Chris Roeder CUAnschutz

test_string_similarity failed for me because the nltk download isn't working. I found a way to get the download to work here: https://stackoverflow.com/questions/38916452/nltk-download-ssl-certificate-verify-failed After failing to get the solutions that fix...

fix #65 no value for merge option does not issue error about multiple…

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Now it shows a friendlier message "Error: Missing option '--clinical_domain'."

fixes #68

**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...

for issue #63

merge option fails with multiple

1

**Describe the bug** If you run with no arguments (as you very likely would not) you get: "ValueError: 'default' must be a list when 'multiple' is true." **To Reproduce** Steps...

Coding: add requirements.txt

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Add a requirements.txt to make it easier to create an environment with required libs.

search in home and current directories to find iri_mappings.txt

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The iri_mappings.txt in the jar doesn't work for my local deployment. I added code that looks in the current working directory, then the user's home directory, before the file in...