Fix saving volume after brushing on mapped fallback buckets (#7833)

* Fix saving volume after brushing on mapped fallback buckets

* changelog

Author: fm3

CHANGELOG.unreleased.md

@@ -17,6 +17,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Changed
 
 ### Fixed
+- Fixed a bug where brushing on a fallback segmentation with active mapping and with segment index file would lead to failed saves. [#7833](https://github.com/scalableminds/webknossos/pull/7833)
 
 ### Removed
 

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

@@ -64,6 +64,7 @@ class DSMeshController @Inject()(
             editableMappingTracingId,
             request.body.segmentId,
             mappingNameForMeshFile,
+            omitMissing = false,
             urlOrHeaderToken(token, request)
           )
           chunkInfos <- meshFileService.listMeshChunksForSegments(organizationName,

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

@@ -654,6 +654,7 @@ class DataSourceController @Inject()(
             request.body.editableMappingTracingId,
             segmentId.toLong,
             mappingNameForMeshFile = None,
+            omitMissing = false,
             urlOrHeaderToken(token, request)
           )
           fileMag <- segmentIndexFileService.readFileMag(organizationName, datasetName, dataLayerName)
@@ -694,6 +695,7 @@ class DataSourceController @Inject()(
                 request.body.editableMappingTracingId,
                 segmentOrAgglomerateId,
                 mappingNameForMeshFile = None,
+                omitMissing = true, // assume agglomerate ids not present in the mapping belong to user-brushed segments
                 urlOrHeaderToken(token, request)
               )
               fileMag <- segmentIndexFileService.readFileMag(organizationName, datasetName, dataLayerName)

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

@@ -134,6 +134,7 @@ class DSFullMeshService @Inject()(dataSourceRepository: DataSourceRepository,
         fullMeshRequest.editableMappingTracingId,
         fullMeshRequest.segmentId,
         mappingNameForMeshFile,
+        omitMissing = false,
         token
       )
       chunkInfos: WebknossosSegmentInfo <- meshFileService.listMeshChunksForSegments(organizationName,

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

@@ -1,8 +1,9 @@
 package com.scalableminds.webknossos.datastore.services
 
 import com.scalableminds.util.tools.Fox
-import com.scalableminds.util.tools.Fox.option2Fox
+import com.scalableminds.util.tools.Fox.{box2Fox, option2Fox}
 import com.scalableminds.webknossos.datastore.storage.AgglomerateFileKey
+import net.liftweb.common.Full
 
 import scala.concurrent.ExecutionContext
 
@@ -20,6 +21,7 @@ trait MeshMappingHelper {
       editableMappingTracingId: Option[String],
       agglomerateId: Long,
       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 =>
@@ -59,10 +61,16 @@ trait MeshMappingHelper {
           case _ =>
             for {
               agglomerateService <- binaryDataServiceHolder.binaryDataService.agglomerateServiceOpt.toFox
-              segmentIds <- agglomerateService.segmentIdsForAgglomerateId(
-                agglomerateFileKey,
-                agglomerateId
-              )
+              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
         }
     }

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

@@ -148,7 +148,7 @@ class VolumeSegmentIndexBuffer(tracingId: String,
     (hits, misses)
   }
 
-  // Get a map from segment index to bucket position (e.g. an index) from all sources (buffer, fossilDB, file)
+  // Get a map from segment to bucket position (e.g. an index) from all sources (buffer, fossilDB, file)
   def getSegmentToBucketIndexMap(segmentIds: List[Long],
                                  mag: Vec3Int,
                                  mappingName: Option[String],