Write wkurl into annotation nml file

CHANGELOG.unreleased.md

@@ -20,6 +20,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Changed
 - Moved the view mode selection in the toolbar next to the position field. [#6949](https://github.com/scalableminds/webknossos/pull/6949)
 - Redesigned welcome toast for new, annonymous users with new branding. [#6961](https://github.com/scalableminds/webknossos/pull/6961)
+- When saving annotations, the URL of the webknossos instance is stored in the resulting NML file. [#6964](https://github.com/scalableminds/webknossos/pull/6964)
 
 ### Fixed
 - Fixed incorrect initial tab when clicking "Show Annotations" for a user in the user list. Also, the datasets tab was removed from that page as it was the same as the datasets table from the main dashboard. [#6957](https://github.com/scalableminds/webknossos/pull/6957)

app/controllers/AnnotationIOController.scala

@@ -43,7 +43,7 @@ import play.api.i18n.{Messages, MessagesProvider}
 import play.api.libs.Files.{TemporaryFile, TemporaryFileCreator}
 import play.api.libs.json.Json
 import play.api.mvc.{Action, AnyContent, MultipartFormData}
-import utils.ObjectId
+import utils.{ObjectId, WkConf}
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -62,6 +62,7 @@ class AnnotationIOController @Inject()(
     temporaryFileCreator: TemporaryFileCreator,
     annotationService: AnnotationService,
     analyticsService: AnalyticsService,
+    conf: WkConf,
     sil: Silhouette[WkEnv],
     provider: AnnotationInformationProvider,
     annotationUploadService: AnnotationUploadService)(implicit ec: ExecutionContext, val materializer: Materializer)
@@ -102,9 +103,9 @@ Expects:
         val attachedFiles = request.body.files.map(f => (f.ref.path.toFile, f.filename))
         val parsedFiles =
           annotationUploadService.extractFromFiles(attachedFiles, useZipName = true, overwritingDataSetName)
-        val parsedFilesWraped =
+        val parsedFilesWrapped =
           annotationUploadService.wrapOrPrefixTrees(parsedFiles.parseResults, shouldCreateGroupForEachFile)
-        val parseResultsFiltered: List[NmlParseResult] = parsedFilesWraped.filter(_.succeeded)
+        val parseResultsFiltered: List[NmlParseResult] = parsedFilesWrapped.filter(_.succeeded)
 
         if (parseResultsFiltered.isEmpty) {
           returnError(parsedFiles)
@@ -113,13 +114,15 @@ Expects:
             parseSuccesses <- Fox.serialCombined(parseResultsFiltered)(r => r.toSuccessBox)
             name = nameForUploaded(parseResultsFiltered.map(_.fileName))
             description = descriptionForNMLs(parseResultsFiltered.map(_.description))
+            wkUrl = wkUrlsForNMLs(parseResultsFiltered.map(_.wkUrl))
             _ <- assertNonEmpty(parseSuccesses)
             skeletonTracings = parseSuccesses.flatMap(_.skeletonTracing)
             // Create a list of volume layers for each uploaded (non-skeleton-only) annotation.
             // This is what determines the merging strategy for volume layers
             volumeLayersGroupedRaw = parseSuccesses.map(_.volumeLayers).filter(_.nonEmpty)
             dataSet <- findDataSetForUploadedAnnotations(skeletonTracings,
-                                                         volumeLayersGroupedRaw.flatten.map(_.tracing))
+                                                         volumeLayersGroupedRaw.flatten.map(_.tracing),
+                                                         wkUrl)
             volumeLayersGrouped <- adaptVolumeTracingsToFallbackLayer(volumeLayersGroupedRaw, dataSet)
             tracingStoreClient <- tracingStoreService.clientFor(dataSet)
             mergedVolumeLayers <- mergeAndSaveVolumeLayers(volumeLayersGrouped,
@@ -198,19 +201,31 @@ Expects:
 
   private def findDataSetForUploadedAnnotations(
       skeletonTracings: List[SkeletonTracing],
-      volumeTracings: List[VolumeTracing])(implicit mp: MessagesProvider, ctx: DBAccessContext): Fox[DataSet] =
+      volumeTracings: List[VolumeTracing],
+      wkUrl: String)(implicit mp: MessagesProvider, ctx: DBAccessContext): Fox[DataSet] =
     for {
       dataSetName <- assertAllOnSameDataSet(skeletonTracings, volumeTracings) ?~> "nml.file.differentDatasets"
       organizationNameOpt <- assertAllOnSameOrganization(skeletonTracings, volumeTracings) ?~> "nml.file.differentDatasets"
       organizationIdOpt <- Fox.runOptional(organizationNameOpt) {
         organizationDAO.findOneByName(_)(GlobalAccessContext).map(_._id)
-      } ?~> Messages("organization.notFound", organizationNameOpt.getOrElse("")) ~> NOT_FOUND
+      } ?~> (if (wkUrl.nonEmpty && conf.Http.uri != wkUrl) {
+               Messages("organization.notFound.wrongHost", organizationNameOpt.getOrElse(""), wkUrl, conf.Http.uri)
+             } else { Messages("organization.notFound", organizationNameOpt.getOrElse("")) }) ~>
+        NOT_FOUND
       organizationId <- Fox.fillOption(organizationIdOpt) {
         dataSetDAO.getOrganizationForDataSet(dataSetName)(GlobalAccessContext)
       } ?~> Messages("dataSet.noAccess", dataSetName) ~> FORBIDDEN
-      dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organizationId) ?~> Messages(
-        "dataSet.noAccess",
-        dataSetName) ~> FORBIDDEN
+      dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organizationId) ?~> (if (wkUrl.nonEmpty && conf.Http.uri != wkUrl) {
+                                                                                             Messages(
+                                                                                               "dataSet.noAccess.wrongHost",
+                                                                                               dataSetName,
+                                                                                               wkUrl,
+                                                                                               conf.Http.uri)
+                                                                                           } else {
+                                                                                             Messages(
+                                                                                               "dataSet.noAccess",
+                                                                                               dataSetName)
+                                                                                           }) ~> FORBIDDEN
     } yield dataSet
 
   private def nameForUploaded(fileNames: Seq[String]) =
@@ -222,6 +237,9 @@ Expects:
   private def descriptionForNMLs(descriptions: Seq[Option[String]]) =
     if (descriptions.size == 1) descriptions.headOption.flatten.getOrElse("") else ""
 
+  private def wkUrlsForNMLs(wkUrls: Seq[Option[String]]) =
+    if (wkUrls.toSet.size == 1) wkUrls.headOption.flatten.getOrElse("") else ""
+
   private def returnError(zipParseResult: NmlResults.MultiNmlParseResult)(implicit messagesProvider: MessagesProvider) =
     if (zipParseResult.containsFailure) {
       val errors = zipParseResult.parseResults.flatMap {
@@ -370,6 +388,7 @@ Expects:
                                           dataSet.scale,
                                           None,
                                           organizationName,
+                                          conf.Http.uri,
                                           dataSet.name,
                                           Some(user),
                                           taskOpt)
@@ -395,15 +414,18 @@ Expects:
         }
         user <- userService.findOneById(annotation._user, useCache = true)
         taskOpt <- Fox.runOptional(annotation._task)(taskDAO.findOne)
-        nmlStream = nmlWriter.toNmlStream(fetchedSkeletonLayers ::: fetchedVolumeLayers,
-                                          Some(annotation),
-                                          dataset.scale,
-                                          None,
-                                          organizationName,
-                                          dataset.name,
-                                          Some(user),
-                                          taskOpt,
-                                          skipVolumeData)
+        nmlStream = nmlWriter.toNmlStream(
+          fetchedSkeletonLayers ::: fetchedVolumeLayers,
+          Some(annotation),
+          dataset.scale,
+          None,
+          organizationName,
+          conf.Http.uri,
+          dataset.name,
+          Some(user),
+          taskOpt,
+          skipVolumeData
+        )
         temporaryFile = temporaryFileCreator.create()
         zipper = ZipIO.startZip(new BufferedOutputStream(new FileOutputStream(new File(temporaryFile.path.toString))))
         _ <- zipper.addFileFromEnumerator(name + ".nml", nmlStream)

app/models/annotation/AnnotationService.scala

@@ -52,7 +52,7 @@ import play.api.i18n.{Messages, MessagesProvider}
 import play.api.libs.Files.{TemporaryFile, TemporaryFileCreator}
 import play.api.libs.iteratee.Enumerator
 import play.api.libs.json.{JsNull, JsObject, JsValue, Json}
-import utils.ObjectId
+import utils.{ObjectId, WkConf}
 
 import java.io.{BufferedOutputStream, File, FileOutputStream}
 import javax.inject.Inject
@@ -104,7 +104,8 @@ class AnnotationService @Inject()(
     nmlWriter: NmlWriter,
     temporaryFileCreator: TemporaryFileCreator,
     meshDAO: MeshDAO,
-    meshService: MeshService
+    meshService: MeshService,
+    conf: WkConf,
 )(implicit ec: ExecutionContext, val materializer: Materializer)
     extends BoxImplicits
     with FoxImplicits
@@ -639,6 +640,7 @@ class AnnotationService @Inject()(
                                         scaleOpt,
                                         Some(name + "_data.zip"),
                                         organizationName,
+                                        conf.Http.uri,
                                         datasetName,
                                         Some(user),
                                         taskOpt)

app/models/annotation/AnnotationUploadService.scala

@@ -38,8 +38,8 @@ class AnnotationUploadService @Inject()(tempFileService: TempFileService) extend
                      isTaskUpload: Boolean,
                      basePath: Option[String] = None)(implicit m: MessagesProvider): NmlParseResult =
     NmlParser.parse(name, inputStream, overwritingDataSetName, isTaskUpload, basePath) match {
-      case Full((skeletonTracing, uploadedVolumeLayers, description)) =>
-        NmlParseSuccess(name, skeletonTracing, uploadedVolumeLayers, description)
+      case Full((skeletonTracing, uploadedVolumeLayers, description, wkUrl)) =>
+        NmlParseSuccess(name, skeletonTracing, uploadedVolumeLayers, description, wkUrl)
       case Failure(msg, _, chain) => NmlParseFailure(name, msg + chain.map(_ => formatChain(chain)).getOrElse(""))
       case Empty                  => NmlParseEmpty(name)
     }
@@ -82,8 +82,8 @@ class AnnotationUploadService @Inject()(tempFileService: TempFileService) extend
 
     if (parseResults.length > 1) {
       parseResults.map {
-        case NmlParseSuccess(name, Some(skeletonTracing), uploadedVolumeLayers, description) =>
-          NmlParseSuccess(name, Some(renameTrees(name, skeletonTracing)), uploadedVolumeLayers, description)
+        case NmlParseSuccess(name, Some(skeletonTracing), uploadedVolumeLayers, description, wkUrl) =>
+          NmlParseSuccess(name, Some(renameTrees(name, skeletonTracing)), uploadedVolumeLayers, description, wkUrl)
         case r => r
       }
     } else {
@@ -104,8 +104,8 @@ class AnnotationUploadService @Inject()(tempFileService: TempFileService) extend
     }
 
     parseResults.map {
-      case NmlParseSuccess(name, Some(skeletonTracing), uploadedVolumeLayers, description) =>
-        NmlParseSuccess(name, Some(wrapTreesInGroup(name, skeletonTracing)), uploadedVolumeLayers, description)
+      case NmlParseSuccess(name, Some(skeletonTracing), uploadedVolumeLayers, description, wkUrl) =>
+        NmlParseSuccess(name, Some(wrapTreesInGroup(name, skeletonTracing)), uploadedVolumeLayers, description, wkUrl)
       case r => r
     }
   }

app/models/annotation/nml/NmlParser.scala

@@ -34,7 +34,7 @@ object NmlParser extends LazyLogging with ProtoGeometryImplicits with ColorGener
             overwritingDataSetName: Option[String],
             isTaskUpload: Boolean,
             basePath: Option[String] = None)(
-      implicit m: MessagesProvider): Box[(Option[SkeletonTracing], List[UploadedVolumeLayer], String)] =
+      implicit m: MessagesProvider): Box[(Option[SkeletonTracing], List[UploadedVolumeLayer], String, Option[String])] =
     try {
       val data = XML.load(nmlInputStream)
       for {
@@ -52,6 +52,7 @@ object NmlParser extends LazyLogging with ProtoGeometryImplicits with ColorGener
       } yield {
         val dataSetName = overwritingDataSetName.getOrElse(parseDataSetName(parameters \ "experiment"))
         val description = parseDescription(parameters \ "experiment")
+        val wkUrl = parseWkUrl(parameters \ "experiment")
         val organizationName =
           if (overwritingDataSetName.isDefined) None else parseOrganizationName(parameters \ "experiment")
         val activeNodeId = parseActiveNode(parameters \ "activeNode")
@@ -115,7 +116,7 @@ object NmlParser extends LazyLogging with ProtoGeometryImplicits with ColorGener
               )
             )
 
-        (skeletonTracingOpt, volumeLayers, description)
+        (skeletonTracingOpt, volumeLayers, description, wkUrl)
       }
     } catch {
       case e: org.xml.sax.SAXParseException if e.getMessage.startsWith("Premature end of file") =>
@@ -232,6 +233,9 @@ object NmlParser extends LazyLogging with ProtoGeometryImplicits with ColorGener
   private def parseDescription(nodes: NodeSeq): String =
     nodes.headOption.map(node => getSingleAttribute(node, "description")).getOrElse(DEFAULT_DESCRIPTION)
 
+  private def parseWkUrl(nodes: NodeSeq): Option[String] =
+    nodes.headOption.map(node => getSingleAttribute(node, "wkUrl"))
+
   private def parseOrganizationName(nodes: NodeSeq): Option[String] =
     nodes.headOption.flatMap(node => getSingleAttributeOpt(node, "organization"))
 

app/models/annotation/nml/NmlResults.scala

@@ -14,6 +14,7 @@ object NmlResults extends LazyLogging {
     def fileName: String
 
     def description: Option[String] = None
+    def wkUrl: Option[String] = None
 
     def succeeded: Boolean
 
@@ -32,11 +33,13 @@ object NmlResults extends LazyLogging {
   case class NmlParseSuccess(fileName: String,
                              skeletonTracing: Option[SkeletonTracing],
                              volumeLayers: List[UploadedVolumeLayer],
-                             _description: String)
+                             _description: String,
+                             _wkUrl: Option[String])
       extends NmlParseResult {
     def succeeded = true
 
     override def description: Option[String] = Some(_description)
+    override def wkUrl: Option[String] = _wkUrl
 
     override def withName(name: String): NmlParseResult = this.copy(fileName = name)
   }

app/models/annotation/nml/NmlWriter.scala

@@ -22,6 +22,7 @@ case class NmlParameters(
     dataSetName: String,
     organizationName: String,
     description: Option[String],
+    wkUrl: String,
     scale: Option[Vec3Double],
     createdTimestamp: Long,
     editPosition: Vec3IntProto,
@@ -40,6 +41,7 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
                   scale: Option[Vec3Double],
                   volumeFilename: Option[String],
                   organizationName: String,
+                  wkUrl: String,
                   datasetName: String,
                   annotationOwner: Option[User],
                   annotationTask: Option[Task],
@@ -53,6 +55,7 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
                    scale,
                    volumeFilename,
                    organizationName,
+                   wkUrl,
                    datasetName,
                    annotationOwner,
                    annotationTask,
@@ -66,6 +69,7 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
             scale: Option[Vec3Double],
             volumeFilename: Option[String],
             organizationName: String,
+            wkUrl: String,
             datasetName: String,
             annotationOwner: Option[User],
             annotationTask: Option[Task],
@@ -82,6 +86,7 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
                                                  volumeLayers,
                                                  annotation: Option[Annotation],
                                                  organizationName,
+                                                 wkUrl,
                                                  datasetName,
                                                  scale)
           _ = writeParameters(parameters)
@@ -103,6 +108,7 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
                                volumeLayers: List[FetchedAnnotationLayer],
                                annotation: Option[Annotation],
                                organizationName: String,
+                               wkUrl: String,
                                datasetName: String,
                                scale: Option[Vec3Double]): Fox[NmlParameters] =
     for {
@@ -113,6 +119,7 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
             datasetName,
             organizationName,
             annotation.map(_.description),
+            wkUrl,
             scale,
             s.createdTimestamp,
             s.editPosition,
@@ -127,6 +134,7 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
             datasetName,
             organizationName,
             annotation.map(_.description),
+            wkUrl,
             scale,
             v.createdTimestamp,
             v.editPosition,
@@ -154,6 +162,7 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
         writer.writeAttribute("name", parameters.dataSetName)
         writer.writeAttribute("organization", parameters.organizationName)
         parameters.description.foreach(writer.writeAttribute("description", _))
+        writer.writeAttribute("wkUrl", parameters.wkUrl)
       }
       Xml.withinElementSync("scale") {
         writer.writeAttribute("x", parameters.scale.map(_.x).getOrElse(-1).toString)

conf/messages

@@ -33,6 +33,7 @@ team.inUse.projects=Team is referenced by {0} projects
 organization.create.forbidden=You are not allowed to create a new organization
 organization.create.failed=Failed to create a new organization
 organization.notFound=Organization {0} could not be found
+organization.notFound.wrongHost=Organization {0} could not be found. Please check whether you are on the correct WEBKNOSSOS instance. The uploaded file indicates {1} while this instance is {2}.
 organization.list.failed=Failed to retrieve list of organizations.
 organization.name.invalid=This organization name contains illegal characters. Please only use letters and numbers.
 organization.name.alreadyInUse=This name is already claimed by a different organization and not available anymore. Please choose a different name.
@@ -75,6 +76,7 @@ dataSet.notFound=Dataset {0} does not exist or could not be accessed
 dataSet.notFoundConsiderLogin=Dataset {0} does not exist or could not be accessed. You may need to log in.
 dataSet.notFoundForAnnotation=The Dataset for this annotation does not exist or could not be accessed.
 dataSet.noAccess=Could not access DataSet {0}. Does your team have access?
+dataSet.noAccess.wrongHost=Could not access DataSet {0}. Please check whether you are on the correct WEBKNOSSOS instance. The uploaded file indicates {1} while this instance is {2}.
 dataSet.noAccessById=Could not access the corresponding DataSet. This is likely because you are not a member of a team that has access to it.
 dataSet.notImported=Dataset {0} is not imported
 dataSet.name.invalid.characters=Dataset name is invalid. Please use only letters, digits, dots, underscores, hypens.

frontend/javascripts/oxalis/model/helpers/nml_helpers.ts

@@ -224,6 +224,7 @@ function serializeParameters(
           name: state.dataset.name,
           description: annotation.description,
           organization: state.dataset.owningOrganization,
+          wkUrl: `${location.protocol}//${location.host}`,
         }),
         serializeTag("scale", {
           x: state.dataset.dataSource.scale[0],