CRS handling in xarray provider properties (geopython#1641)

* update crs handling

* fix epsg code

* config parsing, lean on pyproj

* consolidate code and leverage prior crs work

* update crs handling

* fix epsg code

* config parsing, lean on pyproj

* consolidate code and leverage prior crs work

* fix function call

* bug and flake8 fixes

* documentation updates

* flake8

* Update ogcapi-coverages.rst

* update crs handling

* fix epsg code

* config parsing, lean on pyproj

* consolidate code and leverage prior crs work

* update crs handling

* fix epsg code

* config parsing, lean on pyproj

* consolidate code and leverage prior crs work

* fix function call

* bug and flake8 fixes

* documentation updates

* flake8

* Update ogcapi-coverages.rst

* flake8 fix

* rebase issues

* update import formatting

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>

* update conditional logic

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>

* update error handling

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>

* parse storage crs in init

---------

Co-authored-by: Benjamin Webb <40066515+webb-ben@users.noreply.github.com>

Author: sjordan29

docs/source/data-publishing/ogcapi-coverages.rst

@@ -75,6 +75,9 @@ The `Xarray`_ provider plugin reads and extracts `NetCDF`_ and `Zarr`_ data.
          x_field: lon
          y_field: lat
          time_field: time
+         # optionally specify the coordinate reference system of your dataset
+         # else pygeoapi assumes it is WGS84 (EPSG:4326).
+         storage_crs: 4326
          format:
             name: netcdf
             mimetype: application/x-netcdf
@@ -96,6 +99,11 @@ The `Xarray`_ provider plugin reads and extracts `NetCDF`_ and `Zarr`_ data.
    be sure to provide the full S3 URL. Any parameters required to open the dataset
    using fsspec can be added to the config file under `options` and `s3`.
 
+.. note::
+   When providing a `storage_crs` value in the xarray configuration, specify the 
+   coordinate reference system using any valid input for 
+   `pyproj.CRS.from_user_input`_. 
+
 Data access examples
 --------------------
 
@@ -146,3 +154,4 @@ Data access examples
 .. _`NetCDF`: https://en.wikipedia.org/wiki/NetCDF
 .. _`Zarr`: https://zarr.readthedocs.io/en/stable
 .. _`GDAL raster driver short name`: https://gdal.org/drivers/raster/index.html
+.. _`pyproj.CRS.from_user_input`: https://pyproj4.github.io/pyproj/stable/api/crs/coordinate_system.html#pyproj.crs.CoordinateSystem.from_user_input

docs/source/data-publishing/ogcapi-edr.rst

@@ -47,6 +47,9 @@ The `xarray-edr`_ provider plugin reads and extracts `NetCDF`_ and `Zarr`_ data
          x_field: lon
          y_field: lat
          time_field: time
+         # optionally specify the coordinate reference system of your dataset
+         # else pygeoapi assumes it is WGS84 (EPSG:4326).
+         storage_crs: 4326
          format:
             name: netcdf
             mimetype: application/x-netcdf
@@ -81,6 +84,11 @@ The `xarray-edr`_ provider plugin reads and extracts `NetCDF`_ and `Zarr`_ data
    S3 URL. Any parameters required to open the dataset using fsspec can be added
    to the config file under `options` and `s3`, as shown above.
 
+.. note::
+   When providing a `storage_crs` value in the EDR configuration, specify the 
+   coordinate reference system using any valid input for 
+   `pyproj.CRS.from_user_input`_. 
+
 
 Data access examples
 --------------------
@@ -105,6 +113,7 @@ Data access examples
 .. _`xarray`: https://docs.xarray.dev/en/stable/
 .. _`NetCDF`: https://en.wikipedia.org/wiki/NetCDF
 .. _`Zarr`: https://zarr.readthedocs.io/en/stable
+.. _`pyproj.CRS.from_user_input`: https://pyproj4.github.io/pyproj/stable/api/crs/coordinate_system.html#pyproj.crs.CoordinateSystem.from_user_input
 
 
 .. _`OGC Environmental Data Retrieval (EDR) (API)`: https://github.com/opengeospatial/ogcapi-coverages

pygeoapi/provider/xarray_.py

@@ -37,12 +37,16 @@
 import xarray
 import fsspec
 import numpy as np
+import pyproj
+from pyproj.exceptions import CRSError
+
+from pygeoapi.api import DEFAULT_STORAGE_CRS
 
 from pygeoapi.provider.base import (BaseProvider,
                                     ProviderConnectionError,
                                     ProviderNoDataError,
                                     ProviderQueryError)
-from pygeoapi.util import read_data
+from pygeoapi.util import get_crs_from_uri, read_data
 
 LOGGER = logging.getLogger(__name__)
 
@@ -82,6 +86,7 @@ def __init__(self, provider_def):
                 data_to_open = self.data
 
             self._data = open_func(data_to_open)
+            self.storage_crs = self._parse_storage_crs(provider_def)
             self._coverage_properties = self._get_coverage_properties()
 
             self.axes = [self._coverage_properties['x_axis_label'],
@@ -341,6 +346,7 @@ def gen_covjson(self, metadata, data, fields):
     def _get_coverage_properties(self):
         """
         Helper function to normalize coverage properties
+        :param provider_def: provider definition
 
         :returns: `dict` of coverage properties
         """
@@ -401,16 +407,21 @@ def _get_coverage_properties(self):
             'restime': self.get_time_resolution()
         }
 
-        if 'crs' in self._data.variables.keys():
-            try:
-                properties['bbox_crs'] = f'http://www.opengis.net/def/crs/OGC/1.3/{self._data.crs.epsg_code}'  # noqa
-
-                properties['inverse_flattening'] = self._data.crs.\
-                    inverse_flattening
-
+        # Update properties based on the xarray's CRS
+        epsg_code = self.storage_crs.to_epsg()
+        LOGGER.debug(f'{epsg_code}')
+        if epsg_code == 4326 or self.storage_crs == 'OGC:CRS84':
+            pass
+            LOGGER.debug('Confirmed default of WGS 84')
+        else:
+            properties['bbox_crs'] = \
+                f'https://www.opengis.net/def/crs/EPSG/0/{epsg_code}'
+            properties['inverse_flattening'] = \
+                self.storage_crs.ellipsoid.inverse_flattening
+            if self.storage_crs.is_projected:
                 properties['crs_type'] = 'ProjectedCRS'
-            except AttributeError:
-                pass
+
+        LOGGER.debug(f'properties: {properties}')
 
         properties['axes'] = [
             properties['x_axis_label'],
@@ -476,6 +487,71 @@ def get_time_coverage_duration(self):
 
         return ', '.join(times)
 
+    def _parse_grid_mapping(self):
+        """
+        Identifies grid_mapping.
+
+        :returns: name of xarray data variable that contains CRS information.
+        """
+        LOGGER.debug('Parsing grid mapping...')
+        spatiotemporal_dims = (self.time_field, self.y_field, self.x_field)
+        LOGGER.debug(spatiotemporal_dims)
+        grid_mapping_name = None
+        for var_name, var in self._data.variables.items():
+            if all(dim in var.dims for dim in spatiotemporal_dims):
+                try:
+                    grid_mapping_name = self._data[var_name].attrs['grid_mapping']  # noqa 
+                    LOGGER.debug(f'Grid mapping: {grid_mapping_name}')
+                except KeyError as err:
+                    LOGGER.debug(err)
+                    LOGGER.debug('No grid mapping information found.')
+        return grid_mapping_name
+
+    def _parse_storage_crs(
+        self,
+        provider_def: dict
+    ) -> pyproj.CRS:
+        """
+        Parse the storage CRS from an xarray dataset.
+
+        :param provider_def: provider definition
+
+        :returns: `pyproj.CRS` instance parsed from dataset
+        """
+        storage_crs = None
+
+        try:
+            storage_crs = provider_def['storage_crs']
+            crs_function = pyproj.CRS.from_user_input
+        except KeyError as err:
+            LOGGER.debug(err)
+            LOGGER.debug('No storage_crs found. Attempting to parse the CRS.')
+
+        if storage_crs is None:
+            grid_mapping = self._parse_grid_mapping()
+            if grid_mapping is not None:
+                storage_crs = self._data[grid_mapping].attrs
+                crs_function = pyproj.CRS.from_cf
+            elif 'crs' in self._data.variables.keys():
+                storage_crs = self._data['crs'].attrs
+                crs_function = pyproj.CRS.from_dict
+            else:
+                storage_crs = DEFAULT_STORAGE_CRS
+                crs_function = get_crs_from_uri
+                LOGGER.debug('Failed to parse dataset CRS. Assuming WGS84.')
+
+        LOGGER.debug(f'Parsing CRS {storage_crs} with {crs_function}')
+        try:
+            crs = crs_function(storage_crs)
+        except CRSError as err:
+            LOGGER.debug(f'Unable to parse projection with pyproj: {err}')
+            LOGGER.debug('Assuming default WGS84.')
+            crs = get_crs_from_uri(DEFAULT_STORAGE_CRS)
+
+        LOGGER.debug(crs)
+
+        return crs
+
 
 def _to_datetime_string(datetime_obj):
     """