Add absolute paths to datasets with no mag paths

Author: frcroth

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

@@ -392,7 +392,13 @@ class DataSourceService @Inject()(
               mag =>
                 mag.path match {
                   case Some(pathStr) => mag.copy(path = Some(replaceUri(new URI(pathStr)).toString))
-                  case _             => mag
+                  // If the mag does not have a path, it is an implicit path, we need to make it explicit.
+                  case _ =>
+                    mag.copy(
+                      path = Some(
+                        new URI(newBasePath)
+                          .resolve(List(layerWithMagLocators.name, mag.mag.toMagLiteral(true)).mkString("/"))
+                          .toString))
               },
               attachmentMapping = attachment =>
                 DatasetLayerAttachments(

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/uploading/UploadService.scala

@@ -398,9 +398,12 @@ class UploadService @Inject()(dataSourceService: DataSourceService,
       datasetSizeBytes: Long <- if (uploadToS3) {
         for {
           _ <- Fox.successful(())
-
+          _ = logger.info(
+            s"Starting upload of dataset ${dataSourceId.organizationId}/${dataSourceId.directoryName} to S3.")
           s3ObjectKey = s"${dataStoreConfig.Datastore.S3Upload.objectKeyPrefix}/$uploadId/"
           _ <- uploadDirectoryToS3(unpackToDir, dataStoreConfig.Datastore.S3Upload.bucketName, s3ObjectKey)
+          _ = logger.info(
+            s"Finished upload of dataset ${dataSourceId.organizationId}/${dataSourceId.directoryName} to S3.")
           endPointHost = new URI(dataStoreConfig.Datastore.S3Upload.endpoint).getHost
           s3DataSource <- dataSourceService.prependAllPaths(
             dataSource,