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.
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
Desktop (please complete the following information):
Smartphone (please complete the following information):
Additional context Add any other context about the problem here.