mimic3wdb-matched RECORDS file hast too many entries

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#466 opened on Sep 22, 2023 1 comment 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty: 4/5
Estimated time: 3-5 days
Newbie friendliness: 35/100

Issue type: Bug
Clarity: Mostly clear
Activity status: Stale
Tech stack: python
Domain: backend, data

Research direction

Start with wfdb.io.dl_database and compare the linked mimic3wdb-matched RECORDS file with the database contents, including the missing 3783537_10000.hea URL. Confirm how the extra entries produce download failures, then verify that downloading the database no longer requests nonexistent records; the proposed multithreading change is a separate, broader question.

Written by the indexing model from the issue text.

Description

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

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:

Actual content:

wfdb.io.dl_database generates unique urls using this RECORDS file which then leads to the mentioned error above.

Some questions:

Can someone adapt the RECORDS file to reflect the database content
The download via wfdb.io.dl_database is excruciating slow. Would it make sens to rewrite wfdb.io.dl_database to use multi-threading? Or what approach do you use to dump the whole database efficiently?

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