Script can't handle spaces in the directory path
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 3.4k
- Forks
- 1.7k
- PR merge metrics
- No merged PRs in 30d
Description
Prerequisites
- Put an X between the brackets on this line if you have done all of the following:
- Checked the online documentation: https://mimic.physionet.org/about/mimic/
- Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=
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)
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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