config: - output_elevation_units = self.config.output_elevation_units - well_depth_units = self.config.output_well_depth_units - output_horizontal_datum = self.config.output_horizontal_datum - - lng, lat, datum = transform_horizontal_datum( - x, - y, - input_horizontal_datum, - output_horizontal_datum, - ) - - if not self.in_nm(lng, lat): - self.warn( - f"Skipping site {klassed_record.id}. Coordinates {x}, {y} with datum {input_horizontal_datum} are not within 25km of New Mexico" - ) - return None + if not mrd: + return + d, t = standardize_datetime(mrd, transformed_record["id"]) + transformed_record["date_measured"] = d + transformed_record["time_measured"] = t + + def _apply_datum_transform(self, klassed_record): + y = float(klassed_record.latitude) + x = float(klassed_record.longitude) + if x == 0 or y == 0: + self.warn(f"Skipping site {klassed_record.id}. Latitude or Longitude is 0") + return None + if not (-180 <= x <= 180) or not (-90 <= y <= 90): + self.warn(f"Skipping site {klassed_record.id}. Coordinates out of range: lng={x}, lat={y}") + return None + input_datum = klassed_record.horizontal_datum + if input_datum not in ALLOWED_DATUMS: + self.warn(f"Skipping site {klassed_record.id}. Datum {input_datum} cannot be processed") + return None + output_datum = self.config.output_horizontal_datum if self.config else "WGS84" + lng, lat, datum = transform_horizontal_datum(x, y, input_datum, output_datum) + if not self.in_nm(lng, lat): + self.warn(f"Skipping site {klassed_record.id}. Coordinates {x}, {y} with datum {input_datum} are not within 25km of New Mexico") + return None + klassed_record.update(latitude=lat, longitude=lng, horizontal_datum=datum) + return klassed_record - klassed_record.update(latitude=lat) - klassed_record.update(longitude=lng) - klassed_record.update(horizontal_datum=datum) + def _apply_elevation_transform(self, klassed_record): + units = self.config.output_elevation_units if self.config else "" + elevation, unit = transform_length_units(klassed_record.elevation, klassed_record.elevation_units, units) + klassed_record.update(elevation=elevation, elevation_units=unit) + return klassed_record - elevation, elevation_unit = transform_length_units( - klassed_record.elevation, - klassed_record.elevation_units, - output_elevation_units, - ) - klassed_record.update(elevation=elevation) - klassed_record.update(elevation_units=elevation_unit) + def _apply_well_depth_transform(self, klassed_record): + units = self.config.output_well_depth_units if self.config else "" + depth, unit = transform_length_units(klassed_record.well_depth, klassed_record.well_depth_units, units) + klassed_record.update(well_depth=depth, well_depth_units=unit) + return klassed_record - well_depth, well_depth_unit = transform_length_units( - klassed_record.well_depth, - klassed_record.well_depth_units, - well_depth_units, + def _apply_unit_conversion(self, klassed_record): + output_units = ( + self.config.analyte_output_units + if klassed_record.record_type == "analytes" + else self.config.waterlevel_output_units + ) + source_result = klassed_record.parameter_value + source_unit = klassed_record.source_parameter_units + source_name = klassed_record.source_parameter_name + dt = klassed_record.date_measured + warning_msg = "" + conversion_factor = None + try: + converted_result, conversion_factor, warning_msg = self.converter.convert( + float(source_result), source_unit, output_units, source_name, self.config.parameter, dt ) - klassed_record.update(well_depth=well_depth) - klassed_record.update(well_depth_units=well_depth_unit) - - # update the units to the output unit for analyte records - # this is done after converting the units to the output unit for the analyte records - # convert the parameter value to the output unit specified in the config - elif isinstance(klassed_record, (AnalyteRecord, WaterLevelRecord)): - if isinstance(klassed_record, AnalyteRecord): - output_units = self.config.analyte_output_units - else: - output_units = self.config.waterlevel_output_units - - source_result = klassed_record.parameter_value - source_unit = klassed_record.source_parameter_units - dt = klassed_record.date_measured - source_name = klassed_record.source_parameter_name - conversion_factor = None # conversion factor will remain None if record is kept for time series and cannot be converted, such as non-detects - warning_msg = "" - try: - converted_result, conversion_factor, warning_msg = convert_units( - float(source_result), - source_unit, - output_units, - source_name, - self.config.parameter, - dt, - ) - if warning_msg != "": - msg = f"{warning_msg} for {klassed_record.id}" - self.warn(msg) - except (TypeError, ValueError): - msg = f"Keeping {source_result} for {klassed_record.id} on {klassed_record.date_measured} for time series data" - self.warn(msg) - converted_result = source_result - - if warning_msg == "": - klassed_record.update(conversion_factor=conversion_factor) - klassed_record.update(parameter_value=converted_result) - else: - klassed_record = None - - return klassed_record + if warning_msg: + self.warn(f"{warning_msg} for {klassed_record.id}") + except (TypeError, ValueError): + self.warn(f"Keeping {source_result} for {klassed_record.id} on {dt} for time series data") + converted_result = source_result + if warning_msg == "": + klassed_record.update(conversion_factor=conversion_factor, parameter_value=converted_result) + return klassed_record + return None def in_nm(self, lng: float | int | str, lat: float | int | str) -> bool: """ @@ -594,14 +338,11 @@ def contained( """ config = self.config if config and config.has_bounds() and self.check_contained: - if not self._cached_polygon: - poly = shapely.wkt.loads(config.bounding_wkt()) - self._cached_polygon = poly - else: - poly = self._cached_polygon - - pt = Point(lng, lat) - return poly.contains(pt) + wkt = config.bounding_wkt() + if wkt not in BaseTransformer._polygon_cache: + BaseTransformer._polygon_cache[wkt] = shapely.wkt.loads(wkt) + poly = BaseTransformer._polygon_cache[wkt] + return poly.contains(Point(lng, lat)) return True @@ -683,6 +424,9 @@ def _post_transform(self, *args, **kw): def _get_record_klass(self): raise NotImplementedError + def _get_record_type(self) -> str | None: + return None + class SiteTransformer(BaseTransformer): def _get_record_klass(self) -> type[SiteRecord]: @@ -747,22 +491,8 @@ def _transform(self, record, site_record): rec.update(source_id) return rec - def _transform_terminal_record(self, record, site_id, bookend): - """ - Convert either the earliest or latest record to the standard format. - - Parameters - -------- - record: dict - The record to convert - - site_id: str - The site ID for the record - - bookend: str - The bookend of the record to convert. Either "earliest" or "latest" - """ - if bookend == EARLIEST: + def _transform_terminal_record(self, record, site_id, position): + if position == EARLIEST: datetime_key = "earliest_datetime" date_key = "earliest_date" time_key = "earliest_time" @@ -770,7 +500,7 @@ def _transform_terminal_record(self, record, site_id, bookend): unit_key = "earliest_units" source_units_key = "earliest_source_units" source_name_key = "earliest_source_name" - elif bookend == LATEST: + elif position == LATEST: datetime_key = "latest_datetime" date_key = "latest_date" time_key = "latest_time" @@ -781,7 +511,7 @@ def _transform_terminal_record(self, record, site_id, bookend): dt, tt = standardize_datetime(record[datetime_key], site_id) parameter_name, unit = self._get_parameter_name_and_units() - converted_value, conversion_factor, warning_msg = convert_units( + converted_value, conversion_factor, warning_msg = self.converter.convert( record[value_key], record[source_units_key], unit, @@ -804,23 +534,11 @@ def _transform_latest_record(self, record, site_id): class WaterLevelTransformer(ParameterTransformer): - def _get_record_klass( - self, - ) -> type[WaterLevelRecord] | type[WaterLevelSummaryRecord]: - """ - Returns the WaterLevelRecord class to use for the transformer for - water level records if config.output_summary is False, otherwise - returns the WaterLevelSummaryRecord class + def _get_record_klass(self) -> type[ParameterRecord] | type[SummaryRecord]: + return SummaryRecord if self.config.output_summary else ParameterRecord - Returns - -------- - WaterLevelRecord | WaterLevelSummaryRecord - The record class to use for the transformer - """ - if self.config.output_summary: - return WaterLevelSummaryRecord - else: - return WaterLevelRecord + def _get_record_type(self) -> str: + return "waterlevels" def _get_parameter_name_and_units(self) -> tuple: """ @@ -835,21 +553,11 @@ def _get_parameter_name_and_units(self) -> tuple: class AnalyteTransformer(ParameterTransformer): - def _get_record_klass(self) -> type[AnalyteRecord] | type[AnalyteSummaryRecord]: - """ - Returns the AnalyteRecord class to use for the transformer for - water level records if config.output_summary is False, otherwise - returns the AnalyteSummaryRecord class + def _get_record_klass(self) -> type[ParameterRecord] | type[SummaryRecord]: + return SummaryRecord if self.config.output_summary else ParameterRecord - Returns - -------- - AnalyteRecord | AnalyteSummaryRecord - The record class to use for the transformer - """ - if self.config.output_summary: - return AnalyteSummaryRecord - else: - return AnalyteRecord + def _get_record_type(self) -> str: + return "analytes" def _get_parameter_name_and_units(self) -> tuple: """ diff --git a/backend/unifier.py b/backend/unifier.py index a3a5830..a52f0c6 100644 --- a/backend/unifier.py +++ b/backend/unifier.py @@ -15,11 +15,12 @@ # =============================================================================== import shapely -from backend.config import Config, get_source, OutputFormat -from backend.logger import setup_logging +from backend.config import Config, get_source +from backend.logger import make_logger + +_log = make_logger("unifier") from backend.constants import WATERLEVELS -from backend.persister import BasePersister -from backend.persisters.geoserver import GeoServerPersister +from backend.persisters.factory import make_persister from backend.source import BaseSiteSource from backend.exceptions import USGSRateLimitError, PartialOrNoDataError @@ -46,7 +47,7 @@ def health_check(source: BaseSiteSource) -> bool | None: def unify_analytes(config): - print("Unifying analytes\n") + _log.log("Unifying analytes") # config.report() -- report is done in cli.py, no need to do it twice config.validate() @@ -57,7 +58,7 @@ def unify_analytes(config): def unify_waterlevels(config): - print("Unifying waterlevels\n") + _log.log("Unifying waterlevels") # config.report() -- report is done in cli.py, no need to do it twice config.validate() @@ -69,7 +70,7 @@ def unify_waterlevels(config): def unify_sites(config): - print("Unifying sites only\n") + _log.log("Unifying sites only") # config.report() -- report is done in cli.py, no need to do it twice config.validate() @@ -233,11 +234,10 @@ def _site_wrapper(site_source, parameter_source, persister, config): ] break - except BaseException: + except Exception: import traceback - exc = traceback.format_exc() - config.warn(exc) + config.warn(traceback.format_exc()) config.warn(f"Failed to unify {site_source}") @@ -246,10 +246,7 @@ def _unify_parameter( sources, ): - if config.output_format == OutputFormat.GEOSERVER: - persister = GeoServerPersister(config) - else: - persister = BasePersister(config) + persister = make_persister(config) for site_source, parameter_source in sources: _site_wrapper( @@ -273,17 +270,6 @@ def _unify_parameter( persister.finalize(config.output_name) -def get_sources_in_polygon(polygon): - # polygon = shapely.wkt.loads(polygon) - sources = get_sources() - rets = [] - for source in sources: - print(source) - if source.intersects(polygon): - rets.append(source.tag) - return rets - - def get_county_bounds(county): config = Config() config.county = county @@ -333,84 +319,4 @@ def get_sources(config=None): return sources -def generate_site_bounds(): - source = get_source("bernco") - source.generate_bounding_polygon() - - -def analyte_unification_test(): - cfg = Config() - cfg.county = "chaves" - cfg.county = "eddy" - - cfg.analyte = "TDS" - cfg.output_summary = True - - # analyte testing - cfg.use_source_wqp = False - # cfg.use_source_nmbgmr = False - cfg.use_source_iscsevenrivers = False - cfg.use_source_bor = False - cfg.use_source_dwb = False - cfg.site_limit = 10 - - unify_analytes(cfg) - - -def waterlevel_unification_test(): - cfg = Config() - cfg.county = "chaves" - # cfg.county = "eddy" - # cfg.bbox = "-104.5 32.5,-104 33" - # cfg.start_date = "2020-01-01" - # cfg.end_date = "2020-5-01" - cfg.output_summary = False - cfg.output_name = "test00112233" - # cfg.output_summary = True - cfg.output_single_timeseries = True - - cfg.use_source_nwis = False - cfg.use_source_nmbgmr = False - cfg.use_source_iscsevenrivers = False - cfg.use_source_pvacd = False - # cfg.use_source_oseroswell = False - cfg.use_source_bernco = False - cfg.use_source_iscsevenrivers = False - cfg.use_source_nmose_isc_seven_rivers = False - cfg.use_source_ebid = False - # cfg.site_limit = 10 - - unify_waterlevels(cfg) - - -def get_datastream(siteid): - import httpx - - resp = httpx.get( - f"https://st2.newmexicowaterdata.org/FROST-Server/v1.1/Locations({siteid})?$expand=Things/Datastreams" - ) - obj = resp.json() - return obj["Things"][0]["Datastreams"][0] - - -def get_datastreams(): - s = get_source("pvacd") - for si in s.read_sites(): - ds = get_datastream(si.id) - print(si, si.id, ds["@iot.id"]) - - -# if __name__ == "__main__": -# test_waterlevel_unification() -# root = logging.getLogger() -# root.setLevel(logging.DEBUG) -# shandler = logging.StreamHandler() -# get_sources(Config()) -# setup_logging() -# site_unification_test() -# waterlevel_unification_test() -# analyte_unification_test() -# print(health_check("nwis")) -# generate_site_bounds() - # ============= EOF ============================================= diff --git a/dagster_cloud.yaml b/dagster_cloud.yaml new file mode 100644 index 0000000..7896743 --- /dev/null +++ b/dagster_cloud.yaml @@ -0,0 +1,9 @@ +locations: + - location_name: die-orchestration + code_source: + module_name: orchestration.definitions + build: + # PEX fast-deploy build root. orchestration/pyproject.toml declares the + # dagster deps and the `nmuwd` path-dependency (tool.uv.sources); the + # builder recurses into the repo root to collect backend/ + its deps. + directory: orchestration diff --git a/frontend/api/app.py b/frontend/api/app.py index bddd34d..5b7a06e 100644 --- a/frontend/api/app.py +++ b/frontend/api/app.py @@ -15,9 +15,7 @@ # =============================================================================== import hashlib import json -import multiprocessing import os -import time from typing import Optional from fastapi import FastAPI, HTTPException diff --git a/frontend/cli.py b/frontend/cli.py index 34a3a34..be226cf 100644 --- a/frontend/cli.py +++ b/frontend/cli.py @@ -37,84 +37,84 @@ def cli(): click.option( "--no-bernco", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude Bernalillo County Water Authority data. Default is to include", ), click.option( "--no-bor", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude BoR data. Default is to include", ), click.option( "--no-cabq", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude CABQ data. Default is to include", ), click.option( "--no-ebid", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude EBID data. Default is to include", ), click.option( "--no-nmbgmr-amp", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude NMBGMR AMP data. Default is to include", ), click.option( "--no-nmed-dwb", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude NMED DWB data. Default is to include", ), click.option( "--no-nmose-isc-seven-rivers", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude NMOSE ISC Seven Rivers data. Default is to include", ), click.option( "--no-nmose-pod", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude NMOSE POD data. Default is to include", ), click.option( "--no-nmose-roswell", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude NMOSE Roswell data. Default is to include", ), click.option( "--no-nwis", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude NWIS data. Default is to include", ), click.option( "--no-pvacd", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude PVACD data. Default is to include", ), click.option( "--no-wqp", is_flag=True, - default=True, + default=False, show_default=True, help="Exclude WQP data. Default is to include", ), @@ -317,7 +317,7 @@ def weave( lcs = locals() if config_agencies: for agency in config_agencies: - setattr(config, f"use_source_{agency}", lcs.get(f"no_{agency}", False)) + setattr(config, f"use_source_{agency}", not lcs.get(f"no_{agency}", False)) # dates config.start_date = start_date config.end_date = end_date @@ -400,7 +400,7 @@ def sites( if config_path is None: lcs = locals() for agency in config_agencies: - setattr(config, f"use_source_{agency}", lcs.get(f"no_{agency}", False)) + setattr(config, f"use_source_{agency}", not lcs.get(f"no_{agency}", False)) config.output_dir = output_dir config.sites_only = True diff --git a/mypy.ini b/mypy.ini deleted file mode 100644 index 4904098..0000000 --- a/mypy.ini +++ /dev/null @@ -1,4 +0,0 @@ -[mypy] -ignore_missing_imports = True -exclude = ^(venv|.github|.mypy_cache|.pytest_cache|nmuwd.egg-info|__pycache__|build|tests/archived) -plugins = sqlalchemy.ext.mypy.plugin diff --git a/orchestration/Dockerfile b/orchestration/Dockerfile new file mode 100644 index 0000000..47e54f7 --- /dev/null +++ b/orchestration/Dockerfile @@ -0,0 +1,40 @@ +FROM python:3.12-slim + +WORKDIR /app + +# Install uv +COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv + +# Install system deps needed by geopandas / shapely +RUN apt-get update && apt-get install -y --no-install-recommends \ + libgdal-dev \ + libgeos-dev \ + && rm -rf /var/lib/apt/lists/* + +# Copy lockfiles and project manifests first (layer cache) +COPY pyproject.toml uv.lock ./ +COPY orchestration/pyproject.toml ./orchestration/ + +# Install all deps (root package + orchestration) +RUN uv sync --frozen --extra gcs && \ + uv pip install \ + dagster>=1.8 \ + dagster-gcp>=0.24 \ + google-cloud-storage \ + google-cloud-secret-manager \ + Jinja2 + +# Copy source code +COPY backend/ ./backend/ +COPY frontend/ ./frontend/ +COPY orchestration/ ./orchestration/ + +ENV PYTHONPATH=/app +ENV DAGSTER_HOME=/app/.dagster + +# Cloud Run Job: PRODUCT_ID env var selects which asset to materialize. +# Cloud Scheduler sets PRODUCT_ID in the job invocation. +CMD ["sh", "-c", \ + "uv run dagster asset materialize \ + -f orchestration/definitions.py \ + --select ${PRODUCT_ID}"] diff --git a/orchestration/README.md b/orchestration/README.md new file mode 100644 index 0000000..2577fd1 --- /dev/null +++ b/orchestration/README.md @@ -0,0 +1,83 @@ +# DIE Orchestration + +Dagster-based pipeline that runs on a schedule, fetches data from 12 NM water sources, +and writes OGC Feature Collections to GCS for serving via pygeoapi. + +## Architecture + +``` +Cloud Scheduler → Cloud Run Job (this image) + └── Dagster asset materialize + ├── DIE unifier (backend/) + ├── OGCFeaturesPersister → .geojson + └── GCSResource → gs://die-products/ +``` + +## Products + +Configured in `config/products.yaml`. Each product becomes a Dagster asset + Cloud Scheduler job. + +## Local Development + +```bash +# Install all deps +uv sync --extra gcs +uv pip install dagster dagster-gcp + +# Run a specific product locally (uses local filesystem, no GCS) +PRODUCT_ID=nm_waterlevels_summary \ +uv run dagster asset materialize -f orchestration/definitions.py --select nm_waterlevels_summary + +# View asset graph in Dagster UI +uv run dagster dev -f orchestration/definitions.py +``` + +## Environment Variables + +| Variable | Source | Description | +|----------|--------|-------------| +| `PRODUCT_ID` | Cloud Scheduler | Which asset to materialize | +| `GCS_BUCKET` | Cloud Run env | GCS bucket for output (default: `die-products`) | +| `USGS_API_KEY` | Secret Manager | USGS rate-limit key | + +## GCP Setup + +### Service Account + +```bash +gcloud iam service-accounts create die-orchestration-sa \ + --display-name="DIE Orchestration" + +# GCS write access +gcloud storage buckets add-iam-policy-binding gs://die-products \ + --member="serviceAccount:die-orchestration-sa@PROJECT_ID.iam.gserviceaccount.com" \ + --role="roles/storage.objectAdmin" + +# Secret Manager read +gcloud projects add-iam-policy-binding PROJECT_ID \ + --member="serviceAccount:die-orchestration-sa@PROJECT_ID.iam.gserviceaccount.com" \ + --role="roles/secretmanager.secretAccessor" +``` + +### Build & Deploy + +```bash +# Build image +gcloud builds submit --config orchestration/cloudbuild.yaml . + +# Deploy job +sed -i 's/PROJECT_ID/your-project-id/g' orchestration/cloudrun.yaml +gcloud run jobs replace orchestration/cloudrun.yaml --region us-central1 + +# Create Cloud Scheduler trigger per product +gcloud scheduler jobs create http die-nm_waterlevels_summary \ + --schedule="0 6 * * *" \ + --time-zone="UTC" \ + --uri="https://us-central1-run.googleapis.com/apis/run.googleapis.com/v1/namespaces/PROJECT_ID/jobs/die-orchestration:run" \ + --message-body='{"overrides": {"containerOverrides": [{"env": [{"name": "PRODUCT_ID", "value": "nm_waterlevels_summary"}]}]}}' \ + --oauth-service-account-email=die-orchestration-sa@PROJECT_ID.iam.gserviceaccount.com +``` + +## pygeoapi + +See `pygeoapi/README.md` for serving the GCS-stored products via OGC API - Features. diff --git a/orchestration/__init__.py b/orchestration/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/orchestration/assets/__init__.py b/orchestration/assets/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/orchestration/assets/analytes.py b/orchestration/assets/analytes.py new file mode 100644 index 0000000..da6c1f9 --- /dev/null +++ b/orchestration/assets/analytes.py @@ -0,0 +1,45 @@ +import tempfile +from pathlib import Path + +import dagster as dg + +from backend.unifier import unify_analytes +from backend.persisters.ogc_features import dump_summary_collection +from orchestration.resources.die_config import DIEConfigResource +from orchestration.resources.gcs import GCSResource + + +def build_analyte_summary_asset(product: dict): + @dg.asset(name=product["id"], group_name="analytes") + def _analyte_asset( + die_config: DIEConfigResource, + gcs: GCSResource, + ) -> dg.MaterializeResult: + config = die_config.get_config(product) + config.output_summary = True + + with tempfile.TemporaryDirectory() as tmpdir: + unify_analytes(config) + + persister = getattr(config, "_persister", None) + records = persister.records if persister else [] + + out = Path(tmpdir) / "collection.geojson" + meta = { + "id": product["id"], + "title": product.get("title", product["id"]), + "description": product.get("description", ""), + } + dump_summary_collection(str(out), records, meta) + + info = gcs.upload_product(str(out), product["id"]) + + return dg.MaterializeResult( + metadata={ + "feature_count": dg.MetadataValue.int(info["feature_count"]), + "dated_uri": dg.MetadataValue.url(info["dated_uri"]), + "latest_uri": dg.MetadataValue.url(info["latest_uri"]), + } + ) + + return _analyte_asset diff --git a/orchestration/assets/waterlevels.py b/orchestration/assets/waterlevels.py new file mode 100644 index 0000000..51ac2a4 --- /dev/null +++ b/orchestration/assets/waterlevels.py @@ -0,0 +1,90 @@ +import tempfile +from pathlib import Path + +import dagster as dg + +from backend.unifier import unify_waterlevels +from backend.persisters.ogc_features import dump_summary_collection, dump_timeseries_collection +from orchestration.resources.die_config import DIEConfigResource +from orchestration.resources.gcs import GCSResource + + +def build_waterlevels_summary_asset(product: dict): + @dg.asset(name=product["id"], group_name="waterlevels") + def _wl_summary_asset( + die_config: DIEConfigResource, + gcs: GCSResource, + ) -> dg.MaterializeResult: + config = die_config.get_config(product) + config.output_summary = True + + with tempfile.TemporaryDirectory() as tmpdir: + unify_waterlevels(config) + + persister = getattr(config, "_persister", None) + records = persister.records if persister else [] + + out = Path(tmpdir) / "collection.geojson" + meta = { + "id": product["id"], + "title": product.get("title", product["id"]), + "description": product.get("description", ""), + } + dump_summary_collection(str(out), records, meta) + info = gcs.upload_product(str(out), product["id"]) + + return dg.MaterializeResult( + metadata={ + "feature_count": dg.MetadataValue.int(info["feature_count"]), + "dated_uri": dg.MetadataValue.url(info["dated_uri"]), + "latest_uri": dg.MetadataValue.url(info["latest_uri"]), + } + ) + + return _wl_summary_asset + + +def build_waterlevels_timeseries_asset(product: dict): + """ + §V: ogc_timeseries features MUST be flat (one per observation). + §V: MUST have ISO 8601 `datetime` property. + §V: Each Feature MUST have top-level id. + """ + + @dg.asset(name=product["id"], group_name="waterlevels") + def _wl_ts_asset( + die_config: DIEConfigResource, + gcs: GCSResource, + ) -> dg.MaterializeResult: + config = die_config.get_config(product) + config.output_summary = False + config.output_timeseries_unified = True + + with tempfile.TemporaryDirectory() as tmpdir: + unify_waterlevels(config) + + persister = getattr(config, "_persister", None) + site_records = persister.sites if persister else [] + timeseries = persister.timeseries if persister else [] + + # timeseries is list-of-lists (per site); flatten to list of records + flat_timeseries = [obs for site_ts in timeseries for obs in site_ts] + + out = Path(tmpdir) / "collection.geojson" + meta = { + "id": product["id"], + "title": product.get("title", product["id"]), + "description": product.get("description", ""), + } + dump_timeseries_collection(str(out), site_records, flat_timeseries, meta) + info = gcs.upload_product(str(out), product["id"]) + + return dg.MaterializeResult( + metadata={ + "feature_count": dg.MetadataValue.int(info["feature_count"]), + "dated_uri": dg.MetadataValue.url(info["dated_uri"]), + "latest_uri": dg.MetadataValue.url(info["latest_uri"]), + } + ) + + return _wl_ts_asset diff --git a/orchestration/cloudbuild.yaml b/orchestration/cloudbuild.yaml new file mode 100644 index 0000000..35d75e5 --- /dev/null +++ b/orchestration/cloudbuild.yaml @@ -0,0 +1,27 @@ +steps: + - name: 'gcr.io/cloud-builders/docker' + args: + - 'build' + - '-t' + - '$_REGION-docker.pkg.dev/$PROJECT_ID/die/die-orchestration:$COMMIT_SHA' + - '-t' + - '$_REGION-docker.pkg.dev/$PROJECT_ID/die/die-orchestration:latest' + - '-f' + - 'orchestration/Dockerfile' + - '.' + + - name: 'gcr.io/cloud-builders/docker' + args: + - 'push' + - '--all-tags' + - '$_REGION-docker.pkg.dev/$PROJECT_ID/die/die-orchestration' + +substitutions: + _REGION: us-central1 + +images: + - '$_REGION-docker.pkg.dev/$PROJECT_ID/die/die-orchestration:$COMMIT_SHA' + - '$_REGION-docker.pkg.dev/$PROJECT_ID/die/die-orchestration:latest' + +options: + logging: CLOUD_LOGGING_ONLY diff --git a/orchestration/cloudrun.yaml b/orchestration/cloudrun.yaml new file mode 100644 index 0000000..04db69d --- /dev/null +++ b/orchestration/cloudrun.yaml @@ -0,0 +1,38 @@ +# Cloud Run Job definition for DIE orchestration. +# Deploy with: +# gcloud run jobs replace orchestration/cloudrun.yaml +# +# Each product in products.yaml gets its own Cloud Scheduler trigger +# pointing at this job with PRODUCT_ID set to the product id. + +apiVersion: run.googleapis.com/v1 +kind: Job +metadata: + name: die-orchestration + labels: + app: die +spec: + template: + spec: + taskCount: 1 + timeoutSeconds: 3600 + template: + spec: + containers: + - image: us-central1-docker.pkg.dev/PROJECT_ID/die/die-orchestration:latest + env: + - name: PRODUCT_ID + value: nm_waterlevels_summary # overridden per Cloud Scheduler job + - name: GCS_BUCKET + value: die-products + - name: USGS_API_KEY + valueFrom: + secretKeyRef: + name: usgs-api-key + key: latest + resources: + limits: + cpu: "2" + memory: "4Gi" + serviceAccountName: die-orchestration-sa@PROJECT_ID.iam.gserviceaccount.com + maxRetries: 1 diff --git a/orchestration/config/products.yaml b/orchestration/config/products.yaml new file mode 100644 index 0000000..f0abfcd --- /dev/null +++ b/orchestration/config/products.yaml @@ -0,0 +1,46 @@ +gcs_bucket: die-products + +products: + - id: nm_waterlevels_summary + parameter: waterlevels + output_type: ogc_summary + title: "NM Unified Water Levels Summary" + description: "Summary stats for water levels, all NM sources" + schedule: "0 6 * * *" + spatial_filter: + state: NM + sources: + exclude: [] + + - id: nm_waterlevels_timeseries + parameter: waterlevels + output_type: ogc_timeseries + title: "NM Water Levels Time Series" + description: "Per-observation water level measurements, all NM sources" + schedule: "0 7 * * *" + spatial_filter: + state: NM + sources: + exclude: [] + + - id: bernco_waterlevels_timeseries + parameter: waterlevels + output_type: ogc_timeseries + title: "Bernalillo County Water Level Time Series" + description: "Bernalillo County water level timeseries per well" + schedule: "0 8 * * *" + spatial_filter: + county: Bernalillo + sources: + include: [bernco] + + - id: nm_arsenic_summary + parameter: arsenic + output_type: ogc_summary + title: "NM Arsenic Summary" + description: "Arsenic concentration summary stats, all NM sources" + schedule: "0 9 * * *" + spatial_filter: + state: NM + sources: + exclude: [] diff --git a/orchestration/definitions.py b/orchestration/definitions.py new file mode 100644 index 0000000..0af0de2 --- /dev/null +++ b/orchestration/definitions.py @@ -0,0 +1,68 @@ +from pathlib import Path + +import dagster as dg +import yaml + +from orchestration.resources.die_config import DIEConfigResource +from orchestration.resources.gcs import GCSResource +from orchestration.assets.waterlevels import ( + build_waterlevels_summary_asset, + build_waterlevels_timeseries_asset, +) +from orchestration.assets.analytes import build_analyte_summary_asset + +_PRODUCTS_PATH = Path(__file__).parent / "config" / "products.yaml" + + +def _load_products() -> dict: + return yaml.safe_load(_PRODUCTS_PATH.read_text()) + + +def _build_assets(products_config: dict) -> list: + assets = [] + for product in products_config["products"]: + param = product["parameter"] + output_type = product["output_type"] + + if param == "waterlevels" and output_type == "ogc_summary": + assets.append(build_waterlevels_summary_asset(product)) + elif param == "waterlevels" and output_type == "ogc_timeseries": + assets.append(build_waterlevels_timeseries_asset(product)) + elif output_type == "ogc_summary": + assets.append(build_analyte_summary_asset(product)) + + return assets + + +def _build_schedules(products_config: dict, assets: list) -> list: + asset_names = {a.key.path[-1] for a in assets} + schedules = [] + for product in products_config["products"]: + pid = product["id"] + if pid not in asset_names: + continue + schedules.append( + dg.ScheduleDefinition( + name=f"schedule_{pid}", + target=dg.AssetSelection.keys(pid), + cron_schedule=product.get("schedule", "0 6 * * *"), + execution_timezone="America/Denver", + ) + ) + return schedules + + +_products_config = _load_products() +_assets = _build_assets(_products_config) +_schedules = _build_schedules(_products_config, _assets) + +defs = dg.Definitions( + assets=_assets, + schedules=_schedules, + resources={ + "die_config": DIEConfigResource(), + "gcs": GCSResource( + bucket_name=_products_config.get("gcs_bucket", "die-products"), + ), + }, +) diff --git a/orchestration/deploy_serverless.sh b/orchestration/deploy_serverless.sh new file mode 100755 index 0000000..bd76476 --- /dev/null +++ b/orchestration/deploy_serverless.sh @@ -0,0 +1,41 @@ +#!/bin/bash +# Manual deploy of the DIE code location to Dagster+ Serverless. +# +# Same target as the GitHub Action (.github/workflows/dagster-cloud-deploy.yml): +# a PEX fast-deploy built from dagster_cloud.yaml. Use this to push from a laptop +# without going through CI. +# +# Prerequisites: +# - Docker running locally (build-method=docker builds manylinux-compatible +# wheels so the deploy works regardless of host OS). +# - uv installed (the dagster-cloud CLI is pulled in on the fly via `uv run`). +# +# Required env vars: +# DAGSTER_CLOUD_ORGANIZATION your Dagster+ org name (e.g. "nmwd") +# DAGSTER_CLOUD_API_TOKEN a Dagster+ user/agent token +# Optional: +# DEPLOYMENT target deployment (default: prod) +# +# Usage: +# DAGSTER_CLOUD_ORGANIZATION=nmwd DAGSTER_CLOUD_API_TOKEN=*** \ +# orchestration/deploy_serverless.sh +set -euo pipefail + +: "${DAGSTER_CLOUD_ORGANIZATION:?set DAGSTER_CLOUD_ORGANIZATION to your Dagster+ org}" +: "${DAGSTER_CLOUD_API_TOKEN:?set DAGSTER_CLOUD_API_TOKEN to a Dagster+ token}" +DEPLOYMENT="${DEPLOYMENT:-prod}" + +# Run from repo root so dagster_cloud.yaml + the orchestration build dir resolve. +REPO_ROOT="$(cd "$(dirname "$0")/.." && pwd)" +cd "$REPO_ROOT" + +echo "Deploying location 'die-orchestration' to org '$DAGSTER_CLOUD_ORGANIZATION' deployment '$DEPLOYMENT'..." + +uv run --with dagster-cloud -- \ + dagster-cloud serverless deploy-python-executable \ + --organization "$DAGSTER_CLOUD_ORGANIZATION" \ + --deployment "$DEPLOYMENT" \ + --location-file dagster_cloud.yaml \ + --location-name die-orchestration \ + --python-version 3.10 \ + --build-method docker diff --git a/orchestration/pygeoapi/Dockerfile b/orchestration/pygeoapi/Dockerfile new file mode 100644 index 0000000..b87d49b --- /dev/null +++ b/orchestration/pygeoapi/Dockerfile @@ -0,0 +1,24 @@ +FROM geopython/pygeoapi:latest + +# pygeoapi base image includes GDAL with /vsigs/ GCS support. +# Auth uses Application Default Credentials — no key file needed on Cloud Run. + +WORKDIR /pygeoapi + +# Copy generation inputs +COPY config.yml.j2 /tmp/config.yml.j2 +COPY generate_config.py /tmp/generate_config.py +COPY ../config/products.yaml /tmp/products.yaml + +# Bake config into image at build time. +# §V: config generated from products.yaml, not hand-edited. +RUN pip install jinja2 pyyaml --quiet && \ + python /tmp/generate_config.py \ + --products /tmp/products.yaml \ + --template /tmp/config.yml.j2 \ + --output /pygeoapi/local.config.yml + +EXPOSE 80 + +# pygeoapi reads PYGEOAPI_CONFIG env var; default is local.config.yml +ENV PYGEOAPI_CONFIG=/pygeoapi/local.config.yml diff --git a/orchestration/pygeoapi/cloudbuild.yaml b/orchestration/pygeoapi/cloudbuild.yaml new file mode 100644 index 0000000..dabf080 --- /dev/null +++ b/orchestration/pygeoapi/cloudbuild.yaml @@ -0,0 +1,42 @@ +steps: + - name: 'gcr.io/cloud-builders/docker' + args: + - 'build' + - '-t' + - '$_REGION-docker.pkg.dev/$PROJECT_ID/die/die-pygeoapi:$COMMIT_SHA' + - '-t' + - '$_REGION-docker.pkg.dev/$PROJECT_ID/die/die-pygeoapi:latest' + - '-f' + - 'orchestration/pygeoapi/Dockerfile' + - 'orchestration/pygeoapi' # build context — allows COPY ../config/products.yaml + + - name: 'gcr.io/cloud-builders/docker' + args: + - 'push' + - '--all-tags' + - '$_REGION-docker.pkg.dev/$PROJECT_ID/die/die-pygeoapi' + + - name: 'gcr.io/google.com/cloudsdktool/cloud-sdk' + entrypoint: gcloud + args: + - 'run' + - 'deploy' + - 'die-pygeoapi' + - '--image=$_REGION-docker.pkg.dev/$PROJECT_ID/die/die-pygeoapi:$COMMIT_SHA' + - '--region=$_REGION' + - '--platform=managed' + - '--allow-unauthenticated' + - '--port=80' + - '--memory=512Mi' + - '--set-env-vars=PYGEOAPI_SERVER_URL=https://die-pygeoapi-$_SUFFIX.run.app' + +substitutions: + _REGION: us-central1 + _SUFFIX: placeholder # replace with Cloud Run URL suffix after first deploy + +images: + - '$_REGION-docker.pkg.dev/$PROJECT_ID/die/die-pygeoapi:$COMMIT_SHA' + - '$_REGION-docker.pkg.dev/$PROJECT_ID/die/die-pygeoapi:latest' + +options: + logging: CLOUD_LOGGING_ONLY diff --git a/orchestration/pygeoapi/config.yml.j2 b/orchestration/pygeoapi/config.yml.j2 new file mode 100644 index 0000000..6eb32ba --- /dev/null +++ b/orchestration/pygeoapi/config.yml.j2 @@ -0,0 +1,82 @@ +server: + bind: + host: 0.0.0.0 + port: 80 + url: ${PYGEOAPI_SERVER_URL} + mimetype: application/json + encoding: utf-8 + language: en-US + cors: true + pretty_print: false + limit: 500 + +logging: + level: ERROR + +metadata: + identification: + title: NM Unified Water Data + description: OGC API - Features for New Mexico water data + keywords: + - water + - groundwater + - New Mexico + - NMBGMR + keywords_type: theme + terms_of_service: https://creativecommons.org/licenses/by/4.0/ + url: https://waterdata.nmt.edu + license: + name: CC-BY 4.0 + url: https://creativecommons.org/licenses/by/4.0/ + provider: + name: NM Bureau of Geology & Mineral Resources + url: https://geoinfo.nmt.edu + contact: + address: 801 Leroy Place + city: Socorro + stateorprovince: New Mexico + postalcode: "87801" + country: USA + +resources: +{% for product in products %} + {{ product.id }}: + type: collection + title: {{ product.title | tojson }} + description: {{ product.description | tojson }} + keywords: + - water + - groundwater + - New Mexico + extent: + spatial: + bbox: + - -109.05 + - 31.33 + - -103.00 + - 37.00 + crs: http://www.opengis.net/def/crs/OGC/1.3/CRS84 +{% if product.output_type == 'ogc_timeseries' %} + temporal: + interval: + - - "1900-01-01T00:00:00Z" + - null +{% endif %} + providers: + - type: feature + name: OGR + data: + source_type: GeoJSON + source: /vsigs/{{ gcs_bucket }}/products/{{ product.id }}/latest.geojson + source_options: + GDAL_HTTP_UNSAFESSL: "NO" + gdal_ogr_options: + EMPTY_AS_NULL: "NO" + GDAL_CACHEMAX: "64" + id_field: id + layer: OGRGeoJSON +{% if product.output_type == 'ogc_timeseries' %} + time_field: datetime +{% endif %} + +{% endfor %} diff --git a/orchestration/pygeoapi/generate_config.py b/orchestration/pygeoapi/generate_config.py new file mode 100644 index 0000000..a9e4a90 --- /dev/null +++ b/orchestration/pygeoapi/generate_config.py @@ -0,0 +1,52 @@ +""" +Generate pygeoapi config.yml from products.yaml + Jinja2 template. + +§V: pygeoapi config MUST be generated from products.yaml — never hand-edited. +§V: pygeoapi OGR provider MUST use /vsigs/ path (GCS). + +Usage: + python generate_config.py \ + --products ../config/products.yaml \ + --template config.yml.j2 \ + --output /pygeoapi/local.config.yml +""" +import argparse +from pathlib import Path + +import yaml +from jinja2 import Environment, FileSystemLoader + + +def generate(products_path: Path, template_path: Path, output_path: Path) -> None: + products_config = yaml.safe_load(products_path.read_text()) + env = Environment( + loader=FileSystemLoader(str(template_path.parent)), + keep_trailing_newline=True, + ) + tmpl = env.get_template(template_path.name) + rendered = tmpl.render( + products=products_config["products"], + gcs_bucket=products_config["gcs_bucket"], + ) + + # Sanity check: every product must produce an OGR /vsigs/ entry + for product in products_config["products"]: + pid = product["id"] + bucket = products_config["gcs_bucket"] + expected = f"/vsigs/{bucket}/products/{pid}/latest.geojson" + assert expected in rendered, ( + f"§V violated: OGR provider for '{pid}' missing /vsigs/ path in generated config" + ) + + output_path.parent.mkdir(parents=True, exist_ok=True) + output_path.write_text(rendered) + print(f"Generated {output_path} ({len(products_config['products'])} collections)") + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument("--products", required=True, type=Path) + parser.add_argument("--template", required=True, type=Path) + parser.add_argument("--output", required=True, type=Path) + args = parser.parse_args() + generate(args.products, args.template, args.output) diff --git a/orchestration/pyproject.toml b/orchestration/pyproject.toml new file mode 100644 index 0000000..ca41e35 --- /dev/null +++ b/orchestration/pyproject.toml @@ -0,0 +1,24 @@ +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "die-orchestration" +version = "0.1.0" +description = "DIE Dagster orchestration (internal, not published)" +requires-python = ">=3.10" +dependencies = [ + "dagster>=1.8", + "dagster-gcp>=0.24", + "dagster-webserver>=1.8", + "google-cloud-storage", + "google-cloud-secret-manager", + "Jinja2", + "nmuwd", +] + +[tool.uv.sources] +nmuwd = { path = "..", editable = true } + +[tool.hatch.build.targets.wheel] +packages = ["orchestration"] diff --git a/orchestration/resources/__init__.py b/orchestration/resources/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/orchestration/resources/die_config.py b/orchestration/resources/die_config.py new file mode 100644 index 0000000..ccbf911 --- /dev/null +++ b/orchestration/resources/die_config.py @@ -0,0 +1,41 @@ +from typing import Optional +import dagster as dg +from backend.config import Config + + +class DIEConfigResource(dg.ConfigurableResource): + """Dagster resource that constructs a DIE Config from a product spec dict.""" + + usgs_api_key: Optional[str] = None + + def get_config(self, product: dict) -> Config: + spatial = product.get("spatial_filter", {}) + sources_spec = product.get("sources", {}) + + payload: dict = { + "yes": True, + "output_summary": product.get("output_type") == "ogc_summary", + "output_format": product.get("output_type", "ogc_summary"), + } + + if spatial.get("county"): + payload["county"] = spatial["county"] + if spatial.get("state"): + payload["wkt"] = None + + if sources_spec.get("include"): + all_sources = [ + "bernco", "bor", "cabq", "ebid", "nmbgmr_amp", + "nmed_dwb", "nmose_isc_seven_rivers", "nmose_pod", + "nmose_roswell", "nwis", "pvacd", "wqp", + ] + for s in all_sources: + payload[f"use_source_{s}"] = s in sources_spec["include"] + elif sources_spec.get("exclude"): + for s in sources_spec["exclude"]: + payload[f"use_source_{s}"] = False + + config = Config(payload=payload) + config.parameter = product["parameter"] + config.finalize() + return config diff --git a/orchestration/resources/gcs.py b/orchestration/resources/gcs.py new file mode 100644 index 0000000..f9a1ae9 --- /dev/null +++ b/orchestration/resources/gcs.py @@ -0,0 +1,75 @@ +from datetime import datetime, timezone +from pathlib import Path +from typing import Optional + +import dagster as dg + +try: + from google.cloud import storage + _GCS_AVAILABLE = True +except ImportError: + _GCS_AVAILABLE = False + + +class GCSResource(dg.ConfigurableResource): + """ + Upload OGC Feature Collection GeoJSON files to GCS. + + §V: latest.geojson MUST be overwritten atomically + (copy from dated object, never direct overwrite of in-flight file). + §V: No database — GCS is the sole store. + """ + + bucket_name: str + products_prefix: str = "products" + + def _client(self): + if not _GCS_AVAILABLE: + raise ImportError("google-cloud-storage not installed") + return storage.Client() + + def upload_product( + self, + local_path: str, + product_id: str, + run_date: Optional[str] = None, + ) -> dict: + """ + Upload *local_path* as both a dated archive and latest.geojson. + + Returns dict with: + dated_uri: gs://bucket/products/{product_id}/{date}.geojson + latest_uri: gs://bucket/products/{product_id}/latest.geojson + feature_count: int + file_size_bytes: int + """ + if run_date is None: + run_date = datetime.now(timezone.utc).strftime("%Y-%m-%d") + + client = self._client() + bucket = client.bucket(self.bucket_name) + + dated_key = f"{self.products_prefix}/{product_id}/{run_date}.geojson" + latest_key = f"{self.products_prefix}/{product_id}/latest.geojson" + + file_size = Path(local_path).stat().st_size + + dated_blob = bucket.blob(dated_key) + dated_blob.upload_from_filename(local_path, content_type="application/geo+json") + + # §V: atomic latest — copy from the just-uploaded dated blob, not + # another upload that could race with a concurrent reader. + bucket.copy_blob(dated_blob, bucket, latest_key) + + import json + with open(local_path, encoding="utf-8") as f: + data = json.load(f) + feature_count = data.get("numberReturned", len(data.get("features", []))) + + return { + "dated_uri": f"gs://{self.bucket_name}/{dated_key}", + "latest_uri": f"gs://{self.bucket_name}/{latest_key}", + "feature_count": feature_count, + "file_size_bytes": file_size, + "run_date": run_date, + } diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..a35c373 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,51 @@ +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "nmuwd" +version = "0.10.3" +description = "New Mexico Water Data Integration Engine" +readme = "README.md" +license = { text = "Apache-2.0" } +authors = [{ name = "Jake Ross" }] +requires-python = ">=3.10" +classifiers = [ + "Programming Language :: Python :: 3", + "Operating System :: OS Independent", +] +dependencies = [ + "click>=8.2.1", + "python-dotenv", + "frost_sta_client", + "geopandas", + "httpx", + "pandas", + "pyyaml", + "types-pyyaml", + "urllib3>=2.2.0,<3.0.0", +] + +[project.urls] +Homepage = "https://github.com/DataIntegrationGroup/DataIntegrationEngine" + +[project.optional-dependencies] +dev = ["pytest", "mypy", "flake8"] +geoserver = ["psycopg2-binary", "GeoAlchemy2", "SQLAlchemy"] +gcs = ["google-cloud-storage"] + +[project.scripts] +die = "frontend.cli:cli" + +[tool.hatch.build.targets.wheel] +packages = ["frontend", "backend"] + +[tool.pytest.ini_options] +testpaths = ["tests"] +norecursedirs = ["tests/archived"] + +[tool.mypy] +ignore_missing_imports = true +# Archived tests are excluded from pytest (norecursedirs) and reference an old +# CLI API; don't type-check them either. +exclude = ["tests/archived/"] diff --git a/pytest.ini b/pytest.ini deleted file mode 100644 index 8ea4712..0000000 --- a/pytest.ini +++ /dev/null @@ -1,3 +0,0 @@ -[pytest] -; skip archived tests but keep for reference -norecursedirs = tests/archived \ No newline at end of file diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index bd7f502..0000000 --- a/requirements.txt +++ /dev/null @@ -1,16 +0,0 @@ -click==8.2.1 -python-dotenv -flask -frost_sta_client -Geoalchemy2 -geopandas -google-cloud-storage -gunicorn -httpx -mypy -pandas -psycopg2-binary -pytest -pyyaml -types-pyyaml -urllib3>=2.2.0,<3.0.0 \ No newline at end of file diff --git a/setup.py b/setup.py deleted file mode 100644 index da41f4c..0000000 --- a/setup.py +++ /dev/null @@ -1,69 +0,0 @@ -# =============================================================================== -# Copyright 2024 ross -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# =============================================================================== - -from setuptools import setup, find_packages - -with open("README.md", "r", encoding="utf-8") as fh: - long_description = fh.read() - - -setup( - name="nmuwd", - version="0.10.3", - author="Jake Ross", - description="New Mexico Water Data Integration Engine", - long_description=long_description, - long_description_content_type="text/markdown", - url="https://github.com/DataIntegrationGroup/DataIntegrationEngine", - classifiers=[ - "Programming Language :: Python :: 3", - "Operating System :: OS Independent", - ], - install_requires=[ - "click==8.2.1", - "python-dotenv", - "flask", - "frost_sta_client", - "Geoalchemy2", - "geopandas", - "google-cloud-storage", - "gunicorn", - "httpx", - "mypy", - "pandas", - "psycopg2-binary", - "pytest", - "pyyaml", - "types-pyyaml", - "urllib3>=2.2.0,<3.0.0", - ], - entry_points={ - "console_scripts": [ - "die = frontend.cli:cli", - ], - }, - packages=["frontend", "backend"] - + [f"backend.{p}" for p in find_packages("backend")], - python_requires=">=3.6", - include_package_data=True, - # package_data={ - # If any package contains *.txt or *.rst files, include them: - # "templates": [ - # "*.template", - # ], - # }, -) -# ============= EOF ============================================= diff --git a/tests/test_persisters/__init__.py b/tests/test_persisters/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_persisters/test_ogc_features.py b/tests/test_persisters/test_ogc_features.py new file mode 100644 index 0000000..969b8a5 --- /dev/null +++ b/tests/test_persisters/test_ogc_features.py @@ -0,0 +1,174 @@ +import json +import os +import tempfile + +from backend.persisters.ogc_features import dump_summary_collection, dump_timeseries_collection +from backend.record import SummaryRecord, SiteRecord, ParameterRecord + + +def _make_summary_record(source="nmbgmr_amp", rid="RA-1234", lat=35.0, lon=-106.5): + return SummaryRecord({ + "source": source, + "id": rid, + "name": "Test Well", + "usgs_site_id": "", + "alternate_site_id": "", + "latitude": lat, + "longitude": lon, + "horizontal_datum": "WGS84", + "elevation": 1650.0, + "elevation_units": "ft", + "well_depth": None, + "well_depth_units": "ft", + "parameter_name": "waterlevels", + "parameter_units": "ft", + "nrecords": 10, + "min": 200.0, + "max": 250.0, + "mean": 225.0, + "earliest_date": "1990-01-01", + "earliest_time": "00:00:00", + "earliest_value": 200.0, + "earliest_units": "ft", + "latest_date": "2024-01-01", + "latest_time": "00:00:00", + "latest_value": 220.0, + "latest_units": "ft", + }) + + +def _make_site_record(source="nmbgmr_amp", rid="RA-1234", lat=35.0, lon=-106.5): + return SiteRecord({ + "source": source, + "id": rid, + "name": "Test Well", + "latitude": lat, + "longitude": lon, + "elevation": 1650.0, + "elevation_units": "ft", + "horizontal_datum": "WGS84", + "vertical_datum": "", + "usgs_site_id": "", + "alternate_site_id": "", + "formation": "", + "aquifer": "", + "well_depth": None, + "well_depth_units": "ft", + }) + + +def _make_wl_record(source="nmbgmr_amp", rid="RA-1234", date="2024-01-15", value=212.4): + return ParameterRecord({ + "source": source, + "id": rid, + "parameter_name": "waterlevels", + "parameter_value": value, + "parameter_units": "ft", + "date_measured": date, + "time_measured": "00:00:00", + "source_parameter_name": "depth_to_water", + "source_parameter_units": "ft", + "conversion_factor": 1.0, + "record_type": "waterlevels", + }) + + +class TestDumpSummaryCollection: + def test_ogc_required_fields(self, tmp_path): + """§V: OGC FC MUST include top-level id, type, numberReturned, timeStamp.""" + records = [_make_summary_record()] + out = tmp_path / "summary.geojson" + result = dump_summary_collection(str(out), records, {"id": "nm_waterlevels"}) + + assert result["type"] == "FeatureCollection" + assert result["id"] == "nm_waterlevels" + assert "timeStamp" in result + assert "numberReturned" in result + assert result["numberReturned"] == 1 + + def test_feature_has_top_level_id(self, tmp_path): + """§V: Each Feature MUST have top-level id (not only in properties).""" + records = [_make_summary_record(source="nmbgmr_amp", rid="RA-1234")] + out = tmp_path / "summary.geojson" + result = dump_summary_collection(str(out), records, {"id": "test"}) + + feature = result["features"][0] + assert "id" in feature + assert feature["id"] == "nmbgmr_amp:RA-1234" + + def test_writes_valid_geojson_file(self, tmp_path): + records = [_make_summary_record(), _make_summary_record(rid="RA-5678")] + out = tmp_path / "summary.geojson" + dump_summary_collection(str(out), records, {"id": "test"}) + + with open(str(out)) as f: + data = json.load(f) + assert data["numberReturned"] == 2 + assert len(data["features"]) == 2 + + def test_geometry_has_coordinates(self, tmp_path): + records = [_make_summary_record(lat=35.123, lon=-106.456)] + out = tmp_path / "summary.geojson" + result = dump_summary_collection(str(out), records, {"id": "test"}) + + geom = result["features"][0]["geometry"] + assert geom["type"] == "Point" + assert geom["coordinates"][0] == -106.456 + assert geom["coordinates"][1] == 35.123 + + def test_empty_records(self, tmp_path): + out = tmp_path / "summary.geojson" + result = dump_summary_collection(str(out), [], {"id": "empty"}) + assert result["numberReturned"] == 0 + assert result["features"] == [] + + +class TestDumpTimeseriesCollection: + def test_flat_one_feature_per_observation(self, tmp_path): + """§V: ogc_timeseries MUST be flat (one per observation).""" + site = _make_site_record() + obs1 = _make_wl_record(date="2024-01-15", value=212.4) + obs2 = _make_wl_record(date="2024-04-20", value=218.1) + + out = tmp_path / "ts.geojson" + result = dump_timeseries_collection( + str(out), [site], [obs1, obs2], {"id": "nm_wl_ts"} + ) + + assert result["numberReturned"] == 2 + assert len(result["features"]) == 2 + + def test_iso8601_datetime_property(self, tmp_path): + """§V: MUST have ISO 8601 `datetime` property on each feature.""" + site = _make_site_record() + obs = _make_wl_record(date="2024-01-15") + + out = tmp_path / "ts.geojson" + result = dump_timeseries_collection(str(out), [site], [obs], {"id": "test"}) + + props = result["features"][0]["properties"] + assert "datetime" in props + assert props["datetime"].startswith("2024-01-15T") + + def test_feature_has_top_level_id(self, tmp_path): + """§V: Each Feature MUST have top-level id.""" + site = _make_site_record() + obs = _make_wl_record(date="2024-01-15") + + out = tmp_path / "ts.geojson" + result = dump_timeseries_collection(str(out), [site], [obs], {"id": "test"}) + + feature = result["features"][0] + assert "id" in feature + assert "nmbgmr_amp" in feature["id"] + assert "RA-1234" in feature["id"] + + def test_ogc_required_fields(self, tmp_path): + """§V: OGC FC 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