Write wkurl into annotation nml file (#6964)

Co-authored-by: Philipp Otto <[email protected]>
scalableminds · Apr 18, 2023 · 0e6e6e7 · 0e6e6e7
1 parent 0c7385f
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diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -20,7 +20,8 @@ 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, anonymous users with new branding. [#6961](https://github.com/scalableminds/webknossos/pull/6961)
+- 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 unintended dependencies between segments of different volume layers which used the same segment id. Now, using the same segment id for segments in different volume layers should work without any problems. [#6960](https://github.com/scalableminds/webknossos/pull/6960)

diff --git a/app/controllers/AnnotationIOController.scala b/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 {
@@ -369,6 +387,7 @@ Expects:
                                           dataSet.scale,
                                           None,
                                           organizationName,
+                                          conf.Http.uri,
                                           dataSet.name,
                                           Some(user),
                                           taskOpt)
@@ -394,15 +413,18 @@ 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)

diff --git a/app/models/annotation/AnnotationService.scala b/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)

diff --git a/app/models/annotation/AnnotationUploadService.scala b/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
     }
   }

diff --git a/app/models/annotation/nml/NmlParser.scala b/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"))
 

diff --git a/app/models/annotation/nml/NmlResults.scala b/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)
   }

diff --git a/app/models/annotation/nml/NmlWriter.scala b/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)