Fix edge cases in NGFF dataset upload (#8341)

scalableminds · Jan 20, 2025 · be83f8e · be83f8e
1 parent d71e780
commit be83f8e
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Showing 3 changed files with 9 additions and 2 deletions.
diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -54,6 +54,8 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed the template for neuron inferral using a custom workflow. [#8312](https://github.com/scalableminds/webknossos/pull/8312)
 - Fixed that the list of processing jobs crashed for deleted job types. [#8300](https://github.com/scalableminds/webknossos/pull/8300)
 - Fixed an issue where you could not maximize or reposition the 3D/XZ viewport in Safari. [#8337](https://github.com/scalableminds/webknossos/pull/8337)
+- Fixed upload of NGFF datasets with only one directory named "color". [#8341](https://github.com/scalableminds/webknossos/pull/8341/) 
+- Fixed an issue that could occur if the NGFF multiscale name was set to "/" when exploring. [#8341](https://github.com/scalableminds/webknossos/pull/8341/)
 
 ### Removed
 - Removed support for HTTP API versions 3 and 4. [#8075](https://github.com/scalableminds/webknossos/pull/8075)

diff --git a/...tastore/app/com/scalableminds/webknossos/datastore/explore/ExploreLocalLayerService.scala b/...tastore/app/com/scalableminds/webknossos/datastore/explore/ExploreLocalLayerService.scala
@@ -122,7 +122,12 @@ class ExploreLocalLayerService @Inject()(dataVaultService: DataVaultService)
       explorer: RemoteLayerExplorer)(path: Path, dataSourceId: DataSourceId, layerDirectory: String)(
       implicit ec: ExecutionContext): Fox[DataSourceWithMagLocators] =
     for {
-      fullPath <- Fox.successful(path.resolve(layerDirectory))
+      _ <- Fox.successful(())
+      layer = if (layerDirectory.isEmpty) {
+        val subdirs = Files.list(path).iterator().asScala.toList
+        if (subdirs.size == 1) subdirs.head.getFileName.toString else layerDirectory
+      } else layerDirectory
+      fullPath <- Fox.successful(path.resolve(layer))
       remoteSourceDescriptor <- Fox.successful(RemoteSourceDescriptor(fullPath.toUri, None))
       vaultPath <- dataVaultService.getVaultPath(remoteSourceDescriptor) ?~> "dataVault.setup.failed"
       layersWithVoxelSizes <- explorer.explore(vaultPath, None)

diff --git a/...s-datastore/app/com/scalableminds/webknossos/datastore/explore/NgffExplorationUtils.scala b/...s-datastore/app/com/scalableminds/webknossos/datastore/explore/NgffExplorationUtils.scala
@@ -246,7 +246,7 @@ trait NgffExplorationUtils extends FoxImplicits {
         axisOrder) ?~> "Could not extract voxel size from scale transforms"
       voxelSizeFactor = voxelSizeInAxisUnits * axisUnitFactors
       nameFromPath = remotePath.basename
-      datasetName = multiscale.name.getOrElse(nameFromPath)
+      datasetName = multiscale.name.flatMap(TextUtils.normalizeStrong).getOrElse(nameFromPath)
       layers <- Fox.serialCombined((0 until channelCount).toList)({ channelIndex: Int =>
         createLayer(remotePath,
                     credentialId,