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Import AnSRS directly in Taxonomy Model #144

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puja-trivedi opened this issue Feb 14, 2025 · 0 comments
Open

Import AnSRS directly in Taxonomy Model #144

puja-trivedi opened this issue Feb 14, 2025 · 0 comments
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@puja-trivedi
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puja-trivedi commented Feb 14, 2025

Currently unable to import AnSRS model directly in bke_taxonomy model.

Note: This is an error with schemasheets. If I add import: anatomical_structure in the yaml file, the pydantic generation works as expected; however, if I add the import in the google spreadsheet, schemasheets has an error.

Need to debug this error :


    sys.exit(cli())
             ^^^^^
  File "/Users/pujatrivedi/anaconda3/envs/test_bkbit_20241127/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pujatrivedi/anaconda3/envs/test_bkbit_20241127/lib/python3.11/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/Users/pujatrivedi/anaconda3/envs/test_bkbit_20241127/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pujatrivedi/anaconda3/envs/test_bkbit_20241127/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pujatrivedi/anaconda3/envs/test_bkbit_20241127/lib/python3.11/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pujatrivedi/Desktop/MIT/test_bkbit_20241127/bkbit/bkbit/model_converters/sheets_converter.py", line 284, in schema2model
    schema = schema_maker.repair_schema(schema)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pujatrivedi/anaconda3/envs/test_bkbit_20241127/lib/python3.11/site-packages/schemasheets/schemamaker.py", line 596, in repair_schema
    map_ix = sv.get_mappings(e.name)
             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pujatrivedi/anaconda3/envs/test_bkbit_20241127/lib/python3.11/site-packages/linkml_runtime/utils/schemaview.py", line 1186, in get_mappings
    'self': [self.get_uri(element_name, imports=imports, expand=False)],
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/pujatrivedi/anaconda3/envs/test_bkbit_20241127/lib/python3.11/site-packages/linkml_runtime/utils/schemaview.py", line 1094, in get_uri
    schema = self.schema_map[self.in_schema(e.name)]
             ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: 'anatomical-structure-schema'

@puja-trivedi puja-trivedi self-assigned this Feb 14, 2025
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