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Girder 5 upgrade 2026 - #443

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BryonLewis wants to merge 34 commits into
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girder-5-upgrade-2026
Open

Girder 5 upgrade 2026#443
BryonLewis wants to merge 34 commits into
mainfrom
girder-5-upgrade-2026

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@BryonLewis

@BryonLewis BryonLewis commented Jun 8, 2026

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Replaces the #241 with this more updated version

  • Docker Compose structure upgrade
  • Update docker build files to build web client and spa client
  • Girder DIVE web interface is updated to use vite and modifications to code for Girder 5
  • Notifications Bus uses websockets and the girder web components web socket upgrades
  • Update to notifications to use the new system on the server
  • Upgrade Axios in DIVE-DSA and the dive-dsa-slicer-ui tools, this requires using a new branch of girder web components as well

TODO:

  • Test/fix slicer-cli notifications (don't seem to work right now)
  • Test assetstore imports and conversion afterwards using events
  • Test Metadata Slicer CLI runs for multiple jobs
  • Test DIVE Metadata creation and if it needs to be converted to a task instead of being in the request thread (most likely) - create an example with 10k items

BryonLewis and others added 30 commits June 8, 2026 13:37
Integrate asset import options and dependency bumps from main while
preserving Girder 5 upgrade changes (notifications, worker events, REST).

Co-authored-by: Cursor <cursoragent@cursor.com>
Bumps [websocket-driver](https://github.com/faye/websocket-driver-node) from 0.7.4 to 0.7.5.
- [Changelog](https://github.com/faye/websocket-driver-node/blob/main/CHANGELOG.md)
- [Commits](faye/websocket-driver-node@0.7.4...0.7.5)

---
updated-dependencies:
- dependency-name: websocket-driver
  dependency-version: 0.7.5
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [torch](https://github.com/pytorch/pytorch) from 2.12.0 to 2.13.0.
- [Release notes](https://github.com/pytorch/pytorch/releases)
- [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md)
- [Commits](pytorch/pytorch@v2.12.0...v2.13.0)

---
updated-dependencies:
- dependency-name: torch
  dependency-version: 2.13.0
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps  and [ws](https://github.com/websockets/ws). These dependencies needed to be updated together.

Updates `ws` from 7.5.10 to 7.5.13
- [Release notes](https://github.com/websockets/ws/releases)
- [Commits](websockets/ws@7.5.10...7.5.13)

Updates `ws` from 8.18.3 to 8.21.1
- [Release notes](https://github.com/websockets/ws/releases)
- [Commits](websockets/ws@7.5.10...7.5.13)

---
updated-dependencies:
- dependency-name: ws
  dependency-version: 7.5.13
  dependency-type: indirect
- dependency-name: ws
  dependency-version: 8.21.1
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
BryonLewis and others added 4 commits July 21, 2026 09:04
Resolve dependency conflicts by taking main's axios and pillow bumps,
keeping branch numpy pin, dropping yarn.lock, and regenerating locks.

Co-authored-by: Cursor <cursoragent@cursor.com>
Bring in main commits since Jul 21 (dependency bumps, Slicer CLI UI updates, metadata mismatch fixes). Keep Girder 5 job-based metadata ingest, drop yarn.lock, and port DIVE_DatasetId matching into crud_metadata_ingest.

Co-authored-by: Cursor <cursoragent@cursor.com>
Port combineMetadataFolders create/index support and import row summaries
into the job-based DIVE metadata ingest path while keeping local-queue
enqueue semantics from this branch.

Co-authored-by: Cursor <cursoragent@cursor.com>
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