Add frontend and backend part for job to materialize a volume annotat…

…ion (#6086) * add frontend and backend part for job to apply merger mode tracing * renaming variable * add annotation type as job parameter and make layer names more readable * fix layer selection for merger mode job modal * add job output dataset name to start job modals make start job modals a form * add output dataset name to nuclei & neuron & merger mode job params Add potential volume annotation layer to params of merger mode job all potential annotation cases * refactor starting modal for flood fills to use the same root component as the other job starting modals - Add volume annotation layer name to flood fill job to make it work when there are multiple annotation layers * Apply suggestions from code review Co-authored-by: Philipp Otto <[email protected]> * apply pr feedback * disable jobs * update docs * apply pr feedback * add changelog entry * Update docs/volume_annotation.md Co-authored-by: Philipp Otto <[email protected]> * only show merger mode job button whe jobs are enabled - and apply some feedback * add output segmentation layer name as user input field to apply merger mode job modal * add segmentation output layer name to apply merger mode job api call * make merger job available for volume annotation without skeletons * fix returnLink of materialize job * make materialize volume anotation job better compatible with volume layer without a fallback layer - also incoperate other feedback * update doc images and add merge with fallback layer section to docs * Apply suggestions from code review Co-authored-by: Daniel <[email protected]> * apply review feedback - pass unallowed layer names directly to form item * Update docs/volume_annotation.md Co-authored-by: Philipp Otto <[email protected]> * apply pr feedback * rephrase commennt to make it clearer Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Daniel <[email protected]> Co-authored-by: Florian M <[email protected]>
scalableminds · May 9, 2022 · 95ec9e1 · 95ec9e1
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diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -11,6 +11,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 [Commits](https://github.com/scalableminds/webknossos/compare/22.05.1...HEAD)
 
 ### Added
+- Added a long-running job that applies the merging done via a merger mode tracing to a new output dataset. The job is accessible via a button next to the merger mode button once the merger mode is active. [#6086](https://github.com/scalableminds/webknossos/pull/6086)
  - Added support to stream zarr files using the corresponding [zarr spec](https://zarr.readthedocs.io/en/stable/spec/v2.html#storage). [#6144](https://github.com/scalableminds/webknossos/pull/6144)
 
 ### Changed

diff --git a/app/controllers/JobsController.scala b/app/controllers/JobsController.scala
@@ -126,7 +126,10 @@ class JobsController @Inject()(jobDAO: JobDAO,
       } yield Ok(js)
     }
 
-  def runInferNucleiJob(organizationName: String, dataSetName: String, layerName: Option[String]): Action[AnyContent] =
+  def runInferNucleiJob(organizationName: String,
+                        dataSetName: String,
+                        layerName: String,
+                        newDatasetName: String): Action[AnyContent] =
     sil.SecuredAction.async { implicit request =>
       log(Some(slackNotificationService.noticeFailedJobRequest)) {
         for {
@@ -142,6 +145,7 @@ class JobsController @Inject()(jobDAO: JobDAO,
             "organization_name" -> organizationName,
             "dataset_name" -> dataSetName,
             "layer_name" -> layerName,
+            "new_dataset_name" -> newDatasetName,
             "webknossos_token" -> RpcTokenHolder.webKnossosToken,
           )
           job <- jobService.submitJob(command, commandArgs, request.identity, dataSet._dataStore) ?~> "job.couldNotRunNucleiInferral"
@@ -153,7 +157,8 @@ class JobsController @Inject()(jobDAO: JobDAO,
   def runInferNeuronsJob(organizationName: String,
                          dataSetName: String,
                          layerName: String,
-                         bbox: String): Action[AnyContent] =
+                         bbox: String,
+                         newDatasetName: String): Action[AnyContent] =
     sil.SecuredAction.async { implicit request =>
       log(Some(slackNotificationService.noticeFailedJobRequest)) {
         for {
@@ -167,6 +172,7 @@ class JobsController @Inject()(jobDAO: JobDAO,
           commandArgs = Json.obj(
             "organization_name" -> organizationName,
             "dataset_name" -> dataSetName,
+            "new_dataset_name" -> newDatasetName,
             "layer_name" -> layerName,
             "webknossos_token" -> RpcTokenHolder.webKnossosToken,
             "bbox" -> bbox,
@@ -180,10 +186,11 @@ class JobsController @Inject()(jobDAO: JobDAO,
   def runGlobalizeFloodfills(
       organizationName: String,
       dataSetName: String,
-      newDataSetName: Option[String],
-      layerName: Option[String],
-      annotationId: Option[String],
-      annotationType: Option[String],
+      fallbackLayerName: String,
+      annotationId: String,
+      annotationType: String,
+      newDatasetName: String,
+      volumeLayerName: Option[String]
   ): Action[AnyContent] =
     sil.SecuredAction.async { implicit request =>
       log(Some(slackNotificationService.noticeFailedJobRequest)) {
@@ -201,11 +208,13 @@ class JobsController @Inject()(jobDAO: JobDAO,
           commandArgs = Json.obj(
             "organization_name" -> organizationName,
             "dataset_name" -> dataSetName,
-            "new_dataset_name" -> newDataSetName,
-            "layer_name" -> layerName,
+            "fallback_layer_name" -> fallbackLayerName,
+            "webknossos_token" -> RpcTokenHolder.webKnossosToken,
+            "user_auth_token" -> userAuthToken.id,
             "annotation_id" -> annotationId,
             "annotation_type" -> annotationType,
-            "user_auth_token" -> userAuthToken.id,
+            "new_dataset_name" -> newDatasetName,
+            "volume_layer_name" -> volumeLayerName
           )
           job <- jobService.submitJob(command, commandArgs, request.identity, dataSet._dataStore) ?~> "job.couldNotRunGlobalizeFloodfills"
           js <- jobService.publicWrites(job)
@@ -258,4 +267,44 @@ class JobsController @Inject()(jobDAO: JobDAO,
       }
     }
 
+  def runMaterializeVolumeAnnotationJob(organizationName: String,
+                                        dataSetName: String,
+                                        fallbackLayerName: String,
+                                        annotationId: String,
+                                        annotationType: String,
+                                        newDatasetName: String,
+                                        outputSegmentationLayerName: String,
+                                        mergeSegments: Boolean,
+                                        volumeLayerName: Option[String]): Action[AnyContent] =
+    sil.SecuredAction.async { implicit request =>
+      log(Some(slackNotificationService.noticeFailedJobRequest)) {
+        for {
+          organization <- organizationDAO.findOneByName(organizationName) ?~> Messages("organization.notFound",
+                                                                                       organizationName)
+          _ <- bool2Fox(request.identity._organization == organization._id) ?~> "job.applyMergerMode.notAllowed.organization" ~> FORBIDDEN
+          dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organization._id) ?~> Messages(
+            "dataSet.notFound",
+            dataSetName) ~> NOT_FOUND
+          userAuthToken <- wkSilhouetteEnvironment.combinedAuthenticatorService.findOrCreateToken(
+            request.identity.loginInfo)
+          command = "materialize_volume_annotation"
+          commandArgs = Json.obj(
+            "organization_name" -> organizationName,
+            "dataset_name" -> dataSetName,
+            "fallback_layer_name" -> fallbackLayerName,
+            "webknossos_token" -> RpcTokenHolder.webKnossosToken,
+            "user_auth_token" -> userAuthToken.id,
+            "annotation_id" -> annotationId,
+            "output_segmentation_layer_name" -> outputSegmentationLayerName,
+            "annotation_type" -> annotationType,
+            "new_dataset_name" -> newDatasetName,
+            "merge_segments" -> mergeSegments,
+            "volume_layer_name" -> volumeLayerName
+          )
+          job <- jobService.submitJob(command, commandArgs, request.identity, dataSet._dataStore) ?~> "job.couldNotRunApplyMergerMode"
+          js <- jobService.publicWrites(job)
+        } yield Ok(js)
+      }
+    }
+
 }
diff --git a/app/models/job/Job.scala b/app/models/job/Job.scala
@@ -72,7 +72,7 @@ case class Job(
           }
         case "export_tiff" =>
           Some(s"$dataStorePublicUrl/data/exports/${_id.id}/download")
-        case "infer_nuclei" | "infer_neurons" =>
+        case "infer_nuclei" | "infer_neurons" | "materialize_volume_annotation" =>
           returnValue.map { resultDatasetName =>
             s"/datasets/$organizationName/$resultDatasetName/view"
           }

diff --git a/conf/messages b/conf/messages
@@ -346,6 +346,7 @@ job.couldNotRunComputeMeshFile = Failed to start mesh file computation job.
 job.couldNotRunNucleiInferral = Failed to start nuclei inferral job.
 job.couldNotRunNeuronInferral = Failed to start neuron inferral job.
 job.couldNotRunGlobalizeFloodfills = Failed to start job for globalizing floodfills.
+job.couldNotRunApplyMergerMode = Failed to start job to apply merger mode tracing.
 job.disabled = Long-running jobs are not enabled for this webKnossos instance.
 jobs.worker.notFound = Could not find this worker in the database.
 job.export.fileNotFound = Exported file not found. The link may be expired.
@@ -357,6 +358,7 @@ job.inferNuclei.notAllowed.organization = Currently nuclei inferral is only allo
 job.inferNeurons.notAllowed.organization = Currently neuron inferral is only allowed for datasets of your own organization.
 job.meshFile.notAllowed.organization = Calculating mesh files is only allowed for datasets of your own organization.
 job.globalizeFloodfill.notAllowed.organization = Globalizing floodfills is only allowed for datasets of your own organization.
+job.applyMergerMode.notAllowed.organization = Applying merger mode tracings is only allowed for datasets of your own organization.
 
 agglomerateSkeleton.failed=Could not generate agglomerate skeleton.