Resolve relative local attachment paths

[fm3]

Fixed a bug where layer attachments with relative paths would not be read correctly. Regression from #8829

Steps to test:

• I tested that I can now load both hdf5 and zarr attachments with the following path styles:

segmentation/agglomerates/agglomerate_view_5
./segmentation/agglomerates/agglomerate_view_50
/absolute/path/to/webknossos/binaryData/sample_organization/test-agglomerate-file-zarr/segmentation/agglomerates/agglomerate_view_90
file:///absolute/path/to/webknossos/binaryData/sample_organization/test-agglomerate-file-zarr/segmentation/agglomerates/agglomerate_view_80

---

• Added changelog entry (create a $PR_NUMBER.md file in unreleased_changes or use ./tools/create-changelog-entry.py)
• Needs datastore update after deployment

[coderabbitai]

📝 Walkthrough

Walkthrough

This change introduces a new method to resolve relative file paths for layer attachments, ensuring they are correctly interpreted based on a configurable base directory. Multiple services are updated to use this resolution logic by injecting the configuration and applying the new method when constructing file keys. No other logic is modified.

Changes

Cohort / File(s)	Change Summary
LayerAttachment Path Resolution .../models/datasource/DatasetLayerAttachments.scala	Adds resolvedPath method to LayerAttachment for resolving relative paths against a base directory and data source ID, returning an absolute URI.
Service Constructor Updates & Path Resolution .../services/connectome/ConnectomeFileService.scala, .../services/mapping/AgglomerateService.scala, .../services/mesh/MeshFileService.scala, .../services/segmentindex/SegmentIndexFileService.scala	Updates constructors to require DataStoreConfig and uses the new resolvedPath method to ensure attachments use resolved file paths when constructing file keys. Some minor refactoring (e.g., return type, variable names) in select services.
Documentation unreleased_changes/8834.md	Documents the bugfix for handling layer attachments with relative file paths.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~15–20 minutes

Suggested reviewers

• frcroth

Poem

🐇✨
A hop and a skip through the code we go,
Paths once confused now perfectly so!
Attachments resolved, no longer astray,
With config in paw, we find the right way.
No more lost files—just carrot-filled cheer,
The rabbit ensures your data is near!
🗂️🥕

Note

⚡️ Unit Test Generation is now available in beta!

Learn more here, or try it out under "Finishing Touches" below.

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📜 Recent review details

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Review profile: CHILL
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📥 Commits

Reviewing files that changed from the base of the PR and between e4afd9b and cf027f1.

📒 Files selected for processing (3)

• webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/connectome/ConnectomeFileService.scala (3 hunks)
• webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/mesh/MeshFileService.scala (3 hunks)
• webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/segmentindex/SegmentIndexFileService.scala (3 hunks)

🚧 Files skipped from review as they are similar to previous changes (3)

• webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/segmentindex/SegmentIndexFileService.scala
• webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/connectome/ConnectomeFileService.scala
• webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/mesh/MeshFileService.scala

⏰ Context from checks skipped due to timeout of 90000ms. You can increase the timeout in your CodeRabbit configuration to a maximum of 15 minutes (900000ms). (3)

• GitHub Check: build-smoketest-push
• GitHub Check: backend-tests
• GitHub Check: frontend-tests

✨ Finishing Touches

🧪 Generate unit tests

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch resolve-relative-attachment-paths

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[MichaelBuessemeyer]

Awesome, thanks for fixing this 🎉