Add frontend and backend part for job to materialize a volume annotation

app/controllers/JobsController.scala

@@ -258,4 +258,34 @@ class JobsController @Inject()(jobDAO: JobDAO,
       }
     }
 
+    def runApplyMergerModeJob(organizationName: String,
+                         dataSetName: String,
+                         layerName: String,
+                         annotationId: 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 = "apply_merger_mode"
+          commandArgs = Json.obj(
+            "organization_name" -> organizationName,
+            "dataset_name" -> dataSetName,
+            "layer_name" -> layerName,
+            "webknossos_token" -> RpcTokenHolder.webKnossosToken,
+            "user_auth_token" -> userAuthToken.id,
+            "annotation_id" -> annotationId,
+          )
+          job <- jobService.submitJob(command, commandArgs, request.identity, dataSet._dataStore) ?~> "job.couldNotRunApplyMergerMode"
+          js <- jobService.publicWrites(job)
+        } yield Ok(js)
+      }
+    }
+
 }

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" | "apply_merger_mode" =>
           returnValue.map { resultDatasetName =>
             s"/datasets/$organizationName/$resultDatasetName/view"
           }

conf/messages

@@ -342,6 +342,7 @@ 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.
@@ -353,6 +354,7 @@ 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.
 

conf/webknossos.latest.routes

@@ -209,6 +209,7 @@ POST          /jobs/run/exportTiff/:organizationName/:dataSetName              c
 POST          /jobs/run/inferNuclei/:organizationName/:dataSetName             controllers.JobsController.runInferNucleiJob(organizationName: String, dataSetName: String, layerName: Option[String])
 POST          /jobs/run/inferNeurons/:organizationName/:dataSetName            controllers.JobsController.runInferNeuronsJob(organizationName: String, dataSetName: String, layerName: String, bbox: String)
 POST          /jobs/run/globalizeFloodfills/:organizationName/:dataSetName     controllers.JobsController.runGlobalizeFloodfills(organizationName: String, dataSetName: String, newDataSetName: Option[String], layerName: Option[String], annotationId: Option[String], annotationType: Option[String])
+POST          /jobs/run/applyMergerMode/:organizationName/:dataSetName         controllers.JobsController.runApplyMergerModeJob(organizationName: String, dataSetName: String, layerName: String, annotationId: String)
 GET           /jobs/:id                                                        controllers.JobsController.get(id: String)
 PATCH         /jobs/:id/cancel                                                 controllers.JobsController.cancel(id: String)
 POST          /jobs/:id/status                                                 controllers.WKRemoteWorkerController.updateJobStatus(key: String, id: String)

frontend/javascripts/admin/admin_rest_api.js

@@ -1084,6 +1084,20 @@ export function startGlobalizeFloodfillsJob(
   );
 }
 
+export function startApplyMergerModeJob(
+  organizationName: string,
+  datasetName: string,
+  layerName: string,
+  annotationId: string,
+): Promise<APIJob> {
+  return Request.receiveJSON(
+    `/api/jobs/run/applyMergerMode/${organizationName}/${datasetName}?layerName=${layerName}&annotationId=${annotationId}`,
+    {
+      method: "POST",
+    },
+  );
+}
+
 export function getDatasetDatasource(
   dataset: APIMaybeUnimportedDataset,
 ): Promise<APIDataSourceWithMessages> {

frontend/javascripts/oxalis/view/action-bar/toolbar_view.js

@@ -1,7 +1,7 @@
 // @flow
 import { Radio, Tooltip, Badge, Space, Popover } from "antd";
 import { useSelector, useDispatch } from "react-redux";
-import React, { useEffect } from "react";
+import React, { useEffect, useState } from "react";
 
 import { LogSliderSetting } from "oxalis/view/components/setting_input_views";
 import { addUserBoundingBoxAction } from "oxalis/model/actions/annotation_actions";
@@ -29,6 +29,7 @@ import { updateUserSettingAction } from "oxalis/model/actions/settings_actions";
 import { usePrevious, useKeyPress } from "libs/react_hooks";
 import { userSettings } from "types/schemas/user_settings.schema";
 import ButtonComponent from "oxalis/view/components/button_component";
+import { ApplyMergerModeModal } from "oxalis/view/right-border-tabs/starting_job_modals";
 import Constants, {
   ToolsWithOverwriteCapabilities,
   type AnnotationTool,
@@ -187,6 +188,7 @@ function AdditionalSkeletonModesButtons() {
   const isMergerModeEnabled = useSelector(
     state => state.temporaryConfiguration.isMergerModeEnabled,
   );
+  const [showApplyMergerModeModal, setShowApplyMergerModeModal] = useState<boolean>(false);
   const isNewNodeNewTreeModeOn = useSelector(state => state.userConfiguration.newNodeNewTree);
   const toggleNewNodeNewTreeMode = () =>
     dispatch(updateUserSettingAction("newNodeNewTree", !isNewNodeNewTreeModeOn));
@@ -222,6 +224,18 @@ function AdditionalSkeletonModesButtons() {
           />
         </ButtonComponent>
       </Tooltip>
+      {isMergerModeEnabled && (
+        <Tooltip title="Apply this merger mode tracing.">
+          <ButtonComponent
+            style={narrowButtonStyle}
+            onClick={() => setShowApplyMergerModeModal(true)}
+            faIcon="fa fa-cogs"
+          />
+        </Tooltip>
+      )}
+      {showApplyMergerModeModal && (
+        <ApplyMergerModeModal handleClose={() => setShowApplyMergerModeModal(false)} />
+      )}
     </React.Fragment>
   );
 }

frontend/javascripts/oxalis/view/right-border-tabs/starting_job_modals.js

@@ -2,12 +2,16 @@
 import React, { useEffect, useState, type Node } from "react";
 import { type APIDataset, type APIJob } from "types/api_flow_types";
 import { Modal, Select, Button } from "antd";
-import { startNucleiInferralJob, startNeuronInferralJob } from "admin/admin_rest_api";
+import {
+  startNucleiInferralJob,
+  startNeuronInferralJob,
+  startApplyMergerModeJob,
+} from "admin/admin_rest_api";
 import { useSelector } from "react-redux";
-import { getColorLayers } from "oxalis/model/accessors/dataset_accessor";
+import { getColorLayers, getSegmentationLayers } from "oxalis/model/accessors/dataset_accessor";
 import { getUserBoundingBoxesFromState } from "oxalis/model/accessors/tracing_accessor";
 import Toast from "libs/toast";
-import { type OxalisState, type UserBoundingBox } from "oxalis/store";
+import { type UserBoundingBox } from "oxalis/store";
 import { Unicode, type Vector3 } from "oxalis/constants";
 import { capitalizeWords, computeArrayFromBoundingBox, rgbToHex } from "libs/utils";
 
@@ -28,23 +32,26 @@ type StartingJobModalProps = {
   jobName: string,
   description: Node,
   isBoundingBoxConfigurable?: boolean,
+  chooseSegmentationLayer?: boolean,
 };
 
 function StartingJobModal(props: StartingJobModalProps) {
   const isBoundingBoxConfigurable = props.isBoundingBoxConfigurable || false;
+  const chooseSegmentationLayer = props.chooseSegmentationLayer || false;
   const { dataset, handleClose, jobName, description, jobApiCall } = props;
-  const userBoundingBoxes = useSelector((state: OxalisState) =>
-    getUserBoundingBoxesFromState(state),
-  );
-  const [selectedColorLayerName, setSelectedColorLayerName] = useState<?string>(null);
+  const userBoundingBoxes = useSelector(state => getUserBoundingBoxesFromState(state));
+  const [selectedLayerName, setSelectedLayerName] = useState<?string>(null);
   const [selectedBoundingBox, setSelectedBoundingBox] = useState<?UserBoundingBox>(null);
-  const colorLayerNames = getColorLayers(dataset).map(layer => layer.name);
+  const layerNames = (chooseSegmentationLayer
+    ? getSegmentationLayers(dataset)
+    : getColorLayers(dataset)
+  ).map(layer => layer.name);
   useEffect(() => {
-    if (colorLayerNames.length === 1) {
-      setSelectedColorLayerName(colorLayerNames[0]);
+    if (layerNames.length === 1) {
+      setSelectedLayerName(layerNames[0]);
     }
   });
-  if (colorLayerNames.length < 1) {
+  if (layerNames.length < 1) {
     return null;
   }
   const onChangeBoundingBox = (selectedBBoxId: number) => {
@@ -54,15 +61,15 @@ function StartingJobModal(props: StartingJobModalProps) {
     }
   };
   const startJob = async () => {
-    if (selectedColorLayerName == null) {
+    if (selectedLayerName == null) {
       return;
     }
     try {
       let apiJob;
       if (isBoundingBoxConfigurable) {
-        apiJob = await jobApiCall(selectedColorLayerName, selectedBoundingBox);
+        apiJob = await jobApiCall(selectedLayerName, selectedBoundingBox);
       } else {
-        apiJob = await jobApiCall(selectedColorLayerName);
+        apiJob = await jobApiCall(selectedLayerName);
       }
       if (!apiJob) {
         return;
@@ -87,24 +94,24 @@ function StartingJobModal(props: StartingJobModalProps) {
   };
 
   const ColorLayerSelection = (): Node =>
-    colorLayerNames.length > 1 ? (
+    layerNames.length > 1 ? (
       <React.Fragment>
-        <p>Please select the layer that should be used for the inferral.</p>
+        <p>Please select the layer that should be used for this job.</p>
         <div style={{ textAlign: "center" }}>
           <Select
             showSearch
             style={{ width: 300 }}
             placeholder="Select a color layer"
             optionFilterProp="children"
-            value={selectedColorLayerName}
-            onChange={setSelectedColorLayerName}
+            value={selectedLayerName}
+            onChange={setSelectedLayerName}
             filterOption={(input, option) =>
               option.children.toLowerCase().indexOf(input.toLowerCase()) >= 0
             }
           >
-            {colorLayerNames.map(colorLayerName => (
-              <Select.Option key={colorLayerName} value={colorLayerName}>
-                {colorLayerName}
+            {layerNames.map(layerName => (
+              <Select.Option key={layerName} value={layerName}>
+                {layerName}
               </Select.Option>
             ))}
           </Select>
@@ -166,7 +173,7 @@ function StartingJobModal(props: StartingJobModalProps) {
     ) : null;
 
   const hasUnselectedOptions =
-    selectedColorLayerName == null || (isBoundingBoxConfigurable && selectedBoundingBox == null);
+    selectedLayerName == null || (isBoundingBoxConfigurable && selectedBoundingBox == null);
 
   return (
     <Modal
@@ -198,7 +205,7 @@ function StartingJobModal(props: StartingJobModalProps) {
 }
 
 export function NucleiInferralModal({ handleClose }: Props) {
-  const dataset = useSelector((state: OxalisState) => state.dataset);
+  const dataset = useSelector(state => state.dataset);
   return (
     <StartingJobModal
       dataset={dataset}
@@ -229,7 +236,7 @@ export function NucleiInferralModal({ handleClose }: Props) {
 }
 
 export function NeuronInferralModal({ handleClose }: Props) {
-  const dataset = useSelector((state: OxalisState) => state.dataset);
+  const dataset = useSelector(state => state.dataset);
   return (
     <StartingJobModal
       dataset={dataset}
@@ -268,3 +275,34 @@ export function NeuronInferralModal({ handleClose }: Props) {
     />
   );
 }
+
+export function ApplyMergerModeModal({ handleClose }: Props) {
+  const dataset = useSelector(state => state.dataset);
+  const annotationId = useSelector(store => store.tracing.annotationId);
+  return (
+    <StartingJobModal
+      dataset={dataset}
+      handleClose={handleClose}
+      jobName="apply merger mode"
+      chooseSegmentationLayer
+      jobApiCall={async colorLayerName =>
+        startApplyMergerModeJob(
+          dataset.owningOrganization,
+          dataset.name,
+          colorLayerName,
+          annotationId,
+        )
+      }
+      description={
+        <>
+          <p>
+            Start a job that take the current state of this merger mode tracing and apply it to the
+            segmentation layer. This will create a new dataset which contains the merged
+            segmentation layer. If this dataset has more than one segmentation layer, please select
+            the segmentation layer to the merging should be applied to.
+          </p>
+        </>
+      }
+    />
+  );
+}