MIT-LCP / MIT-LCP/mimic-code

Script can't handle spaces in the directory path

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mimic-iii
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Description

Prerequisites
Description

Description of the issue, including:

  • what you have tried

I've tried loading the data which is stored on an external HD, with the path being "/Volumes/PZ External/MIMIC_comp". I believe this is due to the space between "PZ" and "External". The files are indeed there, however I receive the error pasted below.

To resolve this, I've renamed the folder to be /Volumes/PZ/MIMIC_comp/ and everything seems to work fine.


-- Checking for data --

Data path: /Volumes/PZ External/MIMIC_comp/
Unable to find /Volumes/PZ External/MIMIC_comp/ADMISSIONS.csv.gz - exiting before build.
make: *** [mimic-check-gz] Error 1

  • references to similar issues
  • queries demonstrating your question (if applicable)

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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 mimic-check-gz make target and trace how it reads and checks the configured data path. Reproduce the failure using the reported path, /Volumes/PZ External/MIMIC_comp/, then inspect the relevant script or command handling that path. Done means the check locates ADMISSIONS.csv.gz when the directory name contains spaces.

Written by the indexing model from the issue text.

Assessment

Domain
build-system
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Quiet
Clarity
Needs clarification
Newbie friendliness
45/100

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