Merge branch 'master' into virtual-remote-datasets

Author: frcroth

.github/PULL_REQUEST_TEMPLATE.md

@@ -12,8 +12,8 @@
 
 ------
 (Please delete unneeded items, merge only when none are left open)
-- [ ] Updated [changelog](../blob/master/CHANGELOG.unreleased.md#unreleased)
-- [ ] Updated [migration guide](../blob/master/MIGRATIONS.unreleased.md#unreleased) if applicable
+- [ ] Added changelog entry (create a `$PR_NUMBER.md` file in `unreleased_changes` or use `./tools/create-changelog-entry.py`)
+- [ ] Added migration guide entry if applicable (edit the same file as for the changelog)
 - [ ] Updated [documentation](../blob/master/docs) if applicable
 - [ ] Adapted [wk-libs python client](https://github.com/scalableminds/webknossos-libs/tree/master/webknossos/webknossos/client) if relevant API parts change
 - [ ] Removed dev-only changes like prints and application.conf edits

CHANGELOG.released.md

@@ -7,6 +7,12 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 For upgrade instructions, please check the [migration guide](MIGRATIONS.released.md).
 
+## [25.06.2](https://github.com/scalableminds/webknossos/releases/tag/25.06.2) - 2025-06-17
+[Commits](https://github.com/scalableminds/webknossos/compare/25.06.1...25.06.2)
+
+### Fixed
+- Fixed a regression that led to incorrect behavior when trying to jump to the last branchpoint even though no branchpoint existed. [#8695](https://github.com/scalableminds/webknossos/pull/8695)
+
 ## [25.06.1](https://github.com/scalableminds/webknossos/releases/tag/25.06.1) - 2025-06-03
 [Commits](https://github.com/scalableminds/webknossos/compare/25.06.0...25.06.1)
 

CHANGELOG.unreleased.md

@@ -1,28 +1 @@
-# Changelog (Unreleased)
-
-All notable (yet unreleased) user-facing changes to WEBKNOSSOS are documented in this file.
-See `CHANGELOG.released.md` for the changes which are part of official releases.
-
-The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
-and this project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
-For upgrade instructions, please check the [migration guide](MIGRATIONS.released.md).
-
-## Unreleased
-[Commits](https://github.com/scalableminds/webknossos/compare/25.06.1...HEAD)
-
-### Added
-- Added the ability to duplicate trees in skeleton annotations. Users can create a copy of any tree (including all nodes, edges, and properties) via the context menu in the skeleton tab. [#8662](https://github.com/scalableminds/webknossos/pull/8662)
-- Meshes are now reloaded using their previous opacity value. [#8622](https://github.com/scalableminds/webknossos/pull/8622)
-
-### Changed
-
-### Fixed
-- Improved efficiency of saving bounding box related changes. [#8492](https://github.com/scalableminds/webknossos/pull/8492)
-- When deleting a dataset, its caches are cleared, so that if a new dataset by the same name is uploaded afterwards, only new data is loaded. [#8638](https://github.com/scalableminds/webknossos/pull/8638)
-- Fixed the contrast of the WelcomeToast buttons. Updated `antd` to version `5.22`.[#8688](https://github.com/scalableminds/webknossos/pull/8688)
-- Fixed a race condition when starting proofreading with a split action. [#8676](https://github.com/scalableminds/webknossos/pull/8676)
-- Fixed that activating a mapping got stuck when a dataset was opened in "view" mode. [#8687](https://github.com/scalableminds/webknossos/pull/8687)
-
-### Removed
-
-### Breaking Changes
+WARNING: This file will be deleted in the next release. If you have a merge conflict in this file, please ensure that the file only contains this warning text after the merge. Please execute `./tools/create-changelog-entry.py` and move the changelog for your PR into the file that was created by the script. From now on, this will be the new way of adding changelog and migration guide entries for a PR. The created files will be aggregated when a release is created.

MIGRATIONS.released.md

@@ -6,6 +6,12 @@ See `MIGRATIONS.unreleased.md` for the changes which are not yet part of an offi
 This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 
+## [25.06.2](https://github.com/scalableminds/webknossos/releases/tag/25.06.2) - 2025-06-17
+[Commits](https://github.com/scalableminds/webknossos/compare/25.06.1...25.06.2)
+
+### Postgres Evolutions:
+None.
+
 ## [25.06.1](https://github.com/scalableminds/webknossos/releases/tag/25.06.1) - 2025-06-03
 [Commits](https://github.com/scalableminds/webknossos/compare/25.06.0...25.06.1)
 

MIGRATIONS.unreleased.md

@@ -1,14 +1 @@
-# Migration Guide (Unreleased)
-All migrations (for unreleased versions) of WEBKNOSSOS are documented in this file.
-See `MIGRATIONS.released.md` for the migrations which are part of official releases.
-
-This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
-User-facing changes are documented in the [changelog](CHANGELOG.released.md).
-
-## Unreleased
-[Commits](https://github.com/scalableminds/webknossos/compare/25.06.1...HEAD)
-
-- The default thread pool size was increased from 5 to 10 times the number of available CPUs (capped at 1000). Note that wk may need slightly more memory because of this. [#8686](https://github.com/scalableminds/webknossos/pull/8686)
-
-### Postgres Evolutions:
-- [134-dataset-layer-attachments.sql](conf/evolutions/134-dataset-layer-attachments.sql)
+WARNING: This file will be deleted in the next release. If you have a merge conflict in this file, please ensure that the file only contains this warning text after the merge. Please execute `./tools/create-changelog-entry.py` and move the changelog for your PR into the file that was created by the script. From now on, this will be the new way of adding changelog and migration guide entries for a PR. The created files will be aggregated when a release is created.

app/controllers/AnnotationController.scala

@@ -420,6 +420,8 @@ class AnnotationController @Inject()(
       newAnnotationProto <- tracingStoreClient.duplicateAnnotation(
         annotation._id,
         newAnnotationId,
+        annotation._user,
+        user._id,
         version = None,
         isFromTask = annotation._task.isDefined,
         datasetBoundingBox = dataSource.map(_.boundingBox)

app/controllers/AnnotationIOController.scala

@@ -413,7 +413,7 @@ class AnnotationIOController @Inject()(
 
   private def downloadExplorational(annotationId: ObjectId,
                                     typ: String,
-                                    issuingUser: Option[User],
+                                    requestingUser: Option[User],
                                     version: Option[Long],
                                     skipVolumeData: Boolean,
                                     volumeDataZipFormat: VolumeDataZipFormat)(implicit ctx: DBAccessContext) = {
@@ -425,10 +425,12 @@ class AnnotationIOController @Inject()(
         tracingStoreClient <- tracingStoreService.clientFor(dataset)
         fetchedAnnotationLayers <- Fox.serialCombined(annotation.skeletonAnnotationLayers)(
           tracingStoreClient.getSkeletonTracing(annotation._id, _, version))
-        user <- userService.findOneCached(annotation._user)(GlobalAccessContext)
+        annotationProto <- tracingStoreClient.getAnnotationProto(annotation._id, version)
+        annotationOwner <- userService.findOneCached(annotation._user)(GlobalAccessContext)
         taskOpt <- Fox.runOptional(annotation._task)(taskDAO.findOne)
         nmlStream = nmlWriter.toNmlStream(
           "temp",
+          annotationProto,
           fetchedAnnotationLayers,
           Some(annotation),
           dataset.voxelSize,
@@ -437,10 +439,11 @@ class AnnotationIOController @Inject()(
           conf.Http.uri,
           dataset.name,
           dataset._id,
-          Some(user),
+          annotationOwner,
           taskOpt,
           skipVolumeData,
-          volumeDataZipFormat
+          volumeDataZipFormat,
+          requestingUser
         )
         nmlTemporaryFile = tempFileService.create()
         temporaryFileStream = new BufferedOutputStream(new FileOutputStream(new File(nmlTemporaryFile.toString)))
@@ -467,10 +470,12 @@ class AnnotationIOController @Inject()(
           skeletonAnnotationLayer =>
             tracingStoreClient.getSkeletonTracing(annotation._id, skeletonAnnotationLayer, version)
         } ?~> "annotation.download.fetchSkeletonLayer.failed"
-        user <- userService.findOneCached(annotation._user)(GlobalAccessContext) ?~> "annotation.download.findUser.failed"
+        annotationOwner <- userService.findOneCached(annotation._user)(GlobalAccessContext) ?~> "annotation.download.findUser.failed"
         taskOpt <- Fox.runOptional(annotation._task)(taskDAO.findOne(_)(GlobalAccessContext)) ?~> "task.notFound"
+        annotationProto <- tracingStoreClient.getAnnotationProto(annotation._id, version)
         nmlStream = nmlWriter.toNmlStream(
           name,
+          annotationProto,
           fetchedSkeletonLayers ::: fetchedVolumeLayers,
           Some(annotation),
           dataset.voxelSize,
@@ -479,10 +484,11 @@ class AnnotationIOController @Inject()(
           conf.Http.uri,
           dataset.name,
           dataset._id,
-          Some(user),
+          annotationOwner,
           taskOpt,
           skipVolumeData,
-          volumeDataZipFormat
+          volumeDataZipFormat,
+          requestingUser
         )
         temporaryFile = tempFileService.create()
         zipper = ZipIO.startZip(new BufferedOutputStream(new FileOutputStream(new File(temporaryFile.toString))))
@@ -520,13 +526,13 @@ class AnnotationIOController @Inject()(
         zipMimeType
 
     for {
-      annotation <- provider.provideAnnotation(typ, annotationId, issuingUser) ~> NOT_FOUND
+      annotation <- provider.provideAnnotation(typ, annotationId, requestingUser) ~> NOT_FOUND
       restrictions <- provider.restrictionsFor(typ, annotationId) ?~> "annotation.restrictions.unavailable"
       name <- provider.nameFor(annotation) ?~> "annotation.name.impossible"
       fileExtension = exportExtensionForAnnotation(annotation)
       fileName = name + fileExtension
       mimeType = exportMimeTypeForAnnotation(annotation)
-      _ <- restrictions.allowDownload(issuingUser) ?~> "annotation.download.notAllowed" ~> FORBIDDEN
+      _ <- restrictions.allowDownload(requestingUser) ?~> "annotation.download.notAllowed" ~> FORBIDDEN
       dataset <- datasetDAO.findOne(annotation._dataset)(GlobalAccessContext) ?~> "dataset.notFoundForAnnotation" ~> NOT_FOUND
       organization <- organizationDAO.findOne(dataset._organization)(GlobalAccessContext) ?~> "organization.notFound" ~> NOT_FOUND
       temporaryFile <- annotationToTemporaryFile(dataset, annotation, name, organization._id) ?~> "annotation.writeTemporaryFile.failed"
@@ -538,13 +544,13 @@ class AnnotationIOController @Inject()(
     }
   }
 
-  private def downloadProject(projectId: ObjectId, userOpt: Option[User], skipVolumeData: Boolean)(
+  private def downloadProject(projectId: ObjectId, requestingUserOpt: Option[User], skipVolumeData: Boolean)(
       implicit ctx: DBAccessContext,
       m: MessagesProvider) =
     for {
-      user <- userOpt.toFox ?~> Messages("notAllowed") ~> FORBIDDEN
+      requestingUser <- requestingUserOpt.toFox ?~> Messages("notAllowed") ~> FORBIDDEN
       project <- projectDAO.findOne(projectId) ?~> Messages("project.notFound", projectId) ~> NOT_FOUND
-      _ <- Fox.assertTrue(userService.isTeamManagerOrAdminOf(user, project._team)) ?~> "notAllowed" ~> FORBIDDEN
+      _ <- Fox.assertTrue(userService.isTeamManagerOrAdminOf(requestingUser, project._team)) ?~> "notAllowed" ~> FORBIDDEN
       annotations <- annotationDAO.findAllFinishedForProject(projectId)
       zipTempFilePath <- annotationService.zipAnnotations(annotations,
                                                           project.name,
@@ -556,7 +562,7 @@ class AnnotationIOController @Inject()(
                   fileName = _ => Some(TextUtils.normalize(project.name + "_nmls.zip")))
     }
 
-  private def downloadTask(taskId: ObjectId, userOpt: Option[User], skipVolumeData: Boolean)(
+  private def downloadTask(taskId: ObjectId, requestingUserOpt: Option[User], skipVolumeData: Boolean)(
       implicit ctx: DBAccessContext,
       m: MessagesProvider) = {
     def createTaskZip(task: Task): Fox[Path] = annotationService.annotationsFor(task._id).flatMap { annotations =>
@@ -566,10 +572,10 @@ class AnnotationIOController @Inject()(
     }
 
     for {
-      user <- userOpt.toFox ?~> Messages("notAllowed") ~> FORBIDDEN
+      requestingUser <- requestingUserOpt.toFox ?~> Messages("notAllowed") ~> FORBIDDEN
       task <- taskDAO.findOne(taskId) ?~> Messages("task.notFound") ~> NOT_FOUND
       project <- projectDAO.findOne(task._project) ?~> Messages("project.notFound") ~> NOT_FOUND
-      _ <- Fox.assertTrue(userService.isTeamManagerOrAdminOf(user, project._team)) ?~> Messages("notAllowed") ~> FORBIDDEN
+      _ <- Fox.assertTrue(userService.isTeamManagerOrAdminOf(requestingUser, project._team)) ?~> Messages("notAllowed") ~> FORBIDDEN
       zipTempFilePath <- createTaskZip(task)
     } yield {
       Ok.sendPath(zipTempFilePath,
@@ -578,7 +584,7 @@ class AnnotationIOController @Inject()(
     }
   }
 
-  private def downloadTaskType(taskTypeId: ObjectId, userOpt: Option[User], skipVolumeData: Boolean)(
+  private def downloadTaskType(taskTypeId: ObjectId, requestingUserOpt: Option[User], skipVolumeData: Boolean)(
       implicit ctx: DBAccessContext,
       m: MessagesProvider) = {
     def createTaskTypeZip(taskType: TaskType) =
@@ -593,9 +599,9 @@ class AnnotationIOController @Inject()(
       } yield zip
 
     for {
-      user <- userOpt.toFox ?~> Messages("notAllowed") ~> FORBIDDEN
+      requestingUser <- requestingUserOpt.toFox ?~> Messages("notAllowed") ~> FORBIDDEN
       taskType <- taskTypeDAO.findOne(taskTypeId) ?~> "taskType.notFound" ~> NOT_FOUND
-      _ <- Fox.assertTrue(userService.isTeamManagerOrAdminOf(user, taskType._team)) ?~> "notAllowed" ~> FORBIDDEN
+      _ <- Fox.assertTrue(userService.isTeamManagerOrAdminOf(requestingUser, taskType._team)) ?~> "notAllowed" ~> FORBIDDEN
       zipTempFilePath <- createTaskTypeZip(taskType)
     } yield {
       Ok.sendPath(zipTempFilePath,

app/controllers/AuthenticationController.scala

@@ -215,7 +215,7 @@ class AuthenticationController @Inject()(
     } yield result
 
   def accessibleBySwitching(datasetId: Option[ObjectId],
-                            annotationId: Option[String],
+                            annotationId: Option[ObjectId],
                             workflowHash: Option[String]): Action[AnyContent] = sil.SecuredAction.async {
     implicit request =>
       for {

app/controllers/TaskController.scala

@@ -67,7 +67,8 @@ class TaskController @Inject()(taskCreationService: TaskCreationService,
         taskParametersFull <- taskCreationService.createTracingsFromBaseAnnotations(taskParametersWithIds,
                                                                                     taskType,
                                                                                     dataset,
-                                                                                    dataSource)
+                                                                                    dataSource,
+                                                                                    request.identity._id)
         skeletonBaseOpts: List[Option[SkeletonTracing]] = taskCreationService.createTaskSkeletonTracingBases(
           taskParametersFull)
         volumeBaseOpts: List[Option[(VolumeTracing, Option[File])]] <- taskCreationService.createTaskVolumeTracingBases(

app/controllers/WKRemoteTracingStoreController.scala

@@ -82,8 +82,7 @@ class WKRemoteTracingStoreController @Inject()(tracingStoreService: TracingStore
       tracingStoreService.validateAccess(name, key) { _ =>
         val report = request.body
         for {
-          annotationId <- ObjectId.fromString(report.annotationId)
-          annotation <- annotationDAO.findOne(annotationId)
+          annotation <- annotationDAO.findOne(report.annotationId)
           _ <- ensureAnnotationNotFinished(annotation)
           _ <- annotationDAO.updateModified(annotation._id, Instant.now)
           _ = report.statistics.map(statistics => annotationService.updateStatistics(annotation._id, statistics))