[FIX] Fixed xnat_to_bids ignoring --clobber before pulling data#330
Merged
slimnsour merged 4 commits intoTIGRLab:masterfrom Apr 22, 2022
Merged
[FIX] Fixed xnat_to_bids ignoring --clobber before pulling data#330slimnsour merged 4 commits intoTIGRLab:masterfrom
slimnsour merged 4 commits intoTIGRLab:masterfrom
Conversation
|
Hello @slimnsour, Thank you for updating! Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, Comment last updated at 2022-04-20 20:58:49 UTC |
Codecov Report
@@ Coverage Diff @@
## master #330 +/- ##
==========================================
- Coverage 30.79% 30.75% -0.05%
==========================================
Files 63 63
Lines 9515 9528 +13
==========================================
Hits 2930 2930
- Misses 6585 6598 +13
Continue to review full report at Codecov.
|
DESm1th
previously approved these changes
Apr 20, 2022
DESm1th
approved these changes
Apr 20, 2022
Contributor
DESm1th
left a comment
DESm1th
left a comment
There was a problem hiding this comment.
Thanks for the quick fix Salim!
jerdra
approved these changes
Apr 22, 2022
Contributor
jerdra
left a comment
jerdra
left a comment
There was a problem hiding this comment.
good stuff, thanks for PR!
Contributor
Author
|
Thanks guys! |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Small fix with behavior of
xnat_to_bids: Before it would download the zip from xnat before checking if the subject was already converted to bids in the destination folder, which would add unnecessary time to batch runs. Now it will check the destination folder for the subject before attempting to pull their data (unless the --clobber tag is used of course)I'm also working on a doc page to illustrate how to use
xnat_to_bids, but with this fix we can safely putdm_xnat_extract.py $STUDY --use-dcm2bidsin nightly scripts as it will skip over converted subjects properly.