Fix regression with DiffableMaps and duplicate agglomerate skeletons #8656

philippotto · 2025-05-26T13:12:49Z

This PR fixes an issue with with WK loading duplicate tree when enabling agglomerate skeletons. This bug is a regression from #8596 .

URL of deployed dev instance (used for testing):

https://___.webknossos.xyz

Steps to test:

Load a agglomerate skeleton
Verify that only one tree was loaded
Do any operation (spllit, rename) on the agglomerate skeleton without issue
also see added tests

Issues:

fixes https://scm.slack.com/archives/C02H5T8Q08P/p1748263747190599

(Please delete unneeded items, merge only when none are left open)

Updated changelog
Updated migration guide if applicable
Updated documentation if applicable
Adapted wk-libs python client if relevant API parts change
Removed dev-only changes like prints and application.conf edits
Considered common edge cases
Needs datastore update after deployment

…ld map

coderabbitai · 2025-05-26T13:12:56Z

📝 Walkthrough

Walkthrough

This update fixes a crash during tree import when annotations are non-empty, modifies a test fixture to export a variable, adds tests for tree ID relabeling, and refactors a helper function to use immutable patterns for tree collections.

Changes

Files/Paths	Change Summary
CHANGELOG.unreleased.md	Added an entry describing the fix for crashes during tree import with non-empty annotations.
frontend/javascripts/test/fixtures/hybridtracing_object.ts	Changed `initalTreeOne` from a local constant to a named export.
frontend/javascripts/test/reducers/skeletontracing_reducer.spec.ts	Added tests for tree addition and ID relabeling; no changes to function signatures or core logic.
frontend/javascripts/viewer/model/reducers/skeletontracing_reducer_helpers.ts	Refactored `addTreesAndGroups` to use a new `MutableTreeMap` for immutability, avoiding in-place mutations; no signature changes.

Possibly related PRs

Fix merging trees #8359: Both PRs involve fixes to tree manipulation functions, with this PR addressing crash fixes during tree import and the related PR focusing on tree merging and type consistency.
Expand parent group when new tree node is selected #8585: Both PRs modify skeleton tree behavior, particularly actions and reducer logic for handling tree groups and expansion.
Fix performance bottleneck when deleting a lot of trees at once #8176: Both PRs involve changes to tree deletion logic, with one focusing on batch deletion performance and the other on robust import handling.

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backend

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hotzenklotz

Poem

A bug in the forest, a crash in the trees,
When annotations were full, it brought code to its knees.
Now rabbits rejoice, for imports are sound,
With new tests and exports, stability’s found.
The woods are restored, the mappings are neat—
Hop, hop, hooray, for a bug-free retreat! 🐇🌲

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frontend/javascripts/test/fixtures/hybridtracing_object.ts

hotzenklotz · 2025-05-26T13:43:00Z

frontend/javascripts/test/reducers/skeletontracing_reducer.spec.ts

+    // The original tree id 4 should have survived.
+    expect(ids).toEqual([4]);
+    expect(state.annotation.skeleton?.trees.size()).toBe(1);
+    expect(state.annotation.skeleton?.trees.getNullable(4)).toBeDefined();


Does it make sense to also test that the newly added tree has tree id 5(?) now?

yes, doesn't hurt. luckily, the id will be 4 and not 5 😅

hotzenklotz

LGTM

coderabbitai

Actionable comments posted: 0

♻️ Duplicate comments (1)

frontend/javascripts/test/reducers/skeletontracing_reducer.spec.ts (1)

1813-1817: Test implementation is correct.

The test properly verifies that tree IDs are preserved when adding to an empty skeleton. The assertion confirms the tree retains its original ID of 4.

Note: The past review comment about testing tree id 5 doesn't apply here as this test intentionally uses ID 4 to verify no relabeling occurs.

🧹 Nitpick comments (1)

frontend/javascripts/test/reducers/skeletontracing_reducer.spec.ts (1)
1801-1803: Consider clarifying the comment about ID relabeling.

The current comment could be misinterpreted. Consider rephrasing for clarity.
-      // Id-relabeling is only done if the skeleton is not empty.
-      // Therefore, delete the two existing trees so that the new tree will
-      // be added without id-relabeling.
+      // When the skeleton is empty, ID relabeling is not performed.
+      // Therefore, delete the two existing trees so that the new tree will
+      // retain its original ID.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between eb09162 and 4255fd1.

📒 Files selected for processing (2)

frontend/javascripts/test/fixtures/hybridtracing_object.ts (2 hunks)
frontend/javascripts/test/reducers/skeletontracing_reducer.spec.ts (2 hunks)

⏰ Context from checks skipped due to timeout of 90000ms (3)

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

🔇 Additional comments (3)

frontend/javascripts/test/fixtures/hybridtracing_object.ts (1)

33-33: LGTM!

The export addition follows the existing pattern in the file and is necessary for the new test cases.

frontend/javascripts/test/reducers/skeletontracing_reducer.spec.ts (2)

12-13: Import changes look good.

The imports are properly organized and necessary for the new test cases.

Also applies to: 18-24

1820-1839: Test correctly validates ID relabeling behavior.

The test properly verifies that large tree IDs are relabeled to the next available ID when adding to a non-empty skeleton. Good coverage of both positive (new ID exists) and negative (old ID doesn't exist) assertions.

…8656) * create new tree map when re-assigning tree ids instead of adding to old map * add tests for addTreesAndGroupsAction * update changelog * fix typo * also assert ids

create new tree map when re-assigning tree ids instead of adding to o…

42d2d4f

…ld map

philippotto self-assigned this May 26, 2025

hotzenklotz added frontend bug labels May 26, 2025

hotzenklotz changed the title ~~Fix adding tree with id greater than 1M~~ Fix regression with DiffableMaps and duplicate agglomerate skeletons May 26, 2025

philippotto added 2 commits May 26, 2025 15:37

add tests for addTreesAndGroupsAction

e87e587

update changelog

eb09162

philippotto marked this pull request as ready for review May 26, 2025 13:39

philippotto requested a review from hotzenklotz May 26, 2025 13:39

hotzenklotz reviewed May 26, 2025

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frontend/javascripts/test/fixtures/hybridtracing_object.ts Outdated Show resolved Hide resolved

hotzenklotz reviewed May 26, 2025

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hotzenklotz approved these changes May 26, 2025

View reviewed changes

philippotto added 2 commits May 26, 2025 15:44

fix typo

aedf7fe

also assert ids

4255fd1

philippotto enabled auto-merge (squash) May 26, 2025 13:46

coderabbitai bot reviewed May 26, 2025

View reviewed changes

philippotto merged commit 6ed9baf into master May 26, 2025
5 checks passed

philippotto deleted the fix-id-relabelling-when-adding-trees branch May 26, 2025 13:52

This was referenced Jun 2, 2025

Release 25.06.0 #8654

Merged

Release 25.06.1 #8669

Merged

coderabbitai bot mentioned this pull request Jun 17, 2025

25.06.2 #8696

Merged

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Fix regression with DiffableMaps and duplicate agglomerate skeletons #8656

Fix regression with DiffableMaps and duplicate agglomerate skeletons #8656

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philippotto commented May 26, 2025 •

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Fix regression with DiffableMaps and duplicate agglomerate skeletons #8656

Fix regression with DiffableMaps and duplicate agglomerate skeletons #8656

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philippotto commented May 26, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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URL of deployed dev instance (used for testing):

Steps to test:

Issues:

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philippotto commented May 26, 2025 •

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