implement OGC EDR API (#658)

* implement OGC EDR API
* add docs/tests
* fix tests

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

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

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

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
 --------------------

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

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

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
 ---------------------
 

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

pygeoapi/api.py

@@ -43,6 +43,8 @@ import urllib.parse
 from copy import deepcopy
 
 from dateutil.parser import parse as dateparse
+from shapely.wkt import loads as shapely_loads
+from shapely.errors import WKTReadingError
 import pytz
 
 from pygeoapi import __version__
@@ -79,6 +81,8 @@ HEADERS = {
 FORMATS = ['json', 'html', 'jsonld']
 
 CONFORMANCE = [
+    'http://www.opengis.net/spec/ogcapi-common-1/1.0/conf/core',
+    'http://www.opengis.net/spec/ogcapi-common-2/1.0/conf/collections',
     'http://www.opengis.net/spec/ogcapi-features-1/1.0/conf/core',
     'http://www.opengis.net/spec/ogcapi-features-1/1.0/conf/oas30',
     'http://www.opengis.net/spec/ogcapi-features-1/1.0/conf/html',
@@ -88,13 +92,12 @@ CONFORMANCE = [
     'http://www.opengis.net/spec/ogcapi-coverages-1/1.0/conf/html',
     'http://www.opengis.net/spec/ogcapi-tiles-1/1.0/req/core',
     'http://www.opengis.net/spec/ogcapi-tiles-1/1.0/req/collections',
-    'http://www.opengis.net/spec/ogcapi-common-1/1.0/conf/core',
-    'http://www.opengis.net/spec/ogcapi-common-2/1.0/conf/collections',
     'http://www.opengis.net/spec/ogcapi-records-1/1.0/conf/core',
     'http://www.opengis.net/spec/ogcapi-records-1/1.0/conf/sorting',
     'http://www.opengis.net/spec/ogcapi-records-1/1.0/conf/opensearch',
     'http://www.opengis.net/spec/ogcapi-records-1/1.0/conf/json',
-    'http://www.opengis.net/spec/ogcapi-records-1/1.0/conf/html'
+    'http://www.opengis.net/spec/ogcapi-records-1/1.0/conf/html',
+    'http://www.opengis.net/spec/ogcapi-edr-1/1.0/conf/core'
 ]
 
 OGC_RELTYPES_BASE = 'http://www.opengis.net/def/rel/ogc/1.0'
@@ -532,14 +535,15 @@ class API:
                         p = load_plugin('provider', get_provider_by_type(
                             self.config['resources'][k]['providers'],
                             'coverage'))
+                        collection['crs'] = [p.crs]
+                        collection['domainset'] = p.get_coverage_domainset()
+                        collection['rangetype'] = p.get_coverage_rangetype()
                     except ProviderConnectionError:
                         msg = 'connection error (check logs)'
                         return self.get_exception(
                             500, headers_, format_, 'NoApplicableCode', msg)
-
-                    collection['crs'] = [p.crs]
-                    collection['domainset'] = p.get_coverage_domainset()
-                    collection['rangetype'] = p.get_coverage_rangetype()
+                    except ProviderTypeError:
+                        pass
 
             try:
                 tile = get_provider_by_type(v['providers'], 'tile')
@@ -563,6 +567,45 @@ class API:
                         self.config['server']['url'], k)
                 })
 
+            try:
+                edr = get_provider_by_type(v['providers'], 'edr')
+            except ProviderTypeError:
+                edr = None
+
+            if edr and dataset is not None:
+                LOGGER.debug('Adding EDR links')
+                try:
+                    p = load_plugin('provider', get_provider_by_type(
+                        self.config['resources'][dataset]['providers'],
+                        'edr'))
+                    parameters = p.get_fields()
+                    if parameters:
+                        collection['parameters'] = {}
+                        for f in parameters['field']:
+                            collection['parameters'][f['id']] = f
+
+                    for qt in p.get_query_types():
+                        collection['links'].append({
+                            'type': 'text/json',
+                            'rel': 'data',
+                            'title': '{} query for this collection as JSON'.format(qt),  # noqa
+                            'href': '{}/collections/{}/{}?f=json'.format(
+                                self.config['server']['url'], k, qt)
+                        })
+                        collection['links'].append({
+                            'type': 'text/html',
+                            'rel': 'data',
+                            'title': '{} query for this collection as HTML'.format(qt),  # noqa
+                            'href': '{}/collections/{}/{}?f=html'.format(
+                                self.config['server']['url'], k, qt)
+                        })
+                except ProviderConnectionError:
+                    msg = 'connection error (check logs)'
+                    return self.get_exception(
+                        500, headers_, format_, 'NoApplicableCode', msg)
+                except ProviderTypeError:
+                    pass
+
             if dataset is not None and k == dataset:
                 fcm = collection
                 break
@@ -2115,6 +2158,142 @@ tiles/{{{}}}/{{{}}}/{{{}}}/{{{}}}?f=mvt'
         LOGGER.info(response)
         return {}, http_status, response
 
+    def get_collection_edr_query(self, headers, args, dataset, instance,
+                                 query_type):
+        """
+        Queries collection EDR
+        :param headers: dict of HTTP headers
+        :param args: dict of HTTP request parameters
+        :param dataset: dataset name
+        :param dataset: instance name
+        :param query_type: EDR query type
+        :returns: tuple of headers, status code, content
+        """
+
+        headers_ = HEADERS.copy()
+
+        query_args = {}
+        formats = FORMATS
+        formats.extend(f.lower() for f in PLUGINS['formatter'].keys())
+
+        collections = filter_dict_by_key_value(self.config['resources'],
+                                               'type', 'collection')
+
+        format_ = check_format(args, headers)
+
+        if dataset not in collections.keys():
+            msg = 'Invalid collection'
+            return self.get_exception(
+                400, headers_, format_, 'InvalidParameterValue', msg)
+
+        if format_ is not None and format_ not in formats:
+            msg = 'Invalid format'
+            return self.get_exception(
+                400, headers_, format_, 'InvalidParameterValue', msg)
+
+        LOGGER.debug('Processing query parameters')
+
+        LOGGER.debug('Processing datetime parameter')
+        datetime_ = args.get('datetime')
+        try:
+            datetime_ = validate_datetime(collections[dataset]['extents'],
+                                          datetime_)
+        except ValueError as err:
+            msg = str(err)
+            return self.get_exception(
+                400, headers_, format_, 'InvalidParameterValue', msg)
+
+        LOGGER.debug('Processing parameter-name parameter')
+        parameternames = args.get('parameter-name', [])
+        if parameternames:
+            parameternames = parameternames.split(',')
+
+        LOGGER.debug('Processing coords parameter')
+        wkt = args.get('coords', None)
+
+        if wkt is None:
+            msg = 'missing coords parameter'
+            return self.get_exception(
+                400, headers_, format_, 'InvalidParameterValue', msg)
+
+        try:
+            wkt = shapely_loads(wkt)
+        except WKTReadingError:
+            msg = 'invalid coords parameter'
+            return self.get_exception(
+                400, headers_, format_, 'InvalidParameterValue', msg)
+
+        LOGGER.debug('Processing z parameter')
+        z = args.get('z')
+
+        LOGGER.debug('Loading provider')
+        try:
+            p = load_plugin('provider', get_provider_by_type(
+                collections[dataset]['providers'], 'edr'))
+        except ProviderTypeError:
+            msg = 'invalid provider type'
+            return self.get_exception(
+                500, headers_, format_, 'NoApplicableCode', msg)
+        except ProviderConnectionError:
+            msg = 'connection error (check logs)'
+            return self.get_exception(
+                500, headers_, format_, 'NoApplicableCode', msg)
+        except ProviderQueryError:
+            msg = 'query error (check logs)'
+            return self.get_exception(
+                500, headers_, format_, 'NoApplicableCode', msg)
+
+        if instance is not None and not p.get_instance(instance):
+            msg = 'Invalid instance identifier'
+            return self.get_exception(
+                400, headers_, format_, 'InvalidParameterValue', msg)
+
+        if query_type not in p.get_query_types():
+            msg = 'Unsupported query type'
+            return self.get_exception(
+                400, headers_, format_, 'InvalidParameterValue', msg)
+
+        parametername_matches = list(
+            filter(
+                lambda p: p['id'] in parameternames, p.get_fields()['field']
+            )
+        )
+
+        if len(parametername_matches) < len(parameternames):
+            msg = 'Invalid parameter-name'
+            return self.get_exception(
+                400, headers_, format_, 'InvalidParameterValue', msg)
+
+        query_args = dict(
+            query_type=query_type,
+            instance=instance,
+            format_=format_,
+            datetime_=datetime_,
+            select_properties=parameternames,
+            wkt=wkt,
+            z=z
+        )
+
+        try:
+            data = p.query(**query_args)
+        except ProviderNoDataError:
+            msg = 'No data found'
+            return self.get_exception(
+                204, headers_, format_, 'NoMatch', msg)
+        except ProviderQueryError:
+            msg = 'query error (check logs)'
+            return self.get_exception(
+                500, headers_, format_, 'NoApplicableCode', msg)
+
+        if format_ == 'html':  # render
+            headers_['Content-Type'] = 'text/html'
+            content = render_j2_template(
+                self.config, 'collections/edr/query.html', data)
+        else:
+            content = to_json(data, self.pretty_print)
+
+        return headers_, 200, content
+
     @pre_process
     @jsonldify
     def get_stac_root(self, headers_, format_):

pygeoapi/flask_app.py

@@ -465,6 +465,39 @@ def get_process_job_result_resource(process_id, job_id, resource):
     return response
 
 
+@BLUEPRINT.route('/collections/<collection_id>/position')
+@BLUEPRINT.route('/collections/<collection_id>/area')
+@BLUEPRINT.route('/collections/<collection_id>/cube')
+@BLUEPRINT.route('/collections/<collection_id>/trajectory')
+@BLUEPRINT.route('/collections/<collection_id>/corridor')
+@BLUEPRINT.route('/collections/<collection_id>/instances/<instance_id>/position')  # noqa
+@BLUEPRINT.route('/collections/<collection_id>/instances/<instance_id>/area')
+@BLUEPRINT.route('/collections/<collection_id>/instances/<instance_id>/cube')
+@BLUEPRINT.route('/collections/<collection_id>/instances/<instance_id>/trajectory')  # noqa
+@BLUEPRINT.route('/collections/<collection_id>/instances/<instance_id>/corridor')  # noqa
+def get_collection_edr_query(collection_id, instance_id=None):
+    """
+    OGC EDR API endpoints
+
+    :param collection_id: collection identifier
+    :param instance_id: instance identifier
+
+    :returns: HTTP response
+    """
+
+    query_type = request.path.split('/')[-1]
+
+    headers, status_code, content = api_.get_collection_edr_query(
+        request.headers, request.args, collection_id, instance_id, query_type)
+
+    response = make_response(content, status_code)
+
+    if headers:
+        response.headers = headers
+
+    return response
+
+
 @BLUEPRINT.route('/stac')
 def stac_catalog_root():
     """

pygeoapi/openapi.py

@@ -48,7 +48,8 @@ OPENAPI_YAML = {
     'oacov': 'https://raw.githubusercontent.com/tomkralidis/ogcapi-coverages-1/fix-cis/yaml-unresolved',  # noqa
     'oapit': 'https://raw.githubusercontent.com/opengeospatial/ogcapi-tiles/master/openapi/swaggerhub/tiles.yaml',  # noqa
     'oapimt': 'https://raw.githubusercontent.com/opengeospatial/ogcapi-tiles/master/openapi/swaggerhub/map-tiles.yaml',  # noqa
-    'oapir': 'https://raw.githubusercontent.com/opengeospatial/ogcapi-records/master/core/openapi'  # noqa
+    'oapir': 'https://raw.githubusercontent.com/opengeospatial/ogcapi-records/master/core/openapi',  # noqa
+    'oaedr': 'https://raw.githubusercontent.com/opengeospatial/ogcapi-environmental-data-retrieval/master/candidate-standard/openapi', # noqa
 }
 
 
@@ -726,6 +727,56 @@ def get_oas_30(cfg):
                 }
             }
 
+        LOGGER.debug('setting up tiles endpoints')
+        edr_extension = filter_providers_by_type(
+            collections[k]['providers'], 'edr')
+
+        if edr_extension:
+            ep = load_plugin('provider', edr_extension)
+
+            edr_query_endpoints = []
+
+            for qt in ep.get_query_types():
+                edr_query_endpoints.append({
+                    'path': '{}/{}'.format(collection_name_path, qt),
+                    'qt': qt,
+                    'op_id': 'query{}{}'.format(qt.capitalize(), k.capitalize())  # noqa
+                })
+                if ep.instances:
+                    edr_query_endpoints.append({
+                        'path': '{}/instances/{{instanceId}}/{}'.format(collection_name_path, qt),  # noqa
+                        'qt': qt,
+                        'op_id': 'query{}Instance{}'.format(qt.capitalize(), k.capitalize())  # noqa
+                    })
+
+            for eqe in edr_query_endpoints:
+                paths[eqe['path']] = {
+                    'get': {
+                        'summary': 'query {} by {}'.format(v['description'], eqe['qt']),  # noqa
+                        'description': v['description'],
+                        'tags': [k],
+                        'operationId': eqe['op_id'],
+                        'parameters': [
+                            {'$ref': '{}/parameters/{}Coords.yaml'.format(OPENAPI_YAML['oaedr'], eqe['qt'])},  # noqa
+                            {'$ref': '{}#/components/parameters/datetime'.format(OPENAPI_YAML['oapif'])},  # noqa
+                            {'$ref': '{}/parameters/parameter-name.yaml'.format(OPENAPI_YAML['oaedr'])},  # noqa
+                            {'$ref': '{}/parameters/z.yaml'.format(OPENAPI_YAML['oaedr'])},  # noqa
+                            {'$ref': '#/components/parameters/f'}
+                        ],
+                        'responses': {
+                            '200': {
+                                'description': 'Response',
+                                'content': {
+                                    'application/prs.coverage+json': {
+                                        'schema': {
+                                            '$ref': '{}/schemas/coverageJSON.yaml'.format(OPENAPI_YAML['oaedr'])}  # noqa
+                                        }
+                                    }
+                                }
+                            }
+                        }
+                    }
+
     LOGGER.debug('setting up STAC')
     stac_collections = filter_dict_by_key_value(cfg['resources'],
                                                 'type', 'stac-collection')

pygeoapi/plugin.py

@@ -49,7 +49,8 @@ PLUGINS = {
         'rasterio': 'pygeoapi.provider.rasterio_.RasterioProvider',
         'xarray': 'pygeoapi.provider.xarray_.XarrayProvider',
         'MVT': 'pygeoapi.provider.mvt.MVTProvider',
-        'TinyDBCatalogue': 'pygeoapi.provider.tinydb_.TinyDBCatalogueProvider'
+        'TinyDBCatalogue': 'pygeoapi.provider.tinydb_.TinyDBCatalogueProvider',
+        'xarray-edr': 'pygeoapi.provider.xarray_edr.XarrayEDRProvider'
     },
     'formatter': {
         'CSV': 'pygeoapi.formatter.csv_.CSVFormatter'

pygeoapi/provider/filesystem.py

@@ -70,8 +70,6 @@ class FileSystemProvider(BaseProvider):
 
         thispath = os.path.join(baseurl, urlpath)
 
-        print("THISPATH", thispath)
-
         resource_type = None
         root_link = None
         child_links = []

pygeoapi/provider/xarray_.py

@@ -57,7 +57,7 @@ class XarrayProvider(BaseProvider):
         super().__init__(provider_def)
 
         try:
-            if provider_def['format']['name'] == 'zarr':
+            if provider_def['data'].endswith('.zarr'):
                 open_func = xarray.open_zarr
             else:
                 open_func = xarray.open_dataset
@@ -312,10 +312,19 @@ class XarrayProvider(BaseProvider):
         minx, miny, maxx, maxy = metadata['bbox']
         mint, maxt = metadata['time']
 
-        if data.coords[self.y_field].values[0] > data.coords[self.y_field].values[-1]:  # noqa
+        try:
+            tmp_min = data.coords[self.y_field].values[0]
+        except IndexError:
+            tmp_min = data.coords[self.y_field].values
+        try:
+            tmp_max = data.coords[self.y_field].values[-1]
+        except IndexError:
+            tmp_max = data.coords[self.y_field].values
+
+        if tmp_min > tmp_max:
             LOGGER.debug('Reversing direction of {}'.format(self.y_field))
-            miny = data.coords[self.y_field].values[-1]
-            maxy = data.coords[self.y_field].values[0]
+            miny = tmp_max
+            maxy = tmp_min
 
         cj = {
             'type': 'Coverage',

pygeoapi/provider/xarray_edr.py

@@ -0,0 +1,166 @@
+# =================================================================
+#
+# Authors: Tom Kralidis <tomkralidis@gmail.com>
+#
+# Copyright (c) 2020 Tom Kralidis
+#
+# Permission is hereby granted, free of charge, to any person
+# obtaining a copy of this software and associated documentation
+# files (the "Software"), to deal in the Software without
+# restriction, including without limitation the rights to use,
+# copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following
+# conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+# OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+# HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+# WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+# OTHER DEALINGS IN THE SOFTWARE.
+#
+# =================================================================
+
+import logging
+
+from pygeoapi.provider.base import ProviderNoDataError
+from pygeoapi.provider.xarray_ import _to_datetime_string, XarrayProvider
+
+LOGGER = logging.getLogger(__name__)
+
+
+class XarrayEDRProvider(XarrayProvider):
+    """EDR Provider"""
+
+    def __init__(self, provider_def):
+        """
+        Initialize object
+
+        :param provider_def: provider definition
+
+        :returns: pygeoapi.provider.rasterio_.RasterioProvider
+        """
+
+        XarrayProvider.__init__(self, provider_def)
+        self.instances = []
+
+    def get_fields(self):
+        """
+        Get provider field information (names, types)
+
+        :returns: dict of dicts of parameters
+        """
+
+        return self.get_coverage_rangetype()
+
+    def get_instance(self, instance):
+        """
+        Validate instance identifier
+
+        :returns: `bool` of whether instance is valid
+        """
+
+        return NotImplementedError()
+
+    def get_query_types(self):
+        """
+        Provide supported query types
+
+        :returns: list of EDR query types
+        """
+
+        return ['position']
+
+    def query(self, **kwargs):
+        """
+        Extract data from collection collection
+
+        :param query_type: query type
+        :param wkt: `shapely.geometry` WKT geometry
+        :param datetime_: temporal (datestamp or extent)
+        :param select_properties: list of parameters
+        :param z: vertical level(s)
+        :param format_: data format of output
+
+        :returns: coverage data as dict of CoverageJSON or native format
+        """
+
+        query_params = {}
+
+        LOGGER.debug('Query parameters: {}'.format(kwargs))
+
+        LOGGER.debug('Query type: {}'.format(kwargs.get('query_type')))
+
+        wkt = kwargs.get('wkt')
+        if wkt is not None:
+            LOGGER.debug('Processing WKT')
+            LOGGER.debug('Geometry type: {}'.format(wkt.type))
+            if wkt.type == 'Point':
+                query_params[self._coverage_properties['x_axis_label']] = wkt.x
+                query_params[self._coverage_properties['y_axis_label']] = wkt.y
+            elif wkt.type == 'LineString':
+                query_params[self._coverage_properties['x_axis_label']] = wkt.xy[0]  # noqa
+                query_params[self._coverage_properties['y_axis_label']] = wkt.xy[1]  # noqa
+            elif wkt.type == 'Polygon':
+                query_params[self._coverage_properties['x_axis_label']] = slice(wkt.bounds[0], wkt.bounds[2])  # noqa
+                query_params[self._coverage_properties['y_axis_label']] = slice(wkt.bounds[1], wkt.bounds[3])  # noqa
+                pass
+
+        LOGGER.debug('Processing parameter-name')
+        select_properties = kwargs.get('select_properties')
+
+        # example of fetching instance passed
+        # TODO: apply accordingly
+        instance = kwargs.get('instance')
+        LOGGER.debug('instance: {}'.format(instance))
+
+        datetime_ = kwargs.get('datetime_')
+        if datetime_ is not None:
+            query_params[self._coverage_properties['time_axis_label']] = datetime_  # noqa
+
+        LOGGER.debug('query parameters: {}'.format(query_params))
+
+        try:
+            if select_properties:
+                self.fields = select_properties
+                data = self._data[[*select_properties]]
+            else:
+                data = self._data
+            data = data.sel(query_params, method='nearest')
+        except KeyError:
+            raise ProviderNoDataError()
+
+        if len(data.coords[self.time_field].values) < 1:
+            raise ProviderNoDataError()
+
+        try:
+            height = data.dims[self.y_field]
+        except KeyError:
+            height = 1
+        try:
+            width = data.dims[self.x_field]
+        except KeyError:
+            width = 1
+
+        bbox = wkt.bounds
+        out_meta = {
+            'bbox': [bbox[0], bbox[1], bbox[2], bbox[3]],
+            "time": [
+                _to_datetime_string(data.coords[self.time_field].values[0]),
+                _to_datetime_string(data.coords[self.time_field].values[-1])
+            ],
+            "driver": "xarray",
+            "height": height,
+            "width": width,
+            "time_steps": data.dims[self.time_field],
+            "variables": {var_name: var.attrs
+                          for var_name, var in data.variables.items()}
+        }
+
+        return self.gen_covjson(out_meta, data, self.fields)

pygeoapi/starlette_app.py

@@ -467,6 +467,46 @@ async def get_process_job_result_resource(request: Request, process_id=None,
     return response
 
 
+@app.route('/collections/{collection_id}/position')
+@app.route('/collections/{collection_id}/area')
+@app.route('/collections/{collection_id}/cube')
+@app.route('/collections/{collection_id}/trajectory')
+@app.route('/collections/{collection_id}/corridor')
+@app.route('/collections/{collection_id}/instances/{instance_id}/position')
+@app.route('/collections/{collection_id}/instances/{instance_id}/area')
+@app.route('/collections/{collection_id}/instances/{instance_id}/cube')
+@app.route('/collections/{collection_id}/instances/{instance_id}/trajectory')
+@app.route('/collections/{collection_id}/instances/{instance_id}/corridor')
+async def get_collection_edr_query(request: Request, collection_id=None, instance_id=None):  # noqa
+    """
+    OGC EDR API endpoints
+
+    :param collection_id: collection identifier
+    :param instance_id: instance identifier
+
+    :returns: HTTP response
+    """
+
+    if 'collection_id' in request.path_params:
+        collection_id = request.path_params['collection_id']
+
+    if 'instance_id' in request.path_params:
+        instance_id = request.path_params['instance_id']
+
+    query_type = request.path.split('/')[-1]
+
+    headers, status_code, content = api_.get_collection_edr_query(
+        request.headers, request.query_params, collection_id, instance_id,
+        query_type)
+
+    response = Response(content=content, status_code=status_code)
+
+    if headers:
+        response.headers.update(headers)
+
+    return response
+
+
 @app.route('/stac')
 async def stac_catalog_root(request: Request):
     """

pygeoapi/templates/collections/edr/query.html

@@ -0,0 +1,80 @@
+{% extends "_base.html" %}
+{% block title %}{{ super() }} {{ data['title'] }} {% endblock %}
+{% block crumbs %}{{ super() }}
+/ <a href="{{ data['collections_path'] }}">Collections</a>
+{% for link in data['links'] %}
+  {% if link.rel == 'collection' %} /
+    <a href="{{ data['dataset_path'] }}">{{ link['title'] | truncate( 25 ) }}</a>
+    {% set col_title = link['title'] %}
+  {% endif %}
+{% endfor %}
+/ <a href="{{ data['items_path']}}">Items</a>
+{% endblock %}
+{% block extrahead %}
+    <link rel="stylesheet" href="https://unpkg.com/leaflet@1.3.1/dist/leaflet.css"/>
+    <link rel="stylesheet" type="text/css" href="https://unpkg.com/leaflet-coverage@0.7/leaflet-coverage.css">
+    <script src="https://unpkg.com/leaflet@1.3.1/dist/leaflet.js"></script>
+    <script src="https://unpkg.com/covutils@0.6/covutils.min.js"></script>
+    <script src="https://unpkg.com/covjson-reader@0.16/covjson-reader.src.js"></script>
+    <script src="https://unpkg.com/leaflet-coverage@0.7/leaflet-coverage.min.js"></script>
+{% endblock %}
+
+{% block body %}
+  <section id="coverage">
+    <div id="items-map"></div>
+  </section>
+{% endblock %}
+
+{% block extrafoot %}
+{% if data %}
+<!--
+    <script>
+    var map = L.map('items-map').setView([{{ 45 }}, {{ -75 }}], 5);
+    map.addLayer(new L.TileLayer(
+        '{{ config['server']['map']['url'] }}', {
+            maxZoom: 18,
+            attribution: '{{ config['server']['map']['attribution'] }}'
+        }
+    ));
+
+var cov = CovJSON.read(JSON.parse('{{ data |to_json }}'), parameters: ['SST']);
+
+//var cov = CovJSON.load('https://raw.githubusercontent.com/covjson/cookbook/master/examples/coverages/grid.covjson');
+
+var layer = new C.dataLayer(cov, {parameter: 'SST'});
+
+    </script>
+-->
+
+    <script>
+    var map = L.map('items-map').setView([{{ 45 }}, {{ -75 }}], 5);
+    map.addLayer(new L.TileLayer(
+        '{{ config['server']['map']['url'] }}', {
+            maxZoom: 18,
+            attribution: '{{ config['server']['map']['attribution'] }}'
+        }
+    ));
+
+    var layers = L.control.layers(null, null, {collapsed: false}).addTo(map)
+
+    var layer
+    CovJSON.read(JSON.parse('{{ data | to_json }}')).then(function (coverage) {
+      layer = C.dataLayer(coverage, {parameter: 'SST'})
+        .on('afterAdd', function () {
+          C.legend(layer).addTo(map)
+          map.fitBounds(layer.getBounds())
+        })
+        .addTo(map)
+      layers.addOverlay(layer, 'Temperature')
+      map.setZoom(5)
+    })
+
+    map.on('click', function (e) {
+      new C.DraggableValuePopup({
+        layers: [layer]
+      }).setLatLng(e.latlng).openOn(map)
+    })
+
+</script>
+{% endif %}
+{% endblock %}

requirements.txt

@@ -5,4 +5,5 @@ python-dateutil
 pytz
 PyYAML
 rasterio
+shapely
 unicodecsv

tests/pygeoapi-test-config.yml

@@ -225,6 +225,32 @@ resources:
                   name: GRIB
                   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
+
     hello-world:
         type: process
         processor:

tests/test_api.py

@@ -177,7 +177,7 @@ def test_conformance(config, api_):
 
     assert isinstance(root, dict)
     assert 'conformsTo' in root
-    assert len(root['conformsTo']) == 16
+    assert len(root['conformsTo']) == 17
 
     rsp_headers, code, response = api_.conformance(req_headers, {'f': 'foo'})
     assert code == 400
@@ -201,7 +201,7 @@ def test_describe_collections(config, api_):
     collections = json.loads(response)
 
     assert len(collections) == 2
-    assert len(collections['collections']) == 4
+    assert len(collections['collections']) == 5
     assert len(collections['links']) == 3
 
     rsp_headers, code, response = api_.describe_collections(
@@ -1116,6 +1116,92 @@ def test_delete_process_job(api_):
     assert code == 404
 
 
+def test_get_collection_edr_query(config, api_):
+    # no coords parameter
+    req_headers = make_req_headers()
+    rsp_headers, code, response = api_.get_collection_edr_query(
+        req_headers, {}, 'icoads-sst', instance=None, query_type='position')
+    assert code == 400
+
+    # bad query type
+    req_headers = make_req_headers()
+    rsp_headers, code, response = api_.get_collection_edr_query(
+        req_headers, {'coords': 'POINT(11 11)'}, 'icoads-sst', instance=None,
+        query_type='corridor')
+    assert code == 400
+
+    # bad coords parameter
+    req_headers = make_req_headers()
+    rsp_headers, code, response = api_.get_collection_edr_query(
+        req_headers, {'coords': 'gah'}, 'icoads-sst', instance=None,
+        query_type='position')
+    assert code == 400
+
+    # bad parameter-name parameter
+    req_headers = make_req_headers()
+    rsp_headers, code, response = api_.get_collection_edr_query(
+        req_headers, {'coords': 'POINT(11 11)', 'parameter-name': 'bad'},
+        'icoads-sst', instance=None, query_type='position')
+    assert code == 400
+
+    # all parameters
+    req_headers = make_req_headers()
+    rsp_headers, code, response = api_.get_collection_edr_query(
+        req_headers, {'coords': 'POINT(11 11)'}, 'icoads-sst', instance=None,
+        query_type='position')
+    assert code == 200
+
+    data = json.loads(response)
+
+    axes = list(data['domain']['axes'].keys())
+    axes.sort()
+    assert len(axes) == 3
+    assert axes == ['TIME', 'x', 'y']
+
+    assert data['domain']['axes']['x']['start'] == 11.0
+    assert data['domain']['axes']['x']['stop'] == 11.0
+    assert data['domain']['axes']['y']['start'] == 11.0
+    assert data['domain']['axes']['y']['stop'] == 11.0
+
+    parameters = list(data['parameters'].keys())
+    parameters.sort()
+    assert len(parameters) == 4
+    assert parameters == ['AIRT', 'SST', 'UWND', 'VWND']
+
+    # single parameter
+    req_headers = make_req_headers()
+    rsp_headers, code, response = api_.get_collection_edr_query(
+        req_headers, {'coords': 'POINT(11 11)', 'parameter-name': 'SST'},
+        'icoads-sst', instance=None, query_type='position')
+    assert code == 200
+
+    data = json.loads(response)
+
+    assert len(data['parameters'].keys()) == 1
+    assert list(data['parameters'].keys())[0] == 'SST'
+
+    # some data
+    req_headers = make_req_headers()
+    rsp_headers, code, response = api_.get_collection_edr_query(
+        req_headers, {'coords': 'POINT(11 11)', 'datetime': '2000-01-16'},
+        'icoads-sst', instance=None, query_type='position')
+    assert code == 200
+
+    # no data
+    req_headers = make_req_headers()
+    rsp_headers, code, response = api_.get_collection_edr_query(
+        req_headers, {'coords': 'POINT(11 11)', 'datetime': '2000-01-17'},
+        'icoads-sst', instance=None, query_type='position')
+    assert code == 204
+
+    # no data
+#    req_headers = make_req_headers()
+#    rsp_headers, code, response = api_.get_collection_edr_query(
+#        req_headers, {'coords': 'POINT(11 11)', 'datetime': '2000-01-15'},
+#        'icoads-sst', instance=None, query_type='position')
+#    assert code == 204
+
+
 def test_validate_bbox():
     assert validate_bbox('1,2,3,4') == [1, 2, 3, 4]
     assert validate_bbox('-142,42,-52,84') == [-142, 42, -52, 84]

tests/test_util.py

@@ -124,7 +124,7 @@ def test_filter_dict_by_key_value():
 
     collections = util.filter_dict_by_key_value(d['resources'],
                                                 'type', 'collection')
-    assert len(collections) == 4
+    assert len(collections) == 5
 
     notfound = util.filter_dict_by_key_value(d['resources'],
                                              'type', 'foo')