Traceback (most recent call last):
File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/bin/linkml-validate", line 8, in <module>
sys.exit(cli())
File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/linkml/validators/jsonschemavalidator.py", line 167, in cli
results = validator.validate_object(obj, target_class=py_target_class)
File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/linkml/validators/jsonschemavalidator.py", line 68, in validate_object
return jsonschema.validate(inst_dict, schema=jsonschema_obj, format_checker=jsonschema.Draft7Validator.FORMAT_CHECKER)
File "/home/cpauvert/.cache/pypoetry/virtualenvs/miiid-schema-6-7ZvLG3-py3.9/lib/python3.9/site-packages/jsonschema/validators.py", line 1121, in validate
raise error
jsonschema.exceptions.ValidationError: '1236' is not one of ['NOT_APPLICABLE', 'NOT_COLLECTED', 'NOT_PROVIDED', 'RESTRICTED_ACCESS']
Failed validating 'enum' in schema[1]:
{'description': 'List of missing values reporting terms according '
'based on the International Nucleotide Sequence '
'Database Collaboration (INSDC )',
'enum': ['NOT_APPLICABLE',
'NOT_COLLECTED',
'NOT_PROVIDED',
'RESTRICTED_ACCESS'],
'title': 'MissingValue',
'type': 'string'}
On instance:
'1236'
This could be due to the fact that the any_of is applied to an enum : MissingValue and a custom typeNCBITaxId.
This should is related to #4 but there is an issue with the validation of the data.
fails with:
This could be due to the fact that the
any_of
is applied to anenum
:MissingValue
and a customtype
NCBITaxId
.https://github.com/FAIR-MI/miiid-schema/blob/f99e409b3f153548c7dc4adb7fe019175d11a2d0/src/miiid_schema/schema/miiid_schema.yaml#L78-L85