update linkml to 1.6.2 - Githubissues

poetry run gen-project \
        --exclude excel \
        --exclude graphql \
        --exclude jsonld \
        --exclude markdown \
        --exclude proto \
        --exclude shacl \
        --exclude shex \
        --exclude sqlddl \
        --include jsonldcontext \
        --include jsonschema \
        --include owl \
        --include python \
        --include rdf \
        -d project src/schema/nmdc.yaml && mv project/*.py nmdc_schema

ALL_SCHEMAS = ['src/schema/nmdc.yaml'] INFO:root:Skipping graphql as not in inclusion list: ['jsonldcontext', 'jsonschema', 'owl', 'python', 'rdf'] INFO:root:Generating: jsonldcontext INFO:root: SCHEMA: src/schema/nmdc.yaml INFO:root: PARENT=project/jsonld INFO:root: jsonldcontext ARGS: {'mergeimports': True} INFO:root: WRITING TO: project/jsonld/nmdc.context.jsonld INFO:root:Skipping jsonld as not in inclusion list: ['jsonldcontext', 'jsonschema', 'owl', 'python', 'rdf'] INFO:root:Generating: jsonschema INFO:root: SCHEMA: src/schema/nmdc.yaml INFO:root: PARENT=project/jsonschema INFO:root:Using SchemaView with im=None INFO:root: jsonschema ARGS: {'mergeimports': True} INFO:root:Importing workflow_execution_activity as workflow_execution_activity from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing core as core from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing prov as prov from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing basic_slots as basic_slots from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing external_identifiers as external_identifiers from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing sample_prep as sample_prep from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing portal/sample_id as portal/sample_id from source src/schema/nmdc.yaml; base_dir=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 src/schema/nmdc.yaml; base_dir=None INFO:root:Importing portal/mixs_inspired as portal/mixs_inspired from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing portal/jgi_metatranscriptomics as portal/jgi_metatranscriptomics from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing portal/jgi_metagenomics as portal/jgi_metagenomics from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing portal/emsl as portal/emsl from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing mixs as mixs from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing annotation as annotation from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root: WRITING TO: project/jsonschema/nmdc.schema.json INFO:root:Skipping markdown as not in inclusion list: ['jsonldcontext', 'jsonschema', 'owl', 'python', 'rdf'] INFO:root:Generating: owl INFO:root: SCHEMA: src/schema/nmdc.yaml INFO:root: PARENT=project/owl INFO:root:Using SchemaView with im=None INFO:root: owl ARGS: {'mergeimports': True} INFO:root:Importing workflow_execution_activity as workflow_execution_activity from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing core as core from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing prov as prov from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing basic_slots as basic_slots from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing external_identifiers as external_identifiers from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing sample_prep as sample_prep from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing portal/sample_id as portal/sample_id from source src/schema/nmdc.yaml; base_dir=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 src/schema/nmdc.yaml; base_dir=None INFO:root:Importing portal/mixs_inspired as portal/mixs_inspired from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing portal/jgi_metatranscriptomics as portal/jgi_metatranscriptomics from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing portal/jgi_metagenomics as portal/jgi_metagenomics from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing portal/emsl as portal/emsl from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing mixs as mixs from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing annotation as annotation from source src/schema/nmdc.yaml; base_dir=src/schema INFO:root:Importing linkml:units as /home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/model/schema/units from source None; base_dir=None INFO:root:Importing linkml:mappings as /home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/model/schema/mappings from source None; base_dir=None 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 None; base_dir=None INFO:root:Importing linkml:annotations as /home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/model/schema/annotations from source None; base_dir=None INFO:root:Importing linkml:extensions as /home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml_runtime/linkml_model/model/schema/extensions from source None; base_dir=None WARNING:root:from_schema not populated for element has_input WARNING:root:from_schema not populated for element has_output WARNING:root:from_schema not populated for element id WARNING:root:from_schema not populated for element has_input WARNING:root:from_schema not populated for element has_output WARNING:root:from_schema not populated for element id WARNING:root:from_schema not populated for element has_input WARNING:root:from_schema not populated for element has_output WARNING:root:from_schema not populated for element id WARNING:root:from_schema not populated for element id WARNING:root:from_schema not populated for element has_input WARNING:root:from_schema not populated for element has_output WARNING:root:from_schema not populated for element id WARNING:root:from_schema not populated for element description WARNING:root:from_schema not populated for element id WARNING:root:from_schema not populated for element name WARNING:root:from_schema not populated for element dna_cont_well WARNING:root:from_schema not populated for element dna_cont_type WARNING:root:from_schema not populated for element dna_cont_type WARNING:root:from_schema not populated for element dna_cont_well WARNING:root:from_schema not populated for element rna_cont_well WARNING:root:from_schema not populated for element rna_cont_type WARNING:root:from_schema not populated for element rna_cont_type WARNING:root:from_schema not populated for element rna_cont_well WARNING:root:from_schema not populated for element al_sat WARNING:root:from_schema not populated for element al_sat_meth WARNING:root:from_schema not populated for element alternative_identifiers WARNING:root:from_schema not populated for element annual_precpt WARNING:root:from_schema not populated for element climate_environment WARNING:root:from_schema not populated for element cur_vegetation WARNING:root:from_schema not populated for element cur_vegetation_meth WARNING:root:from_schema not populated for element elev WARNING:root:from_schema not populated for element env_broad_scale WARNING:root:from_schema not populated for element env_local_scale WARNING:root:from_schema not populated for element env_medium WARNING:root:from_schema not populated for element extreme_event WARNING:root:from_schema not populated for element fire WARNING:root:from_schema not populated for element flooding WARNING:root:from_schema not populated for element gaseous_environment WARNING:root:from_schema not populated for element gold_biosample_identifiers WARNING:root:from_schema not populated for element heavy_metals WARNING:root:from_schema not populated for element heavy_metals_meth WARNING:root:from_schema not populated for element id WARNING:root:from_schema not populated for element lat_lon WARNING:root:from_schema not populated for element oxy_stat_samp WARNING:root:Multiple owl types {rdflib.term.URIRef('http://www.w3.org/2002/07/owl#Thing'), rdflib.term.URIRef('http://www.w3.org/2000/01/rdf-schema#Literal')} WARNING:root:from_schema not populated for element part_of WARNING:root:from_schema not populated for element ph_meth WARNING:root:from_schema not populated for element salinity_meth WARNING:root:from_schema not populated for element season_precpt WARNING:root:from_schema not populated for element sieving WARNING:root:from_schema not populated for element slope_aspect WARNING:root:from_schema not populated for element slope_gradient WARNING:root:from_schema not populated for element source_mat_id WARNING:root:from_schema not populated for element tot_carb WARNING:root:from_schema not populated for element tot_nitro_cont_meth WARNING:root:from_schema not populated for element tot_nitro_content WARNING:root:from_schema not populated for element tot_org_c_meth WARNING:root:from_schema not populated for element tot_org_carb WARNING:root:from_schema not populated for element water_cont_soil_meth WARNING:root:from_schema not populated for element water_content WARNING:root:from_schema not populated for element watering_regm Traceback (most recent call last): File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/bin/gen-project", line 8, in sys.exit(cli()) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, kwargs) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/projectgen.py", line 243, in cli gen.generate(yamlfile, project_config) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/projectgen.py", line 145, in generate gen_dump = gen.serialize(serialize_args) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 199, in serialize self.as_graph() File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 185, in as_graph self.add_class(cls) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 352, in add_class pre_node = condition_to_bnode(rule.preconditions) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 344, in condition_to_bnode ixn_listnode = self.transform_class_expression(expr, quantifier_predicate=OWL.someValuesFrom) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 428, in transform_class_expression x = self.transform_class_slot_expression(cls, slot, slot) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 494, in transform_class_slot_expression self._union_of([self.transform_class_slot_expression(cls, x, main_slot) for x in slot.any_of]) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 871, in _union_of return self._boolean_expression(exprs, OWL.unionOf, **kwargs) File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-_1824IzR-py3.9/lib/python3.9/site-packages/linkml/generators/owlgen.py", line 894, in _boolean_expression raise ValueError(f"None in exprs: {exprs}") ValueError: None in exprs: [None, None] make: *** [Makefile:102: gen-project] Error 1

microbiomedata / nmdc-schema

update linkml to 1.6.2 #1374

1365