callahantiff / OMOP2OBO

OMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies
http://tiffanycallahan.com/OMOP2OBO_Dashboard
MIT License
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running without a mrconso file has an error‘ #68

Open chrisroederucdenver opened 2 years ago

chrisroederucdenver commented 2 years ago

Describe the bug running without a mrconso file creates an error

To Reproduce Steps to reproduce the behavior: (test_env) CARD-CRoeder:OMOP2OBO christopherroeder$ time ./main.py --clinical_domain condition --clinical_data resources/clinical_data/sample_conditions.csv

Expected behavior no error

Screenshots

*** Annotating Level: concept
Performing UMLS CUI + Semantic Type Annotation
Traceback (most recent call last):
  File "./main.py", line 149, in <module>
    main()
  File "/Users/christopherroeder/work/git_misc/OMOP2OBO/test_env/lib/python3.8/site-packages/click/core.py", line 1025, in __call__
    return self.main(*args, **kwargs)
  File "/Users/christopherroeder/work/git_misc/OMOP2OBO/test_env/lib/python3.8/site-packages/click/core.py", line 955, in main
    rv = self.invoke(ctx)
  File "/Users/christopherroeder/work/git_misc/OMOP2OBO/test_env/lib/python3.8/site-packages/click/core.py", line 1279, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/christopherroeder/work/git_misc/OMOP2OBO/test_env/lib/python3.8/site-packages/click/core.py", line 710, in invoke
    return callback(*args, **kwargs)
  File "./main.py", line 97, in main
    mappings = mapper.clinical_concept_mapper()
  File "/Users/christopherroeder/work/git_misc/OMOP2OBO/omop2obo/clinical_concept_annotator.py", line 373, in clinical_concept_mapper
    if self.umls_cui_data is not None and self.umls_tui_data is not None:
AttributeError: 'ConceptAnnotator' object has no attribute 'umls_cui_data'

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