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[FIX] Allow (but discourage) task, acquisition and run entities for coordsystem.json and electrodes.tsv #1888

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merged 3 commits into from
Oct 10, 2024

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effigies
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We've run into a situation where the regular validator regular expressions were written more laxly than the specification, leading to datasets that use entities that are against the spec but perfectly interpretable. In particular, the task entity has been permitted for coordsystem.json across EEG, iEEG, MEG and NIRS.

Following the pattern established in #1722, instead of marking these datasets invalid with a schema-based validator, we relax the spec but add warnings.

cc @bids-standard/raw-electrophys and @rob-luke @lpollonini (we should make a NIRS team...).

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codecov bot commented Aug 14, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 88.06%. Comparing base (0e506f0) to head (c0915eb).

Additional details and impacted files
@@           Coverage Diff           @@
##           master    #1888   +/-   ##
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  Coverage   88.06%   88.06%           
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  Files          16       16           
  Lines        1391     1391           
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  Hits         1225     1225           
  Misses        166      166           

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@effigies
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@dorahermes @VisLab WDYT?

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Just noting that if a _task- entity is allowed for an _coordsystem.json it should also be allowed for an _electrodes.tsv.

@effigies effigies changed the title [FIX] Allow (but discourage) task entity for coordsystem.json [FIX] Allow (but discourage) task, acquisition and run entities for coordsystem.json and electrodes.tsv Oct 10, 2024
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Good catch. task, acquisition and run were all permitted in the legacy validator for both electrodes.tsv and coordsystem.json, and all six combinations exist on OpenNeuro. For consistency, I've updated this PR to treat these all the same.

@effigies effigies force-pushed the fix/coordsystem-task branch from f67775e to eaaeca2 Compare October 10, 2024 18:47
@rwblair rwblair merged commit 2e86e99 into bids-standard:master Oct 10, 2024
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4 participants