Unable to extract D_ICD_PROCEDURES.csv

MIT-LCP / mimic-code

MIMIC Code Repository: Code shared by the research community for the MIMIC family of databases

https://mimic.mit.edu

MIT License

2.41k stars 1.5k forks source link

Closed weronikazak closed 7 months ago

weronikazak commented 8 months ago

[x] Put an X between the brackets on this line if you have done all of the following:
- Checked the online documentation: https://mimic.mit.edu/
- Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=

I was trying to get the csv file for D_ICD_PROCEDURES.csv from the PhysioNet, but upon the extraction I get the following error:

Any idea how to resolve this?

alistairewj commented 7 months ago

Can you verify the file is downloaded correctly by comparing the checksum hash (SHA) with the ones provided on the website?

alistairewj commented 7 months ago

Going to close this. Feel free to reopen if you still have the issue.

I will say that there is a bug in libarchive where plain text files are misinterpreted as mtree files, and the archive agent fails to extract the data. https://github.com/libarchive/libarchive/issues/1051

I don't have a good workaround for this aside from using a different program like gzip.