Add UI to globalize incomplete floodfill(s)

app/controllers/JobsController.scala

@@ -131,6 +131,39 @@ class JobsController @Inject()(jobDAO: JobDAO,
       }
     }
 
+  def runGlobalizeFloodfills(
+      organizationName: String,
+      dataSetName: String,
+      newDataSetName: Option[String],
+      layerName: Option[String],
+      annotationId: Option[String],
+      annotationType: 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.globalizeFloodfill.notAllowed.organization" ~> FORBIDDEN
+          dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organization._id) ?~> Messages(
+            "dataSet.notFound",
+            dataSetName) ~> NOT_FOUND
+          command = "globalize_floodfills"
+          commandArgs = Json.obj(
+            "organization_name" -> organizationName,
+            "dataset_name" -> dataSetName,
+            "new_dataset_name" -> newDataSetName,
+            "layer_name" -> layerName,
+            "annotation_id" -> annotationId,
+            "annotation_type" -> annotationType,
+            "webknossos_token" -> RpcTokenHolder.webKnossosToken,
+          )
+          job <- jobService.submitJob(command, commandArgs, request.identity, dataSet._dataStore) ?~> "job.couldNotRunGlobalizeFloodfills"
+          js <- jobService.publicWrites(job)
+        } yield Ok(js)
+      }
+    }
+
   def runExportTiffJob(organizationName: String,
                        dataSetName: String,
                        bbox: String,

conf/application.conf

@@ -78,7 +78,7 @@ features {
   taskReopenAllowedInSeconds = 30
   allowDeleteDatasets = true
   # to enable jobs for local development, use "yarn enable-jobs" to also activate it in the database
-  jobsEnabled = false
+  jobsEnabled = true
   # For new users, the dashboard will show a banner which encourages the user to check out the following dataset.
   # If isDemoInstance == true, `/createExplorative/hybrid/true` is appended to the URL so that a new tracing is opened.
   # If isDemoInstance == false, `/view` is appended to the URL so that it's opened in view mode (since the user might not

conf/messages

@@ -334,6 +334,7 @@ job.couldNotRunCubing = Failed to start WKW conversion job.
 job.couldNotRunTiffExport = Failed to start Tiff export job.
 job.couldNotRunComputeMeshFile = Failed to start mesh file computation job.
 job.couldNotRunNucleiInferral = Failed to start nuclei inferral job.
+job.couldNotRunGlobalizeFloodfills = Failed to start job for globalizing floodfills.
 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.
@@ -343,6 +344,7 @@ job.export.tiff.edgeLengthExceeded = An edge length of the selected bounding box
 job.export.notAllowed.organization = Currently tiff export is only allowed for datasets of your own organization.
 job.inferNuclei.notAllowed.organization = Currently nuclei 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.
 
 agglomerateSkeleton.failed=Could not generate agglomerate skeleton.
 

conf/webknossos.latest.routes

@@ -204,6 +204,7 @@ GET           /jobs/run/convertToWkw/:organizationName/:dataSetName            c
 GET           /jobs/run/computeMeshFile/:organizationName/:dataSetName         controllers.JobsController.runComputeMeshFileJob(organizationName: String, dataSetName: String, layerName: String, mag: String, agglomerateView: Option[String])
 GET           /jobs/run/exportTiff/:organizationName/:dataSetName              controllers.JobsController.runExportTiffJob(organizationName: String, dataSetName: String, bbox: String, layerName: Option[String], tracingId: Option[String], tracingVersion: Option[String], annotationId: Option[String], annotationType: Option[String], hideUnmappedIds: Option[Boolean], mappingName: Option[String], mappingType: Option[String])
 GET           /jobs/run/inferNuclei/:organizationName/:dataSetName             controllers.JobsController.runInferNucleiJob(organizationName: String, dataSetName: String, layerName: Option[String])
+GET           /jobs/run/globalizeFloodfills/:organizationName/:dataSetName     controllers.JobsController.runGlobalizeFloodfills(organizationName: String, dataSetName: String, newDataSetName: Option[String], layerName: Option[String], annotationId: Option[String], annotationType: Option[String])
 GET           /jobs/:id                                                        controllers.JobsController.get(id: String)
 GET           /jobs/:id/downloadExport/:exportFileName                         controllers.JobsController.downloadExport(id: String, exportFileName: String)
 POST          /jobs/:id/status                                                 controllers.WKRemoteWorkerController.updateJobStatus(id: String)

frontend/javascripts/admin/admin_rest_api.js

@@ -1011,6 +1011,19 @@ export function startNucleiInferralJob(
   );
 }
 
+export function startGlobalizeFloodfillsJob(
+  organizationName: string,
+  datasetName: string,
+  newDataSetName: string,
+  layerName: string,
+  annotationId: string,
+  annotationType: APIAnnotationType,
+): Promise<APIJob> {
+  return Request.receiveJSON(
+    `/api/jobs/run/globalizeFloodfills/${organizationName}/${datasetName}?newDataSetName=${newDataSetName}&layerName=${layerName}&annotationId=${annotationId}&annotationType=${annotationType}`,
+  );
+}
+
 export function getDatasetDatasource(
   dataset: APIMaybeUnimportedDataset,
 ): Promise<APIDataSourceWithMessages> {

frontend/javascripts/dashboard/advanced_dataset/dataset_table.js

@@ -1,30 +1,35 @@
 // @flow
 
-import { Table, Tag } from "antd";
+import {
+  CheckCircleOutlined,
+  CloseCircleOutlined,
+  PlusOutlined,
+  WarningOutlined,
+} from "@ant-design/icons";
+import { Link } from "react-router-dom";
+import { Table, Tag, Tooltip } from "antd";
 import * as React from "react";
-import { CheckCircleOutlined, CloseCircleOutlined, PlusOutlined } from "@ant-design/icons";
 import _ from "lodash";
-import { Link } from "react-router-dom";
 import dice from "dice-coefficient";
 import update from "immutability-helper";
 
-import EditableTextIcon from "oxalis/view/components/editable_text_icon";
 import type {
   APITeam,
   APIMaybeUnimportedDataset,
   APIDatasetId,
   APIDataset,
 } from "types/api_flow_types";
-import { stringToColor, formatScale } from "libs/format_utils";
 import type { DatasetFilteringMode } from "dashboard/dataset_view";
-import DatasetAccessListView from "dashboard/advanced_dataset/dataset_access_list_view";
-import DatasetActionView from "dashboard/advanced_dataset/dataset_action_view";
-import FormattedDate from "components/formatted_date";
 import { getDatasetExtentAsString } from "oxalis/model/accessors/dataset_accessor";
+import { stringToColor, formatScale } from "libs/format_utils";
 import { trackAction } from "oxalis/model/helpers/analytics";
+import CategorizationLabel from "oxalis/view/components/categorization_label";
+import DatasetAccessListView from "dashboard/advanced_dataset/dataset_access_list_view";
+import DatasetActionView from "dashboard/advanced_dataset/dataset_action_view";
+import EditableTextIcon from "oxalis/view/components/editable_text_icon";
 import FixedExpandableTable from "components/fixed_expandable_table";
+import FormattedDate from "components/formatted_date";
 import * as Utils from "libs/utils";
-import CategorizationLabel from "oxalis/view/components/categorization_label";
 
 const { Column } = Table;
 
@@ -255,9 +260,9 @@ class DatasetTable extends React.PureComponent<Props, State> {
                 />
               </div>
             ) : (
-              <div style={{ color: "@disabled-color" }}>
-                Not tags available for inactive datasets.
-              </div>
+              <Tooltip title="No tags available for inactive datasets">
+                <WarningOutlined style={{ color: "@disabled-color" }} />
+              </Tooltip>
             )
           }
         />

frontend/javascripts/oxalis/view/components/categorization_label.js

@@ -22,7 +22,13 @@ type FilterProps = {|
 export default function CategorizationLabel({ tag, kind, onClick, onClose, closable }: LabelProps) {
   return (
     <Tooltip title={`Click to only show ${kind} with this tag.`}>
-      <Tag color={stringToColor(tag)} onClick={onClick} onClose={onClose} closable={closable}>
+      <Tag
+        color={stringToColor(tag)}
+        onClick={onClick}
+        onClose={onClose}
+        closable={closable}
+        style={{ cursor: "pointer" }}
+      >
         {tag}
       </Tag>
     </Tooltip>
@@ -63,6 +69,7 @@ export function CategorizationSearch({ searchTags, setTags, localStorageSavingKe
           onClose={() => {
             removeTag(tag);
           }}
+          style={{ cursor: "pointer" }}
           closable
         >
           {tag}

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

@@ -1,30 +1,32 @@
-/**
- * tracing_settings_view.js
- * @flow
- */
-import { Tooltip } from "antd";
+// @flow
+import { Button, Tooltip } from "antd";
 import { PlusSquareOutlined } from "@ant-design/icons";
 import { useSelector, useDispatch } from "react-redux";
 import React, { useState } from "react";
 import _ from "lodash";
 
-import { setPositionAction } from "oxalis/model/actions/flycam_actions";
-import type { Vector3, Vector6, BoundingBoxType } from "oxalis/constants";
 import { UserBoundingBoxInput } from "oxalis/view/components/setting_input_views";
-import { getSomeTracing } from "oxalis/model/accessors/tracing_accessor";
+import type { Vector3, Vector6, BoundingBoxType } from "oxalis/constants";
 import {
   changeUserBoundingBoxAction,
   addUserBoundingBoxAction,
   deleteUserBoundingBoxAction,
 } from "oxalis/model/actions/annotation_actions";
+import { getSomeTracing } from "oxalis/model/accessors/tracing_accessor";
+import { hasVolumeTracings } from "oxalis/model/accessors/volumetracing_accessor";
+import { setPositionAction } from "oxalis/model/actions/flycam_actions";
+import { startGlobalizeFloodfillsJob } from "admin/admin_rest_api";
+import ExportBoundingBoxModal from "oxalis/view/right-border-tabs/export_bounding_box_modal";
 import * as Utils from "libs/utils";
+import features from "features";
 
-import ExportBoundingBoxModal from "oxalis/view/right-border-tabs/export_bounding_box_modal";
+const GLOBALIZE_FLOODFILL_REGEX = /Limits of flood-fill \(source_id=(\d+), target_id=(\d+), seed=([\d,]+), timestamp=(\d+)\)/;
 
 export default function BoundingBoxTab() {
   const [selectedBoundingBoxForExport, setSelectedBoundingBoxForExport] = useState(null);
   const tracing = useSelector(state => state.tracing);
   const dataset = useSelector(state => state.dataset);
+  const activeUser = useSelector(state => state.activeUser);
   const { userBoundingBoxes } = getSomeTracing(tracing);
 
   const dispatch = useDispatch();
@@ -60,8 +62,38 @@ export default function BoundingBoxTab() {
     setPosition(center);
   }
 
+  const showGlobalizeFloodfillsButton =
+    features().jobsEnabled &&
+    activeUser != null &&
+    hasVolumeTracings(tracing) != null &&
+    userBoundingBoxes.some(bbox => bbox.name.match(GLOBALIZE_FLOODFILL_REGEX) != null);
+
+  const onGlobalizeFloodfills = () => {
+    startGlobalizeFloodfillsJob(
+      dataset.owningOrganization,
+      dataset.name,
+      `${dataset.name}_with_floodfills`,
+      "segmentation",
+      tracing.annotationId,
+      tracing.annotationType,
+    );
+  };
+
   return (
     <div className="padded-tab-content" style={{ minWidth: 300 }}>
+      {showGlobalizeFloodfillsButton ? (
+        <Tooltip title="For this annotation some floodfill operations were aborted prematurely, because they covered a too big volume. webKnossos can finish these operations via a long-running job.">
+          <Button size="small" style={{ marginBottom: 4 }} onClick={onGlobalizeFloodfills}>
+            <i
+              className="fas fa-fill-drip"
+              style={{
+                opacity: false ? 0.5 : 1,
+              }}
+            />
+            Globalize Flood-Fills
+          </Button>
+        </Tooltip>
+      ) : null}
       {userBoundingBoxes.length > 0 ? (
         userBoundingBoxes.map(bb => (
           <UserBoundingBoxInput