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microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model
https://microbiomedata.github.io/nmdc-schema/
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update linkml-runtime to 1.6.1 #1370

Closed turbomam closed 11 months ago

turbomam commented 11 months ago 
poetry run python -m unittest discover
poetry run python -m unittest discover
..INFO:root:Using SchemaView with im=None
INFO:root:Importing workflow_execution_activity as workflow_execution_activity from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing core as core from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing prov as prov from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing basic_slots as basic_slots from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing external_identifiers as external_identifiers from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing sample_prep as sample_prep from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing portal/sample_id as portal/sample_id from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing linkml:types as /home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/model/schema/types from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=None
INFO:root:Importing portal/mixs_inspired as portal/mixs_inspired from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing portal/jgi_metatranscriptomics as portal/jgi_metatranscriptomics from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing portal/jgi_metagenomics as portal/jgi_metagenomics from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing portal/emsl as portal/emsl from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing mixs as mixs from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing annotation as annotation from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Using SchemaView with im=None
INFO:root:Importing workflow_execution_activity as workflow_execution_activity from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing core as core from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing prov as prov from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing basic_slots as basic_slots from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing external_identifiers as external_identifiers from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing sample_prep as sample_prep from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing portal/sample_id as portal/sample_id from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing linkml:types as /home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/model/schema/types from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=None
INFO:root:Importing portal/mixs_inspired as portal/mixs_inspired from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing portal/jgi_metatranscriptomics as portal/jgi_metatranscriptomics from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing portal/jgi_metagenomics as portal/jgi_metagenomics from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing portal/emsl as portal/emsl from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing mixs as mixs from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
INFO:root:Importing annotation as annotation from source /home/mark/gitrepos/nmdc-schema/tests/../src/schema/nmdc.yaml; base_dir=/home/mark/gitrepos/nmdc-schema/tests/../src/schema
.......EE.
======================================================================
ERROR: test_create_nmdc_mixs_view (tests.test_nmdc_mixs_merged_view.TestNmdcMixsMergedView)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/mark/gitrepos/nmdc-schema/tests/test_nmdc_mixs_merged_view.py", line 11, in test_create_nmdc_mixs_view
    nmdc_mixs_merged_view = SchemaView(nmdc_mixs_url)
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/schemaview.py", line 138, in __init__
    schema = load_schema_wrap(schema)
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/schemaview.py", line 70, in load_schema_wrap
    schema = yaml_loader.load(path, target_class=SchemaDefinition, **kwargs)
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/loaders/loader_root.py", line 71, in load
    results = self.load_any(*args, **kwargs)
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/loaders/yaml_loader.py", line 41, in load_any
    return self._construct_target_class(data_as_dict, target_class)
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/loaders/loader_root.py", line 132, in _construct_target_class
    return target_class(**data_as_dict)
  File "<string>", line 66, in __init__
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/meta.py", line 564, in __post_init__
    self.imports = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.imports]
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/meta.py", line 564, in <listcomp>
    self.imports = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.imports]
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/metamodelcore.py", line 104, in __init__
    raise ValueError(f"{v} is not a valid URI or CURIE")
ValueError: MIXS_yaml:agriculture is not a valid URI or CURIE

======================================================================
ERROR: test_is_merged (tests.test_nmdc_mixs_merged_view.TestNmdcMixsMergedView)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/mark/gitrepos/nmdc-schema/tests/test_nmdc_mixs_merged_view.py", line 17, in test_is_merged
    nmdc_mixs_merged_view = SchemaView(nmdc_mixs_url)
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/schemaview.py", line 138, in __init__
    schema = load_schema_wrap(schema)
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/schemaview.py", line 70, in load_schema_wrap
    schema = yaml_loader.load(path, target_class=SchemaDefinition, **kwargs)
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/loaders/loader_root.py", line 71, in load
    results = self.load_any(*args, **kwargs)
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/loaders/yaml_loader.py", line 41, in load_any
    return self._construct_target_class(data_as_dict, target_class)
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/loaders/loader_root.py", line 132, in _construct_target_class
    return target_class(**data_as_dict)
  File "<string>", line 66, in __init__
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/meta.py", line 564, in __post_init__
    self.imports = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.imports]
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/meta.py", line 564, in <listcomp>
    self.imports = [v if isinstance(v, URIorCURIE) else URIorCURIE(v) for v in self.imports]
  File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/utils/metamodelcore.py", line 104, in __init__
    raise ValueError(f"{v} is not a valid URI or CURIE")
ValueError: MIXS_yaml:agriculture is not a valid URI or CURIE

----------------------------------------------------------------------
Ran 12 tests in 29.320s

FAILED (errors=2)
turbomam commented 11 months ago

added 

    @unittest.skip(
        "runtime 1.6.1 complains about MIXS_yaml prefix. Will disappear when we start importing GSC's MIxS 6.2")