MIT-LCP / MIT-LCP/mimic-code

mimic3wdb-matched RECORDS file hast too many entries

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Description

Prerequisites
Description

Description of the issue, including:

  • what you have tried
    Tried downloading mimic3wdb-matched using wfdb-python:
  • references to similar issues
    https://github.com/MIT-LCP/wfdb-python/issues/466
  • queries demonstrating your question (if applicable)
    wfdb.io.dl_database("mimic3wdb-matched", "mimic3wdb-matched", records='all', annotators='all', keep_subdirs=True, overwrite=False)

We are trying to download the mimic3wdb-matched database via wfdb.io.dl_database:

wfdb.io.dl_database("mimic3wdb-matched", "mimic3wdb-matched", records='all', annotators='all', keep_subdirs=True, overwrite=False)

After a long wait, we get an error indicating a missing file:
wfdb.io._url.NetFileNotFoundError: 404 Error: Not Found for url: https://physionet.org/files/mimic3wdb-matched/1.0/p01/p017488/3783537_10000.hea

While investigating we found that the corresponding RECORDS file contains more records than there are in the database:
https://physionet.org/files/mimic3wdb-matched/1.0/p01/p017488/RECORDS

RECORDS file:
image

Actual content:
image

Can someone adapt the RECORDS file to reflect the database content

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the mimic3wdb-matched p01/p017488/RECORDS file and the reported wfdb.io.dl_database call, then compare the listed records with the files actually available at the PhysioNet URL. Done means the RECORDS contents accurately reflect the database so the download no longer requests the missing 3783537_10000.hea file.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
databases
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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