backend conversion route for tracings to hybrid (#3324)

* create a make-hybrid route which lets you turn any non-hybrid tracing into a hybrid tracing #3288 * implement pr feedback #3324
scalableminds · Oct 9, 2018 · b673829 · b673829
1 parent 851a435
commit b673829
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Showing 5 changed files with 65 additions and 20 deletions.
diff --git a/app/controllers/AnnotationController.scala b/app/controllers/AnnotationController.scala
@@ -150,6 +150,18 @@ class AnnotationController @Inject()(annotationDAO: AnnotationDAO,
       }
     }
 
+  def makeHybrid(typ: String, id: String) = sil.SecuredAction.async { implicit request =>
+    for {
+      _ <- bool2Fox(AnnotationType.Explorational.toString == typ) ?~> "annotation.makeHybrid.explorationalsOnly"
+      annotation <- provider.provideAnnotation(typ, id, request.identity)
+      _ <- annotationService.makeAnnotationHybrid(request.identity, annotation) ?~> "annotation.makeHybrid.failed"
+      updated <- provider.provideAnnotation(typ, id, request.identity)
+      json <- annotationService.publicWrites(updated, Some(request.identity)) ?~> "annotation.write.failed"
+    } yield {
+      JsonOk(json)
+    }
+  }
+
   private def finishAnnotation(typ: String, id: String, issuingUser: User)(implicit ctx: DBAccessContext): Fox[(Annotation, String)] = {
     for {
       annotation <- provider.provideAnnotation(typ, id, issuingUser) ?~> "annotation.notFound"

diff --git a/app/models/annotation/Annotation.scala b/app/models/annotation/Annotation.scala
@@ -286,6 +286,12 @@ class AnnotationDAO @Inject()(sqlClient: SQLClient)(implicit ec: ExecutionContex
       _ <- run(sqlu"update webknossos.annotations set skeletonTracingId = ${newSkeletonTracingId} where _id = ${id.id}")
     } yield ()
 
+  def updateVolumeTracingId(id: ObjectId, newVolumeTracingId: String)(implicit ctx: DBAccessContext): Fox[Unit] =
+    for {
+      _ <- assertUpdateAccess(id)
+      _ <- run(sqlu"update webknossos.annotations set volumeTracingId = ${newVolumeTracingId} where _id = ${id.id}")
+    } yield ()
+
   def updateStatistics(id: ObjectId, statistics: JsObject)(implicit ctx: DBAccessContext): Fox[Unit] =
     for {
       _ <- assertUpdateAccess(id)

diff --git a/app/models/annotation/AnnotationService.scala b/app/models/annotation/AnnotationService.scala
@@ -97,35 +97,35 @@ class AnnotationService @Inject()(annotationInformationProvider: AnnotationInfor
     )
   }
 
+  def createTracings(dataSet: DataSet, dataSource: DataSource, tracingType: TracingType.Value, withFallback: Boolean)(implicit ctx: DBAccessContext): Fox[(Option[String], Option[String])] = tracingType match {
+    case TracingType.skeleton =>
+      for {
+        handler <- dataSetService.handlerFor(dataSet)
+        skeletonTracingId <- handler.saveSkeletonTracing(SkeletonTracingDefaults.createInstance.copy(dataSetName = dataSet.name, editPosition = dataSource.center))
+      } yield (Some(skeletonTracingId), None)
+    case TracingType.volume =>
+      for {
+        handler <- dataSetService.handlerFor(dataSet)
+        volumeTracingId <- handler.saveVolumeTracing(createVolumeTracing(dataSource, withFallback))
+      } yield (None, Some(volumeTracingId))
+    case TracingType.hybrid =>
+      for {
+        handler <- dataSetService.handlerFor(dataSet)
+        skeletonTracingId <- handler.saveSkeletonTracing(SkeletonTracingDefaults.createInstance.copy(dataSetName = dataSet.name, editPosition = dataSource.center))
+        volumeTracingId <- handler.saveVolumeTracing(createVolumeTracing(dataSource, withFallback))
+      } yield (Some(skeletonTracingId), Some(volumeTracingId))
+  }
+
   def createExplorationalFor(
                               user: User,
                               _dataSet: ObjectId,
                               tracingType: TracingType.Value,
                               withFallback: Boolean)(implicit ctx: DBAccessContext): Fox[Annotation] = {
-
-    def createTracings(dataSet: DataSet, dataSource: DataSource): Fox[(Option[String], Option[String])] = tracingType match {
-      case TracingType.skeleton =>
-        for {
-          handler <- dataSetService.handlerFor(dataSet)
-          skeletonTracingId <- handler.saveSkeletonTracing(SkeletonTracingDefaults.createInstance.copy(dataSetName = dataSet.name, editPosition = dataSource.center))
-        } yield (Some(skeletonTracingId), None)
-      case TracingType.volume =>
-        for {
-          handler <- dataSetService.handlerFor(dataSet)
-          volumeTracingId <- handler.saveVolumeTracing(createVolumeTracing(dataSource, withFallback))
-        } yield (None, Some(volumeTracingId))
-      case TracingType.hybrid =>
-        for {
-          handler <- dataSetService.handlerFor(dataSet)
-          skeletonTracingId <- handler.saveSkeletonTracing(SkeletonTracingDefaults.createInstance.copy(dataSetName = dataSet.name, editPosition = dataSource.center))
-          volumeTracingId <- handler.saveVolumeTracing(createVolumeTracing(dataSource, withFallback))
-        } yield (Some(skeletonTracingId), Some(volumeTracingId))
-    }
     for {
       dataSet <- dataSetDAO.findOne(_dataSet)
       dataSource <- dataSetService.dataSourceFor(dataSet)
       usableDataSource <- dataSource.toUsable ?~> "DataSet is not imported."
-      tracingIds <- createTracings(dataSet, usableDataSource)
+      tracingIds <- createTracings(dataSet, usableDataSource, tracingType, withFallback)
       teamId <- selectSuitableTeam(user, dataSet)
       annotation = Annotation(
         ObjectId.generate,
@@ -142,6 +142,27 @@ class AnnotationService @Inject()(annotationInformationProvider: AnnotationInfor
     }
   }
 
+  def makeAnnotationHybrid(user: User, annotation: Annotation)(implicit ctx: DBAccessContext) = {
+    def createNewTracings(dataSet: DataSet, dataSource: DataSource) = annotation.tracingType match {
+      case TracingType.skeleton => createTracings(dataSet, dataSource, TracingType.volume, false).flatMap {
+        case (_, Some(volumeId)) => annotationDAO.updateVolumeTracingId(annotation._id, volumeId)
+        case _ => Fox.failure("unexpectedReturn")
+      }
+      case TracingType.volume => createTracings(dataSet, dataSource, TracingType.skeleton, false).flatMap {
+        case (Some(skeletonId), _) => annotationDAO.updateSkeletonTracingId(annotation._id, skeletonId)
+        case _ => Fox.failure("unexpectedReturn")
+      }
+      case _ => Fox.failure("annotation.makeHybrid.alreadyHybrid")
+    }
+
+    for {
+      dataSet <- dataSetDAO.findOne(annotation._dataSet)
+      dataSource <- dataSetService.dataSourceFor(dataSet).flatMap(_.toUsable)
+      _ <- createNewTracings(dataSet, dataSource)
+    } yield ()
+
+  }
+
   // WARNING: needs to be repeatable, might be called multiple times for an annotation
   def finish(annotation: Annotation, user: User, restrictions: AnnotationRestrictions)(implicit ctx: DBAccessContext): Fox[String] = {
     def executeFinish: Fox[String] = {

diff --git a/conf/messages b/conf/messages
@@ -177,6 +177,9 @@ annotation.transferee.noDataSetAccess=Cannot transfer annotation to a user who h
 annotation.timelogging.read.failed=Time
 annotation.write.failed=Could not convert annotation to json
 annotation.noSkeleton=No skeleton tracing found for this annotation
+annotation.makeHybrid.explorationalsOnly=Could not convert annotation to hybrid annotation because it is only allowed for explorational annotations.
+annotation.makeHybrid.failed=Could not convert to hybrid.
+annotation.makeHybrid.alreadyHybrid=Could not convert annotation to hybrid annotation because it is already a hybrid annotation.
 
 task.create.success=Task successfully created
 task.create.failed=Failed to create Task
@@ -215,3 +218,5 @@ serialization.failed=Failed to serialize data.
 
 initialData.notEnabled=Initial Data Insertion is not enabled in the configuration of this wK instance
 initialData.organizationsNotEmpty=There are already organizations present in the database. Please refresh the db schema and try again
+
+unexpectedReturn=Unexpected return of parameters
diff --git a/conf/webknossos.routes b/conf/webknossos.routes
@@ -94,6 +94,7 @@ GET           /api/annotations/:typ/:id/revert
 POST          /api/annotations/:typ/:id/transfer                                    controllers.AnnotationController.transfer(typ: String, id: String)
 
 GET           /api/annotations/:typ/:id/info                                        controllers.AnnotationController.info(typ: String, id: String)
+PATCH         /api/annotations/:typ/:id/makeHybrid                                  controllers.AnnotationController.makeHybrid(typ: String, id: String)
 DELETE        /api/annotations/:typ/:id                                             controllers.AnnotationController.cancel(typ: String, id: String)
 GET           /api/annotations/:typ/:id/merge/:mergedTyp/:mergedId                  controllers.AnnotationController.merge(typ: String, id: String, mergedTyp: String, mergedId: String)
 GET           /api/annotations/:typ/:id/download                                    controllers.AnnotationIOController.download(typ: String, id: String)