Send baseMappingName when forwarding FullMeshRequest from TS to DS (#…

…7887)

* correctly use base mapping in FullMeshRequest when forwarding from TS to DS

* changelog

---------

Co-authored-by: MichaelBuessemeyer <39529669+MichaelBuessemeyer@users.noreply.github.com>

CHANGELOG.unreleased.md

@@ -33,6 +33,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed a bug where sometimes old mismatching javascript code would be served after upgrades. [#7854](https://github.com/scalableminds/webknossos/pull/7854)
 - Fixed a bug where dataset uploads of zipped tiff data via the UI would be rejected. [#7856](https://github.com/scalableminds/webknossos/pull/7856)
 - Fixed a bug with incorrect valiation of layer names in the animation modal. [#7882](https://github.com/scalableminds/webknossos/pull/7882)
+- Fixed a bug in the fullMesh.stl route used by the render_animation worker job, where some meshes in proofreading annotations could not be loaded. [#7887](https://github.com/scalableminds/webknossos/pull/7887)
 
 ### Removed
 - If the datasource-properties.json file for a dataset is missing or contains errors, WEBKNOSSOS no longer attempts to guess its contents from the raw data. Exploring remote datasets will still create the file. [#7697](https://github.com/scalableminds/webknossos/pull/7697)

webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DSMeshController.scala

@@ -44,6 +44,7 @@ class DSMeshController @Inject()(
                                            the oversegmentation. Collect mesh chunks of all *unmapped* segment ids
                                            belonging to the supplied agglomerate id.
                                            If it is not set, use meshfile as is, assume passed id is present in meshfile
+                                  Note: in case of an editable mapping, targetMappingName is its baseMapping name.
                                 */
                                targetMappingName: Option[String],
                                editableMappingTracingId: Option[String]): Action[ListMeshChunksRequest] =

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/MeshMappingHelper.scala

@@ -23,55 +23,59 @@ trait MeshMappingHelper {
       mappingNameForMeshFile: Option[String],
       omitMissing: Boolean, // If true, failing lookups in the agglomerate file will just return empty list.
       token: Option[String])(implicit ec: ExecutionContext): Fox[List[Long]] =
-    targetMappingName match {
-      case None =>
+    (targetMappingName, editableMappingTracingId) match {
+      case (None, None) =>
         // No mapping selected, assume id matches meshfile
         Fox.successful(List(agglomerateId))
-      case Some(mappingName) if mappingNameForMeshFile.contains(mappingName) =>
+      case (Some(mappingName), None) if mappingNameForMeshFile.contains(mappingName) =>
         // Mapping selected, but meshfile has the same mapping name in its metadata, assume id matches meshfile
         Fox.successful(List(agglomerateId))
-      case Some(mappingName) =>
+      case (Some(mappingName), None) =>
         // Mapping selected, but meshfile does not have matching mapping name in its metadata,
         // assume agglomerate id, fetch oversegmentation segment ids for it
-        val agglomerateFileKey = AgglomerateFileKey(
-          organizationName,
-          datasetName,
-          dataLayerName,
-          mappingName
-        )
-        editableMappingTracingId match {
-          case Some(tracingId) =>
-            for {
-              tracingstoreUri <- dsRemoteWebknossosClient.getTracingstoreUri
-              segmentIdsResult <- dsRemoteTracingstoreClient.getEditableMappingSegmentIdsForAgglomerate(tracingstoreUri,
-                                                                                                        tracingId,
-                                                                                                        agglomerateId,
-                                                                                                        token)
-              segmentIds <- if (segmentIdsResult.agglomerateIdIsPresent)
-                Fox.successful(segmentIdsResult.segmentIds)
-              else
-                for {
-                  agglomerateService <- binaryDataServiceHolder.binaryDataService.agglomerateServiceOpt.toFox
-                  localSegmentIds <- agglomerateService.segmentIdsForAgglomerateId(
-                    agglomerateFileKey,
-                    agglomerateId
-                  )
-                } yield localSegmentIds
-            } yield segmentIds
-          case _ =>
+        for {
+          agglomerateService <- binaryDataServiceHolder.binaryDataService.agglomerateServiceOpt.toFox
+          segmentIdsBox <- agglomerateService
+            .segmentIdsForAgglomerateId(
+              AgglomerateFileKey(
+                organizationName,
+                datasetName,
+                dataLayerName,
+                mappingName
+              ),
+              agglomerateId
+            )
+            .futureBox
+          segmentIds <- segmentIdsBox match {
+            case Full(segmentIds) => Fox.successful(segmentIds)
+            case _                => if (omitMissing) Fox.successful(List.empty) else segmentIdsBox.toFox
+          }
+        } yield segmentIds
+      case (Some(mappingName), Some(tracingId)) =>
+        // An editable mapping tracing id is supplied. Ask the tracingstore for the segment ids. If it doesn’t know,
+        // use the mappingName (here the editable mapping’s base mapping) to look it up from file.
+        for {
+          tracingstoreUri <- dsRemoteWebknossosClient.getTracingstoreUri
+          segmentIdsResult <- dsRemoteTracingstoreClient.getEditableMappingSegmentIdsForAgglomerate(tracingstoreUri,
+                                                                                                    tracingId,
+                                                                                                    agglomerateId,
+                                                                                                    token)
+          segmentIds <- if (segmentIdsResult.agglomerateIdIsPresent)
+            Fox.successful(segmentIdsResult.segmentIds)
+          else // the agglomerate id is not present in the editable mapping. Fetch its info from the base mapping.
             for {
               agglomerateService <- binaryDataServiceHolder.binaryDataService.agglomerateServiceOpt.toFox
-              segmentIdsBox <- agglomerateService
-                .segmentIdsForAgglomerateId(
-                  agglomerateFileKey,
-                  agglomerateId
-                )
-                .futureBox
-              segmentIds <- segmentIdsBox match {
-                case Full(segmentIds) => Fox.successful(segmentIds)
-                case _                => if (omitMissing) Fox.successful(List.empty) else segmentIdsBox.toFox
-              }
-            } yield segmentIds
-        }
+              localSegmentIds <- agglomerateService.segmentIdsForAgglomerateId(
+                AgglomerateFileKey(
+                  organizationName,
+                  datasetName,
+                  dataLayerName,
+                  mappingName
+                ),
+                agglomerateId
+              )
+            } yield localSegmentIds
+        } yield segmentIds
+      case _ => Fox.failure("Cannot determine segment ids for editable mapping without base mapping")
     }
 }

webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/TSRemoteDatastoreClient.scala

@@ -133,7 +133,7 @@ class TSRemoteDatastoreClient @Inject()(
   def querySegmentIndex(remoteFallbackLayer: RemoteFallbackLayer,
                         segmentId: Long,
                         mag: Vec3Int,
-                        mappingName: Option[String],
+                        mappingName: Option[String], // should be the baseMappingName in case of editable mappings
                         editableMappingTracingId: Option[String],
                         userToken: Option[String]): Fox[Seq[Vec3Int]] =
     for {
@@ -152,12 +152,13 @@ class TSRemoteDatastoreClient @Inject()(
       indices = positions.map(_.scale(1f / DataLayer.bucketLength)) // Route returns positions to use the same interface as tracing store, we want indices
     } yield indices
 
-  def querySegmentIndexForMultipleSegments(remoteFallbackLayer: RemoteFallbackLayer,
-                                           segmentIds: Seq[Long],
-                                           mag: Vec3Int,
-                                           mappingName: Option[String],
-                                           editableMappingTracingId: Option[String],
-                                           userToken: Option[String]): Fox[Seq[(Long, Seq[Vec3Int])]] =
+  def querySegmentIndexForMultipleSegments(
+      remoteFallbackLayer: RemoteFallbackLayer,
+      segmentIds: Seq[Long],
+      mag: Vec3Int,
+      mappingName: Option[String], // should be the baseMappingName in case of editable mappings
+      editableMappingTracingId: Option[String],
+      userToken: Option[String]): Fox[Seq[(Long, Seq[Vec3Int])]] =
     for {
       remoteLayerUri <- getRemoteLayerUri(remoteFallbackLayer)
       result <- rpc(s"$remoteLayerUri/segmentIndex")

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

@@ -44,8 +44,9 @@ class TSFullMeshService @Inject()(volumeTracingService: VolumeTracingService,
       fullMeshRequest: FullMeshRequest)(implicit ec: ExecutionContext): Fox[Array[Byte]] =
     for {
       remoteFallbackLayer <- remoteFallbackLayerFromVolumeTracing(tracing, tracingId)
+      baseMappingName <- volumeTracingService.baseMappingName(tracing)
       fullMeshRequestAdapted = if (tracing.mappingIsEditable.getOrElse(false))
-        fullMeshRequest.copy(mappingName = tracing.mappingName,
+        fullMeshRequest.copy(mappingName = baseMappingName,
                              editableMappingTracingId = Some(tracingId),
                              mappingType = Some("HDF5"))
       else fullMeshRequest