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[electrophysiology_browser] Replace Physiological Annotations with Events #9032

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jeffersoncasimir
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@jeffersoncasimir jeffersoncasimir commented Jan 31, 2024

This PR aims to improve the current compliance to the BIDS standard. Loris-MRI counterpart: #1041
Partially addresses #8910.

This replaces references to annotation files with references to event files.

This PR deletes *_annotation_* tables. The corresponding required event tables already exist.

+minor improvements to the EventManager and AnnotationForm components.

This PR brings in the following limitations:

  • Events can no longer be created via the interface (support coming soon)
  • Events can be modified, but the currently supported fields are by default read-only or disabled (Name and time)
  • HED tag support is extremely limited (better support in imminent PR: [electrophysiology_browser] HED Tag Support #9033)

TODO: Raisinbread modifications

TODO: Get official server-side solution + Add to documentation.

  • Determine required request time limit
  • Determine required memory allocation limit
  • Determine procedure for increasing when needed

Both of the above needed to be increased for certain requests.

jeffersoncasimir added a commit to jeffersoncasimir/Loris that referenced this pull request Feb 1, 2024
@christinerogers christinerogers added Add to Release Notes PR change should be highlighted in Release notes (important security, features and bugfixes) Cleanup PR or issue introducing/requiring at least one clean-up operation Caveat for Existing Projects PR contains changes that might impact the code or accepted practices of current active projects Document at Release PR adds or changes a feature such that the wiki (or other documentation) must be updated Critical to release PR or issue is key for the release to which it has been assigned Priority: High PR or issue should be prioritised over others for review and testing labels Feb 6, 2024
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driusan commented Feb 6, 2024

@regisoc can you review this?

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Nice work!

  • global logic looks good. Some questions for the back-end class.
  • Still some TODOs in the code. I avoided repeating all comments. The comment on the first one should be valid for all similar following it.
  • rename permission electrophysiology_browser_edit_annotations to electrophysiology_browser_edit_events?
  • Some cleaning to do (commented lines to remove/keep)?
  • Not tested yet. I might need help setting up testing env.

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regisoc commented Feb 14, 2024

I will put that here so we do not forget them. Note after tests:

  • Event download button disabled or not working.
  • Error epoch.properties is undefined following that process:
    • open event panel
    • edit one event
    • submit this event
    • close the event submit with the top-right "x".

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regisoc commented Feb 14, 2024

@jeffersoncasimir let me know if you need another round of test this morning.

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New pass:

  • error on epoch resolved.
  • new errors due to multiple config db calls that can vary from config.xml. Unify calls for config check to $config->getSetting("dataDirBasepath"); in electrophysiologyevents.class.inc (one in _updateArchives one in update).
  • Archive events file tgz created and downloadable, but archive is corrupted. Not corrupted, but not a gzip archive? Using tar xf <file> works, but not when using tar xzf <file>?

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LGTM

@christinerogers christinerogers added this to the 26.0.0 milestone Feb 23, 2024
@laemtl laemtl assigned driusan and unassigned regisoc Feb 27, 2024
@driusan driusan merged commit 1112e1a into aces:main Feb 27, 2024
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5 participants