Add UI to globalize incomplete floodfill(s)

app/controllers/AuthenticationController.scala

@@ -29,7 +29,7 @@ import play.api.data.Forms.{email, _}
 import play.api.data.validation.Constraints._
 import play.api.i18n.Messages
 import play.api.libs.json._
-import play.api.mvc.{Action, AnyContent, PlayBodyParsers, _}
+import play.api.mvc.{Action, AnyContent, PlayBodyParsers}
 import utils.{ObjectId, WkConf}
 
 import scala.concurrent.{ExecutionContext, Future}
@@ -384,32 +384,17 @@ class AuthenticationController @Inject()(
   }
 
   def getToken: Action[AnyContent] = sil.SecuredAction.async { implicit request =>
-    val futureOfFuture: Future[Future[Result]] =
-      combinedAuthenticatorService.findByLoginInfo(request.identity.loginInfo).map {
-        case Some(token) => Future.successful(Ok(Json.obj("token" -> token.id)))
-        case _ =>
-          combinedAuthenticatorService.createToken(request.identity.loginInfo).map { newToken =>
-            Ok(Json.obj("token" -> newToken.id))
-          }
-      }
     for {
-      resultFuture <- futureOfFuture
-      result <- resultFuture
-    } yield result
+      token <- combinedAuthenticatorService.findOrCreateToken(request.identity.loginInfo)
+    } yield Ok(Json.obj("token" -> token.id))
   }
 
   def deleteToken(): Action[AnyContent] = sil.SecuredAction.async { implicit request =>
-    val futureOfFuture: Future[Future[Result]] =
-      combinedAuthenticatorService.findByLoginInfo(request.identity.loginInfo).map {
-        case Some(token) =>
-          combinedAuthenticatorService.discard(token, Ok(Json.obj("messages" -> Messages("auth.tokenDeleted"))))
-        case _ => Future.successful(Ok)
-      }
-
-    for {
-      resultFuture <- futureOfFuture
-      result <- resultFuture
-    } yield result
+    combinedAuthenticatorService.findTokenByLoginInfo(request.identity.loginInfo).flatMap {
+      case Some(token) =>
+        combinedAuthenticatorService.discard(token, Ok(Json.obj("messages" -> Messages("auth.tokenDeleted"))))
+      case _ => Future.successful(Ok)
+    }
   }
 
   def logout: Action[AnyContent] = sil.UserAwareAction.async { implicit request =>

app/controllers/JobsController.scala

@@ -9,7 +9,7 @@ import javax.inject.Inject
 import models.binary.DataSetDAO
 import models.job.{JobDAO, JobService, JobState, WorkerDAO, WorkerService}
 import models.organization.OrganizationDAO
-import oxalis.security.WkEnv
+import oxalis.security.{WkEnv, WkSilhouetteEnvironment}
 import oxalis.telemetry.SlackNotificationService
 import play.api.i18n.Messages
 import play.api.libs.json._
@@ -25,6 +25,7 @@ class JobsController @Inject()(jobDAO: JobDAO,
                                workerService: WorkerService,
                                workerDAO: WorkerDAO,
                                wkconf: WkConf,
+                               wkSilhouetteEnvironment: WkSilhouetteEnvironment,
                                slackNotificationService: SlackNotificationService,
                                organizationDAO: OrganizationDAO)(implicit ec: ExecutionContext)
     extends Controller {
@@ -149,6 +150,42 @@ 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)(GlobalAccessContext) ?~> Messages(
+            "organization.notFound",
+            organizationName)
+          _ <- bool2Fox(request.identity._organization == organization._id) ?~> "job.globalizeFloodfill.notAllowed.organization" ~> FORBIDDEN
+          userAuthToken <- wkSilhouetteEnvironment.combinedAuthenticatorService.findOrCreateToken(
+            request.identity.loginInfo)
+          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,
+            "user_auth_token" -> userAuthToken.id,
+          )
+          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,

app/models/job/Job.scala

@@ -319,7 +319,7 @@ class JobService @Inject()(wkConf: WkConf,
       Json.obj(
         "id" -> job._id.id,
         "command" -> job.command,
-        "commandArgs" -> (job.commandArgs - "webknossos_token"),
+        "commandArgs" -> (job.commandArgs - "webknossos_token" - "user_auth_token"),
         "state" -> job.state,
         "manualState" -> job.manualState,
         "latestRunId" -> job.latestRunId,

app/oxalis/security/CombinedAuthenticatorService.scala

@@ -64,6 +64,13 @@ case class CombinedAuthenticatorService(cookieSettings: CookieAuthenticatorSetti
     tokenAuthenticator.map(CombinedAuthenticator(_))
   }
 
+  def findOrCreateToken(loginInfo: LoginInfo): Future[CombinedAuthenticator] =
+    findTokenByLoginInfo(loginInfo).flatMap {
+      case Some(token) => Future.successful(token)
+      case _ =>
+        createToken(loginInfo)
+    }
+
   override def retrieve[B](implicit request: ExtractableRequest[B]): Future[Option[CombinedAuthenticator]] =
     for {
       optionCookie <- cookieAuthenticatorService.retrieve(request)
@@ -73,7 +80,7 @@ case class CombinedAuthenticatorService(cookieSettings: CookieAuthenticatorSetti
     }
 
   // only called in token case
-  def findByLoginInfo(loginInfo: LoginInfo): Future[Option[CombinedAuthenticator]] =
+  def findTokenByLoginInfo(loginInfo: LoginInfo): Future[Option[CombinedAuthenticator]] =
     tokenDao.findOneByLoginInfo(loginInfo, TokenType.Authentication).map(opt => opt.map(CombinedAuthenticator(_)))
 
   // only called in the cookie case

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

@@ -337,6 +337,7 @@ 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.
@@ -346,6 +347,7 @@ 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

@@ -206,6 +206,7 @@ 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)
 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

@@ -1039,6 +1039,19 @@ 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/admin/dataset/dataset_components.js

@@ -31,12 +31,19 @@ export function CardContainer({
   }
 }
 
-export function DatasetNameFormItem({ activeUser }: { activeUser: ?APIUser }) {
+export function DatasetNameFormItem({
+  activeUser,
+  initialName,
+}: {
+  activeUser: ?APIUser,
+  initialName?: string,
+}) {
   return (
     <FormItem
       name="name"
       label="Dataset Name"
       hasFeedback
+      initialValue={initialName}
       rules={[
         { required: true, message: messages["dataset.import.required.name"] },
         { min: 3 },

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" }}>
-                Tags not available for inactive datasets.
-              </div>
+              <Tooltip title="No tags available for inactive datasets">
+                <WarningOutlined style={{ color: "@disabled-color" }} />
+              </Tooltip>
             )
           }
         />

frontend/javascripts/oxalis/model/sagas/volumetracing_saga.js

@@ -55,6 +55,7 @@ import {
   getSegmentsForLayer,
   isVolumeAnnotationDisallowedForZoom,
 } from "oxalis/model/accessors/volumetracing_accessor";
+import { getBBoxNameForPartialFloodfill } from "oxalis/view/right-border-tabs/bounding_box_tab";
 import {
   getPosition,
   getFlooredPosition,
@@ -638,9 +639,7 @@ export function* floodFill(): Saga<void> {
       yield* put(
         addUserBoundingBoxAction({
           boundingBox: coveredBoundingBox,
-          name: `Limits of flood-fill (source_id=${oldSegmentIdAtSeed}, target_id=${activeCellId}, seed=${seedPosition.join(
-            ",",
-          )}, timestamp=${new Date().getTime()})`,
+          name: getBBoxNameForPartialFloodfill(oldSegmentIdAtSeed, activeCellId, seedPosition),
           color: Utils.getRandomColor(),
           isVisible: true,
         }),

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>