Fix uploading zipped tiff (should set needsConversion=true) (#7856)

* Fix uploading zipped tiff (should set needsConversion=true) * changelog * rephrase code comment --------- Co-authored-by: MichaelBuessemeyer <[email protected]>
scalableminds · Jun 11, 2024 · 08ce2ba · 08ce2ba
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diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -26,6 +26,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed a bug where the warning to zoom in to see the agglomerate mapping was shown to the user even when the 3D viewport was maximized and no volume data was shown. [#7865](https://github.com/scalableminds/webknossos/issues/7865) 
 - 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)
 - 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)
 
 ### Removed
 

diff --git a/conf/messages b/conf/messages
@@ -109,6 +109,7 @@ dataset.upload.linkRestricted=Can only link layers of datasets that are either p
 dataset.upload.invalidLinkedLayers=Could not link all requested layers
 dataset.upload.noFiles=Tried to finish upload with no files. May be a retry of a failed finish request, see previous errors.
 dataset.upload.storageExceeded=Cannot upload dataset because the storage quota of the organization is exceeded.
+dataset.upload.finishFailed=Failed to finalize dataset upload.
 dataset.explore.failed.readFile=Failed to read remote file
 dataset.explore.magDtypeMismatch=Element class must be the same for all mags of a layer. Got {0}
 dataset.explore.autoAdd.failed=Failed to automatically import the explored dataset.

diff --git a/frontend/javascripts/admin/dataset/dataset_upload_view.tsx b/frontend/javascripts/admin/dataset/dataset_upload_view.tsx
@@ -511,9 +511,9 @@ class DatasetUploadView extends React.Component<PropsWithFormAndRouter, State> {
             zipFile: [],
           });
         }
-        // We return here since not more than 1 zip archive is supported anyway. This is guarded
-        // against via form validation.
-        return;
+        // The loop breaks here in case of zip because at most one zip archive is supported anyway.
+        // Form validation takes care of that assertion.
+        break;
       }
     }
 

diff --git a/...tastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala b/...tastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala
@@ -195,7 +195,7 @@ class DataSourceController @Inject()(
           result <- accessTokenService.validateAccess(UserAccessRequest.writeDataSource(dataSourceId),
                                                       urlOrHeaderToken(token, request)) {
             for {
-              (dataSourceId, datasetSizeBytes) <- uploadService.finishUpload(request.body)
+              (dataSourceId, datasetSizeBytes) <- uploadService.finishUpload(request.body) ?~> "finishUpload.failed"
               _ <- remoteWebknossosClient.reportUpload(
                 dataSourceId,
                 datasetSizeBytes,

diff --git a/...tastore/app/com/scalableminds/webknossos/datastore/services/uploading/UploadService.scala b/...tastore/app/com/scalableminds/webknossos/datastore/services/uploading/UploadService.scala
@@ -290,7 +290,8 @@ class UploadService @Inject()(dataSourceRepository: DataSourceRepository,
             } yield explored)
           .toList)
       combinedLayers = exploreLocalLayerService.makeLayerNamesUnique(dataSources.flatMap(_.dataLayers))
-      dataSource = GenericDataSource[DataLayer](dataSourceId, combinedLayers, dataSources.head.scale)
+      firstExploredDatasource <- dataSources.headOption.toFox
+      dataSource = GenericDataSource[DataLayer](dataSourceId, combinedLayers, firstExploredDatasource.scale)
       path <- Fox.runIf(combinedLayers.nonEmpty)(
         exploreLocalLayerService.writeLocalDatasourceProperties(dataSource, path))
     } yield path
@@ -418,7 +419,8 @@ class UploadService @Inject()(dataSourceRepository: DataSourceRepository,
 
   private def looksLikeN5Multilayer(dataSourceDir: Path): Box[Boolean] =
     for {
-      _ <- containsMatchingFile(List(FILENAME_ATTRIBUTES_JSON), dataSourceDir, 1) // root attributes.json
+      matchingFileIsPresent <- containsMatchingFile(List(FILENAME_ATTRIBUTES_JSON), dataSourceDir, 1) // root attributes.json
+      _ <- bool2Box(matchingFileIsPresent)
       directories <- PathUtils.listDirectories(dataSourceDir, silent = false)
       detectedLayerBoxes = directories.map(looksLikeN5MultiscalesLayer)
       _ <- bool2Box(detectedLayerBoxes.forall(_.openOr(false)))
@@ -433,7 +435,8 @@ class UploadService @Inject()(dataSourceRepository: DataSourceRepository,
     //        - directories 0 to n
     //        - attributes.json (N5Header, dimension, compression,...)
     for {
-      _ <- containsMatchingFile(List(FILENAME_ATTRIBUTES_JSON), dataSourceDir, 1) // root attributes.json
+      matchingFileIsPresent <- containsMatchingFile(List(FILENAME_ATTRIBUTES_JSON), dataSourceDir, 1) // root attributes.json
+      _ <- bool2Box(matchingFileIsPresent)
       datasetDir <- PathUtils.listDirectories(dataSourceDir, silent = false).map(_.headOption)
       scaleDirs <- datasetDir.map(PathUtils.listDirectories(_, silent = false)).getOrElse(Full(Seq.empty))
       _ <- bool2Box(scaleDirs.length == 1) // Must be 1, otherwise it is a multiscale dataset