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Fix appending task bbox to user bbox in annotation nml upload #8280

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merged 2 commits into from
Dec 16, 2024

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MichaelBuessemeyer
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@MichaelBuessemeyer MichaelBuessemeyer commented Dec 16, 2024

URL of deployed dev instance (used for testing):

  • https://___.webknossos.xyz

Steps to test:

  • Upload the annotation from the slack thread in the wk dashboard.
  • The opened annotation should have 2 bboxes (one the task bbox)

Issues:


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

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coderabbitai bot commented Dec 16, 2024

📝 Walkthrough
📝 Walkthrough

Walkthrough

The changes in the NmlParser.scala file focus on modifying the getParametersFromNML method's handling of userBoundingBoxes. The primary modification involves changing the variable from immutable (val) to mutable (var), enabling dynamic updates during the parsing process. The approach for populating bounding boxes has been updated from a map operation to a foreach operation, allowing direct appending of bounding boxes based on specific parsing conditions. Additionally, the changelog has been updated to reflect various new features and fixes in the WEBKNOSSOS system.

Changes

File Change Summary
app/models/annotation/nml/NmlParser.scala Modified getParametersFromNML method to use mutable userBoundingBoxes and updated bounding box population logic.
CHANGELOG.unreleased.md Updated changelog with new features, fixes, and changes related to dataset management, performance optimizations, and error handling.

Possibly related PRs

Suggested reviewers

  • dieknolle3333

Poem

🐰 In the realm of parsing XML's might,
A rabbit hops through bounding box delight!
Mutable lists now dance and sway,
Flexible parsing finds its way.
Code evolves with each soft bound 🌟


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Reviewing files that changed from the base of the PR and between d1d103c and 7462836.

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  • CHANGELOG.unreleased.md (1 hunks)
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CHANGELOG.unreleased.md (1)

33-33: LGTM! The changelog entry is well-documented.

The entry accurately describes the fix, follows the changelog format, and provides proper traceability by linking to PR #8280.


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Actionable comments posted: 0

🧹 Nitpick comments (1)
app/models/annotation/nml/NmlParser.scala (1)

160-160: Consider using immutable operations instead of mutable state.

While changing to var works, consider using immutable operations for better maintainability and thread safety:

-        var userBoundingBoxes = parseBoundingBoxes(parameters \ "userBoundingBox")
+        val initialBoundingBoxes = parseBoundingBoxes(parameters \ "userBoundingBox")
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Reviewing files that changed from the base of the PR and between 6febb57 and d1d103c.

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  • app/models/annotation/nml/NmlParser.scala (1 hunks)
🔇 Additional comments (1)
app/models/annotation/nml/NmlParser.scala (1)

161-163: LGTM: Correct fix for task bbox handling.

The conditional logic correctly ensures that task bounding box is only appended to user bounding boxes when it's not a task upload, fixing the issue mentioned in the PR objectives.

Let's verify the task bbox handling in other parts of the codebase:

✅ Verification successful

Task bounding box handling is consistent across the codebase

The codebase shows consistent handling of task bounding boxes:

  • In NmlParser.scala, task bounding box is only added to user bounding boxes when !isTaskUpload
  • In SkeletonTracingService.scala, task bounding box is handled similarly with a fromTask flag that controls the behavior
  • The task bounding box is properly maintained as a separate field in the data structures (NmlResults.scala, NmlWriter.scala)
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Search for other places where task bounding box is handled
rg -A 3 "taskBoundingBox" --type scala

Length of output: 4526

Comment on lines 158 to +163
else None
userBoundingBoxes = parseBoundingBoxes(parameters \ "userBoundingBox")
} yield {
var userBoundingBoxes = parseBoundingBoxes(parameters \ "userBoundingBox")
if (!sharedParsingParameters.isTaskUpload) {
parseTaskBoundingBoxAsUserBoundingBox(parameters \ "taskBoundingBox", userBoundingBoxes)
.map(asUserBoundingBox => userBoundingBoxes :+ asUserBoundingBox)
.foreach(asUserBoundingBox => userBoundingBoxes = userBoundingBoxes :+ asUserBoundingBox)
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The changes to userBoundingBoxes weren't saved. These changes now work close to what the logic was before the #8075 pr. cf:

var taskBoundingBox: Option[BoundingBox] = None
parseTaskBoundingBox(parameters \ "taskBoundingBox", isTaskUpload, userBoundingBoxes).foreach {
case Left(value) => taskBoundingBox = Some(value)
case Right(value) => userBoundingBoxes = userBoundingBoxes :+ value
}

@MichaelBuessemeyer MichaelBuessemeyer merged commit e1dd067 into master Dec 16, 2024
3 checks passed
@MichaelBuessemeyer MichaelBuessemeyer deleted the fix-taskbb-to-userbb-in-nml-upload branch December 16, 2024 13:11
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