Error when downloading records from the mimic3db database

[Favourj-bit]

I'm trying to download records from the mimic3wdb:MIMIC-III Waveform Database using the code given in the demo

import os
import wfdb

cwd = os.getcwd()
dl_dir = os.path.join(cwd, 'tmp_dl_dir')

wfdb.dl_database('mimic3wdb', dl_dir=dl_dir)
display(os.listdir(dl_dir))

But I keep on getting the error shown:

Please how could I solve this?

[tompollard]

@Favourj-bit please could you provide code to reproduce the issue?

[Favourj-bit]

Hi @tompollard I just did that. I got the same error when trying to access the 'mimic3wdb-matched', 'MIMIC-III Waveform Database Matched Subset' database

[tompollard]

Thanks for adding the content @Favourj-bit. The code in your example works okay for me. Please could you show me the output to the following code?

import wfdb
print(wfdb.__version__)

A quick fix might be to upgrade to the latest version (e.g. with pip install wfdb --upgrade)

[Favourj-bit]

Hi @tompollard
here is the output from the code:

[Favourj-bit]

hi @tompollard, I have tried updating the wfdb but I'm still getting the same error.

NetFileNotFoundError: 404 Error: Not Found for url: https://physionet.org/files/mimic3wdb/1.0/30/3000003/.hea

[tompollard]

thanks @Favourj-bit I'll take a look into this as soon as I have the opportunity. There is a problem with the path that is being generated, so you are getting a 404 not found error.

Side note, but he MIMIC-III database that you are looking to work with is hosted at: https://physionet.org/content/mimic3wdb/1.0/

[Favourj-bit]

Hi @tompollard , I wanted to find out if you have been able to look into this

[tompollard]

I'm sorry, not yet. I have some other commitments that I need to focus on, but will take a look at this when I can (if someone doesn't get there before me).

[briangow]

@Favourj-bit , are you still having trouble with this? I cannot reproduce your problem. The files are downloading properly for me using this code.

[Favourj-bit]

@briangow
Yes, I am.
Which code is that?

[Favourj-bit]

@briangow

What app are you using?
I used jupyter lab for that code

[briangow]

I used Jupyter Notebook, could you give it a try?

[Favourj-bit]

ok, i will do that. thanks

[Favourj-bit]

i just tried with jupyter notebook, gives the same error. I wanted to let you know however that I'm just copying the code for my usecase, I did not clone the notebook. Could that cause an issue?

[briangow]

You should be able to simply copy the code and have it work, so I don't think that is the problem. To properly debug this we'd need to inspect record_list and nested_records in the dl_database function here: https://github.com/MIT-LCP/wfdb-python/blob/main/wfdb/io/record.py#L2971 . Feel free to give that a try. These lists should point the files here https://physionet.org/content/mimic3wdb/1.0/ (at the bottom). Your error shows a url which doesn't have the filename before the .hea, which isn't correct.

I won't be able help with this again until later next week. If you are anxious to get started using the mimic3wdb files, I'd suggest you download them directly from the physionet.org link above. Keep in mind that these files do take a substantial amount of disk space.

If you don't need to download them locally I'd suggest reading directly from the database (without saving them locally). See this section in the demo.ipynb for an example on how to do this for the matched subset of MIMIC-III waveforms (https://physionet.org/content/mimic3wdb-matched/1.0/):

# Can also read the same files hosted on PhysioNet (takes long to stream the many large files)
signals, fields = wfdb.rdsamp('3269321_0001', pn_dir = 'mimic3wdb/matched/p00/p000878')
wfdb.plot_items(signal=signals, fs=fields['fs'], title='Record p000878/3269321_0001')
display((signals, fields))