diff --git a/.env.example b/.env.example index bf2a02b6..70b4b505 100644 --- a/.env.example +++ b/.env.example @@ -1,36 +1,54 @@ -PYGEOAPI_CONFIG=data/pygeoapi/pygeoapi-config.yml -PYGEOAPI_OPENAPI=data/pygeoapi/pygeoapi-openapi.yml - -# DHIS2 Connection -DHIS2_BASE_URL=https://play.im.dhis2.org/stable-2-42-4/api -DHIS2_USERNAME=admin -DHIS2_PASSWORD=district - -# CDS API (required for ERA5-Land downloads) -# Get your API key from: https://cds.climate.copernicus.eu/how-to-api -CDSAPI_URL=https://cds.climate.copernicus.eu/api -CDSAPI_KEY=your-cds-api-key - -# Download cache directory for climate data -# DOWNLOAD_DIR=./target/data - -# Default EO download extent when a dataset requires bbox and the request does not provide one +# ── Instance configuration ──────────────────────────────────────────────────── +# Path to the instance config file (extent, optional datasets_dir). +# Copy the example before editing: cp climate-api.yaml.example climate-api.yaml +# climate-api.yaml is gitignored so your local extent stays out of version control. +# When running via `make run` from the repo root, the relative path below works. +# When running the installed `climate-api` CLI from another directory, use an +# absolute path instead: CLIMATE_API_CONFIG=/path/to/your/climate-api.yaml +CLIMATE_API_CONFIG=./climate-api.yaml + +# ── pygeoapi ────────────────────────────────────────────────────────────────── +# Absolute paths are set automatically at startup; override only if you move the files. +# PYGEOAPI_CONFIG=/absolute/path/to/pygeoapi-config.yml +# PYGEOAPI_OPENAPI=/absolute/path/to/pygeoapi-openapi.yml + +# ── ERA5-Land (DestinE Earth Data Hub) ──────────────────────────────────────── +# Authentication uses ~/.netrc — no API key is required here. +# See docs/setup_guide.md for registration and .netrc setup instructions. + +# ── Download and ingestion ──────────────────────────────────────────────────── +# Override the download cache directory (default: data/downloads). +# CACHE_OVERRIDE=/path/to/cache + +# Fallback bounding box used when a request does not include an explicit bbox. # Format: xmin,ymin,xmax,ymax # DOWNLOAD_BBOX=-13.5,6.9,-10.1,10.0 -# Default country code for datasets that require one (for example WorldPop) +# Country code for datasets that require one (e.g. WorldPop). # COUNTRY_CODE=SLE -# OGC API base URL (used by Prefect tasks to call back into the API) -# OGCAPI_BASE_URL=http://localhost:8000/ogcapi - -# Public Climate API base URL used for absolute STAC links behind a reverse proxy +# ── API deployment ──────────────────────────────────────────────────────────── +# Set when running behind a reverse proxy so that STAC hrefs and native dataset +# links use the public address instead of the internal request URL. +# Note: pygeoapi's OGC self/root links are controlled separately via server.url +# in config/pygeoapi/base.yml and are not affected by this variable. # CLIMATE_API_BASE_URL=http://localhost:8000 -# TiTiler tile server base URL -# TITILER_BASE_URL=http://127.0.0.1:8000 +# Fallback used to derive the native API base URL when CLIMATE_API_BASE_URL is not set. +# Only needed if CLIMATE_API_BASE_URL is unset and the OGC API path is known. +# Note: pygeoapi's server.url is controlled separately in config/pygeoapi/base.yml. +# OGCAPI_BASE_URL=http://localhost:8000/ogcapi -# Prefect (embedded server) -PREFECT_API_URL=http://localhost:8000/prefect/api -PREFECT_SERVER_ANALYTICS_ENABLED=false -PREFECT_SERVER_UI_SHOW_PROMOTIONAL_CONTENT=false +# Comma-separated list of origins used for extra browser/private-network headers +# on Zarr responses (default: https://inspect.geozarr.org). +# This does not restrict general CORS access; the API allows all origins globally. +# CLIMATE_API_ZARR_BROWSER_ORIGINS=http://localhost:3000 + +# ── DHIS2 connection ────────────────────────────────────────────────────────── +# Required for DHIS2 org unit lookups (Step 2 — spatial aggregation). +# Not needed for Step 1 (data ingestion, sync, and serving). +# DHIS2_BASE_URL=https://play.im.dhis2.org/stable-2-42-4/api +# DHIS2_USERNAME=admin +# DHIS2_PASSWORD=district +# DHIS2_HTTP_TIMEOUT_SECONDS=30 +# DHIS2_HTTP_RETRIES=3 diff --git a/.gitignore b/.gitignore index f25225c3..b14363f4 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,7 @@ __pycache__/ .venv/ .env +climate-api.yaml eo_api.egg-info/ data/downloads data/artifacts diff --git a/CLAUDE.md b/CLAUDE.md index f167bcda..ebb6860b 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -8,7 +8,7 @@ Key concepts: - **Dataset templates** — YAML files in `data/datasets/` describing a data source (variable, period type, download function). These are blueprints. - **Artifacts / managed datasets** — ingested instances of a template for a specific spatial extent and time range. Exposed under `/datasets` and `/zarr/{dataset_id}`. -- **Extents** — named spatial bounding boxes configured at instance setup time (`id`, `bbox`, optional `country_code`). +- **Extent** — a single named spatial bounding box configured at instance setup time (`id`, `bbox`, optional `country_code`). Exposed at `GET /extent`. ## Repository layout @@ -41,11 +41,11 @@ The `.env` file is required for `make run` and `make openapi`. Copy `.env.exampl ## Dataset templates -Each YAML in `data/datasets/` defines a dataset template. The `cache_info` block controls download and zarr build behaviour: +Each YAML in `data/datasets/` defines a dataset template. The `ingestion` block controls download and zarr build behaviour: ```yaml -cache_info: - eo_function: dhis2eo.data.worldpop.pop_total.yearly.download +ingestion: + function: dhis2eo.data.worldpop.pop_total.yearly.download default_params: {} # passed to the download function multiscales: # optional — triggers pyramid build levels: 4 diff --git a/README.md b/README.md index 41cf16b9..f8baeb05 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ Climate and Earth Observation data is distributed across dozens of providers — Each instance is configured for a specific country or region, and all data extraction, processing, and storage is scoped to that spatial extent. It abstracts data access across heterogeneous sources (CHIRPS, ERA5, WorldPop, and others), stores outputs as GeoZarr, and exposes them through standards-based endpoints. -The platform is designed to operate independently of DHIS2 and can be deployed on local, cloud-hosted, or sovereign country infrastructure. See [docs/project_description.md](docs/project_description.md) for a full description of the vision and technical architecture, [docs/managed_data_api_guide.md](docs/managed_data_api_guide.md) for the current API surface, and [docs/roadmap.md](docs/roadmap.md) for the planned development steps. +The platform is designed to operate independently of DHIS2 and can be deployed on local, cloud-hosted, or sovereign country infrastructure. See [docs/setup_guide.md](docs/setup_guide.md) for a step-by-step setup walkthrough, [docs/user_guide.md](docs/user_guide.md) for data access examples, [docs/managed_data_api_guide.md](docs/managed_data_api_guide.md) for the full API reference, and [docs/roadmap.md](docs/roadmap.md) for the planned development steps. > **Status: active development.** Current focus is on dataset ingestion, sync workflows, and GeoZarr storage. APIs and data models may change without notice. @@ -18,13 +18,7 @@ Install dependencies (requires [uv](https://docs.astral.sh/uv/)): uv sync ``` -Copy `.env.example` to `.env` and adjust values as needed. Environment variables are loaded automatically from `.env` at runtime. - -Key environment variables: - -- `DHIS2_BASE_URL` — DHIS2 API base URL (defaults to play server in `.env.example`) -- `DHIS2_USERNAME` — DHIS2 username -- `DHIS2_PASSWORD` — DHIS2 password +Copy `.env.example` to `.env` and adjust values as needed. Environment variables are loaded automatically from `.env` at runtime. See `.env.example` for the full list of available options. Start the app: @@ -40,7 +34,7 @@ If you cannot use uv (e.g. mixed conda/forge environments): python -m venv .venv source .venv/bin/activate pip install -e . -uvicorn climate_api.main:app --reload +python -m uvicorn climate_api.main:app --reload ``` ### Using conda @@ -49,7 +43,7 @@ uvicorn climate_api.main:app --reload conda create -n dhis2-climate-api python=3.13 conda activate dhis2-climate-api pip install -e . -uvicorn climate_api.main:app --reload +python -m uvicorn climate_api.main:app --reload ``` ## Development @@ -73,33 +67,43 @@ Once running, the API is available at: | Endpoint | Description | | ----------------------------------------- | ------------------------------------------ | -| `http://localhost:8000/` | Welcome / health check | +| `http://localhost:8000/` | Navigation document | +| `http://localhost:8000/health` | Health check | | `http://localhost:8000/docs` | Interactive API documentation (Swagger UI) | +| `http://localhost:8000/extent` | Configured spatial extent | +| `http://localhost:8000/datasets` | Managed dataset catalogue | | `http://localhost:8000/stac/catalog.json` | STAC catalog for published GeoZarr data | +| `http://localhost:8000/zarr/{dataset_id}` | GeoZarr store for a managed dataset | | `http://localhost:8000/ogcapi` | OGC API root | -| `http://localhost:8000/zarr/{dataset_id}` | GeoZarr store for a published dataset | ## STAC -Published Zarr-backed managed datasets are exposed under `/stac` as one STAC Collection per dataset. +Published GeoZarr datasets are discoverable under `/stac` as one STAC Collection per dataset. Each collection includes a `zarr` asset with direct xarray-compatible access metadata derived from the live Zarr store. -- `/stac/catalog.json` is the entrypoint catalog -- `/stac/collections/{dataset_id}` exposes a Collection with a direct `/zarr/{dataset_id}` asset href -- `xstac` derives Datacube metadata from the real Zarr-backed dataset -- `pygeoapi` remains the OGC query layer under `/ogcapi` +Discover available datasets and open one with xarray: -Minimal example: +The catalog is populated once at least one dataset has been ingested and published (see [docs/setup_guide.md](docs/setup_guide.md)). ```python -import requests +import httpx import xarray as xr -collection = requests.get( - "http://127.0.0.1:8000/stac/collections/chirps3_precipitation_daily_sle" -).json() - -asset = collection["assets"]["zarr"] -ds = xr.open_zarr(asset["href"], consolidated=asset["xarray:open_kwargs"]["consolidated"]) +catalog = httpx.get("http://127.0.0.1:8000/stac/catalog.json").json() +children = [link for link in catalog["links"] if link["rel"] == "child"] + +if not children: + print("No published datasets found. Run an ingestion first.") +else: + for link in children: + print(link["title"], "—", link["href"]) + + collection = httpx.get(children[0]["href"]).json() + asset = collection["assets"]["zarr"] + ds = xr.open_zarr( + asset["href"], + consolidated=asset["xarray:open_kwargs"]["consolidated"], + ) + print(ds) ``` ## pygeoapi diff --git a/climate-api.yaml.example b/climate-api.yaml.example new file mode 100644 index 00000000..a041fd84 --- /dev/null +++ b/climate-api.yaml.example @@ -0,0 +1,11 @@ +# Climate API instance configuration. +# Replace the extent below with your country before deploying. +# See docs/setup_guide.md for field descriptions. + +extent: + id: sle + name: Sierra Leone + bbox: [-13.5, 6.9, -10.1, 10.0] + country_code: SLE + +# datasets_dir: ./datasets/ # optional — custom templates merged with built-ins diff --git a/data/extents.yaml b/data/extents.yaml deleted file mode 100644 index 5528044d..00000000 --- a/data/extents.yaml +++ /dev/null @@ -1,6 +0,0 @@ -extents: - - id: sle - name: Sierra Leone - description: National extent for Sierra Leone. - bbox: [-13.5, 6.9, -10.1, 10.0] - country_code: SLE diff --git a/docs/adding_custom_datasets.md b/docs/adding_custom_datasets.md new file mode 100644 index 00000000..52f96274 --- /dev/null +++ b/docs/adding_custom_datasets.md @@ -0,0 +1,194 @@ +# Custom Dataset Guide + +This guide explains how to add a new dataset source to your Climate API instance — for example a national meteorological service, a regional satellite product, or a custom model output. + +The built-in dataset templates (CHIRPS3, ERA5-Land, WorldPop) ship as package data. Custom datasets are layered on top by pointing `datasets_dir` in your `climate-api.yaml` at a directory containing your own YAML template files. + +## Overview + +Adding a custom dataset involves two things: + +1. **A download function** — a Python function that downloads data and writes it as one or more NetCDF files to a given directory. +2. **A dataset template YAML** — a file that describes the dataset and tells the API which download function to call. + +## Step 1: Write the download function + +The download function must be importable as a dotted Python path. The API calls it with keyword arguments and ignores the return value — the function is expected to write NetCDF files to `dirname` using `prefix` as the filename prefix. + +```python +# mypackage/sources/enacts.py +from pathlib import Path + +def download( + *, + start: str, # ISO 8601 date or datetime + end: str, + dirname: Path, # directory to write output files into + prefix: str, # filename prefix (use e.g. f"{prefix}_{year}.nc") + overwrite: bool, + bbox: list[float], # [xmin, ymin, xmax, ymax] — include only if your source needs it + **kwargs: object, # absorbs default_params from the YAML template +) -> None: + """Download ENACTS rainfall and write NetCDF files to dirname.""" + ... +``` + +**Required parameters** — always passed by the API: + +| Parameter | Type | Description | +| ----------- | ---------- | ----------- | +| `start` | `str` | Start of the requested time range (ISO 8601) | +| `end` | `str` | End of the requested time range (ISO 8601) | +| `dirname` | `Path` | Directory to write output NetCDF files into | +| `prefix` | `str` | Filename prefix for output files | +| `overwrite` | `bool` | Whether to overwrite existing cached files | + +**Optional parameters** — passed only when present in the function signature: + +| Parameter | Type | Description | +| -------------- | --------------- | ----------- | +| `bbox` | `list[float]` | Bounding box as `[xmin, ymin, xmax, ymax]` — include this if your source requires a spatial filter | +| `country_code` | `str` | ISO 3166-1 alpha-3 code — include this if your source (e.g. WorldPop) requires a country code | + +Any extra keyword arguments from `default_params` in the YAML template are forwarded as additional kwargs. + +The API normalises coordinate names at write time: `valid_time` → `time`, `lat`/`y` → `latitude`, `lon`/`x` → `longitude`. Using the canonical names in your output avoids any ambiguity, but upstream names are handled automatically. + +Install your package in the same environment as the Climate API: + +```bash +pip install ./mypackage +``` + +## Step 2: Create a dataset template YAML + +Create a directory for your custom templates and add a YAML file. Each file contains a list of templates (even if there is only one): + +```yaml +# datasets/enacts_rainfall.yaml +- id: enacts_rainfall_daily + name: ENACTS Rainfall (daily) + short_name: Rainfall + variable: rainfall + period_type: daily + sync_kind: temporal + sync_execution: append + ingestion: + function: mypackage.sources.enacts.download + units: mm + resolution: 4 km x 4 km + source: ENACTS + source_url: https://enacts.example.org +``` + +### Template field reference + +**Identity** + +| Field | Required | Description | +| ------------ | -------- | ----------- | +| `id` | Yes | Unique template identifier. Dataset IDs in the API are `{id}_{extent_id}`, e.g. `enacts_rainfall_daily_rwa` | +| `name` | Yes | Full human-readable name shown in API responses and STAC metadata | +| `short_name` | No | Short label used in compact displays | +| `variable` | Yes | Name of the data variable in the Zarr store (e.g. `precip`, `t2m`, `rainfall`) | +| `source` | No | Name of the upstream data source | +| `source_url` | No | URL to the upstream dataset documentation or landing page | + +**Period and sync** + +| Field | Required | Values | Description | +| ---------------- | -------- | ------ | ----------- | +| `period_type` | Yes | `hourly`, `daily`, `monthly`, `yearly` | Temporal resolution; controls Zarr chunk sizes | +| `sync_kind` | Yes | `temporal` | Data grows over time — sync appends new time steps | +| | | `release` | Data is published as versioned releases — sync checks for a newer release | +| | | `static` | Data does not change — never synced automatically | +| `sync_execution` | No | `append` | New time steps are appended to the existing Zarr store | +| | | `rematerialize` | The full store is rebuilt on each sync | + +**Download function** + +| Field | Required | Description | +| ------------------------------ | -------- | ----------- | +| `ingestion.function` | Yes | Dotted import path to the download function | +| `ingestion.default_params` | No | Extra keyword arguments forwarded to the download function | +| `ingestion.multiscales` | No | Build a multi-resolution Zarr pyramid (see below) | + +**Sync availability** — how the API determines the latest available data: + +```yaml +sync_availability: + latest_available_function: mypackage.sources.enacts.latest_available + lag_hours: 48 # optional: data is delayed by this many hours + allow_future: false # optional: allow requesting future dates (e.g. forecasts) +``` + +`latest_available_function` must accept a `dataset` dict and return a `datetime`. Omit `sync_availability` entirely for `static` datasets or when you always want to sync up to the requested end date. + +**Units** + +| Field | Required | Description | +| --------------- | -------- | ----------- | +| `units` | No | Physical units of the raw download (e.g. `mm`, `kelvin`, `m`) | +| `convert_units` | No | Target unit; the API converts automatically using Pint (e.g. `degC`, `mm`) | + +**Multiscale pyramid** — for high-resolution raster datasets rendered in map viewers: + +```yaml +ingestion: + function: mypackage.sources.enacts.download + multiscales: + levels: 4 # number of pyramid levels (default: 4) + method: mean # aggregation method (default: mean) +``` + +## Step 3: Point the instance at your templates directory + +Add `datasets_dir` to your `climate-api.yaml`: + +```yaml +extent: + id: rwa + name: Rwanda + bbox: [28.8, -2.9, 30.9, -1.0] + +datasets_dir: ./datasets/ +``` + +All `*.yaml` and `*.yml` files in `datasets_dir` are loaded and merged with the built-in templates (CHIRPS3, ERA5-Land, WorldPop). Custom templates are additive — the built-ins remain available unless you deliberately override one by using the same `id`. + +## Step 4: Ingest and publish + +Once the API is running with `CLIMATE_API_CONFIG` pointing to your updated config, ingest as usual: + +```bash +curl -s -X POST http://127.0.0.1:8000/ingestions \ + -H "Content-Type: application/json" \ + -d '{ + "dataset_id": "enacts_rainfall_daily", + "start": "2024-01-01", + "end": "2024-01-31", + "extent_id": "rwa", + "prefer_zarr": true, + "publish": true + }' | jq +``` + +Verify it appears in the STAC catalog: + +```bash +curl -s http://127.0.0.1:8000/stac/catalog.json | jq '.links[] | select(.rel == "child")' +``` + +## Minimal example + +The smallest valid template for a static dataset with no sync: + +```yaml +- id: my_static_dataset + name: My static dataset + variable: value + period_type: daily + sync_kind: static + ingestion: + function: mypackage.sources.my_source.download +``` diff --git a/docs/implementation-status.md b/docs/implementation-status.md index 89a3d2cb..ec7b8d6b 100644 --- a/docs/implementation-status.md +++ b/docs/implementation-status.md @@ -1,4 +1,4 @@ -# Implementation Status: Dataset Publication Slice +# Implementation Status ## Purpose @@ -6,14 +6,14 @@ This note captures the current implementation state of the branch after the API It is intended to answer: -1. what the branch now exposes +1. what the main branch now exposes 2. what is intentionally internal 3. how the current pieces fit together 4. what remains to be refined -## Branch Direction +## Current API surface -The branch now centers on one narrow vertical slice: +The main branch now centers on one narrow vertical slice: 1. define dataset templates in the Climate API registry 2. define configured extents for the Climate API instance @@ -25,7 +25,7 @@ The branch now centers on one narrow vertical slice: The public surface is intentionally small: - `/ingestions` -- `/extents` +- `/extent` - `/datasets` - `/stac/...` - `/zarr/{dataset_id}` @@ -47,13 +47,13 @@ The public surface is intentionally small: - [src/climate_api/providers/availability.py](../src/climate_api/providers/availability.py) - provider-specific sync availability policies - [src/climate_api/extents/routes.py](../src/climate_api/extents/routes.py) - - extent discovery endpoints + - extent discovery endpoint - [src/climate_api/extents/services.py](../src/climate_api/extents/services.py) - - YAML-backed extent registry + - extent registry backed by CLIMATE_API_CONFIG - [src/climate_api/publications/services.py](../src/climate_api/publications/services.py) - pygeoapi publication and stable managed dataset id logic -- [data/extents.yaml](../data/extents.yaml) - - configured extents for the Climate API instance +- `extent:` block in `climate-api.yaml` (CLIMATE_API_CONFIG) + - configured spatial extent for this Climate API instance ## What Was Achieved @@ -93,8 +93,7 @@ Internal artifact records still exist, but they no longer define the public resp The branch exposes: -- `GET /extents` -- `GET /extents/{extent_id}` +- `GET /extent` Extents are configured in YAML and currently include: @@ -252,8 +251,7 @@ Implemented sync behavior: - `POST /ingestions` - `GET /ingestions` - `GET /ingestions/{ingestion_id}` -- `GET /extents` -- `GET /extents/{extent_id}` +- `GET /extent` - `GET /datasets` - `GET /datasets/{dataset_id}` - `GET /datasets/{dataset_id}/download` diff --git a/docs/managed_data_api_guide.md b/docs/managed_data_api_guide.md index 0c1527bb..1670053f 100644 --- a/docs/managed_data_api_guide.md +++ b/docs/managed_data_api_guide.md @@ -5,7 +5,7 @@ This guide describes the current native FastAPI surface for Climate API and how The current public story is: - run and inspect ingestion operations with `/ingestions` -- discover configured extents with `/extents` +- discover the configured extent with `/extent` - discover managed datasets with `/datasets` - discover published GeoZarr datasets with `/stac/catalog.json` - access raw Zarr data with `/zarr/{dataset_id}` @@ -23,8 +23,7 @@ Operational note: - `POST /ingestions` - `GET /ingestions` - `GET /ingestions/{ingestion_id}` -- `GET /extents` -- `GET /extents/{extent_id}` +- `GET /extent` - `GET /datasets` - `GET /datasets/{dataset_id}` - `GET /datasets/{dataset_id}/download` @@ -39,29 +38,24 @@ Operational note: - `GET /ogcapi/collections/{dataset_id}` - `GET /ogcapi/collections/{dataset_id}/coverage` -## 1. Discover configured extents +## 1. Discover the configured extent -Configured extents are setup-time Climate API configuration. They are read-only at runtime and are identified by `extent_id`. +The configured extent is setup-time Climate API configuration. It is read-only at runtime and is identified by `extent_id`. Example: ```bash -curl -s http://127.0.0.1:8000/extents | jq +curl -s http://127.0.0.1:8000/extent | jq ``` Example response: ```json { - "kind": "ExtentList", - "items": [ - { - "extent_id": "sle", - "name": "Sierra Leone", - "description": "National extent for Sierra Leone.", - "bbox": [-13.5, 6.9, -10.1, 10.0] - } - ] + "extent_id": "sle", + "name": "Sierra Leone", + "description": null, + "bbox": [-13.5, 6.9, -10.1, 10.0] } ``` @@ -418,10 +412,10 @@ curl -s -X POST "http://127.0.0.1:8000/sync/chirps3_precipitation_daily_sle" \ These commands assume the API is running on `http://127.0.0.1:8000` and that `jq` is available. -### 1. Confirm configured extents +### 1. Confirm configured extent ```bash -curl -s "http://127.0.0.1:8000/extents" | jq +curl -s "http://127.0.0.1:8000/extent" | jq ``` Use an extent that has enough spatial metadata for the selected dataset. The @@ -627,7 +621,7 @@ The current branch is no longer an artifact-first API. The public contract is now: - ingest with `/ingestions` -- discover extents with `/extents` +- discover the configured extent with `/extent` - discover managed datasets with `/datasets` - discover published Zarr-backed datasets with `/stac/catalog.json` - access raw native data with `/zarr/{dataset_id}` diff --git a/docs/ogcapi.md b/docs/ogcapi.md index 860db24d..3878e478 100644 --- a/docs/ogcapi.md +++ b/docs/ogcapi.md @@ -235,7 +235,7 @@ Note: `chirps3-dhis2-pipeline` has its own contract (`start_date`, `end_date`, f ### ERA5-Land (`era5-land-download`) -Downloads ERA5-Land hourly climate data via the CDS API. +Downloads ERA5-Land hourly climate data via the [DestinE Earth Data Hub](https://earthdatahub.destine.eu). Authentication uses `~/.netrc` — see [setup_guide.md](setup_guide.md#era5-land-via-destine-earth-data-hub) for registration and setup. Additional inputs: diff --git a/docs/setup_guide.md b/docs/setup_guide.md new file mode 100644 index 00000000..68527a1a --- /dev/null +++ b/docs/setup_guide.md @@ -0,0 +1,219 @@ +# Setup Guide + +This guide walks through configuring a new Climate API instance for a specific country, using Rwanda as the example. + +## Prerequisites + +- Python 3.13 or higher +- [uv](https://docs.astral.sh/uv/) for dependency management +- Git +- Make (`make` — available by default on macOS and most Linux distributions; on Windows use [WSL](https://learn.microsoft.com/en-us/windows/wsl/) or run the commands in the Makefile directly) +- [jq](https://jqlang.org/download/) for pretty-printing API responses in the curl examples (optional — omit `| jq` if not installed) + +## Step 1: Clone and install + +```bash +git clone https://github.com/dhis2/climate-api.git +cd climate-api +make sync +``` + +## Step 2: Configure the spatial extent + +The repo includes `climate-api.yaml.example` with Sierra Leone as a starting point. Copy it to `climate-api.yaml` (which is gitignored so your local extent stays out of version control) and replace the entry with your country: + +```bash +cp climate-api.yaml.example climate-api.yaml +``` + +```yaml +extent: + id: rwa + name: Rwanda + bbox: [28.8, -2.9, 30.9, -1.0] + country_code: RWA +``` + +Field reference: + +| Field | Required | Description | +| -------------- | -------- | ----------- | +| `id` | Yes | Short identifier used in dataset IDs and API paths (e.g. `chirps3_precipitation_daily_rwa`) | +| `name` | No | Human-readable name shown in API responses | +| `bbox` | Yes | Bounding box as `[xmin, ymin, xmax, ymax]` in WGS84 decimal degrees | +| `country_code` | No | ISO 3166-1 alpha-3 code — required for WorldPop downloads | + +To find the bounding box for a country, [bboxfinder.com](http://bboxfinder.com) is a useful tool. + +Values can reference environment variables using `${VAR:-default}` syntax: + +```yaml +extent: + id: ${EXTENT_ID:-rwa} + name: ${EXTENT_NAME:-Rwanda} + bbox: [28.8, -2.9, 30.9, -1.0] +``` + +## Step 3: Configure environment variables + +Copy the example environment file: + +```bash +cp .env.example .env +``` + +`CLIMATE_API_CONFIG=./climate-api.yaml` is already set in `.env.example`. The remaining defaults are sufficient to run the API and ingest CHIRPS3 and WorldPop data. Review the file and adjust as needed — the comments explain each variable. + +For ERA5-Land downloads see [ERA5-Land setup](#era5-land-via-destine-earth-data-hub) below. + +## Step 4: Start the API + +```bash +make run +``` + +The API starts on `http://127.0.0.1:8000`. Open `http://127.0.0.1:8000/docs` for the interactive API documentation. + +Alternatively, if the package is installed (e.g. via `pip install .`), you can start it with: + +```bash +climate-api +``` + +When running the `climate-api` command from a directory other than the repo root, the relative path `./climate-api.yaml` in `CLIMATE_API_CONFIG` will not resolve correctly. Use an absolute path in that case: + +```bash +CLIMATE_API_CONFIG=/path/to/your/climate-api.yaml climate-api +``` + +## Step 5: Verify the configured extent + +```bash +curl -s http://127.0.0.1:8000/extent | jq +``` + +Expected response: + +```json +{ + "extent_id": "rwa", + "name": "Rwanda", + "description": null, + "bbox": [28.8, -2.9, 30.9, -1.0] +} +``` + +## Step 6: Ingest your first dataset + +CHIRPS3 (daily precipitation) requires no API key and is a good first dataset to verify the setup. + +Replace `rwa` with the `id` you set in Step 2. + +```bash +curl -s -X POST http://127.0.0.1:8000/ingestions \ + -H "Content-Type: application/json" \ + -d '{ + "dataset_id": "chirps3_precipitation_daily", + "start": "2024-01-01", + "end": "2024-01-31", + "extent_id": "rwa", + "prefer_zarr": true, + "publish": true + }' | jq +``` + +A successful response returns `"status": "completed"` and a `dataset` object with `dataset_id` matching `chirps3_precipitation_daily_{extent_id}` (e.g. `chirps3_precipitation_daily_rwa`). + +## Step 7: Access the data + +Browse the STAC catalog to confirm the dataset is published: + +```bash +curl -s http://127.0.0.1:8000/stac/catalog.json | jq +``` + +Open the dataset with xarray — the catalog discovery picks up whichever extent you configured: + +```python +import httpx +import xarray as xr + +catalog = httpx.get("http://127.0.0.1:8000/stac/catalog.json").json() +children = [link for link in catalog["links"] if link["rel"] == "child"] +collection_url = children[0]["href"] + +collection = httpx.get(collection_url).json() +asset = collection["assets"]["zarr"] +ds = xr.open_zarr( + asset["href"], + consolidated=asset["xarray:open_kwargs"]["consolidated"], +) +print(ds) +``` + +See [user_guide.md](user_guide.md) for more usage examples. + +--- + +## ERA5-Land via DestinE Earth Data Hub + +ERA5-Land hourly temperature and precipitation data is downloaded from the [DestinE Earth Data Hub](https://earthdatahub.destine.eu). Access is free but requires registration. + +### 1. Register + +Create a free account at [earthdatahub.destine.eu](https://earthdatahub.destine.eu). Free accounts include a monthly request limit of 500,000 — sufficient for national-scale downloads. + +### 2. Configure authentication + +DestinE authentication uses a `.netrc` file in your home directory. Create or append to `~/.netrc`: + +``` +machine earthdatahub.destine.eu +login your@email.com +password your-password +``` + +Set the correct permissions: + +```bash +chmod 600 ~/.netrc +``` + +### 3. Ingest ERA5-Land data + +Once authenticated, ingest ERA5-Land temperature for Rwanda: + +```bash +curl -s -X POST http://127.0.0.1:8000/ingestions \ + -H "Content-Type: application/json" \ + -d '{ + "dataset_id": "era5land_temperature_hourly", + "start": "2024-01-01T00", + "end": "2024-01-31T23", + "extent_id": "rwa", + "prefer_zarr": true, + "publish": true + }' | jq +``` + +ERA5-Land data has a configured lag of 120 hours (5 days) — the sync planner will not request data from the last 120 hours. This can be adjusted by supplying a custom `era5_land.yaml` via `datasets_dir` in your `climate-api.yaml`. + +--- + +## Keeping datasets up to date + +Use the sync endpoint to advance an existing dataset to the latest available data. Replace `rwa` with your extent `id` from Step 2: + +```bash +# Check what would be downloaded without executing +curl -s "http://127.0.0.1:8000/sync/chirps3_precipitation_daily_rwa/plan" | jq + +# Execute the sync +curl -s -X POST "http://127.0.0.1:8000/sync/chirps3_precipitation_daily_rwa" \ + -H "Content-Type: application/json" \ + -d '{"prefer_zarr": true, "publish": true}' | jq +``` + +See [managed_data_api_guide.md](managed_data_api_guide.md) for the full sync API reference. + +See [adding_custom_datasets.md](adding_custom_datasets.md) for adding new dataset sources beyond the built-in templates. diff --git a/docs/user_guide.md b/docs/user_guide.md new file mode 100644 index 00000000..94b53b9f --- /dev/null +++ b/docs/user_guide.md @@ -0,0 +1,104 @@ +# User Guide + +This guide shows how to discover and access data from a running Climate API instance. It assumes the API is running locally at `http://127.0.0.1:8000` and that at least one dataset has been ingested and published. + +For configuring a new instance for your country, see [setup_guide.md](setup_guide.md). For the full ingestion and sync API reference, see [managed_data_api_guide.md](managed_data_api_guide.md). + +## Discovering datasets + +The STAC catalog is the starting point for data discovery. It lists all published GeoZarr datasets as STAC Collections. + +```bash +curl -s http://127.0.0.1:8000/stac/catalog.json | jq +``` + +Each entry in `links` with `"rel": "child"` points to one dataset collection. Use the `href` from the catalog to fetch it: + +```bash +# Replace {dataset_id} with any id from the catalog above, e.g. chirps3_precipitation_daily_sle +curl -s http://127.0.0.1:8000/stac/collections/{dataset_id} | jq +``` + +The `assets.zarr` field contains everything needed to open the dataset: + +```json +{ + "assets": { + "zarr": { + "href": "http://127.0.0.1:8000/zarr/chirps3_precipitation_daily_rwa", + "xarray:open_kwargs": { "consolidated": true } + } + } +} +``` + +## Opening a dataset with xarray + +The `climate_api.client` module provides a `Client` class for discovering and opening datasets: + +```python +from climate_api.client import Client + +api = Client("http://127.0.0.1:8000") + +datasets = api.catalog() +for link in datasets: + print(link["id"], "—", link["title"]) + +ds = api.open(datasets[0]["id"]) # open whichever dataset is published first +print(ds) +``` + +The `base_url` defaults to the `CLIMATE_API_BASE_URL` environment variable (falling back to `http://127.0.0.1:8000`), so module-level functions work without any argument when the env var is set: + +```python +from climate_api.client import list_datasets, open_dataset # reads CLIMATE_API_BASE_URL + +dataset_id = list_datasets()[0]["id"] +ds = open_dataset(dataset_id) +``` + +Each dataset has a `time` dimension, `longitude` and `latitude` spatial dimensions, and a data variable matching the variable (e.g. `precip` for CHIRPS, `t2m` for ERA5-Land temperature). + +Select the first time step: + +```python +snapshot = ds.isel(time=0) +print(snapshot) +``` + +Select a spatial point by sampling the centre of the domain: + +```python +variable = list(ds.data_vars)[0] # precip, t2m, tp, or pop_total depending on the dataset +centre_lat = ds.latitude.mean().item() +centre_lon = ds.longitude.mean().item() +point = ds.sel(latitude=centre_lat, longitude=centre_lon, method="nearest") +print(point[variable].values) +``` + +Compute the spatial mean over the first 10 time steps (slicing first avoids reading the full dataset over HTTP): + +```python +spatial_mean = ds[variable].isel(time=slice(10)).mean(dim=["latitude", "longitude"]) +print(spatial_mean.to_dataframe()) +``` + +## Dataset IDs + +Dataset IDs follow the pattern `{source_dataset_id}_{extent_id}`, for example `chirps3_precipitation_daily_sle` for CHIRPS3 daily precipitation over Sierra Leone (`sle`). + +Available datasets in the built-in catalogue: + +| Dataset ID prefix | Variable | Period | Source | +| ------------------------------- | ----------- | ------ | --------- | +| `chirps3_precipitation_daily` | `precip` | Daily | CHIRPS v3 | +| `era5land_temperature_hourly` | `t2m` | Hourly | ERA5-Land | +| `era5land_precipitation_hourly` | `tp` | Hourly | ERA5-Land | +| `worldpop_population_yearly` | `pop_total` | Yearly | WorldPop | + +## What's next + +- See [`examples/stac_discover_and_open.py`](../examples/stac_discover_and_open.py) for a complete discovery and access script. +- See [`examples/zarr_direct_access.py`](../examples/zarr_direct_access.py) for direct Zarr access and spatial/temporal subsetting. +- See [managed_data_api_guide.md](managed_data_api_guide.md) for the full ingestion and sync API reference. diff --git a/examples/stac_discover_and_open.py b/examples/stac_discover_and_open.py new file mode 100644 index 00000000..3e845274 --- /dev/null +++ b/examples/stac_discover_and_open.py @@ -0,0 +1,44 @@ +"""Discover published datasets via the STAC catalog and open one with xarray. + +Requires a running Climate API instance and at least one published dataset. +Adjust BASE_URL if the API is not running on the default local address. +""" + +import json + +from climate_api.client import Client + +BASE_URL = "http://127.0.0.1:8000" + + +def main() -> None: + """Discover and open the first published dataset.""" + api = Client(BASE_URL) + datasets = api.catalog() + + if not datasets: + print("No published datasets found. Run an ingestion first.") + return + + print(json.dumps(datasets, indent=2)) + + first = datasets[0] + print(f"\nOpening: {first['title']}") + + ds = api.open(first["id"]) + print(ds) + + print(f"\nTime range: {ds.time.values[0]} → {ds.time.values[-1]}") + print(f"Time steps: {ds.sizes['time']}") + print(f"Latitude: {ds.latitude.min().item()} → {ds.latitude.max().item()}") + print(f"Longitude: {ds.longitude.min().item()} → {ds.longitude.max().item()}") + + variable = list(ds.data_vars)[0] + centre_lat = ds.latitude.mean().item() + centre_lon = ds.longitude.mean().item() + sample = ds[variable].isel(time=0).sel(latitude=centre_lat, longitude=centre_lon, method="nearest") + print(f"\n{variable} at domain centre, t=0: {sample.item()}") + + +if __name__ == "__main__": + main() diff --git a/examples/zarr_direct_access.py b/examples/zarr_direct_access.py new file mode 100644 index 00000000..5cc722df --- /dev/null +++ b/examples/zarr_direct_access.py @@ -0,0 +1,53 @@ +"""Open a published GeoZarr dataset directly and demonstrate spatial and temporal subsetting. + +Requires a running Climate API instance with at least one published dataset. +Adjust BASE_URL if the API is not running on the default local address. +""" + +from climate_api.client import Client + +BASE_URL = "http://127.0.0.1:8000" + + +def main() -> None: + """Open a Zarr store directly and demonstrate spatial and temporal subsetting.""" + api = Client(BASE_URL) + datasets = api.catalog() + if not datasets: + print("No published datasets found. Run an ingestion first.") + return + + first = datasets[0] + print(f"Opening: {first['title']}\n") + + ds = api.open(first["id"]) + print(ds) + + print(f"\nDimensions: {dict(ds.sizes)}") + print(f"Time range: {ds.time.values[0]} → {ds.time.values[-1]}") + print(f"Latitude: {ds.latitude.min().item()} → {ds.latitude.max().item()}") + print(f"Longitude: {ds.longitude.min().item()} → {ds.longitude.max().item()}") + + variable = list(ds.data_vars)[0] + + # Select a single time step + t0 = ds.time.values[0] + snapshot = ds[variable].sel(time=t0) + print(f"\n{variable} snapshot at {t0}:") + print(f" shape: {snapshot.shape}, min: {snapshot.min().item()}, max: {snapshot.max().item()}") + + # Select the point closest to the spatial centre of the domain + centre_lat = ds.latitude.mean().item() + centre_lon = ds.longitude.mean().item() + point = ds[variable].sel(latitude=centre_lat, longitude=centre_lon, method="nearest") + print(f"\n{variable} at domain centre ({centre_lat:.2f}, {centre_lon:.2f}):") + print(point.to_dataframe()[[variable]].head(10)) + + # Spatial mean over the full domain — first 10 time steps + spatial_mean = ds[variable].isel(time=slice(10)).mean(dim=["latitude", "longitude"]) + print(f"\nSpatial mean {variable} time series (first 10 steps):") + print(spatial_mean.to_dataframe()[[variable]]) + + +if __name__ == "__main__": + main() diff --git a/pyproject.toml b/pyproject.toml index 6314109c..4965eaa0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,6 +6,7 @@ build-backend = "uv_build" name = "climate-api" version = "0.1.0" requires-python = ">=3.13" +description = "Climate and Earth Observation data API for DHIS2" dependencies = [ "fastapi>=0.100.0", "starlette>=0.27.0", @@ -25,6 +26,9 @@ dependencies = [ "topozarr==0.0.*", ] +[project.scripts] +climate-api = "climate_api.cli:main" + [tool.ruff] target-version = "py313" line-length = 120 diff --git a/src/climate_api/cli.py b/src/climate_api/cli.py new file mode 100644 index 00000000..bfc9d039 --- /dev/null +++ b/src/climate_api/cli.py @@ -0,0 +1,8 @@ +"""Command-line entry point for running the Climate API with uvicorn.""" + +import uvicorn + + +def main() -> None: + """Start the Climate API server.""" + uvicorn.run("climate_api.main:app", host="0.0.0.0", port=8000) diff --git a/src/climate_api/client.py b/src/climate_api/client.py new file mode 100644 index 00000000..11762997 --- /dev/null +++ b/src/climate_api/client.py @@ -0,0 +1,91 @@ +"""Lightweight client for discovering and opening published Climate API datasets.""" + +import os + +import httpx +import xarray as xr + +_FALLBACK_BASE_URL = "http://127.0.0.1:8000" + + +def _default_base_url() -> str: + return os.environ.get("CLIMATE_API_BASE_URL", _FALLBACK_BASE_URL) + + +class Client: + """Client for a Climate API instance. + + Args: + base_url: Base URL of the running Climate API (e.g. ``http://localhost:8000``). + """ + + def __init__(self, base_url: str) -> None: + self.base_url = base_url.rstrip("/") + + def catalog(self) -> list[dict]: + """Return all published datasets from the STAC catalog. + + Each entry is a STAC child link dict with at least ``id``, ``title``, and ``href``. + """ + return list_datasets(self.base_url) + + def open(self, dataset_id: str) -> xr.Dataset: + """Open a published dataset as an xarray Dataset. + + Fetches the STAC collection for ``dataset_id``, reads the Zarr asset + metadata, and returns the opened dataset. Coordinates are always + ``time``, ``latitude``, and ``longitude``. + """ + return open_dataset(dataset_id, base_url=self.base_url) + + +def list_datasets(base_url: str | None = None) -> list[dict]: + """Return all published datasets from the STAC catalog. + + Each entry is a STAC child link dict with at least ``id``, ``title``, and ``href``. + ``base_url`` defaults to the ``CLIMATE_API_BASE_URL`` environment variable, + falling back to ``http://127.0.0.1:8000``. + """ + url = (base_url or _default_base_url()).rstrip("/") + response = httpx.get(f"{url}/stac/catalog.json", timeout=30) + response.raise_for_status() + catalog = response.json() + raw_links = catalog.get("links") + if not isinstance(raw_links, list): + raise ValueError(f"Invalid STAC catalog response from {url}: missing or non-list 'links' field") + links = [] + for link in raw_links: + if isinstance(link, dict) and link.get("rel") == "child": + href = link.get("href") + if not isinstance(href, str) or not href: + raise ValueError(f"STAC child link from {url} has a missing or invalid href") + links.append({**link, "id": href.rstrip("/").rsplit("/", 1)[-1]}) + return links + + +def open_dataset(dataset_id: str, *, base_url: str | None = None) -> xr.Dataset: + """Open a published dataset as an xarray Dataset. + + Fetches the STAC collection for ``dataset_id``, reads the Zarr asset + metadata, and returns the opened dataset. Coordinates are always + ``time``, ``latitude``, and ``longitude``. + ``base_url`` defaults to the ``CLIMATE_API_BASE_URL`` environment variable, + falling back to ``http://127.0.0.1:8000``. + """ + url = (base_url or _default_base_url()).rstrip("/") + response = httpx.get(f"{url}/stac/collections/{dataset_id}", timeout=30) + response.raise_for_status() + collection = response.json() + assets = collection.get("assets") + if not isinstance(assets, dict): + raise ValueError(f"STAC collection for '{dataset_id}' from {url} has a missing or invalid 'assets' field") + asset = assets.get("zarr") + if not isinstance(asset, dict): + raise ValueError(f"Dataset '{dataset_id}' has no Zarr asset in the STAC collection") + href = asset.get("href") + if not isinstance(href, str) or not href: + raise ValueError(f"Zarr asset for '{dataset_id}' has a missing or invalid href") + open_kwargs = asset.get("xarray:open_kwargs", {}) + if not isinstance(open_kwargs, dict): + raise ValueError(f"Zarr asset for '{dataset_id}' has a malformed xarray:open_kwargs field") + return xr.open_zarr(href, **open_kwargs) # type: ignore[no-any-return] diff --git a/src/climate_api/config.py b/src/climate_api/config.py new file mode 100644 index 00000000..134976f7 --- /dev/null +++ b/src/climate_api/config.py @@ -0,0 +1,56 @@ +"""Instance configuration loaded from CLIMATE_API_CONFIG.""" + +import os +import re +from pathlib import Path +from typing import Any + +import yaml + + +def _substitute_env_vars(text: str) -> str: + """Replace ${VAR:-default} patterns with values from the environment.""" + + def _replace(match: re.Match[str]) -> str: + var, _, default = match.group(1).partition(":-") + return os.environ.get(var, default) + + return re.sub(r"\$\{([^}]+)\}", _replace, text) + + +def get_config_path() -> Path | None: + """Return the resolved Path of CLIMATE_API_CONFIG, or None if unset.""" + raw = os.environ.get("CLIMATE_API_CONFIG") + return Path(raw).resolve() if raw else None + + +def get_config() -> dict[str, Any]: + """Load and return the instance config from CLIMATE_API_CONFIG. + + Results are cached for the lifetime of the process; the config file is + read once and reused on subsequent calls. Returns an empty dict if + CLIMATE_API_CONFIG is not set. Raises FileNotFoundError if the path is + set but does not exist. + """ + return _load_config() + + +# Module-level cache — reset between tests via monkeypatch on _cache. +_cache: dict[str, Any] | None = None + + +def _load_config() -> dict[str, Any]: + global _cache + if _cache is not None: + return _cache + path = get_config_path() + if path is None: + return {} + if not path.exists(): + raise FileNotFoundError(f"CLIMATE_API_CONFIG not found: {path}") + text = _substitute_env_vars(path.read_text(encoding="utf-8")) + loaded = yaml.safe_load(text) + if loaded is not None and not isinstance(loaded, dict): + raise ValueError(f"CLIMATE_API_CONFIG must be a YAML mapping at the top level: {path}") + _cache = dict(loaded or {}) + return _cache diff --git a/data/datasets/chirps3.yaml b/src/climate_api/data/datasets/chirps3.yaml similarity index 85% rename from data/datasets/chirps3.yaml rename to src/climate_api/data/datasets/chirps3.yaml index 6f6a2064..b977bb2d 100644 --- a/data/datasets/chirps3.yaml +++ b/src/climate_api/data/datasets/chirps3.yaml @@ -7,8 +7,8 @@ sync_execution: append sync_availability: latest_available_function: climate_api.providers.availability.chirps3_daily_latest_available - cache_info: - eo_function: dhis2eo.data.chc.chirps3.daily.download + ingestion: + function: dhis2eo.data.chc.chirps3.daily.download units: mm resolution: 5 km x 5 km source: CHIRPS v3 diff --git a/data/datasets/era5_land.yaml b/src/climate_api/data/datasets/era5_land.yaml similarity index 73% rename from data/datasets/era5_land.yaml rename to src/climate_api/data/datasets/era5_land.yaml index 7c03f811..91716520 100644 --- a/data/datasets/era5_land.yaml +++ b/src/climate_api/data/datasets/era5_land.yaml @@ -8,15 +8,15 @@ sync_availability: latest_available_function: climate_api.providers.availability.lagged_latest_available lag_hours: 120 - cache_info: - eo_function: dhis2eo.data.destine.era5_land.hourly.download + ingestion: + function: dhis2eo.data.destine.era5_land.hourly.download default_params: variables: ['t2m'] units: kelvin convert_units: degC resolution: 9 km x 9 km source: ERA5-Land Reanalysis - source_url: https://cds.climate.copernicus.eu/datasets/reanalysis-era5-land + source_url: https://earthdatahub.destine.eu/collections/era5/datasets/reanalysis-era5-land - id: era5land_precipitation_hourly name: Total precipitation (ERA5-Land) @@ -28,8 +28,8 @@ sync_availability: latest_available_function: climate_api.providers.availability.lagged_latest_available lag_hours: 120 - cache_info: - eo_function: dhis2eo.data.destine.era5_land.hourly.download + ingestion: + function: dhis2eo.data.destine.era5_land.hourly.download default_params: variables: ['tp'] pre_process: ['deaccumulate_era5'] @@ -37,4 +37,4 @@ convert_units: mm resolution: 9 km x 9 km source: ERA5-Land Reanalysis - source_url: https://cds.climate.copernicus.eu/datasets/reanalysis-era5-land + source_url: https://earthdatahub.destine.eu/collections/era5/datasets/reanalysis-era5-land diff --git a/data/datasets/worldpop.yaml b/src/climate_api/data/datasets/worldpop.yaml similarity index 88% rename from data/datasets/worldpop.yaml rename to src/climate_api/data/datasets/worldpop.yaml index 4d56a3f8..ead982b9 100644 --- a/data/datasets/worldpop.yaml +++ b/src/climate_api/data/datasets/worldpop.yaml @@ -8,8 +8,8 @@ latest_available_function: climate_api.providers.availability.worldpop_release_latest_available # WorldPop projections are intentionally request-driven for future years. allow_future: true - cache_info: - eo_function: dhis2eo.data.worldpop.pop_total.yearly.download + ingestion: + function: dhis2eo.data.worldpop.pop_total.yearly.download multiscales: levels: 4 default_params: diff --git a/src/climate_api/data/pygeoapi/base.yml b/src/climate_api/data/pygeoapi/base.yml new file mode 100644 index 00000000..987290af --- /dev/null +++ b/src/climate_api/data/pygeoapi/base.yml @@ -0,0 +1,47 @@ +server: + bind: + host: 0.0.0.0 + port: 8000 + url: http://127.0.0.1:8000/ogcapi + mimetype: application/json; charset=UTF-8 + encoding: utf-8 + languages: + - en-US + limits: + default_items: 20 + max_items: 50 + map: + url: https://tile.openstreetmap.org/{z}/{x}/{y}.png + attribution: "© OpenStreetMap contributors" + admin: false + +logging: + level: ERROR + +metadata: + identification: + title: + en: DHIS2 Climate API + description: + en: Published EO gridded data collections + keywords: + en: + - EO + - coverage + - raster + - zarr + - netcdf + terms_of_service: https://dhis2.org + url: https://dhis2.org + provider: + name: DHIS2 Climate API + url: https://dhis2.org + contact: + name: DHIS2 Climate Team + email: climate@dhis2.org + url: https://dhis2.org + license: + name: CC-BY 4.0 + url: https://creativecommons.org/licenses/by/4.0/ + +resources: {} diff --git a/src/climate_api/data_manager/services/downloader.py b/src/climate_api/data_manager/services/downloader.py index 748cf27d..7e1a5abc 100644 --- a/src/climate_api/data_manager/services/downloader.py +++ b/src/climate_api/data_manager/services/downloader.py @@ -21,12 +21,20 @@ logger = logging.getLogger(__name__) -SCRIPT_DIR = Path(__file__).parent.resolve() -_download_dir = SCRIPT_DIR.parent.parent.parent.parent / "data" / "downloads" -CACHE_OVERRIDE = os.getenv("CACHE_OVERRIDE") -if CACHE_OVERRIDE: - _download_dir = Path(CACHE_OVERRIDE) -DOWNLOAD_DIR = _download_dir + +def _resolve_download_dir() -> Path: + # CACHE_OVERRIDE keeps existing Docker/dev deployments working unchanged. + override = os.getenv("CACHE_OVERRIDE") + if override: + return Path(override) + # Default to an XDG-compliant user-writable location so the package works + # when installed with pip (where a package-relative path would land inside + # site-packages and typically be non-writable). + xdg_data = Path(os.getenv("XDG_DATA_HOME", Path.home() / ".local" / "share")) + return xdg_data / "climate-api" / "downloads" + + +DOWNLOAD_DIR = _resolve_download_dir() CRS = "EPSG:4326" @@ -47,12 +55,12 @@ def download_dataset( When running in the background-task path, the download is deferred and this function returns an empty list because no files have been created yet. """ - cache_info = dataset["cache_info"] - eo_download_func_path = cache_info["eo_function"] + ingestion = dataset["ingestion"] + eo_download_func_path = ingestion["function"] eo_download_func = _get_dynamic_function(eo_download_func_path) before_files = {path.resolve(): path.stat().st_mtime_ns for path in get_cache_files(dataset)} - params = dict(cache_info.get("default_params", {})) + params = dict(ingestion.get("default_params", {})) params.update( { "start": start, @@ -109,7 +117,7 @@ def build_dataset_zarr(dataset: dict[str, Any], *, start: str | None = None, end """Collect dataset cache files into one optimised Zarr archive, clipped to request scope.""" logger.info(f"Optimizing cache for dataset {dataset['id']}") - cache_info = dataset["cache_info"] + ingestion = dataset["ingestion"] files = get_cache_files(dataset) logger.info(f"Opening {len(files)} files from cache") ds = xr.open_mfdataset(files) @@ -124,6 +132,17 @@ def build_dataset_zarr(dataset: dict[str, Any], *, start: str | None = None, end keep_coords = [get_time_dim(ds)] + dims drop_coords = [c for c in ds.coords if c not in keep_coords] ds = ds.drop_vars(drop_coords) + + # Normalise to canonical names (time/longitude/latitude) so all stored Zarr files + # are consistent regardless of what the upstream source uses (e.g. lon/lat, x/y). + # Downstream readers — pygeoapi, the /zarr endpoint, and the client — rely on this. + time_dim = get_time_dim(ds) + rename_map = {k: v for k, v in [(time_dim, "time"), (lon_dim, "longitude"), (lat_dim, "latitude")] if k != v} + if rename_map: + ds = ds.rename(rename_map) + lon_dim, lat_dim = "longitude", "latitude" + dims = [lon_dim, lat_dim] + ds = _select_time_range(ds, dataset=dataset, start=start, end=end) xmin = ds[lon_dim].min().item() @@ -145,7 +164,7 @@ def build_dataset_zarr(dataset: dict[str, Any], *, start: str | None = None, end logger.info("Saving to optimized zarr file") zarr_path = DOWNLOAD_DIR / f"{_get_cache_prefix(dataset)}.zarr" - multiscales = dict(cache_info.get("multiscales", {})) + multiscales = dict(ingestion.get("multiscales", {})) if multiscales: levels = multiscales.get("levels", 4) diff --git a/src/climate_api/data_registry/services/datasets.py b/src/climate_api/data_registry/services/datasets.py index 9f394681..c61e501d 100644 --- a/src/climate_api/data_registry/services/datasets.py +++ b/src/climate_api/data_registry/services/datasets.py @@ -1,23 +1,89 @@ """Dataset registry backed by YAML config files.""" +import importlib.resources import logging from pathlib import Path from typing import Any import yaml +from climate_api import config as api_config + logger = logging.getLogger(__name__) -SCRIPT_DIR = Path(__file__).parent.resolve() -CONFIGS_DIR = SCRIPT_DIR.parent.parent.parent.parent / "data" / "datasets" +# Overridden in tests via monkeypatch to point to a temporary directory. +# When set, only this directory is loaded (no built-ins, no config override). +CONFIGS_DIR: Path | None = None + SUPPORTED_SYNC_KINDS = {"temporal", "release", "static"} SUPPORTED_SYNC_EXECUTIONS = {"append", "rematerialize"} def list_datasets() -> list[dict[str, Any]]: - """Load all YAML files in the registry folder and return a flat list of datasets.""" + """Load all dataset templates and return a flat list. + + Built-in templates from climate_api/data/datasets/ are always loaded. When + datasets_dir is set in CLIMATE_API_CONFIG, templates from that directory are + merged on top — a custom template with the same id overrides the built-in one. + + CONFIGS_DIR (test override via monkeypatch) bypasses this and loads only + from the given directory, as tests supply a fully controlled set. + """ + if CONFIGS_DIR is not None: + return _load_from_dir(CONFIGS_DIR) + + merged: dict[str, dict[str, Any]] = {d["id"]: d for d in _load_builtin_datasets()} + + config_datasets_dir = api_config.get_config().get("datasets_dir") + if config_datasets_dir: + if not isinstance(config_datasets_dir, (str, Path)): + raise ValueError( + f"datasets_dir in CLIMATE_API_CONFIG must be a path string, got {type(config_datasets_dir).__name__}" + ) + config_path = api_config.get_config_path() + resolved = (config_path.parent / config_datasets_dir).resolve() if config_path else Path(config_datasets_dir) + for dataset in _load_from_dir(resolved): + merged[dataset["id"]] = dataset + + return list(merged.values()) + + +def get_dataset(dataset_id: str) -> dict[str, Any] | None: + """Get dataset dict for a given id.""" + datasets_lookup = {d["id"]: d for d in list_datasets()} + return datasets_lookup.get(dataset_id) + + +def _load_builtin_datasets() -> list[dict[str, Any]]: + """Load built-in dataset templates from package data via importlib.resources. + + Using importlib.resources instead of __file__-relative path arithmetic ensures + this works correctly in both editable installs and wheel installs, where the + package lives inside site-packages with no guarantee that the project root + directory (and its data/ folder) is accessible. + """ + pkg = importlib.resources.files("climate_api") / "data" / "datasets" + datasets: list[dict[str, Any]] = [] + for resource in pkg.iterdir(): + if not resource.name.endswith((".yaml", ".yml")): + continue + try: + content = resource.read_text(encoding="utf-8") + file_datasets = yaml.safe_load(content) + if not isinstance(file_datasets, list): + raise ValueError(f"{resource.name} must contain a list of dataset templates") + for dataset in file_datasets: + _validate_dataset_template(dataset, source=resource.name) + datasets.extend(file_datasets) + except Exception: + logger.exception("Error loading %s", resource.name) + raise + return datasets + + +def _load_from_dir(folder: Path) -> list[dict[str, Any]]: + """Load dataset templates from a directory on disk.""" datasets: list[dict[str, Any]] = [] - folder = CONFIGS_DIR if not folder.is_dir(): raise ValueError(f"Path is not a directory: {folder}") @@ -29,7 +95,7 @@ def list_datasets() -> list[dict[str, Any]]: if not isinstance(file_datasets, list): raise ValueError(f"{file_path.name} must contain a list of dataset templates") for dataset in file_datasets: - _validate_dataset_template(dataset, file_path=file_path) + _validate_dataset_template(dataset, source=str(file_path)) datasets.extend(file_datasets) except Exception: logger.exception("Error loading %s", file_path.name) @@ -38,54 +104,56 @@ def list_datasets() -> list[dict[str, Any]]: return datasets -def get_dataset(dataset_id: str) -> dict[str, Any] | None: - """Get dataset dict for a given id.""" - datasets_lookup = {d["id"]: d for d in list_datasets()} - return datasets_lookup.get(dataset_id) - - -def _validate_dataset_template(dataset: object, *, file_path: Path) -> None: +def _validate_dataset_template(dataset: object, *, source: str) -> None: """Validate registry fields required by runtime sync planning.""" if not isinstance(dataset, dict): - raise ValueError(f"{file_path.name} contains a non-object dataset template") + raise ValueError(f"{source} contains a non-object dataset template") - dataset_id = str(dataset.get("id", "")) + dataset_id = dataset.get("id") + if not isinstance(dataset_id, str) or not dataset_id: + raise ValueError(f"{source} contains a dataset template with a missing or invalid id") sync_kind = dataset.get("sync_kind") if not isinstance(sync_kind, str) or not sync_kind: - raise ValueError(f"Dataset template '{dataset_id}' in {file_path.name} must define sync_kind") + raise ValueError(f"Dataset template '{dataset_id}' in {source} must define sync_kind") if sync_kind not in SUPPORTED_SYNC_KINDS: supported = ", ".join(sorted(SUPPORTED_SYNC_KINDS)) raise ValueError( - f"Dataset template '{dataset_id}' in {file_path.name} has unsupported sync_kind " + f"Dataset template '{dataset_id}' in {source} has unsupported sync_kind " f"'{sync_kind}'. Supported values: {supported}" ) sync_execution = dataset.get("sync_execution") if sync_execution is not None: if not isinstance(sync_execution, str) or not sync_execution: - raise ValueError(f"Dataset template '{dataset_id}' in {file_path.name} has invalid sync_execution") + raise ValueError(f"Dataset template '{dataset_id}' in {source} has invalid sync_execution") if sync_execution not in SUPPORTED_SYNC_EXECUTIONS: supported = ", ".join(sorted(SUPPORTED_SYNC_EXECUTIONS)) raise ValueError( - f"Dataset template '{dataset_id}' in {file_path.name} has unsupported sync_execution " + f"Dataset template '{dataset_id}' in {source} has unsupported sync_execution " f"'{sync_execution}'. Supported values: {supported}" ) + ingestion = dataset.get("ingestion") + if not isinstance(ingestion, dict): + raise ValueError(f"Dataset template '{dataset_id}' in {source} must define an 'ingestion' block") + function = ingestion.get("function") + if not isinstance(function, str) or not function: + raise ValueError(f"Dataset template '{dataset_id}' in {source} must define ingestion.function") + sync_availability = dataset.get("sync_availability") if sync_availability is not None: - _validate_sync_availability(sync_availability, dataset_id=dataset_id, file_path=file_path) + _validate_sync_availability(sync_availability, dataset_id=dataset_id, source=source) -def _validate_sync_availability(sync_availability: object, *, dataset_id: str, file_path: Path) -> None: +def _validate_sync_availability(sync_availability: object, *, dataset_id: str, source: str) -> None: """Validate optional source availability policy metadata.""" if not isinstance(sync_availability, dict): - raise ValueError(f"Dataset template '{dataset_id}' in {file_path.name} has invalid sync_availability") + raise ValueError(f"Dataset template '{dataset_id}' in {source} has invalid sync_availability") latest_available_function = sync_availability.get("latest_available_function") if latest_available_function is not None and ( not isinstance(latest_available_function, str) or not latest_available_function ): raise ValueError( - f"Dataset template '{dataset_id}' in {file_path.name} has invalid " - "sync_availability.latest_available_function" + f"Dataset template '{dataset_id}' in {source} has invalid sync_availability.latest_available_function" ) diff --git a/src/climate_api/extents/routes.py b/src/climate_api/extents/routes.py index 9e617ece..fce65717 100644 --- a/src/climate_api/extents/routes.py +++ b/src/climate_api/extents/routes.py @@ -1,24 +1,20 @@ """FastAPI routes for configured extent discovery.""" -from fastapi import APIRouter +from fastapi import APIRouter, HTTPException from climate_api.extents import services -from climate_api.extents.schemas import ExtentListResponse, ExtentRecord +from climate_api.extents.schemas import ExtentRecord router = APIRouter() -@router.get("", response_model=ExtentListResponse) -def list_extents() -> ExtentListResponse: - """List configured extents for this Climate API instance.""" - items = [_build_extent_record(extent) for extent in services.list_extents()] - return ExtentListResponse(items=items) - - -@router.get("/{extent_id}", response_model=ExtentRecord) -def get_extent(extent_id: str) -> ExtentRecord: - """Get one configured extent for this Climate API instance.""" - return _build_extent_record(services.get_extent_or_404(extent_id)) +@router.get("", response_model=ExtentRecord) +def get_extent() -> ExtentRecord: + """Return the configured extent for this Climate API instance.""" + extent = services.get_extent() + if extent is None: + raise HTTPException(status_code=404, detail="No extent configured") + return _build_extent_record(extent) def _build_extent_record(extent: dict[str, object]) -> ExtentRecord: diff --git a/src/climate_api/extents/schemas.py b/src/climate_api/extents/schemas.py index e1a40dae..425702ff 100644 --- a/src/climate_api/extents/schemas.py +++ b/src/climate_api/extents/schemas.py @@ -12,27 +12,3 @@ class ExtentRecord(BaseModel): bbox: tuple[float, float, float, float] = Field( description="Configured bounding box for the extent as xmin, ymin, xmax, ymax." ) - - -class ExtentListResponse(BaseModel): - """Envelope response for configured extents.""" - - kind: str = Field( - default="ExtentList", - description="Self-describing envelope type for this collection response.", - examples=["ExtentList"], - ) - items: list[ExtentRecord] = Field( - default_factory=list, - description="Configured extents available in this Climate API instance.", - examples=[ - [ - { - "extent_id": "sle", - "name": "Sierra Leone", - "description": "National extent for Sierra Leone.", - "bbox": [-13.5, 6.9, -10.1, 10.0], - } - ] - ], - ) diff --git a/src/climate_api/extents/services.py b/src/climate_api/extents/services.py index 3dcccedd..4c7e1d52 100644 --- a/src/climate_api/extents/services.py +++ b/src/climate_api/extents/services.py @@ -1,29 +1,29 @@ -"""Extent registry backed by YAML config files.""" +"""Extent registry backed by CLIMATE_API_CONFIG.""" -from pathlib import Path from typing import Any -import yaml from fastapi import HTTPException -SCRIPT_DIR = Path(__file__).parent.resolve() -EXTENTS_PATH = SCRIPT_DIR.parent.parent.parent / "data" / "extents.yaml" +from climate_api import config as api_config -def list_extents() -> list[dict[str, Any]]: - """Return configured extents for this Climate API instance.""" - if not EXTENTS_PATH.exists(): - return [] - payload = yaml.safe_load(EXTENTS_PATH.read_text(encoding="utf-8")) or {} - extents = payload.get("extents", []) - if not isinstance(extents, list): - raise ValueError(f"Expected 'extents' list in {EXTENTS_PATH}") - return [extent for extent in extents if isinstance(extent, dict)] +def get_extent() -> dict[str, Any] | None: + """Return the configured extent for this Climate API instance, or None if not set.""" + extent = api_config.get_config().get("extent") + if extent is None: + return None + if not isinstance(extent, dict): + raise ValueError("extent in CLIMATE_API_CONFIG must be a mapping") + if not isinstance(extent.get("id"), str) or not extent["id"]: + raise ValueError("extent.id in CLIMATE_API_CONFIG must be a non-empty string") + if not isinstance(extent.get("bbox"), list) or len(extent["bbox"]) != 4: + raise ValueError("extent.bbox in CLIMATE_API_CONFIG must be a list of four numbers [xmin, ymin, xmax, ymax]") + return extent def get_extent_or_404(extent_id: str) -> dict[str, Any]: - """Return one configured extent or raise 404.""" - for extent in list_extents(): - if extent.get("id") == extent_id: - return extent + """Return the configured extent if its id matches, or raise 404.""" + extent = get_extent() + if extent is not None and extent.get("id") == extent_id: + return extent raise HTTPException(status_code=404, detail=f"Extent '{extent_id}' not found") diff --git a/src/climate_api/ingestions/services.py b/src/climate_api/ingestions/services.py index 6b41b48f..dfc5efd4 100644 --- a/src/climate_api/ingestions/services.py +++ b/src/climate_api/ingestions/services.py @@ -47,8 +47,17 @@ logger = logging.getLogger(__name__) -DATA_DIR = Path(__file__).resolve().parent.parent.parent.parent / "data" -ARTIFACTS_DIR = DATA_DIR / "artifacts" + +def _resolve_artifacts_dir() -> Path: + # CACHE_OVERRIDE keeps existing Docker/dev deployments working unchanged. + override = os.getenv("CACHE_OVERRIDE") + if override: + return Path(override) / "artifacts" + xdg_data = Path(os.getenv("XDG_DATA_HOME", Path.home() / ".local" / "share")) + return xdg_data / "climate-api" / "artifacts" + + +ARTIFACTS_DIR = _resolve_artifacts_dir() ARTIFACTS_INDEX_PATH = ARTIFACTS_DIR / "records.json" diff --git a/src/climate_api/ingestions/sync_engine.py b/src/climate_api/ingestions/sync_engine.py index e0870fd5..26a031bb 100644 --- a/src/climate_api/ingestions/sync_engine.py +++ b/src/climate_api/ingestions/sync_engine.py @@ -363,12 +363,12 @@ def _supports_append(source_dataset: dict[str, Any]) -> bool: """Return whether this template opts into V1 delta-download sync execution.""" if source_dataset.get("sync_execution") != SyncAction.APPEND.value: return False - cache_info = source_dataset.get("cache_info") - if not isinstance(cache_info, dict): + ingestion = source_dataset.get("ingestion") + if not isinstance(ingestion, dict): return False # Multiscale stores are rebuilt as pyramids today; keep append opt-in to flat # canonical stores until pyramid delta behavior is explicitly designed. - if cache_info.get("multiscales"): + if ingestion.get("multiscales"): logger.warning( "Sync append execution is not supported for multiscale dataset '%s'; falling back to rematerialize", source_dataset.get("id", ""), diff --git a/src/climate_api/main.py b/src/climate_api/main.py index 9aa3c573..824bb887 100644 --- a/src/climate_api/main.py +++ b/src/climate_api/main.py @@ -15,16 +15,6 @@ from climate_api.stac import routes as stac_routes from climate_api.system import routes as system_routes -app = FastAPI() - -app.add_middleware( - CORSMiddleware, - allow_origins=["*"], - allow_credentials=True, - allow_methods=["*"], - allow_headers=["*"], -) - def _zarr_browser_access_origins() -> set[str]: """Return allowlisted remote origins permitted to inspect local Zarr endpoints.""" @@ -44,44 +34,66 @@ def _append_vary_value(response: Response, value: str) -> None: response.headers["Vary"] = ", ".join([*values, value]) -@app.middleware("http") -async def add_zarr_browser_access_headers( - request: Request, - call_next: Callable[[Request], Awaitable[Response]], -) -> Response: - """Add browser access headers needed by remote Zarr inspectors calling localhost.""" - origin = request.headers.get("origin") - allowed_origin = origin if origin in _zarr_browser_access_origins() else None - if ( - request.method == "OPTIONS" - and (request.url.path == "/zarr" or request.url.path.startswith("/zarr/")) - and request.headers.get("access-control-request-private-network") == "true" - and allowed_origin is not None - ): - response = Response(status_code=200) - else: - response = await call_next(request) - if request.url.path == "/zarr" or request.url.path.startswith("/zarr/"): - if allowed_origin is not None: - response.headers["Access-Control-Allow-Origin"] = allowed_origin - _append_vary_value(response, "Origin") - response.headers.setdefault("Access-Control-Allow-Methods", "GET, HEAD, OPTIONS") - response.headers.setdefault( - "Access-Control-Allow-Headers", - request.headers.get("access-control-request-headers", "*"), - ) - if allowed_origin is not None and request.headers.get("access-control-request-private-network") == "true": - response.headers["Access-Control-Allow-Private-Network"] = "true" - return response - - -app.include_router(system_routes.router, tags=["System"]) -app.include_router(stac_routes.router, prefix="/stac", tags=["STAC"]) -app.include_router(extent_routes.router, prefix="/extents", tags=["Extents"]) -app.include_router(dataset_template_routes.router, prefix="/dataset-templates", tags=["Dataset templates"]) -app.include_router(ingestion_routes.datasets_router, prefix="/datasets", tags=["Datasets"]) -app.include_router(ingestion_routes.ingestions_router, prefix="/ingestions", tags=["Ingestions"]) -app.include_router(ingestion_routes.zarr_router, prefix="/zarr", tags=["Zarr"]) -app.include_router(ingestion_routes.sync_router, prefix="/sync", tags=["Sync"]) - -mount_pygeoapi(app) +def create_app() -> FastAPI: + """Create and configure the Climate API FastAPI application. + + This is the public entry point for embedding the API in a larger application: + + from climate_api.main import create_app + app = create_app() + """ + _app = FastAPI() + + _app.add_middleware( + CORSMiddleware, + allow_origins=["*"], + allow_credentials=False, + allow_methods=["*"], + allow_headers=["*"], + ) + + @_app.middleware("http") + async def add_zarr_browser_access_headers( + request: Request, + call_next: Callable[[Request], Awaitable[Response]], + ) -> Response: + """Add browser access headers needed by remote Zarr inspectors calling localhost.""" + origin = request.headers.get("origin") + allowed_origin = origin if origin in _zarr_browser_access_origins() else None + if ( + request.method == "OPTIONS" + and (request.url.path == "/zarr" or request.url.path.startswith("/zarr/")) + and request.headers.get("access-control-request-private-network") == "true" + and allowed_origin is not None + ): + response = Response(status_code=200) + else: + response = await call_next(request) + if request.url.path == "/zarr" or request.url.path.startswith("/zarr/"): + if allowed_origin is not None: + response.headers["Access-Control-Allow-Origin"] = allowed_origin + _append_vary_value(response, "Origin") + response.headers.setdefault("Access-Control-Allow-Methods", "GET, HEAD, OPTIONS") + response.headers.setdefault( + "Access-Control-Allow-Headers", + request.headers.get("access-control-request-headers", "*"), + ) + if allowed_origin is not None and request.headers.get("access-control-request-private-network") == "true": + response.headers["Access-Control-Allow-Private-Network"] = "true" + return response + + _app.include_router(system_routes.router, tags=["System"]) + _app.include_router(stac_routes.router, prefix="/stac", tags=["STAC"]) + _app.include_router(extent_routes.router, prefix="/extent", tags=["Extent"]) + _app.include_router(dataset_template_routes.router, prefix="/dataset-templates", tags=["Dataset templates"]) + _app.include_router(ingestion_routes.datasets_router, prefix="/datasets", tags=["Datasets"]) + _app.include_router(ingestion_routes.ingestions_router, prefix="/ingestions", tags=["Ingestions"]) + _app.include_router(ingestion_routes.zarr_router, prefix="/zarr", tags=["Zarr"]) + _app.include_router(ingestion_routes.sync_router, prefix="/sync", tags=["Sync"]) + + mount_pygeoapi(_app) + + return _app + + +app = create_app() diff --git a/src/climate_api/publications/services.py b/src/climate_api/publications/services.py index e7c28a14..cc531dd8 100644 --- a/src/climate_api/publications/services.py +++ b/src/climate_api/publications/services.py @@ -2,6 +2,7 @@ from __future__ import annotations +import importlib.resources import os from datetime import UTC, datetime from importlib import import_module @@ -16,10 +17,16 @@ from climate_api.data_manager.services.utils import get_lon_lat_dims, get_time_dim from climate_api.ingestions.schemas import ArtifactFormat, ArtifactRecord, PublicationStatus -DATA_DIR = Path(__file__).resolve().parent.parent.parent.parent / "data" -CONFIG_DIR = Path(__file__).resolve().parent.parent.parent.parent / "config" / "pygeoapi" -PYGEOAPI_BASE_CONFIG_PATH = CONFIG_DIR / "base.yml" -PYGEOAPI_DIR = DATA_DIR / "pygeoapi" + +def _resolve_pygeoapi_dir() -> Path: + override = os.getenv("CACHE_OVERRIDE") + if override: + return Path(override) / "pygeoapi" + xdg_data = Path(os.getenv("XDG_DATA_HOME", Path.home() / ".local" / "share")) + return xdg_data / "climate-api" / "pygeoapi" + + +PYGEOAPI_DIR = _resolve_pygeoapi_dir() PYGEOAPI_CONFIG_PATH = PYGEOAPI_DIR / "pygeoapi-config.yml" PYGEOAPI_OPENAPI_PATH = PYGEOAPI_DIR / "pygeoapi-openapi.yml" @@ -199,5 +206,6 @@ def _native_dataset_href(dataset_id: str) -> str: def _load_base_config() -> dict[str, Any]: - """Load the checked-in base pygeoapi config used for generated publication docs.""" - return cast(dict[str, Any], yaml.safe_load(PYGEOAPI_BASE_CONFIG_PATH.read_text(encoding="utf-8"))) + """Load the bundled base pygeoapi config via importlib.resources.""" + resource = importlib.resources.files("climate_api") / "data" / "pygeoapi" / "base.yml" + return cast(dict[str, Any], yaml.safe_load(resource.read_text(encoding="utf-8"))) diff --git a/src/climate_api/stac/services.py b/src/climate_api/stac/services.py index ce6bba40..4a0c730e 100644 --- a/src/climate_api/stac/services.py +++ b/src/climate_api/stac/services.py @@ -286,10 +286,10 @@ def _public_zarr_asset_href( artifact: ArtifactRecord, source_dataset: dict[str, Any], ) -> str: - cache_info = source_dataset.get("cache_info") + ingestion = source_dataset.get("ingestion") # Use dataset-template multiscale metadata so local and remote stores map to # the same public href contract without filesystem probing. - if isinstance(cache_info, dict) and cache_info.get("multiscales"): + if isinstance(ingestion, dict) and ingestion.get("multiscales"): return _abs_url(request, f"/zarr/{dataset_id}/0") return _abs_url(request, f"/zarr/{dataset_id}") diff --git a/src/climate_api/startup.py b/src/climate_api/startup.py index 9cc5c01d..086a9fce 100644 --- a/src/climate_api/startup.py +++ b/src/climate_api/startup.py @@ -6,17 +6,16 @@ import logging import os -from pathlib import Path from dotenv import load_dotenv # noqa: E402 # -- Load .env (must happen before pygeoapi reads PYGEOAPI_CONFIG) ------------ load_dotenv() -DEFAULT_PYGEOAPI_CONFIG = Path(__file__).resolve().parent.parent.parent / "data" / "pygeoapi" / "pygeoapi-config.yml" -DEFAULT_PYGEOAPI_OPENAPI = Path(__file__).resolve().parent.parent.parent / "data" / "pygeoapi" / "pygeoapi-openapi.yml" -os.environ.setdefault("PYGEOAPI_CONFIG", str(DEFAULT_PYGEOAPI_CONFIG)) -os.environ.setdefault("PYGEOAPI_OPENAPI", str(DEFAULT_PYGEOAPI_OPENAPI)) +from climate_api.publications.services import PYGEOAPI_CONFIG_PATH, PYGEOAPI_OPENAPI_PATH # noqa: E402 + +os.environ.setdefault("PYGEOAPI_CONFIG", str(PYGEOAPI_CONFIG_PATH)) +os.environ.setdefault("PYGEOAPI_OPENAPI", str(PYGEOAPI_OPENAPI_PATH)) # -- climate_api / third-party logging setup --------------------------------------- eo_logger = logging.getLogger("climate_api") diff --git a/src/climate_api/system/routes.py b/src/climate_api/system/routes.py index b2bdd055..7f367eac 100644 --- a/src/climate_api/system/routes.py +++ b/src/climate_api/system/routes.py @@ -19,7 +19,7 @@ def read_index(request: Request) -> RootResponse: links=[ Link(href=f"{base}/ogcapi/", rel="ogcapi", title="OGC API"), Link(href=f"{base}/stac/catalog.json", rel="stac", title="STAC Catalog"), - Link(href=f"{base}/extents", rel="extents", title="Extents"), + Link(href=f"{base}/extent", rel="extent", title="Extent"), Link(href=f"{base}/ingestions", rel="ingestions", title="Ingestions"), Link(href=f"{base}/datasets", rel="datasets", title="Datasets"), Link(href=f"{base}/docs", rel="docs", title="API Docs"), diff --git a/tests/conftest.py b/tests/conftest.py index f796ad54..1f66391f 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,8 +1,40 @@ +import os +from collections.abc import Generator + import pytest from fastapi.testclient import TestClient +from climate_api import config as api_config from climate_api.main import app +_TEST_CONFIG = """\ +extent: + id: sle + name: Sierra Leone + bbox: [-13.5, 6.9, -10.1, 10.0] + country_code: SLE +""" + + +@pytest.fixture(autouse=True, scope="session") +def _test_climate_api_config(tmp_path_factory: pytest.TempPathFactory) -> Generator[None, None, None]: + config_file = tmp_path_factory.mktemp("config") / "climate-api.yaml" + config_file.write_text(_TEST_CONFIG, encoding="utf-8") + old = os.environ.get("CLIMATE_API_CONFIG") + os.environ["CLIMATE_API_CONFIG"] = str(config_file) + yield + if old is None: + os.environ.pop("CLIMATE_API_CONFIG", None) + else: + os.environ["CLIMATE_API_CONFIG"] = old + + +@pytest.fixture(autouse=True) +def _reset_config_cache() -> Generator[None, None, None]: + api_config._cache = None + yield + api_config._cache = None + @pytest.fixture def client() -> TestClient: diff --git a/tests/test_client.py b/tests/test_client.py new file mode 100644 index 00000000..47c990e4 --- /dev/null +++ b/tests/test_client.py @@ -0,0 +1,161 @@ +from pathlib import Path +from unittest.mock import MagicMock, patch + +import numpy as np +import pandas as pd +import pytest +import xarray as xr + +from climate_api.client import Client, list_datasets, open_dataset + + +def _make_catalog(hrefs: list[str]) -> dict: + return { + "links": [{"rel": "child", "href": href, "title": href.split("/")[-1]} for href in hrefs] + + [{"rel": "root", "href": "http://localhost/stac/catalog.json"}] + } + + +def _make_collection(zarr_href: str) -> dict: + return { + "assets": { + "zarr": { + "href": zarr_href, + "xarray:open_kwargs": {"consolidated": True}, + } + } + } + + +def _make_response(json_body: dict, status_code: int = 200) -> MagicMock: + resp = MagicMock() + resp.status_code = status_code + resp.json.return_value = json_body + resp.raise_for_status.return_value = None + return resp + + +def test_list_datasets_returns_child_links() -> None: + catalog = _make_catalog(["http://localhost/stac/collections/chirps3_precipitation_daily_rwa"]) + with patch("climate_api.client.httpx.get", return_value=_make_response(catalog)) as mock_get: + result = list_datasets("http://localhost") + + mock_get.assert_called_once_with("http://localhost/stac/catalog.json", timeout=30) + assert len(result) == 1 + assert result[0]["rel"] == "child" + assert "chirps3" in result[0]["href"] + + +def test_list_datasets_returns_empty_for_no_children() -> None: + catalog = {"links": [{"rel": "root", "href": "http://localhost/stac/catalog.json"}]} + with patch("climate_api.client.httpx.get", return_value=_make_response(catalog)): + result = list_datasets("http://localhost") + + assert result == [] + + +def test_list_datasets_raises_on_http_error() -> None: + import httpx + + with patch("climate_api.client.httpx.get") as mock_get: + mock_get.return_value.raise_for_status.side_effect = httpx.HTTPStatusError( + "404", request=MagicMock(), response=MagicMock() + ) + with pytest.raises(httpx.HTTPStatusError): + list_datasets("http://localhost") + + +def test_open_dataset_fetches_collection_and_opens_zarr(tmp_path: Path) -> None: + zarr_path = tmp_path / "test.zarr" + ds = xr.Dataset( + {"precip": (["time", "latitude", "longitude"], np.ones((2, 3, 3), dtype="float32"))}, + coords={ + "time": pd.date_range("2024-01-01", periods=2, freq="D"), + "latitude": [3.0, 2.0, 1.0], + "longitude": [10.0, 11.0, 12.0], + }, + ) + ds.to_zarr(str(zarr_path), mode="w", consolidated=True) + + collection = _make_collection(str(zarr_path)) + with patch("climate_api.client.httpx.get", return_value=_make_response(collection)): + result = open_dataset("chirps3_precipitation_daily_rwa", base_url="http://localhost") + + try: + assert "precip" in result.data_vars + assert result.sizes["time"] == 2 + assert "latitude" in result.coords + assert "longitude" in result.coords + finally: + result.close() + + +def test_open_dataset_raises_on_http_error() -> None: + import httpx + + with patch("climate_api.client.httpx.get") as mock_get: + mock_get.return_value.raise_for_status.side_effect = httpx.HTTPStatusError( + "404", request=MagicMock(), response=MagicMock() + ) + with pytest.raises(httpx.HTTPStatusError): + open_dataset("nonexistent", base_url="http://localhost") + + +def test_open_dataset_uses_default_base_url() -> None: + collection = _make_collection("/dev/null") + with patch("climate_api.client.httpx.get", return_value=_make_response(collection)) as mock_get: + with patch("climate_api.client.xr.open_zarr", return_value=MagicMock()): + open_dataset("any_dataset") + + mock_get.assert_called_once_with("http://127.0.0.1:8000/stac/collections/any_dataset", timeout=30) + + +def test_open_dataset_uses_env_var_base_url(monkeypatch: pytest.MonkeyPatch) -> None: + monkeypatch.setenv("CLIMATE_API_BASE_URL", "http://env-host:9000") + collection = _make_collection("/dev/null") + with patch("climate_api.client.httpx.get", return_value=_make_response(collection)) as mock_get: + with patch("climate_api.client.xr.open_zarr", return_value=MagicMock()): + open_dataset("any_dataset") + + mock_get.assert_called_once_with("http://env-host:9000/stac/collections/any_dataset", timeout=30) + + +def test_client_catalog_delegates_to_module_function() -> None: + catalog = _make_catalog(["http://localhost/stac/collections/chirps3_precipitation_daily_rwa"]) + with patch("climate_api.client.httpx.get", return_value=_make_response(catalog)) as mock_get: + result = Client("http://localhost").catalog() + + mock_get.assert_called_once_with("http://localhost/stac/catalog.json", timeout=30) + assert len(result) == 1 + assert result[0]["rel"] == "child" + + +def test_client_open_dataset_delegates_to_module_function(tmp_path: Path) -> None: + zarr_path = tmp_path / "test.zarr" + ds = xr.Dataset( + {"precip": (["time", "latitude", "longitude"], np.ones((2, 3, 3), dtype="float32"))}, + coords={ + "time": pd.date_range("2024-01-01", periods=2, freq="D"), + "latitude": [3.0, 2.0, 1.0], + "longitude": [10.0, 11.0, 12.0], + }, + ) + ds.to_zarr(str(zarr_path), mode="w", consolidated=True) + + collection = _make_collection(str(zarr_path)) + with patch("climate_api.client.httpx.get", return_value=_make_response(collection)): + result = Client("http://localhost").open("chirps3_precipitation_daily_rwa") + + try: + assert "precip" in result.data_vars + assert result.sizes["time"] == 2 + finally: + result.close() + + +def test_client_strips_trailing_slash() -> None: + catalog = _make_catalog(["http://localhost/stac/collections/chirps3_precipitation_daily_rwa"]) + with patch("climate_api.client.httpx.get", return_value=_make_response(catalog)) as mock_get: + Client("http://localhost/").catalog() + + mock_get.assert_called_once_with("http://localhost/stac/catalog.json", timeout=30) diff --git a/tests/test_config.py b/tests/test_config.py new file mode 100644 index 00000000..34f452e3 --- /dev/null +++ b/tests/test_config.py @@ -0,0 +1,174 @@ +from pathlib import Path + +import pytest + +from climate_api.config import get_config +from climate_api.data_registry.services import datasets as dataset_registry +from climate_api.extents import services as extent_services + + +def test_get_config_returns_empty_when_unset(monkeypatch: pytest.MonkeyPatch) -> None: + monkeypatch.delenv("CLIMATE_API_CONFIG", raising=False) + assert get_config() == {} + + +def test_get_config_raises_when_path_missing(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> None: + monkeypatch.setenv("CLIMATE_API_CONFIG", str(tmp_path / "nonexistent.yaml")) + with pytest.raises(FileNotFoundError, match="CLIMATE_API_CONFIG not found"): + get_config() + + +def test_get_config_loads_extent(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> None: + config_file = tmp_path / "climate-api.yaml" + config_file.write_text( + """ +extent: + id: rwa + name: Rwanda + bbox: [28.8, -2.9, 30.9, -1.0] + country_code: RWA +""", + encoding="utf-8", + ) + monkeypatch.setenv("CLIMATE_API_CONFIG", str(config_file)) + + config = get_config() + assert config["extent"]["id"] == "rwa" + assert config["extent"]["bbox"] == [28.8, -2.9, 30.9, -1.0] + + +def test_get_config_substitutes_env_vars(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> None: + config_file = tmp_path / "climate-api.yaml" + config_file.write_text( + """ +extent: + id: ${EXTENT_ID:-sle} + name: ${EXTENT_NAME:-Sierra Leone} +""", + encoding="utf-8", + ) + monkeypatch.setenv("CLIMATE_API_CONFIG", str(config_file)) + monkeypatch.setenv("EXTENT_ID", "rwa") + monkeypatch.delenv("EXTENT_NAME", raising=False) + + config = get_config() + assert config["extent"]["id"] == "rwa" + assert config["extent"]["name"] == "Sierra Leone" + + +def test_extents_service_reads_from_config(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> None: + config_file = tmp_path / "climate-api.yaml" + config_file.write_text( + """ +extent: + id: rwa + name: Rwanda + bbox: [28.8, -2.9, 30.9, -1.0] +""", + encoding="utf-8", + ) + monkeypatch.setenv("CLIMATE_API_CONFIG", str(config_file)) + + extent = extent_services.get_extent() + assert extent is not None + assert extent["id"] == "rwa" + + +def test_extent_service_returns_none_when_config_unset(monkeypatch: pytest.MonkeyPatch) -> None: + monkeypatch.delenv("CLIMATE_API_CONFIG", raising=False) + + assert extent_services.get_extent() is None + + +def test_builtin_datasets_include_chirps_era5_worldpop(monkeypatch: pytest.MonkeyPatch) -> None: + monkeypatch.setattr(dataset_registry, "CONFIGS_DIR", None) + monkeypatch.delenv("CLIMATE_API_CONFIG", raising=False) + + ids = {d["id"] for d in dataset_registry.list_datasets()} + assert "chirps3_precipitation_daily" in ids + assert "era5land_temperature_hourly" in ids + assert "era5land_precipitation_hourly" in ids + assert "worldpop_population_yearly" in ids + + +def test_datasets_dir_in_config_adds_to_bundled(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> None: + datasets_dir = tmp_path / "datasets" + datasets_dir.mkdir() + (datasets_dir / "custom.yaml").write_text( + """ +- id: custom_dataset + name: Custom dataset + variable: val + period_type: daily + sync_kind: static + ingestion: + function: mypackage.sources.download +""", + encoding="utf-8", + ) + config_file = tmp_path / "climate-api.yaml" + config_file.write_text(f"datasets_dir: {datasets_dir}\n", encoding="utf-8") + + monkeypatch.setattr(dataset_registry, "CONFIGS_DIR", None) + monkeypatch.setenv("CLIMATE_API_CONFIG", str(config_file)) + + ids = {d["id"] for d in dataset_registry.list_datasets()} + assert "custom_dataset" in ids + assert "chirps3_precipitation_daily" in ids + + +def test_datasets_dir_resolved_relative_to_config_file(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> None: + """datasets_dir is resolved relative to the config file, not CWD. + + This matters when running the installed `climate-api` CLI from a directory + other than the repo root, where a relative datasets_dir in the config must + still point at the correct sibling directory. + """ + deployment_dir = tmp_path / "deployment" + deployment_dir.mkdir() + datasets_dir = deployment_dir / "datasets" + datasets_dir.mkdir() + (datasets_dir / "custom.yaml").write_text( + """ +- id: deployed_dataset + variable: val + period_type: daily + sync_kind: static + ingestion: + function: mypackage.sources.download +""", + encoding="utf-8", + ) + config_file = deployment_dir / "climate-api.yaml" + config_file.write_text("datasets_dir: ./datasets\n", encoding="utf-8") + + monkeypatch.setattr(dataset_registry, "CONFIGS_DIR", None) + monkeypatch.setenv("CLIMATE_API_CONFIG", str(config_file)) + + ids = {d["id"] for d in dataset_registry.list_datasets()} + assert "deployed_dataset" in ids + + +def test_datasets_dir_in_config_overrides_bundled_by_id(monkeypatch: pytest.MonkeyPatch, tmp_path: Path) -> None: + datasets_dir = tmp_path / "datasets" + datasets_dir.mkdir() + (datasets_dir / "chirps3.yaml").write_text( + """ +- id: chirps3_precipitation_daily + name: Custom CHIRPS override + variable: precip + period_type: daily + sync_kind: static + ingestion: + function: mypackage.sources.download +""", + encoding="utf-8", + ) + config_file = tmp_path / "climate-api.yaml" + config_file.write_text(f"datasets_dir: {datasets_dir}\n", encoding="utf-8") + + monkeypatch.setattr(dataset_registry, "CONFIGS_DIR", None) + monkeypatch.setenv("CLIMATE_API_CONFIG", str(config_file)) + + datasets = {d["id"]: d for d in dataset_registry.list_datasets()} + assert datasets["chirps3_precipitation_daily"]["name"] == "Custom CHIRPS override" diff --git a/tests/test_dataset_registry.py b/tests/test_dataset_registry.py index cca324d1..7bb60c76 100644 --- a/tests/test_dataset_registry.py +++ b/tests/test_dataset_registry.py @@ -55,6 +55,8 @@ def test_dataset_registry_accepts_supported_sync_kind( variable: value period_type: daily sync_kind: temporal + ingestion: + function: mypackage.sources.download """, encoding="utf-8", ) @@ -75,6 +77,8 @@ def test_dataset_registry_rejects_unsupported_sync_execution( variable: value period_type: daily sync_kind: temporal + ingestion: + function: mypackage.sources.download sync_execution: sometimes """, encoding="utf-8", @@ -97,6 +101,8 @@ def test_dataset_registry_rejects_non_string_sync_execution( variable: value period_type: daily sync_kind: temporal + ingestion: + function: mypackage.sources.download sync_execution: - append """, @@ -120,6 +126,8 @@ def test_dataset_registry_accepts_supported_sync_execution( variable: value period_type: daily sync_kind: temporal + ingestion: + function: mypackage.sources.download sync_execution: append """, encoding="utf-8", @@ -141,6 +149,8 @@ def test_dataset_registry_rejects_invalid_sync_availability_function( variable: value period_type: daily sync_kind: temporal + ingestion: + function: mypackage.sources.download sync_availability: latest_available_function: 42 """, @@ -164,6 +174,8 @@ def test_dataset_registry_accepts_sync_availability_function( variable: value period_type: daily sync_kind: temporal + ingestion: + function: mypackage.sources.download sync_availability: latest_available_function: climate_api.providers.availability.lagged_latest_available """, diff --git a/tests/test_datasets_sync.py b/tests/test_datasets_sync.py index 9711ec3c..1f035da1 100644 --- a/tests/test_datasets_sync.py +++ b/tests/test_datasets_sync.py @@ -98,7 +98,7 @@ def test_sync_dataset_returns_up_to_date_when_no_new_period_is_due(monkeypatch: "id": "chirps3_precipitation_daily", "period_type": "daily", "sync_kind": "temporal", - "cache_info": {}, + "ingestion": {}, }, ) monkeypatch.setattr(services, "get_dataset_or_404", lambda _: _dataset_detail(dataset_id)) @@ -175,7 +175,7 @@ def test_sync_dataset_append_policy_downloads_only_delta_but_preserves_full_scop "period_type": "daily", "sync_kind": "temporal", "sync_execution": "append", - "cache_info": {}, + "ingestion": {}, }, ) @@ -227,7 +227,7 @@ def test_sync_dataset_append_policy_falls_back_to_rematerialize_for_multiscales( "period_type": "yearly", "sync_kind": "temporal", "sync_execution": "append", - "cache_info": {"multiscales": {"levels": 4}}, + "ingestion": {"multiscales": {"levels": 4}}, }, ) @@ -509,7 +509,7 @@ def today(cls) -> "FixedDate": "period_type": "daily", "sync_kind": "temporal", "sync_execution": "append", - "cache_info": {}, + "ingestion": {}, }, latest_artifact=_artifact(artifact_id="a1", end="2024-02-29"), requested_end="", @@ -587,7 +587,7 @@ def today(cls) -> "FixedDate": "period_type": "daily", "sync_kind": "temporal", "sync_execution": "append", - "cache_info": {}, + "ingestion": {}, }, latest_artifact=_artifact(artifact_id="a1", end="2024-02-29"), requested_end=None, @@ -608,7 +608,7 @@ def test_plan_sync_marks_request_target_clamped_by_availability(monkeypatch: pyt "period_type": "daily", "sync_kind": "temporal", "sync_execution": "append", - "cache_info": {}, + "ingestion": {}, "sync_availability": { "latest_available_function": "climate_api.providers.availability.chirps3_daily_latest_available" }, diff --git a/tests/test_downloader.py b/tests/test_downloader.py index f4d036c1..3e3ba64b 100644 --- a/tests/test_downloader.py +++ b/tests/test_downloader.py @@ -1,3 +1,4 @@ +import tempfile from pathlib import Path from typing import Any @@ -12,6 +13,35 @@ from climate_api.data_accessor.services.accessor import open_zarr_dataset from climate_api.data_manager.services import downloader +from climate_api.ingestions import services as ingestion_services + + +def test_resolve_download_dir_uses_cache_override(monkeypatch: pytest.MonkeyPatch) -> None: + with tempfile.TemporaryDirectory() as override: + monkeypatch.setenv("CACHE_OVERRIDE", override) + monkeypatch.delenv("XDG_DATA_HOME", raising=False) + assert downloader._resolve_download_dir() == Path(override) + + +def test_resolve_download_dir_uses_xdg_data_home(monkeypatch: pytest.MonkeyPatch) -> None: + with tempfile.TemporaryDirectory() as xdg: + monkeypatch.delenv("CACHE_OVERRIDE", raising=False) + monkeypatch.setenv("XDG_DATA_HOME", xdg) + assert downloader._resolve_download_dir() == Path(xdg) / "climate-api" / "downloads" + + +def test_resolve_artifacts_dir_uses_cache_override(monkeypatch: pytest.MonkeyPatch) -> None: + with tempfile.TemporaryDirectory() as override: + monkeypatch.setenv("CACHE_OVERRIDE", override) + monkeypatch.delenv("XDG_DATA_HOME", raising=False) + assert ingestion_services._resolve_artifacts_dir() == Path(override) / "artifacts" + + +def test_resolve_artifacts_dir_uses_xdg_data_home(monkeypatch: pytest.MonkeyPatch) -> None: + with tempfile.TemporaryDirectory() as xdg: + monkeypatch.delenv("CACHE_OVERRIDE", raising=False) + monkeypatch.setenv("XDG_DATA_HOME", xdg) + assert ingestion_services._resolve_artifacts_dir() == Path(xdg) / "climate-api" / "artifacts" def test_download_dataset_returns_400_when_country_code_is_required(monkeypatch: pytest.MonkeyPatch) -> None: @@ -28,7 +58,7 @@ def fake_download( dataset: dict[str, Any] = { "id": "worldpop_population_yearly", - "cache_info": {"eo_function": "ignored.path"}, + "ingestion": {"function": "ignored.path"}, } monkeypatch.delenv("COUNTRY_CODE", raising=False) monkeypatch.setattr(downloader, "_get_dynamic_function", lambda _: fake_download) @@ -62,7 +92,7 @@ def fake_download( dataset: dict[str, Any] = { "id": "chirps3_precipitation_daily", - "cache_info": {"eo_function": "ignored.path"}, + "ingestion": {"function": "ignored.path"}, } monkeypatch.delenv("DOWNLOAD_BBOX", raising=False) monkeypatch.delenv("DEFAULT_DOWNLOAD_BBOX", raising=False) @@ -99,7 +129,7 @@ def fake_download( dataset: dict[str, Any] = { "id": "worldpop_population_yearly", - "cache_info": {"eo_function": "ignored.path"}, + "ingestion": {"function": "ignored.path"}, } monkeypatch.setattr(downloader, "_get_dynamic_function", lambda _: fake_download) @@ -173,14 +203,14 @@ def _write_daily_nc_file(tmp_path: Path) -> list[Path]: "id": "my_dataset", "variable": "pop_total", "period_type": "yearly", - "cache_info": {}, + "ingestion": {}, } _PYRAMID_DATASET: dict[str, Any] = { "id": "my_dataset", "variable": "pop_total", "period_type": "yearly", - "cache_info": {"multiscales": {"levels": 2, "method": "mean"}}, + "ingestion": {"multiscales": {"levels": 2, "method": "mean"}}, } @@ -264,6 +294,78 @@ def test_build_dataset_zarr_flat_creates_zarr(tmp_path: Path, monkeypatch: pytes result.close() +def test_build_dataset_zarr_normalises_coordinate_names(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None: + """Source coordinates (lat/lon, valid_time, x/y) are renamed to longitude/latitude/time.""" + # Simulate ERA5-Land source with valid_time and lon/lat + ds_era5 = xr.Dataset( + {"t2m": (["valid_time", "lat", "lon"], np.ones((2, 3, 3), dtype="float32"))}, + coords={ + "valid_time": pd.date_range("2024-01-01", periods=2, freq="h"), + "lat": [10.0, 9.0, 8.0], + "lon": [30.0, 31.0, 32.0], + }, + ) + path = tmp_path / "era5_t2m_2024-01.nc" + ds_era5.to_netcdf(path) + + dataset: dict[str, Any] = { + "id": "era5land_temperature_hourly", + "variable": "t2m", + "period_type": "hourly", + "ingestion": {}, + } + monkeypatch.setattr(downloader, "DOWNLOAD_DIR", tmp_path) + monkeypatch.setattr(downloader, "get_cache_files", lambda _: [path]) + + downloader.build_dataset_zarr(dataset) + + result = open_zarr_dataset(str(tmp_path / "era5land_temperature_hourly.zarr")) + try: + assert "time" in result.coords + assert "longitude" in result.coords + assert "latitude" in result.coords + assert "valid_time" not in result.coords + assert "lat" not in result.coords + assert "lon" not in result.coords + finally: + result.close() + + +def test_build_dataset_zarr_normalises_xy_coordinate_names(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None: + """Source coordinates using x/y spatial names are renamed to longitude/latitude.""" + ds_xy = xr.Dataset( + {"precip": (["time", "y", "x"], np.ones((2, 3, 3), dtype="float32"))}, + coords={ + "time": pd.date_range("2024-01-01", periods=2, freq="D"), + "y": [10.0, 9.0, 8.0], + "x": [30.0, 31.0, 32.0], + }, + ) + path = tmp_path / "chirps_xy_2024-01.nc" + ds_xy.to_netcdf(path) + + dataset: dict[str, Any] = { + "id": "chirps3_precipitation_daily", + "variable": "precip", + "period_type": "daily", + "ingestion": {}, + } + monkeypatch.setattr(downloader, "DOWNLOAD_DIR", tmp_path) + monkeypatch.setattr(downloader, "get_cache_files", lambda _: [path]) + + downloader.build_dataset_zarr(dataset) + + result = open_zarr_dataset(str(tmp_path / "chirps3_precipitation_daily.zarr")) + try: + assert "time" in result.coords + assert "longitude" in result.coords + assert "latitude" in result.coords + assert "x" not in result.coords + assert "y" not in result.coords + finally: + result.close() + + def test_build_dataset_zarr_clips_to_requested_daily_range( tmp_path: Path, monkeypatch: pytest.MonkeyPatch, @@ -274,7 +376,7 @@ def test_build_dataset_zarr_clips_to_requested_daily_range( "id": "chirps3_precipitation_daily", "variable": "precip", "period_type": "daily", - "cache_info": {}, + "ingestion": {}, } monkeypatch.setattr(downloader, "DOWNLOAD_DIR", tmp_path) monkeypatch.setattr(downloader, "get_cache_files", lambda _: nc_files) @@ -298,7 +400,7 @@ def test_build_dataset_zarr_clips_to_requested_daily_range( def _make_fake_pyramid(ds: xr.Dataset, zarr_path: Path) -> Pyramid: """Return a Pyramid whose .dt.to_zarr writes a minimal two-level DataTree store.""" level0 = ds - level1 = ds.coarsen(lat=2, lon=2, boundary="trim").mean() # pyright: ignore[reportAttributeAccessIssue] + level1 = ds.coarsen(latitude=2, longitude=2, boundary="trim").mean() # pyright: ignore[reportAttributeAccessIssue] dt = DataTree.from_dict({"0": level0, "1": level1}) return Pyramid(datatree=dt, encoding={}) @@ -340,3 +442,41 @@ def fake_create_pyramid(ds: xr.Dataset, levels: int, x_dim: str, y_dim: str, met assert result.sizes["time"] == 2 finally: result.close() + + +def test_build_dataset_zarr_pyramid_normalises_coordinate_names( + tmp_path: Path, monkeypatch: pytest.MonkeyPatch +) -> None: + """Pyramid zarr store uses canonical longitude/latitude/time coordinate names.""" + # Source files use lat/lon (WorldPop-style); canonical names must appear in the written store. + nc_files = _write_nc_files(tmp_path) + monkeypatch.setattr(downloader, "DOWNLOAD_DIR", tmp_path) + monkeypatch.setattr(downloader, "get_cache_files", lambda _: nc_files) + + received: list[xr.Dataset] = [] + + def fake_create_pyramid(ds: xr.Dataset, levels: int, x_dim: str, y_dim: str, method: str) -> Pyramid: + received.append(ds) + return _make_fake_pyramid(ds, tmp_path / "my_dataset.zarr") + + monkeypatch.setattr(downloader, "create_pyramid", fake_create_pyramid) + + downloader.build_dataset_zarr(_PYRAMID_DATASET) + + # The dataset handed to create_pyramid must already carry canonical names. + assert len(received) == 1 + ds_in = received[0] + assert "longitude" in ds_in.coords + assert "latitude" in ds_in.coords + assert "time" in ds_in.coords + assert "lon" not in ds_in.coords + assert "lat" not in ds_in.coords + + # The written store must also expose canonical names when opened. + result = open_zarr_dataset(str(tmp_path / "my_dataset.zarr")) + try: + assert "longitude" in result.coords + assert "latitude" in result.coords + assert "time" in result.coords + finally: + result.close() diff --git a/tests/test_extents.py b/tests/test_extents.py index a851d82b..298ed539 100644 --- a/tests/test_extents.py +++ b/tests/test_extents.py @@ -1,28 +1,11 @@ from fastapi.testclient import TestClient -def test_list_extents_returns_configured_items(client: TestClient) -> None: - response = client.get("/extents") - - assert response.status_code == 200 - payload = response.json() - assert payload["kind"] == "ExtentList" - assert "items" in payload - assert payload["items"][0]["extent_id"] == "sle" - assert payload["items"][0]["bbox"] == [-13.5, 6.9, -10.1, 10.0] - assert "country_code" not in payload["items"][0] - - -def test_get_extent_returns_one_configured_extent(client: TestClient) -> None: - response = client.get("/extents/sle") +def test_get_extent_returns_configured_extent(client: TestClient) -> None: + response = client.get("/extent") assert response.status_code == 200 payload = response.json() assert payload["extent_id"] == "sle" - assert payload["name"] == "Sierra Leone" - - -def test_get_extent_returns_404_for_unknown_extent(client: TestClient) -> None: - response = client.get("/extents/unknown") - - assert response.status_code == 404 + assert payload["bbox"] == [-13.5, 6.9, -10.1, 10.0] + assert "country_code" not in payload diff --git a/tests/test_publications.py b/tests/test_publications.py index 356074af..403d3508 100644 --- a/tests/test_publications.py +++ b/tests/test_publications.py @@ -3,6 +3,32 @@ from climate_api.publications import services +def test_load_base_config_returns_mapping() -> None: + config = services._load_base_config() + assert isinstance(config, dict) + assert "server" in config + + +def test_resolve_pygeoapi_dir_uses_cache_override(monkeypatch: pytest.MonkeyPatch, tmp_path: object) -> None: + import tempfile + + with tempfile.TemporaryDirectory() as override: + monkeypatch.setenv("CACHE_OVERRIDE", override) + monkeypatch.delenv("XDG_DATA_HOME", raising=False) + result = services._resolve_pygeoapi_dir() + assert str(result) == f"{override}/pygeoapi" + + +def test_resolve_pygeoapi_dir_uses_xdg_data_home(monkeypatch: pytest.MonkeyPatch, tmp_path: object) -> None: + import tempfile + + with tempfile.TemporaryDirectory() as xdg: + monkeypatch.delenv("CACHE_OVERRIDE", raising=False) + monkeypatch.setenv("XDG_DATA_HOME", xdg) + result = services._resolve_pygeoapi_dir() + assert str(result) == f"{xdg}/climate-api/pygeoapi" + + def test_native_dataset_href_defaults_to_relative_path(monkeypatch: pytest.MonkeyPatch) -> None: monkeypatch.delenv("CLIMATE_API_BASE_URL", raising=False) monkeypatch.delenv("OGCAPI_BASE_URL", raising=False) diff --git a/tests/test_root.py b/tests/test_root.py index 421b6e7f..abccd6c7 100644 --- a/tests/test_root.py +++ b/tests/test_root.py @@ -20,7 +20,7 @@ def test_root_returns_links(client: TestClient) -> None: response = client.get("/") result = RootResponse.model_validate(response.json()) rels = [link.rel for link in result.links] - assert "extents" in rels + assert "extent" in rels assert "ingestions" in rels assert "datasets" in rels assert "docs" in rels diff --git a/tests/test_stac.py b/tests/test_stac.py index a5a8235e..d81948bf 100644 --- a/tests/test_stac.py +++ b/tests/test_stac.py @@ -2,8 +2,11 @@ from pathlib import Path from types import SimpleNamespace +import numpy as np +import pandas as pd import pystac import pytest +import xarray as xr from fastapi.testclient import TestClient from climate_api.ingestions import services as ingestion_services @@ -286,7 +289,7 @@ def test_collection_uses_level0_href_for_multiscale_store( monkeypatch.setattr( stac_services.registry_datasets, "get_dataset", - lambda _: {"period_type": "daily", "source": "CHIRPS v3", "cache_info": {"multiscales": {"levels": 2}}}, + lambda _: {"period_type": "daily", "source": "CHIRPS v3", "ingestion": {"multiscales": {"levels": 2}}}, ) monkeypatch.setattr( stac_services, @@ -322,7 +325,7 @@ def test_collection_uses_level0_href_for_remote_multiscale_store( monkeypatch.setattr( stac_services.registry_datasets, "get_dataset", - lambda _: {"period_type": "daily", "source": "CHIRPS v3", "cache_info": {"multiscales": {"levels": 2}}}, + lambda _: {"period_type": "daily", "source": "CHIRPS v3", "ingestion": {"multiscales": {"levels": 2}}}, ) monkeypatch.setattr( stac_services, @@ -375,6 +378,7 @@ def test_catalog_prefers_latest_artifact_per_managed_dataset( payload = response.json() child_links = [link for link in payload["links"] if link["rel"] == "child"] assert len(child_links) == 1 + assert "chirps3_precipitation_daily_sle" in child_links[0]["href"] def test_catalog_sorts_child_links_by_managed_dataset_id(client: TestClient, monkeypatch: pytest.MonkeyPatch) -> None: @@ -577,3 +581,39 @@ def raise_file_not_found(_: str) -> None: assert response.status_code == 503 assert "temporarily unavailable" in response.json()["detail"] + + +def test_build_collection_with_xstac_reads_normalised_zarr_coordinates(tmp_path: Path) -> None: + """STAC collection metadata is derived correctly from a normalised longitude/latitude/time store.""" + zarr_path = tmp_path / "chirps3_precipitation_daily_sle.zarr" + ds = xr.Dataset( + {"precip": (["time", "latitude", "longitude"], np.ones((5, 3, 3), dtype="float32"))}, + coords={ + "time": pd.date_range("2026-01-01", periods=5, freq="D"), + "latitude": [4.0, 3.0, 2.0], + "longitude": [1.0, 2.0, 3.0], + }, + ) + ds.to_zarr(str(zarr_path), mode="w", consolidated=True) + + artifact = _artifact(artifact_id="a1", path=str(zarr_path)) + + template = pystac.Collection( + id="chirps3_precipitation_daily_sle", + description="test", + extent=pystac.Extent( + spatial=pystac.SpatialExtent([[1.0, 2.0, 3.0, 4.0]]), + temporal=pystac.TemporalExtent([[datetime(2026, 1, 1, tzinfo=UTC), datetime(2026, 1, 5, tzinfo=UTC)]]), + ), + ) + + payload = stac_services._build_collection_with_xstac(artifact=artifact, template=template) + + assert payload["type"] == "Collection" + cube_dims = payload["cube:dimensions"] + assert "longitude" in cube_dims, f"expected 'longitude' in cube:dimensions, got {list(cube_dims)}" + assert "latitude" in cube_dims, f"expected 'latitude' in cube:dimensions, got {list(cube_dims)}" + assert "time" in cube_dims, f"expected 'time' in cube:dimensions, got {list(cube_dims)}" + assert cube_dims["longitude"]["axis"] == "x" + assert cube_dims["latitude"]["axis"] == "y" + assert cube_dims["time"]["type"] == "temporal" diff --git a/uv.lock b/uv.lock index 0097b732..383dd7d1 100644 --- a/uv.lock +++ b/uv.lock @@ -136,20 +136,20 @@ 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