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3mcloud / MDACE

The project was to build and release the first publicly available code evidence dataset called MDACE on a subset of the MIMIC-III clinical records. We believe that the release of MDACE will greatly improve the understanding and application of deep learning technologies for medical coding, and benefit machine learning models for classification.
MIT License
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Error Injecting Text #6

Closed yradsmikham closed 10 months ago

yradsmikham commented 10 months ago

I attempting to follow the instructions to inject text into JSON by running the following command:

python3 inject-note-text.py --noteevents NOTEEVENTS.csv \ --data-dir data/ \ --out-dir with_text/gold

However, I am receiving the following error:

➜  MDACE git:(main) ✗ python3 inject-note-text.py --noteevents NOTEEVENTS.csv --data-dir data --out-dir with_text/gold
INFO:inject-note-text.py:Loading NOTEEVENTS.csv
INFO:inject-note-text.py:Injecting text and persisting to /Users/yvonne/microsoft/MDACE/with_text/gold
Traceback (most recent call last):
  File "/Users/yvonne/microsoft/MDACE/inject-note-text.py", line 90, in <module>
    main(parser.parse_args())
  File "/Users/yvonne/microsoft/MDACE/inject-note-text.py", line 67, in main
    inject_and_persist(notes_map, args.data_dir, args.out_dir)
  File "/Users/yvonne/microsoft/MDACE/inject-note-text.py", line 37, in inject_and_persist
    admission = inject_note_text(notes_map, json.load(ifp))
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/yvonne/microsoft/MDACE/inject-note-text.py", line 15, in inject_note_text
    text = notes_map[note["note_id"]]
           ~~~~~~~~~^^^^^^^^^^^^^^^^^
KeyError: 44580

Any idea what is causing this error and how to resolve it?

Python version 3.11.7, running on Macbook Pro M1.

Thank you!

yradsmikham commented 10 months ago

I was able to resolve this by redownloading the mimic-iii dataset and trying again.