Fix volume tasks from file without specified Bbox

CHANGELOG.unreleased.md

@@ -20,6 +20,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Fixed
 - Fixed a bug where some values in the project list were displayed incorrectly after pausing/unpausing the project. [#5339](https://github.com/scalableminds/webknossos/pull/5339)
 - Fixed that editing a task type would always re-add the default values to the recommended configuration (if enabled). [#5341](https://github.com/scalableminds/webknossos/pull/5341)
+- Fixed a bug where tasks created from existing volume annotations that did not have a specified bounding box were broken. [#5362](https://github.com/scalableminds/webknossos/pull/5361)
 
 ### Removed
 -

app/controllers/TaskController.scala

@@ -80,7 +80,9 @@ class TaskController @Inject()(taskCreationService: TaskCreationService,
       extractedFiles = nmlService.extractFromFiles(inputFiles.map(f => (f.ref.path.toFile, f.filename)),
                                                    useZipName = false,
                                                    isTaskUpload = true)
-      extractedTracingBoxes: List[TracingBoxContainer] = extractedFiles.toBoxes
+      extractedTracingBoxesRaw: List[TracingBoxContainer] = extractedFiles.toBoxes
+      extractedTracingBoxes: List[TracingBoxContainer] <- taskCreationService
+        .addVolumeFallbackBoundingBoxes(extractedTracingBoxesRaw, request.identity._organization)
       fullParams: List[Box[TaskParameters]] = taskCreationService.buildFullParamsFromFiles(params,
                                                                                            extractedTracingBoxes)
       (skeletonBases, volumeBases) <- taskCreationService.fillInMissingTracings(extractedTracingBoxes.map(_.skeleton),
@@ -93,7 +95,6 @@ class TaskController @Inject()(taskCreationService: TaskCreationService,
       result <- taskCreationService.createTasks(fullParamsWithTracings, request.identity)
     } yield Ok(Json.toJson(result))
   }
-
   def update(taskId: String): Action[TaskParameters] = sil.SecuredAction.async(validateJson[TaskParameters]) {
     implicit request =>
       val params = request.body

app/models/task/TaskCreationService.scala

@@ -2,7 +2,7 @@ package models.task
 
 import java.io.File
 
-import com.scalableminds.util.accesscontext.DBAccessContext
+import com.scalableminds.util.accesscontext.{DBAccessContext, GlobalAccessContext}
 import com.scalableminds.util.geometry.{BoundingBox, Point3D, Vector3D}
 import com.scalableminds.util.tools.{Fox, FoxImplicits}
 import com.scalableminds.webknossos.datastore.SkeletonTracing.{SkeletonTracing, SkeletonTracingOpt, SkeletonTracings}
@@ -21,7 +21,7 @@ import models.annotation.{
   TracingStoreRpcClient,
   TracingStoreService
 }
-import models.binary.{DataSet, DataSetDAO}
+import models.binary.{DataSet, DataSetDAO, DataSetService}
 import models.project.{Project, ProjectDAO}
 import models.team.{Team, TeamDAO}
 import models.user.{User, UserExperiencesDAO, UserService, UserTeamRolesDAO}
@@ -47,6 +47,7 @@ class TaskCreationService @Inject()(taskTypeService: TaskTypeService,
                                     userExperiencesDAO: UserExperiencesDAO,
                                     scriptDAO: ScriptDAO,
                                     dataSetDAO: DataSetDAO,
+                                    dataSetService: DataSetService,
                                     tracingStoreService: TracingStoreService,
 )(implicit ec: ExecutionContext)
     extends FoxImplicits
@@ -212,6 +213,27 @@ class TaskCreationService @Inject()(taskTypeService: TaskTypeService,
                                             boxContainer.description)
     }
 
+  // Used in createFromFiles. For all volume tracings that have an empty bounding box, reset it to the dataset bounding box
+  def addVolumeFallbackBoundingBoxes(tracingBoxes: List[TracingBoxContainer],
+                                     organizationId: ObjectId): Fox[List[TracingBoxContainer]] =
+    Fox.serialCombined(tracingBoxes) { tracingBox: TracingBoxContainer =>
+      tracingBox.volume match {
+        case Full(v) =>
+          for { volumeAdapted <- addVolumeFallbackBoundingBox(v._1, organizationId) } yield
+            tracingBox.copy(volume = Full(volumeAdapted, v._2))
+        case _ => Fox.successful(tracingBox)
+      }
+    }
+
+  // Used in createFromFiles. Called once per requested task if volume tracing is passed
+  private def addVolumeFallbackBoundingBox(volume: VolumeTracing, organizationId: ObjectId): Fox[VolumeTracing] =
+    if (volume.boundingBox.isEmpty) {
+      for {
+        dataSet <- dataSetDAO.findOneByNameAndOrganization(volume.dataSetName, organizationId)(GlobalAccessContext)
+        dataSource <- dataSetService.dataSourceFor(dataSet).flatMap(_.toUsable)
+      } yield volume.copy(boundingBox = dataSource.boundingBox)
+    } else Fox.successful(volume)
+
   // Used in createFromFiles. Called once per requested task
   private def buildFullParamsFromFilesForSingleTask(
       nmlFormParams: NmlTaskParameters,