Add route to add segment index to existing volume annotations

app/controllers/AnnotationController.scala

@@ -356,6 +356,20 @@ class AnnotationController @Inject()(
       } yield result
   }
 
+  @ApiOperation(hidden = true, value = "")
+  def addSegmentIndex(id: String, tracingId: String): Action[AnyContent] = sil.SecuredAction.async { implicit request =>
+    for {
+      annotation <- provider.provideAnnotation(id, request.identity)
+      _ <- bool2Fox(AnnotationType.Explorational == annotation.typ) ?~> "annotation.addSegmentIndex.explorationalsOnly"
+      annotationLayer <- annotation.annotationLayers
+        .find(_.tracingId == tracingId)
+        .toFox ?~> "annotation.addSegmentIndex.layerNotFound"
+      _ <- annotationService.addSegmentIndex(annotation, annotationLayer) ?~> "annotation.addSegmentIndex.failed"
+      updated <- provider.provideAnnotation(id, request.identity)
+      json <- annotationService.publicWrites(updated, Some(request.identity)) ?~> "annotation.write.failed"
+    } yield JsonOk(json)
+  }
+
   private def finishAnnotation(typ: String, id: String, issuingUser: User, timestamp: Instant)(
       implicit ctx: DBAccessContext): Fox[(Annotation, String)] =
     for {

app/models/annotation/AnnotationService.scala

@@ -393,14 +393,27 @@ class AnnotationService @Inject()(
       implicit ctx: DBAccessContext): Fox[Unit] =
     for {
       dataSet <- dataSetDAO.findOne(annotation._dataSet) ?~> "dataSet.notFoundForAnnotation"
-      _ <- bool2Fox(annotation.volumeAnnotationLayers.nonEmpty) ?~> "annotation.downsample.volumeOnly"
+      _ <- bool2Fox(volumeAnnotationLayer.typ == AnnotationLayerType.Volume) ?~> "annotation.downsample.volumeOnly"
       rpcClient <- tracingStoreService.clientFor(dataSet)
       newVolumeTracingId <- rpcClient.duplicateVolumeTracing(volumeAnnotationLayer.tracingId, downsample = true)
       _ = logger.info(
         s"Replacing volume tracing ${volumeAnnotationLayer.tracingId} by downsampled copy $newVolumeTracingId for annotation ${annotation._id}.")
       _ <- annotationLayersDAO.replaceTracingId(annotation._id, volumeAnnotationLayer.tracingId, newVolumeTracingId)
     } yield ()
 
+  def addSegmentIndex(annotation: Annotation, volumeAnnotationLayer: AnnotationLayer)(
+      implicit ctx: DBAccessContext): Fox[Unit] =
+    for {
+      dataSet <- dataSetDAO.findOne(annotation._dataSet) ?~> "dataSet.notFoundForAnnotation"
+      _ <- bool2Fox(volumeAnnotationLayer.typ == AnnotationLayerType.Volume) ?~> "annotation.downsample.volumeOnly"
+      rpcClient <- tracingStoreService.clientFor(dataSet)
+      // duplicate in tracingstore will add segment index if possible
+      newVolumeTracingId <- rpcClient.duplicateVolumeTracing(volumeAnnotationLayer.tracingId)
+      _ = logger.info(
+        s"Replacing volume tracing ${volumeAnnotationLayer.tracingId} by copy with added segment index $newVolumeTracingId for annotation ${annotation._id}.")
+      _ <- annotationLayersDAO.replaceTracingId(annotation._id, volumeAnnotationLayer.tracingId, newVolumeTracingId)
+    } yield ()
+
   // WARNING: needs to be repeatable, might be called multiple times for an annotation
   def finish(annotation: Annotation, user: User, restrictions: AnnotationRestrictions)(
       implicit ctx: DBAccessContext): Fox[String] = {

conf/messages

@@ -203,13 +203,17 @@ annotation.transferee.noDataSetAccess=Cannot transfer annotation to a user who h
 annotation.timelogging.read.failed=Time
 annotation.write.failed=Could not convert annotation to json
 annotation.needsEitherSkeletonOrVolume=Annotation needs at least one of skeleton or volume
-annotation.downsample.layerNotFound=Could not downsample volume annotation (annotation layer not found)
 annotation.addLayer.explorationalsOnly=Could not add annotation layer because it is only allowed for explorational annotations.
 annotation.addLayer.nameInUse=An annotation layer with this name already exists in this annotation. Please change it to prevent duplicates.
 annotation.makeHybrid.failed=Could not convert annotation to hybrid.
 annotation.makeHybrid.alreadyHybrid=Could not convert annotation to hybrid annotation because it is already a hybrid annotation.
+annotation.downsample.layerNotFound=Could not downsample volume annotation (annotation layer not found)
 annotation.downsample.explorationalsOnly=Could not downsample annotation because it is only allowed for explorational annotations.
-annotation.downsample.volumeOnly=Downsampling is only possible for volume or hybrid annotations.
+annotation.downsample.volumeOnly=Downsampling is only possible for volume annotation layers.
+annotation.addSegmentIndex.layerNotFound=Could not add segment index to volume annotation (annotation layer not found)
+annotation.addSegmentIndex.explorationalsOnly=Could not add segment index to annotation because it is only allowed for explorational annotations.
+annotation.addSegmentIndex.volumeOnly=Adding segment index is only possible for volume annotation layers.
+annotation.addSegmentIndex.failed=Failed to add segment index.
 annotationType.notFound=Could not find the specified annotation type.
 annotation.cantMergeVolumes=This annotation collection contains volume tracings. Merging volume tracings is not yet supported. Please use download instead.
 annotation.reopen.tooLate=The annotation cannot be reopened anymore, since it has been finished for too long.

conf/webknossos.latest.routes

@@ -144,6 +144,7 @@ DELETE        /annotations/:id
 POST          /annotations/:id/merge/:mergedTyp/:mergedId                                       controllers.AnnotationController.mergeWithoutType(id: String, mergedTyp: String, mergedId: String)
 GET           /annotations/:id/download                                                         controllers.AnnotationIOController.downloadWithoutType(id: String, skeletonVersion: Option[Long], volumeVersion: Option[Long], skipVolumeData: Option[Boolean])
 POST          /annotations/:id/acquireMutex                                                     controllers.AnnotationController.tryAcquiringAnnotationMutex(id: String)
+PATCH         /annotations/:id/addSegmentIndex                                                  controllers.AnnotationController.addSegmentIndex(id: String, tracingId: String)
 
 GET           /annotations/:typ/:id/info                                                        controllers.AnnotationController.info(typ: String, id: String, timestamp: Long)
 PATCH         /annotations/:typ/:id/makeHybrid                                                  controllers.AnnotationController.makeHybrid(typ: String, id: String, fallbackLayerName: Option[String])

webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeTracingService.scala

@@ -358,6 +358,7 @@ class VolumeTracingService @Inject()(
       boundingBox = boundingBoxOptToProto(boundingBox).getOrElse(tracingWithResolutionRestrictions.boundingBox),
       mappingName = mappingName.orElse(tracingWithResolutionRestrictions.mappingName),
       version = 0,
+      // Adding segment index on duplication if the volume tracing allows it. This will be used in duplicateData
       hasSegmentIndex = VolumeSegmentIndexService.canHaveSegmentIndex(tracingWithResolutionRestrictions.fallbackLayer)
     )
     for {