xarray-edr netcdf position query TypeError: |S1 type <class 'numpy.dtypes.BytesDType'> not serializable

[n-o-tud]

Hey,

I'm trying to provide a NetCDF file using xarray-edr to query raster data at a specific position. However, I'm encountering an error with some NetCDF files and am unsure how to troubleshoot it. Below, you'll find a link to the NetCDF file, the corresponding API call, the resulting error, and the configuration file.

How to get rid of the error and make the position query working?

Link to Netcdf file: 60 Arc-Second Resolution Bedrock elevation netCDF https://www.ngdc.noaa.gov/thredds/catalog/global/ETOPO2022/60s/60s_bed_elev_netcdf/catalog.html?dataset=globalDatasetScan/ETOPO2022/60s/60s_bed_elev_netcdf/ETOPO_2022_v1_60s_N90W180_bed.nc

API call: http://localhost:5000/collections/ETOPO_2022_v1_60s_N90W180_bed_orig/position?f=json&coords=POINT(-75%2045)

Error: TypeError: |S1 type <class 'numpy.dtypes.BytesDType'> not serializable

pygeoapi config:

 server:
  bind:
    host: 0.0.0.0
    port: 5000
  url: http://localhost:5000
  mimetype: application/json; charset=UTF-8
  encoding: utf-8
  gzip: false
  languages:
    # First language is the default language
    - en-US
    - fr-CA
  # cors: true
  pretty_print: true
  limits:
    default_items: 20
    max_items: 50
  # templates:
  # path: /path/to/Jinja2/templates
  # static: /path/to/static/folder # css/js/img
  map:
    url: https://tile.openstreetmap.org/{z}/{x}/{y}.png
    attribution: '&copy; <a href="https://openstreetmap.org/copyright">OpenStreetMap contributors</a>'
  #    manager:
  #        name: TinyDB
  #        connection: /tmp/pygeoapi-process-manager.db
  #        output_dir: /tmp/
  # ogc_schemas_location: /opt/schemas.opengis.net
  admin: false # enable admin api

logging:
  level: DEBUG
  #logfile: /tmp/pygeoapi.log

metadata:
  identification:
    title:
      en: pygeoapi default instance
      fr: instance par défaut de pygeoapi
    description:
      en: pygeoapi provides an API to geospatial data
      fr: pygeoapi fournit une API aux données géospatiales
    keywords:
      en:
        - geospatial
        - data
        - api
      fr:
        - géospatiale
        - données
        - api
    keywords_type: theme
    terms_of_service: https://creativecommons.org/licenses/by/4.0/
    url: https://example.org
  license:
    name: CC-BY 4.0 license
    url: https://creativecommons.org/licenses/by/4.0/
  provider:
    name: Organization Name
    url: https://pygeoapi.io
  contact:
    name: Lastname, Firstname
    position: Position Title
    address: Mailing Address
    city: City
    stateorprovince: Administrative Area
    postalcode: Zip or Postal Code
    country: Country
    phone: +xx-xxx-xxx-xxxx
    fax: +xx-xxx-xxx-xxxx
    email: [email protected]
    url: Contact URL
    hours: Mo-Fr 08:00-17:00
    instructions: During hours of service. Off on weekends.
    role: pointOfContact

resources:
  ETOPO_2022_v1_60s_N90W180_bed_orig:
    type: collection
    title: ETOPO Global Relief Model
    description: ETOPO Global Relief Model 60 Arc-Second Resolution Bedrock elevation netCDF
    keywords:
      - observations
      - monitoring
    extents:
      spatial:
        bbox: [-180, -90, 180, 90]
        crs: 4326
    providers:
      - type: coverage
        name: xarray
        data: tests/data/ETOPO_2022_v1_60s_N90W180_bed_orig.nc
        x_field: lon
        y_field: lat
        storage_crs: 4326
        format:
          name: netcdf
          mimetype: application/x-netcdf
    providers:
      - type: edr
        name: xarray-edr
        data: tests/data/ETOPO_2022_v1_60s_N90W180_bed_orig.nc
        x_field: lon
        y_field: lat
        storage_crs: 4326
        format:
          name: netcdf
          mimetype: application/x-netcdf

[n-o-tud]

Entire error message:

File "/home/Development/Python/pygeoapi/lib/python3.11/site-packages/flask/app.py", line 1536, in call
return self.wsgi_app(environ, start_response)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/Development/Python/pygeoapi/lib/python3.11/site-packages/flask/app.py", line 1514, in wsgi_app
response = self.handle_exception(e)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/Development/Python/pygeoapi/lib/python3.11/site-packages/flask/app.py", line 1511, in wsgi_app
response = self.full_dispatch_request()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/Development/Python/pygeoapi/lib/python3.11/site-packages/flask/app.py", line 919, in full_dispatch_request
rv = self.handle_user_exception(e)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/Development/Python/pygeoapi/lib/python3.11/site-packages/flask/app.py", line 917, in full_dispatch_request
rv = self.dispatch_request()
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/Development/Python/pygeoapi/lib/python3.11/site-packages/flask/app.py", line 902, in dispatch_request
return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args) # type: ignore[no-any-return]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/Development/Python/pygeoapi/lib/python3.11/site-packages/pygeoapi-0.20.dev0-py3.11.egg/pygeoapi/flask_app.py", line 510, in get_collection_edr_query
return execute_from_flask(

File "/home/Development/Python/pygeoapi/lib/python3.11/site-packages/pygeoapi-0.20.dev0-py3.11.egg/pygeoapi/flask_app.py", line 153, in execute_from_flask
headers, status, content = api_function(actual_api, api_request, *args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/Development/Python/pygeoapi/lib/python3.11/site-packages/pygeoapi-0.20.dev0-py3.11.egg/pygeoapi/api/environmental_data_retrieval.py", line 420, in get_collection_edr_query
content = to_json(data, api.pretty_print)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/Development/Python/pygeoapi/lib/python3.11/site-packages/pygeoapi-0.20.dev0-py3.11.egg/pygeoapi/util.py", line 284, in to_json
return json.dumps(dict_, default=json_serial, indent=indent,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/json/init.py", line 238, in dumps
**kw).encode(obj)
^^^^^^^^^^^
File "/usr/local/lib/python3.11/json/encoder.py", line 202, in encode
chunks = list(chunks)
^^^^^^^^^^^^
File "/usr/local/lib/python3.11/json/encoder.py", line 432, in _iterencode
yield from _iterencode_dict(o, _current_indent_level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/json/encoder.py", line 406, in _iterencode_dict
yield from chunks
^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/json/encoder.py", line 406, in _iterencode_dict
yield from chunks
^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/json/encoder.py", line 406, in _iterencode_dict
yield from chunks
^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/json/encoder.py", line 439, in _iterencode
o = _default(o)
^^^^^^^^^^^
File "/home/Development/Python/pygeoapi/lib/python3.11/site-packages/pygeoapi-0.20.dev0-py3.11.egg/pygeoapi/util.py", line 417, in json_serial
raise TypeError(msg)
^^^^^^^^^^^^^^^^^^^^
TypeError: |S1 type <class 'numpy.dtypes.BytesDType'> not serializable