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[electrophysiology_browser] Replace Physiological Annotations with Events #9032

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driusan merged 23 commits into from
Feb 27, 2024
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[electrophysiology_browser] Replace Physiological Annotations with Events #9032

driusan merged 23 commits into from
Feb 27, 2024

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@jeffersoncasimir
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@jeffersoncasimir jeffersoncasimir commented Jan 31, 2024 •
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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.

This was referenced Jan 31, 2024
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jeffersoncasimir added a commit to jeffersoncasimir/Loris that referenced this pull request Feb 1, 2024
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HED Tag Support + HED Tag Manager (Rebased with aces#9032 CI fixes)
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@christinerogers christinerogers added Release: Add to release notes PR whose changes should be highlighted in the release notes Category: Cleanup PR or issue introducing/requiring at least one clean-up operation Release: Breaking changes PR that contains changes that might impact the code or accepted practices of active projects Release: Document at release PR whose changes need to be documented in the wiki (or other documentation) at release 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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regisoc reviewed Feb 12, 2024
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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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regisoc requested changes Feb 14, 2024
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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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regisoc approved these changes Feb 14, 2024
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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
@christinerogers christinerogers mentioned this pull request Mar 4, 2025
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@regisoc regisoc regisoc approved these changes

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Category: Cleanup PR or issue introducing/requiring at least one clean-up operation 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 Release: Add to release notes PR whose changes should be highlighted in the release notes Release: Breaking changes PR that contains changes that might impact the code or accepted practices of active projects Release: Document at release PR whose changes need to be documented in the wiki (or other documentation) at release

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@jeffersoncasimir @driusan @regisoc @christinerogers @laemtl