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running without a mrconso file has an error‘ #68

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chrisroederucdenver opened this issue Mar 17, 2022 · 0 comments
Open

running without a mrconso file has an error‘ #68

chrisroederucdenver opened this issue Mar 17, 2022 · 0 comments
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@chrisroederucdenver
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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'

Desktop (please complete the following information):

  • OS: [e.g. iOS]
  • Browser [e.g. chrome, safari]
  • Version [e.g. 22]

Smartphone (please complete the following information):

  • Device: [e.g. iPhone6]
  • OS: [e.g. iOS8.1]
  • Browser [e.g. stock browser, safari]
  • Version [e.g. 22]

Additional context
Add any other context about the problem here.

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