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allenai / scispacy

A full spaCy pipeline and models for scientific/biomedical documents.
https://allenai.github.io/scispacy/
Apache License 2.0
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export_umls_json.py failing #509

Closed ethanhkim closed 4 months ago

ethanhkim commented 4 months ago

Hi! I noticed that while I was trying to build my own Linker, the script export_umls_json.py is currently failing, and may have been for the past 10 months. Traceback below:

  Traceback (most recent call last):
    File "/dir/to/project/export_umls_json.py", line 115, in <module>
      main(args.meta_path, args.output_path, args.lang, args.source, args.non_suppressed)
  TypeError: main() takes from 2 to 4 positional arguments but 5 were given

Commenting out the last argument (lines 109-113) doesn't resolve the issue as well, creating an empty jsonl file.

For now, I'm using the previous commit's code but the current script may need to be reverted. Thanks!

dakinggg commented 4 months ago

Ah looks like a mistake in the last pr that touched that file! Would you be interested in opening a PR to fix it?

ethanhkim commented 4 months ago

For sure, I'll look into fixing it! Should also be useful for anyone following up #237 .

ethanhkim commented 4 months ago

@dakinggg, PR's open for review: #511.

dakinggg commented 4 months ago

Thank you!