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Fix use of session_id in collect_data #909

Merged
merged 33 commits into from
Jan 14, 2025
Merged

Fix use of session_id in collect_data #909

merged 33 commits into from
Jan 14, 2025

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tsalo
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@tsalo tsalo commented Jan 9, 2025

Closes #908. collect_data wasn't using session_id except when there's a BIDS filter field.

Changes proposed in this pull request

  • Fix collect_data's handling of session_id.
  • Add tests using simulated datasets.

@tsalo tsalo added the testing label Jan 9, 2025
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codecov-commenter commented Jan 9, 2025

Codecov Report

Attention: Patch coverage is 80.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 45.84%. Comparing base (fa4dbe0) to head (3c49cd6).
Report is 3 commits behind head on master.

Files with missing lines Patch % Lines
qsiprep/utils/bids.py 80.00% 0 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master     #909      +/-   ##
==========================================
+ Coverage   44.23%   45.84%   +1.60%     
==========================================
  Files          66       65       -1     
  Lines        9839     9725     -114     
  Branches     1097     1063      -34     
==========================================
+ Hits         4352     4458     +106     
+ Misses       5263     5040     -223     
- Partials      224      227       +3     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@tsalo tsalo mentioned this pull request Jan 10, 2025
@tsalo tsalo changed the title Draft test for parsing Fix use of session_id in collect_data Jan 13, 2025
@tsalo tsalo marked this pull request as ready for review January 13, 2025 21:12
@tsalo tsalo requested a review from mattcieslak January 13, 2025 22:05
@tsalo tsalo added bug Something isn't working and removed testing labels Jan 14, 2025
@@ -226,6 +230,11 @@ def collect_data(bids_dir, participant_label, session_id=None, filters=None, bid
for dtype, query in queries.items()
}

config.loggers.workflow.log(
25,
f'Collected data:\n{yaml.dump(subj_data, default_flow_style=False, indent=4)}',
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nice!

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@mattcieslak mattcieslak left a comment

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THANK YOU

@mattcieslak mattcieslak merged commit 0e047bb into master Jan 14, 2025
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@mattcieslak mattcieslak deleted the fix-session-wise branch January 14, 2025 20:41
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Session-wise processing is not actually session-wise
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