Relabel too-high tree ids in backend (#5484)

* [WIP] relabel too-high tree ids in backend * return skeleton with new trees
scalableminds · May 12, 2021 · f41f4ae · f41f4ae
1 parent ab6be10
commit f41f4ae
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Showing 5 changed files with 15 additions and 4 deletions.
diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -20,6 +20,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Fixed
 - Fixed that the row selection in the user table wasn't properly preserved when filtering the table and (un)selecting rows. [#5486](https://github.com/scalableminds/webknossos/pull/5486)
 - Fixed a bug where histograms generation failed for tiny datasets. [#5458](https://github.com/scalableminds/webknossos/pull/5458)
+- Fixed a bug where NMLs with huge tree IDs uploaded via back-end produced broken annotations. [#5484](https://github.com/scalableminds/webknossos/pull/5484)
 - Fixed a bug where the upload of multiple NMLs failed if some of them have an organization attribute and others don’t. [#5483](https://github.com/scalableminds/webknossos/pull/5483)
 
 ### Removed

diff --git a/app/models/annotation/TracingStoreRpcClient.scala b/app/models/annotation/TracingStoreRpcClient.scala
@@ -27,7 +27,7 @@ object TracingStoreRpcClient {
 class TracingStoreRpcClient(tracingStore: TracingStore, dataSet: DataSet, rpc: RPC)(implicit ec: ExecutionContext)
     extends LazyLogging {
 
-  def baseInfo = s"Dataset: ${dataSet.name} Tracingstore: ${tracingStore.url}"
+  def baseInfo = s" Dataset: ${dataSet.name} Tracingstore: ${tracingStore.url}"
 
   def getSkeletonTracing(tracingId: String, version: Option[Long]): Fox[SkeletonTracing] = {
     logger.debug("Called to get SkeletonTracing." + baseInfo)

diff --git a/...app/com/scalableminds/webknossos/tracingstore/controllers/SkeletonTracingController.scala b/...app/com/scalableminds/webknossos/tracingstore/controllers/SkeletonTracingController.scala
@@ -38,9 +38,10 @@ class SkeletonTracingController @Inject()(val tracingService: SkeletonTracingSer
           AllowRemoteOrigin {
             val tracings: List[Option[SkeletonTracing]] = request.body
             val mergedTracing = tracingService.merge(tracings.flatten)
-            tracingService.save(mergedTracing, None, mergedTracing.version, toCache = !persist).map { newId =>
-              Ok(Json.toJson(newId))
-            }
+            val processedTracing = tracingService.remapTooLargeTreeIds(mergedTracing)
+            for {
+              newId <- tracingService.save(processedTracing, None, processedTracing.version, toCache = !persist)
+            } yield Ok(Json.toJson(newId))
           }
         }
       }

diff --git a/...-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/TracingService.scala b/...-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/TracingService.scala
@@ -172,6 +172,8 @@ trait TracingService[T <: GeneratedMessage with Message[T]]
 
   def merge(tracings: Seq[T]): T
 
+  def remapTooLargeTreeIds(tracing: T): T = tracing
+
   def mergeVolumeData(tracingSelectors: Seq[TracingSelector],
                       tracings: Seq[T],
                       newId: String,

diff --git a/.../com/scalableminds/webknossos/tracingstore/tracings/skeleton/SkeletonTracingService.scala b/.../com/scalableminds/webknossos/tracingstore/tracings/skeleton/SkeletonTracingService.scala
@@ -176,6 +176,13 @@ class SkeletonTracingService @Inject()(tracingDataStore: TracingDataStore,
     )
   }
 
+  // Can be removed again when https://github.com/scalableminds/webknossos/issues/5009 is fixed
+  override def remapTooLargeTreeIds(skeletonTracing: SkeletonTracing): SkeletonTracing =
+    if (skeletonTracing.trees.exists(_.treeId > 1048576)) {
+      val newTrees = for ((tree, index) <- skeletonTracing.trees.zipWithIndex) yield tree.withTreeId(index + 1)
+      skeletonTracing.withTrees(newTrees)
+    } else skeletonTracing
+
   def mergeVolumeData(tracingSelectors: Seq[TracingSelector],
                       tracings: Seq[SkeletonTracing],
                       newId: String,