implement OGC EDR API (geopython#658)

* implement OGC EDR API * add docs/tests * fix tests
francbartoli · Mar 15, 2021 · b26280d · b26280d
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diff --git a/Dockerfile b/Dockerfile
@@ -68,7 +68,7 @@ ARG ADD_DEB_PACKAGES="python3-gdal python3-psycopg2 python3-xarray python3-scipy
 ENV TZ=${TIMEZONE} \
 	DEBIAN_FRONTEND="noninteractive" \
 	DEB_BUILD_DEPS="software-properties-common curl unzip" \
-	DEB_PACKAGES="python3-pip python3-setuptools python3-distutils python3-yaml python3-dateutil python3-tz python3-flask python3-flask-cors python3-unicodecsv python3-click python3-greenlet python3-gevent python3-wheel gunicorn libsqlite3-mod-spatialite ${ADD_DEB_PACKAGES}"
+	DEB_PACKAGES="python3-pip python3-setuptools python3-distutils python3-shapely python3-yaml python3-dateutil python3-tz python3-flask python3-flask-cors python3-unicodecsv python3-click python3-greenlet python3-gevent python3-wheel gunicorn libsqlite3-mod-spatialite ${ADD_DEB_PACKAGES}"
 
 RUN mkdir -p /pygeoapi/pygeoapi
 # Add files required for pip/setuptools

diff --git a/docs/source/configuration.rst b/docs/source/configuration.rst
@@ -170,7 +170,7 @@ default.
               # see pygeoapi.plugin for supported providers
               # for custom built plugins, use the import path (e.g. mypackage.provider.MyProvider)
               # see Plugins section for more information
-              - type: feature # underlying data geospatial type: (allowed values are: feature, coverage, record, tile)
+              - type: feature # underlying data geospatial type: (allowed values are: feature, coverage, record, tile, edr)
                 default: true  # optional: if not specified, the first provider definition is considered the default
                 name: CSV
                 data: tests/data/obs.csv  # required: the data filesystem path or URL, depending on plugin setup

diff --git a/docs/source/data-publishing/index.rst b/docs/source/data-publishing/index.rst
@@ -23,4 +23,5 @@ return back data to the pygeoapi API framework in a plug and play fashion.
    ogcapi-tiles
    ogcapi-processes
    ogcapi-records
+   ogcapi-edr
    stac
diff --git a/docs/source/data-publishing/ogcapi-coverages.rst b/docs/source/data-publishing/ogcapi-coverages.rst
@@ -79,7 +79,7 @@ The `xarray`_ provider plugin reads and extracts `NetCDF`_ and `Zarr`_ data.
 
 .. note::
    `Zarr`_ files are directories with files and subdirectories.  Therefore
-    a zip file is returned upon request for said format.
+   a zip file is returned upon request for said format.
 
 Data access examples
 --------------------

diff --git a/docs/source/data-publishing/ogcapi-edr.rst b/docs/source/data-publishing/ogcapi-edr.rst
@@ -0,0 +1,84 @@
+.. _ogcapi-edr:
+
+Publishing data to OGC API - Environmental Data Retrieval
+=========================================================
+
+The `OGC Environmental Data Retrieval (EDR) (API)`_ provides a family of
+lightweight query interfaces to access spatio-temporal data resources.
+
+To add spatio-temporal data to pygeoapi for EDR query interfaces, you
+can use the dataset example in :ref:`configuration` as a baseline and
+modify accordingly.
+
+Providers
+---------
+
+pygeoapi core EDR providers are listed below, along with a matrix of supported query
+parameters.
+
+.. csv-table::
+   :header: Provider, coords, parameter-name, datetime
+   :align: left
+
+   xarray-edr,✅,✅,✅
+
+
+Below are specific connection examples based on supported providers.
+
+Connection examples
+-------------------
+
+xarray-edr
+^^^^^^^^^^
+
+The `xarray-edr`_ provider plugin reads and extracts `NetCDF`_ and `Zarr`_ data via `xarray`_.
+
+.. code-block:: yaml
+
+   providers:
+       - type: edr
+         name: xarray-edr
+         data: tests/data/coads_sst.nc
+         # optionally specify x/y/time fields, else provider will attempt
+         # to derive automagically
+         x_field: lat
+         x_field: lon
+         time_field: time
+         format:
+            name: netcdf
+            mimetype: application/x-netcdf
+
+   providers:
+       - type: edr
+         name: xarray-edr
+         data: tests/data/analysed_sst.zarr
+         format:
+            name: zarr
+            mimetype: application/zip
+
+.. note::
+
+   `Zarr`_ files are directories with files and subdirectories.  Therefore
+   a zip file is returned upon request for said format.
+
+Data access examples
+--------------------
+
+- list all collections
+  - http://localhost:5000/collections
+- overview of dataset
+  - http://localhost:5000/collections/foo
+- dataset position query
+  - http://localhost:5000/collections/foo/position?coords=POINT(-75%2045)
+- dataset position query for a specific parameter
+  - http://localhost:5000/collections/foo/position?coords=POINT(-75%2045)&parameter-name=SST
+- dataset position query for a specific parameter and time step
+  - http://localhost:5000/collections/foo/position?coords=POINT(-75%2045)&parameter-name=SST&datetime=2000-01-16
+
+
+.. _`xarray`: https://xarray.pydata.org
+.. _`NetCDF`: https://en.wikipedia.org/wiki/NetCDF
+.. _`Zarr`: https://zarr.readthedocs.io/en/stable
+
+
+.. _`OGC Environmental Data Retrieval (EDR) (API)`: https://github.com/opengeospatial/ogcapi-coverages
diff --git a/docs/source/introduction.rst b/docs/source/introduction.rst
@@ -10,7 +10,12 @@ Features
 
 - out of the box modern OGC API server
 - certified OGC Compliant and Reference Implementation for OGC API - Features
-- additionally implements OGC API - Coverages, OGC API - Tiles, OGC API - Processes, OGC API - Records and SpatioTemporal Asset Library
+- additionally implements
+  - OGC API - Coverages
+  - OGC API - Tiles
+  - OGC API - Processes
+  - OGC API - Environmental Data Retrieval
+  - SpatioTemporal Asset Library
 - out of the box data provider plugins for rasterio, GDAL/OGR, Elasticsearch, PostgreSQL/PostGIS
 - easy to use OpenAPI / Swagger documentation for developers
 - supports JSON, GeoJSON, HTML and CSV output
@@ -41,6 +46,7 @@ Standards are at the core of pygeoapi.  Below is the project's standards support
    `OGC API - Tiles`_,Implementing
    `OGC API - Processes`_,Implementing
    `OGC API - Records`_,Implementing
+   `OGC API - Environmental Data Retrieval`_,Implementing
    `SpatioTemporal Asset Catalog`_,Implementing
 
 
@@ -51,4 +57,5 @@ Standards are at the core of pygeoapi.  Below is the project's standards support
 .. _`OGC API - Tiles`: https://github.com/opengeospatial/ogcapi-tiles
 .. _`OGC API - Processes`: https://github.com/opengeospatial/ogcapi-processes
 .. _`OGC API - Records`: https://github.com/opengeospatial/ogcapi-records
+.. _`OGC API - Environmental Data Retrieval`: https://github.com/opengeospatial/ogcapi-environmental-data-retrieval
 .. _`SpatioTemporal Asset Catalog`: https://stacspec.org
diff --git a/docs/source/tour.rst b/docs/source/tour.rst
@@ -148,6 +148,7 @@ This page provides metadata catalogue search capabilities
 .. seealso::
    :ref:`ogcapi-records` for more OGC API - Records request examples.
 
+
 Processes
 ---------
 
@@ -160,6 +161,25 @@ The processes page provides a list of process integrated onto the server, along
    :ref:`ogcapi-processes` for more OGC API - Processes request examples.
 
 
+Environmental data retrieval
+----------------------------
+
+http://localhost:5000/collections/edr-test
+
+This page provides, in addition to a common collection description, specific
+link relations for EDR queries if the collection has an EDR capability, as
+well as supported parameter names to select.
+
+http://localhost:5000/collections/edr-test/position?coords=POINT(111 13)&parameter-name=SST&f=json
+
+This page executes a position query against a given parameter name, providing
+a response in CoverageJSON.
+
+
+.. seealso::
+   :ref:`ogcapi-edr` for more OGC API - EDR request examples.
+
+
 SpatioTemporal Assets
 ---------------------
 

diff --git a/pygeoapi-config.yml b/pygeoapi-config.yml
@@ -180,6 +180,32 @@ resources:
                   name: GRIB2
                   mimetype: application/x-grib2
 
+    icoads-sst:
+        type: collection
+        title: International Comprehensive Ocean-Atmosphere Data Set (ICOADS)
+        description: International Comprehensive Ocean-Atmosphere Data Set (ICOADS)
+        keywords:
+            - icoads
+            - sst
+            - air temperature
+        extents:
+            spatial:
+                bbox: [-180,-90,180,90]
+                crs: http://www.opengis.net/def/crs/OGC/1.3/CRS84
+        links:
+            - type: text/html
+              rel: canonical
+              title: information
+              href: https://psl.noaa.gov/data/gridded/data.coads.1deg.html
+              hreflang: en-US
+        providers:
+            - type: edr
+              name: xarray-edr
+              data: tests/data/coads_sst.nc
+              format:
+                  name: NetCDF
+                  mimetype: application/x-netcdf
+
     test-data:
         type: stac-collection
         title: pygeoapi test data