Adds OME-TIFF export

app/controllers/JobsController.scala

@@ -1,13 +1,10 @@
 package controllers
 
-import java.util.Date
-
 import com.mohiva.play.silhouette.api.Silhouette
 import com.scalableminds.util.accesscontext.GlobalAccessContext
 import com.scalableminds.util.tools.Fox
-import javax.inject.Inject
 import models.binary.DataSetDAO
-import models.job.{JobDAO, JobService, JobState, WorkerDAO, WorkerService}
+import models.job._
 import models.organization.OrganizationDAO
 import oxalis.security.{WkEnv, WkSilhouetteEnvironment}
 import oxalis.telemetry.SlackNotificationService
@@ -16,6 +13,8 @@ import play.api.libs.json._
 import play.api.mvc.{Action, AnyContent}
 import utils.{ObjectId, WkConf}
 
+import java.util.Date
+import javax.inject.Inject
 import scala.concurrent.ExecutionContext
 
 class JobsController @Inject()(jobDAO: JobDAO,
@@ -226,12 +225,10 @@ class JobsController @Inject()(jobDAO: JobDAO,
                        dataSetName: String,
                        bbox: String,
                        layerName: Option[String],
+                       mag: Option[String],
                        annotationLayerName: Option[String],
                        annotationId: Option[String],
-                       annotationType: Option[String],
-                       hideUnmappedIds: Option[Boolean],
-                       mappingName: Option[String],
-                       mappingType: Option[String]): Action[AnyContent] =
+                       asOmeTiff: Boolean): Action[AnyContent] =
     sil.SecuredAction.async { implicit request =>
       log(Some(slackNotificationService.noticeFailedJobRequest)) {
         for {
@@ -242,20 +239,20 @@ class JobsController @Inject()(jobDAO: JobDAO,
           userAuthToken <- wkSilhouetteEnvironment.combinedAuthenticatorService.findOrCreateToken(
             request.identity.loginInfo)
           command = "export_tiff"
-          exportFileName = s"${formatDateForFilename(new Date())}__${dataSetName}__${annotationLayerName.map(_ => "volume").getOrElse(layerName.getOrElse(""))}.zip"
+          exportFileName = if (asOmeTiff)
+            s"${formatDateForFilename(new Date())}__${dataSetName}__${annotationLayerName.map(_ => "volume").getOrElse(layerName.getOrElse(""))}.ome.tif"
+          else
+            s"${formatDateForFilename(new Date())}__${dataSetName}__${annotationLayerName.map(_ => "volume").getOrElse(layerName.getOrElse(""))}.zip"
           commandArgs = Json.obj(
             "organization_name" -> organizationName,
             "dataset_name" -> dataSetName,
             "bbox" -> bbox,
             "export_file_name" -> exportFileName,
             "layer_name" -> layerName,
+            "mag" -> mag,
             "user_auth_token" -> userAuthToken.id,
             "annotation_layer_name" -> annotationLayerName,
-            "annotation_id" -> annotationId,
-            "annotation_type" -> annotationType,
-            "mapping_name" -> mappingName,
-            "mapping_type" -> mappingType,
-            "hide_unmapped_ids" -> hideUnmappedIds
+            "annotation_id" -> annotationId
           )
           job <- jobService.submitJob(command, commandArgs, request.identity, dataSet._dataStore) ?~> "job.couldNotRunTiffExport"
           js <- jobService.publicWrites(job)

conf/webknossos.latest.routes

@@ -251,7 +251,7 @@ GET           /jobs
 GET           /jobs/status                                                              controllers.JobsController.status
 POST          /jobs/run/convertToWkw/:organizationName/:dataSetName                     controllers.JobsController.runConvertToWkwJob(organizationName: String, dataSetName: String, scale: String)
 POST          /jobs/run/computeMeshFile/:organizationName/:dataSetName                  controllers.JobsController.runComputeMeshFileJob(organizationName: String, dataSetName: String, layerName: String, mag: String, agglomerateView: Option[String])
-POST          /jobs/run/exportTiff/:organizationName/:dataSetName                       controllers.JobsController.runExportTiffJob(organizationName: String, dataSetName: String, bbox: String, layerName: Option[String], annotationLayerName: Option[String], annotationId: Option[String], annotationType: Option[String], hideUnmappedIds: Option[Boolean], mappingName: Option[String], mappingType: Option[String])
+POST          /jobs/run/exportTiff/:organizationName/:dataSetName                       controllers.JobsController.runExportTiffJob(organizationName: String, dataSetName: String, bbox: String, layerName: Option[String], mag: Option[String], annotationLayerName: Option[String], annotationId: Option[String], asOmeTiff: Boolean)
 POST          /jobs/run/inferNuclei/:organizationName/:dataSetName                      controllers.JobsController.runInferNucleiJob(organizationName: String, dataSetName: String, layerName: String, newDatasetName: String)
 POST          /jobs/run/inferNeurons/:organizationName/:dataSetName                     controllers.JobsController.runInferNeuronsJob(organizationName: String, dataSetName: String, layerName: String, bbox: String, newDatasetName: String)
 POST          /jobs/run/globalizeFloodfills/:organizationName/:dataSetName              controllers.JobsController.runGlobalizeFloodfills(organizationName: String, dataSetName: String, fallbackLayerName: String, annotationId: String, annotationType: String, newDatasetName: String, volumeLayerName: Option[String])

frontend/javascripts/admin/admin_rest_api.ts

@@ -1086,6 +1086,29 @@ export async function getJobs(): Promise<APIJob[]> {
   );
 }
 
+export async function getJob(jobId: string): Promise<APIJob> {
+  const job = await Request.receiveJSON(`/api/jobs/${jobId}`);
+  return {
+    id: job.id,
+    type: job.command,
+    datasetName: job.commandArgs.dataset_name,
+    organizationName: job.commandArgs.organization_name,
+    layerName: job.commandArgs.layer_name || job.commandArgs.volume_layer_name,
+    annotationLayerName: job.commandArgs.annotation_layer_name,
+    boundingBox: job.commandArgs.bbox,
+    exportFileName: job.commandArgs.export_file_name,
+    tracingId: job.commandArgs.volume_tracing_id,
+    annotationId: job.commandArgs.annotation_id,
+    annotationType: job.commandArgs.annotation_type,
+    mergeSegments: job.commandArgs.merge_segments,
+    state: adaptJobState(job.command, job.state, job.manualState),
+    manualState: job.manualState,
+    result: job.returnValue,
+    resultLink: job.resultLink,
+    createdAt: job.created,
+  };
+}
+
 function adaptJobState(
   command: string,
   celeryState: APIJobCeleryState,
@@ -1141,26 +1164,26 @@ export async function startExportTiffJob(
   organizationName: string,
   bbox: Vector6,
   layerName: string | null | undefined,
+  mag: string | null | undefined,
   annotationId: string | null | undefined,
-  annotationType: APIAnnotationType | null | undefined,
   annotationLayerName: string | null | undefined,
-  mappingName: string | null | undefined,
-  mappingType: string | null | undefined,
-  hideUnmappedIds: boolean | null | undefined,
+  asOmeTiff: boolean,
 ): Promise<APIJob> {
-  const layerNameSuffix = layerName != null ? `&layerName=${layerName}` : "";
-  const annotationIdSuffix = annotationId != null ? `&annotationId=${annotationId}` : "";
-  const annotationTypeSuffix = annotationType != null ? `&annotationType=${annotationType}` : "";
-  const annotationLayerNameSuffix =
-    annotationLayerName != null ? `&annotationLayerName=${annotationLayerName}` : "";
-  const mappingNameSuffix = mappingName != null ? `&mappingName=${mappingName}` : "";
-  const mappingTypeSuffix = mappingType != null ? `&mappingType=${mappingType}` : "";
-  const hideUnmappedIdsSuffix =
-    hideUnmappedIds != null ? `&hideUnmappedIds=${hideUnmappedIds.toString()}` : "";
+  const params = new URLSearchParams({ bbox: bbox.join(","), asOmeTiff: asOmeTiff.toString() });
+  if (layerName != null) {
+    params.append("layerName", layerName);
+  }
+  if (mag != null) {
+    params.append("mag", mag);
+  }
+  if (annotationId != null) {
+    params.append("annotationId", annotationId);
+  }
+  if (annotationLayerName != null) {
+    params.append("annotationLayerName", annotationLayerName);
+  }
   return Request.receiveJSON(
-    `/api/jobs/run/exportTiff/${organizationName}/${datasetName}?bbox=${bbox.join(
-      ",",
-    )}${layerNameSuffix}${annotationIdSuffix}${annotationTypeSuffix}${annotationLayerNameSuffix}${mappingNameSuffix}${mappingTypeSuffix}${hideUnmappedIdsSuffix}`,
+    `/api/jobs/run/exportTiff/${organizationName}/${datasetName}?${params}`,
     {
       method: "POST",
     },

frontend/javascripts/admin/job/job_list_view.tsx

@@ -283,7 +283,6 @@ class JobListView extends React.PureComponent<Props, State> {
   };
 
   renderState = (__: any, job: APIJob) => {
-    // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
     const { tooltip, icon } = TOOLTIP_MESSAGES_AND_ICONS[job.state];
 
     const jobStateNormalized = _.capitalize(job.state.toLowerCase());
@@ -299,75 +298,68 @@ class JobListView extends React.PureComponent<Props, State> {
   render() {
     return (
       <div className="container">
+        <div className="pull-right">
+          <Search
+            style={{
+              width: 200,
+            }}
+            onPressEnter={this.handleSearch}
+            onChange={this.handleSearch}
+            value={this.state.searchQuery}
+          />
+        </div>
+        <h3>Jobs</h3>
         <div
+          className="clearfix"
           style={{
-            // @ts-expect-error ts-migrate(2322) FIXME: Type '{ marginTag: number; }' is not assignable to... Remove this comment to see the full error message
-            marginTag: 20,
+            margin: "20px 0px",
           }}
-        >
-          <div className="pull-right">
-            <Search
-              style={{
-                width: 200,
-              }}
-              onPressEnter={this.handleSearch}
-              onChange={this.handleSearch}
-              value={this.state.searchQuery}
-            />
-          </div>
-          <h3>Jobs</h3>
-          <div
-            className="clearfix"
+        />
+
+        <Spin spinning={this.state.isLoading} size="large">
+          <Table
+            dataSource={Utils.filterWithSearchQueryAND(
+              this.state.jobs,
+              ["datasetName"],
+              this.state.searchQuery,
+            )}
+            rowKey="id"
+            pagination={{
+              defaultPageSize: 50,
+            }}
             style={{
-              margin: "20px 0px",
+              marginTop: 30,
+              marginBottom: 30,
             }}
-          />
-
-          <Spin spinning={this.state.isLoading} size="large">
-            <Table
-              dataSource={Utils.filterWithSearchQueryAND(
-                this.state.jobs,
-                ["datasetName"],
-                this.state.searchQuery,
-              )}
-              rowKey="id"
-              pagination={{
-                defaultPageSize: 50,
-              }}
-              style={{
-                marginTop: 30,
-                marginBottom: 30,
-              }}
-            >
-              <Column
-                title="Job Id"
-                dataIndex="id"
-                key="id"
-                sorter={Utils.localeCompareBy(typeHint, (job) => job.id)}
-              />
-              <Column title="Description" key="datasetName" render={this.renderDescription} />
-              <Column
-                title="Created at"
-                key="createdAt"
-                render={(job) => <FormattedDate timestamp={job.createdAt} />}
-                sorter={Utils.compareBy(typeHint, (job) => job.createdAt)}
-              />
-              <Column
-                title="State"
-                key="state"
-                render={this.renderState}
-                sorter={Utils.localeCompareBy(typeHint, (job) => job.state)}
-              />
-              <Column
-                title="Action"
-                key="actions"
-                fixed="right"
-                width={150}
-                render={this.renderActions}
-              />
-            </Table>
-          </Spin>
-        </div>
+          >
+            <Column
+              title="Job Id"
+              dataIndex="id"
+              key="id"
+              sorter={Utils.localeCompareBy(typeHint, (job) => job.id)}
+            />
+            <Column title="Description" key="datasetName" render={this.renderDescription} />
+            <Column
+              title="Created at"
+              key="createdAt"
+              render={(job) => <FormattedDate timestamp={job.createdAt} />}
+              sorter={Utils.compareBy(typeHint, (job) => job.createdAt)}
+            />
+            <Column
+              title="State"
+              key="state"
+              render={this.renderState}
+              sorter={Utils.localeCompareBy(typeHint, (job) => job.state)}
+            />
+            <Column
+              title="Action"
+              key="actions"
+              fixed="right"
+              width={150}
+              render={this.renderActions}
+            />
+          </Table>
+        </Spin>
       </div>
     );
   }

frontend/javascripts/dashboard/dataset_view.tsx

@@ -459,7 +459,6 @@ function NewJobsAlert({ jobs }: { jobs: APIJob[] }) {
       }}
     >
       {newJobs.slice(0, MAX_JOBS_TO_DISPLAY).map((job) => {
-        // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
         const { tooltip, icon } = TOOLTIP_MESSAGES_AND_ICONS[job.state];
         return (
           <Row key={job.id} gutter={16}>

frontend/javascripts/libs/utils.ts

@@ -299,6 +299,10 @@ export function computeArrayFromBoundingBox(bb: BoundingBoxType): Vector6 {
   ];
 }
 
+export function computeShapeFromBoundingBox(bb: BoundingBoxType): Vector3 {
+  return [bb.max[0] - bb.min[0], bb.max[1] - bb.min[1], bb.max[2] - bb.min[2]];
+}
+
 export function aggregateBoundingBox(boundingBoxes: Array<BoundingBoxObject>): BoundingBoxType {
   if (boundingBoxes.length === 0) {
     return {

frontend/javascripts/messages.tsx

@@ -331,9 +331,9 @@ instead. Only enable this option if you understand its effect. All layers will n
     "Updating the sharing options for the annotation failed. Please retry or see the error message in the console.",
   "annotation.download": "The following annotation data is available for download immediately.",
   "annotation.export":
-    "Exporting this annotation as TIFF images will trigger a background job to prepare data for download. This may take a while depending on the size of your dataset as well as bounding box and layer selection. You can monitor the progress and start the download from the ",
+    "Export this annotation as TIFF image(s). This may take a few moments depending on the size of your configured export.",
   "annotation.export_no_worker":
-    "This WEBKNOSSOS instance is not configured to run TIFF export jobs on a dedicated background worker. To learn more about this feature please contact us at ",
+    "This WEBKNOSSOS instance is not configured to run export jobs. To learn more about this feature please contact us at ",
   "annotation.python_do_not_share":
     "These snippets are pre-configured and contain your personal access token and annotation meta data. Do not share this information with anyone you do not trust!",
   "annotation.register_for_token": "Please log in to get an access token for the script below.",