Accessing a file in a subfolder on PhysioNet using pn_dir

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#467 opened on Nov 14, 2023 2 comments 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

Research direction

Start at wfdb.rdrecord and follow how record and pn_dir are combined for PhysioNet downloads. Reproduce both failing examples, then read the semi-complete PR #346 for the existing path-parsing approach. Done means nested MIMIC-IV-ECG records resolve without requiring an unintuitive files segment, with regression coverage for the shown paths.

Written by the indexing model from the issue text.

Description

I'm using wfdb 4.1.2, and when I try to run this code it fails with a 404:

import wfdb
record = wfdb.rdrecord('p1003/p10030753/s40735970/40735970', pn_dir='mimic-iv-ecg')

NetFileNotFoundError: 404 Error: Not Found for url: https://physionet.org/files/mimic-iv-ecg/1.0/40735970.hea

Looks like this relates to hacky path parsing which there is an open (semi-complete) PR for (#346).

I also tried:

import wfdb
record = wfdb.rdrecord('40735970', pn_dir='mimic-iv-ecg/1.0/p1003/p10030753/s40735970')

NetFileNotFoundError: 404 Error: Not Found for url: https://physionet.org/files/mimic-iv-ecg/1.0/p1003/p10030753/s40735970/40735970.hea

So I played with the path, and this ends up working:

import wfdb
record = wfdb.rdrecord('40735970', pn_dir='mimic-iv-ecg/1.0/files/p1003/p10030753/s40735970')

Seems a bit unintuitive to me that you have to put files in there, am I doing something wrong?

Dominant language: Jupyter Notebook
Stars: 853
Forks: 322
PR merge metrics: No merged PRs in 30d

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