Call wk-worker nuclei inferral job (#5626)

* [WIP] call wk-worker nuclei inferral job * add token, show result in job list view * changelog * remove unused import
scalableminds · Jul 26, 2021 · 6f91d7b · 6f91d7b
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diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -12,6 +12,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 
 ### Added
 - Fixed a bug where non-existing resolutions could be selected for wk-worker-based meshfile computations [#5631](https://github.com/scalableminds/webknossos/pull/5631)
+- Added a route to call new webknossos-worker job for nuclei inferral. [#5626](https://github.com/scalableminds/webknossos/pull/5626)
 
 ### Changed
 - 

diff --git a/app/controllers/JobsController.scala b/app/controllers/JobsController.scala
@@ -97,6 +97,26 @@ class JobsController @Inject()(jobDAO: JobDAO,
       } yield Ok(js)
     }
 
+  def runInferNucleiJob(organizationName: String, dataSetName: String, layerName: 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.export.notAllowed.organization" ~> FORBIDDEN
+          command = "infer_nuclei"
+          commandArgs = Json.obj(
+            "organization_name" -> organizationName,
+            "dataset_name" -> dataSetName,
+            "layer_name" -> layerName,
+            "webknossos_token" -> TracingStoreRpcClient.webKnossosToken,
+          )
+          job <- jobService.runJob(command, commandArgs, request.identity) ?~> "job.couldNotRunNucleiInferral"
+          js <- jobService.publicWrites(job)
+        } yield Ok(js)
+      }
+    }
+
   def runExportTiffJob(organizationName: String,
                        dataSetName: String,
                        bbox: String,

diff --git a/conf/messages b/conf/messages
@@ -322,6 +322,7 @@ job.notFound = Job with id {0} could not be found.
 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.disabled = Long-running jobs are not enabled for this webKnossos instance.
 job.export.fileNotFound = Exported file not found. The link may be expired.
 job.export.tiff.invalidBoundingBox = The selected bounding box could not be parsed, must be x,y,z,width,height,depth

diff --git a/conf/webknossos.latest.routes b/conf/webknossos.latest.routes
@@ -201,3 +201,4 @@ GET           /jobs/:id/downloadExport/:exportFileName                         c
 GET           /jobs/run/convertToWkw/:organizationName/:dataSetName            controllers.JobsController.runConvertToWkwJob(organizationName: String, dataSetName: String, scale: String)
 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])
diff --git a/frontend/javascripts/admin/admin_rest_api.js b/frontend/javascripts/admin/admin_rest_api.js
@@ -838,6 +838,7 @@ export async function getJobs(): Promise<Array<APIJob>> {
     annotationType: job.commandArgs.kwargs.annotation_type,
     state: adaptJobState(job.command, job.celeryInfo.state, job.manualState),
     manualState: job.manualState,
+    result: job.celeryInfo.result,
     createdAt: job.created,
   }));
 }

diff --git a/frontend/javascripts/admin/job/job_list_view.js b/frontend/javascripts/admin/job/job_list_view.js
@@ -123,6 +123,20 @@ class JobListView extends React.PureComponent<Props, State> {
           </Link>{" "}
         </span>
       );
+    } else if (
+      job.type === "infer_nuclei" &&
+      job.organizationName &&
+      job.datasetName &&
+      job.layerName
+    ) {
+      return (
+        <span>
+          Nuclei inferral for layer {job.layerName} of{" "}
+          <Link to={`/datasets/${job.organizationName}/${job.datasetName}/view`}>
+            {job.datasetName}
+          </Link>{" "}
+        </span>
+      );
     } else {
       return <span>{job.type}</span>;
     }
@@ -154,6 +168,20 @@ class JobListView extends React.PureComponent<Props, State> {
           )}
         </span>
       );
+    } else if (job.type === "infer_nuclei") {
+      return (
+        <span>
+          {job.state === "SUCCESS" && job.result && this.props.activeUser && (
+            <Link
+              to={`/datasets/${this.props.activeUser.organization}/${job.result}/view`}
+              title="View Segmentation"
+            >
+              <EyeOutlined />
+              View
+            </Link>
+          )}
+        </span>
+      );
     } else return null;
   };
 

diff --git a/frontend/javascripts/types/api_flow_types.js b/frontend/javascripts/types/api_flow_types.js
@@ -568,6 +568,7 @@ export type APIJob = {
   +type: string,
   +state: string,
   +manualState: string,
+  +result: ?string,
   +createdAt: number,
 };