gen-owl error(s)

[dwinston]

For example, trying gen-owl schema/prov.yaml for this file raises

Traceback (most recent call last):
  File "/opt/miniconda3/envs/nmdc/bin/gen-owl", line 8, in <module>
    sys.exit(cli())
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/generators/owlgen.py", line 298, in cli
    print(OwlSchemaGenerator(yamlfile, **kwargs).serialize(**kwargs))
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/generators/owlgen.py", line 34, in __init__
    super().__init__(schema, **kwargs)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/utils/generator.py", line 92, in __init__
    loader.resolve()
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/utils/schemaloader.py", line 156, in resolve
    self.raise_value_error(f'Class "{cls.name}" - unknown slot: "{slotname}"', slotname)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/utils/schemaloader.py", line 679, in raise_value_error
    raise ValueError(f'{TypedNode.yaml_loc(loc_str)} {error}')
ValueError: File "/Users/dwinston/repos/nmdc/nmdc-metadata/schema/prov.yaml", line 28, col 9:  Class "activity" - unknown slot: "id"

and a larger example, gen-owl schema/nmdc.yaml for this file raises

Traceback (most recent call last):
  File "/opt/miniconda3/envs/nmdc/bin/gen-owl", line 8, in <module>
    sys.exit(cli())
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/generators/owlgen.py", line 298, in cli
    print(OwlSchemaGenerator(yamlfile, **kwargs).serialize(**kwargs))
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/generators/owlgen.py", line 39, in __init__
    SchemaLoader(METAMODEL_YAML_URI, base_dir=META_BASE_URI, importmap=kwargs.get('importmap', None),
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/utils/schemaloader.py", line 50, in __init__
    self.schema = load_raw_schema(data, base_dir=base_dir, merge_modules=mergeimports,
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/utils/rawloader.py", line 66, in load_raw_schema
    return load_raw_schema(response, fname, response.info()['Last-Modified'],
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/utils/rawloader.py", line 150, in load_raw_schema
    for sname, sdef in {k: SchemaDefinition(name=k, **v) for k, v in schemadefs.items()}.items():
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/utils/rawloader.py", line 150, in <dictcomp>
    for sname, sdef in {k: SchemaDefinition(name=k, **v) for k, v in schemadefs.items()}.items():
  File "<string>", line 49, in __init__
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/meta.py", line 399, in __post_init__
    super().__post_init__(**kwargs)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/meta.py", line 272, in __post_init__
    super().__post_init__(**kwargs)
  File "/opt/miniconda3/envs/nmdc/lib/python3.8/site-packages/biolinkml/utils/yamlutils.py", line 32, in __post_init__
    raise ValueError('\n'.join(messages))
ValueError: File "<file>", line 1130, col 1:  Unknown argument: enums = {'pv_formula_options': {'description': '

I am using python 3.8 and biolinkml==1.6.1 via pip install. I'm not sure how to troubleshoot. Thanks @cmungall for suggesting I note the issue here to track.

[hsolbrig]

On it.

[dwinston]

whoops, duplicate of #333