Merge branch 'master' of github.com:scalableminds/webknossos into mes…

…sages

* 'master' of github.com:scalableminds/webknossos:
  Remove superfluous datastoreName param for convertToWkw job (#6606)
  When downloading with skipVolumeData, keep volume tag (#6566)
  Fix getNullBucket crash and remove dead code (#6603)
  Hotfix Dataset View Mode

CHANGELOG.unreleased.md

@@ -21,6 +21,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Node positions are always handled as integers. They have always been persisted as integers by the server, anyway, but the session in which a node was created handled the position as floating point in earlier versions. [#6589](https://github.com/scalableminds/webknossos/pull/6589)
 - When merging annotations, bounding boxes are no longer duplicated. [#6576](https://github.com/scalableminds/webknossos/pull/6576)
 - Jobs can no longer be started on datastores without workers. [#6595](https://github.com/scalableminds/webknossos/pull/6595)
+- When downloading volume annotations with volume data skipped, the nml volume tag is now included anyway (but has no location attribute in this case). [#6566](https://github.com/scalableminds/webknossos/pull/6566)
 
 ### Fixed
 

app/controllers/JobsController.scala

@@ -75,26 +75,25 @@ class JobsController @Inject()(jobDAO: JobDAO,
     } yield Ok(js)
   }
 
-  def runConvertToWkwJob(organizationName: String,
-                         dataSetName: String,
-                         scale: String,
-                         dataStoreName: String): Action[AnyContent] =
+  // Note that the dataset has to be registered by reserveUpload via the datastore first.
+  def runConvertToWkwJob(organizationName: String, dataSetName: String, scale: String): Action[AnyContent] =
     sil.SecuredAction.async { implicit request =>
       log(Some(slackNotificationService.noticeFailedJobRequest)) {
         for {
-          _ <- workerService.assertDataStoreHasWorkers(dataStoreName)
           organization <- organizationDAO.findOneByName(organizationName) ?~> Messages("organization.notFound",
                                                                                        organizationName)
           _ <- bool2Fox(request.identity._organization == organization._id) ~> FORBIDDEN
+          dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organization._id) ?~> Messages(
+            "dataSet.notFound",
+            dataSetName) ~> NOT_FOUND
           command = "convert_to_wkw"
           commandArgs = Json.obj(
             "organization_name" -> organizationName,
             "dataset_name" -> dataSetName,
             "scale" -> scale,
             "webknossos_token" -> RpcTokenHolder.webKnossosToken
           )
-
-          job <- jobService.submitJob(command, commandArgs, request.identity, dataStoreName) ?~> "job.couldNotRunCubing"
+          job <- jobService.submitJob(command, commandArgs, request.identity, dataSet._dataStore) ?~> "job.couldNotRunCubing"
           js <- jobService.publicWrites(job)
         } yield Ok(js)
       }
@@ -114,7 +113,6 @@ class JobsController @Inject()(jobDAO: JobDAO,
         dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organization._id) ?~> Messages(
           "dataSet.notFound",
           dataSetName) ~> NOT_FOUND
-        _ <- workerService.assertDataStoreHasWorkers(dataSet._dataStore)
         command = "compute_mesh_file"
         commandArgs = Json.obj(
           "organization_name" -> organizationName,
@@ -142,7 +140,6 @@ class JobsController @Inject()(jobDAO: JobDAO,
           dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organization._id) ?~> Messages(
             "dataSet.notFound",
             dataSetName) ~> NOT_FOUND
-          _ <- workerService.assertDataStoreHasWorkers(dataSet._dataStore)
           command = "infer_nuclei"
           commandArgs = Json.obj(
             "organization_name" -> organizationName,
@@ -171,7 +168,6 @@ class JobsController @Inject()(jobDAO: JobDAO,
           dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organization._id) ?~> Messages(
             "dataSet.notFound",
             dataSetName) ~> NOT_FOUND
-          _ <- workerService.assertDataStoreHasWorkers(dataSet._dataStore)
           command = "infer_neurons"
           commandArgs = Json.obj(
             "organization_name" -> organizationName,
@@ -208,7 +204,6 @@ class JobsController @Inject()(jobDAO: JobDAO,
           dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organization._id) ?~> Messages(
             "dataSet.notFound",
             dataSetName) ~> NOT_FOUND
-          _ <- workerService.assertDataStoreHasWorkers(dataSet._dataStore)
           command = "globalize_floodfills"
           commandArgs = Json.obj(
             "organization_name" -> organizationName,
@@ -244,7 +239,6 @@ class JobsController @Inject()(jobDAO: JobDAO,
             "dataSet.notFound",
             dataSetName) ~> NOT_FOUND
           _ <- jobService.assertTiffExportBoundingBoxLimits(bbox)
-          _ <- workerService.assertDataStoreHasWorkers(dataSet._dataStore)
           userAuthToken <- wkSilhouetteEnvironment.combinedAuthenticatorService.findOrCreateToken(
             request.identity.loginInfo)
           command = "export_tiff"
@@ -287,7 +281,6 @@ class JobsController @Inject()(jobDAO: JobDAO,
           dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organization._id) ?~> Messages(
             "dataSet.notFound",
             dataSetName) ~> NOT_FOUND
-          _ <- workerService.assertDataStoreHasWorkers(dataSet._dataStore)
           userAuthToken <- wkSilhouetteEnvironment.combinedAuthenticatorService.findOrCreateToken(
             request.identity.loginInfo)
           command = "materialize_volume_annotation"

app/controllers/WKRemoteDataStoreController.scala

@@ -45,7 +45,7 @@ class WKRemoteDataStoreController @Inject()(
   val bearerTokenService: WebknossosBearerTokenAuthenticatorService =
     wkSilhouetteEnvironment.combinedAuthenticatorService.tokenAuthenticatorService
 
-  def validateDataSetUpload(name: String, key: String, token: String): Action[ReserveUploadInformation] =
+  def reserveDataSetUpload(name: String, key: String, token: String): Action[ReserveUploadInformation] =
     Action.async(validateJson[ReserveUploadInformation]) { implicit request =>
       dataStoreService.validateAccess(name, key) { dataStore =>
         val uploadInfo = request.body

app/models/annotation/nml/NmlWriter.scala

@@ -206,21 +206,21 @@ class NmlWriter @Inject()(implicit ec: ExecutionContext) extends FoxImplicits {
                         isSingle: Boolean,
                         volumeFilename: Option[String],
                         skipVolumeData: Boolean)(implicit writer: XMLStreamWriter): Unit =
-    if (skipVolumeData) {
-      writer.writeComment(
-        f"A volume layer named ${volumeLayer.name} (id = $index) was omitted here while downloading this annotation without volume data.")
-    } else {
-      Xml.withinElementSync("volume") {
-        writer.writeAttribute("id", index.toString)
+    Xml.withinElementSync("volume") {
+      writer.writeAttribute("id", index.toString)
+      writer.writeAttribute("name", volumeLayer.name)
+      if (!skipVolumeData) {
         writer.writeAttribute("location", volumeFilename.getOrElse(volumeLayer.volumeDataZipName(index, isSingle)))
-        writer.writeAttribute("name", volumeLayer.name)
-        volumeLayer.tracing match {
-          case Right(volumeTracing) =>
-            volumeTracing.fallbackLayer.foreach(writer.writeAttribute("fallbackLayer", _))
-            volumeTracing.largestSegmentId.foreach(id => writer.writeAttribute("largestSegmentId", id.toString))
-            writeVolumeSegmentMetadata(volumeTracing.segments)
-          case _ => ()
-        }
+      }
+      volumeLayer.tracing match {
+        case Right(volumeTracing) =>
+          volumeTracing.fallbackLayer.foreach(writer.writeAttribute("fallbackLayer", _))
+          volumeTracing.largestSegmentId.foreach(id => writer.writeAttribute("largestSegmentId", id.toString))
+          if (skipVolumeData) {
+            writer.writeComment(f"Note that volume data was omitted when downloading this annotation.")
+          }
+          writeVolumeSegmentMetadata(volumeTracing.segments)
+        case _ => ()
       }
     }
 

app/models/job/Job.scala

@@ -264,6 +264,7 @@ class JobService @Inject()(wkConf: WkConf,
                            userDAO: UserDAO,
                            multiUserDAO: MultiUserDAO,
                            jobDAO: JobDAO,
+                           workerDAO: WorkerDAO,
                            dataStoreDAO: DataStoreDAO,
                            organizationDAO: OrganizationDAO,
                            dataSetDAO: DataSetDAO,
@@ -360,14 +361,22 @@ class JobService @Inject()(wkConf: WkConf,
       "job_kwargs" -> job.commandArgs
     )
 
-  def submitJob(command: String, commandArgs: JsObject, owner: User, dataStoreName: String): Fox[Job] =
+  def submitJob(command: String, commandArgs: JsObject, owner: User, dataStoreName: String)(
+      implicit ctx: DBAccessContext): Fox[Job] =
     for {
       _ <- bool2Fox(wkConf.Features.jobsEnabled) ?~> "job.disabled"
+      _ <- assertDataStoreHasWorkers(dataStoreName) ?~> "job.noWorkerForDatastore"
       job = Job(ObjectId.generate, owner._id, dataStoreName, command, commandArgs)
       _ <- jobDAO.insertOne(job)
       _ = analyticsService.track(RunJobEvent(owner, command))
     } yield job
 
+  private def assertDataStoreHasWorkers(dataStoreName: String)(implicit ctx: DBAccessContext): Fox[Unit] =
+    for {
+      _ <- dataStoreDAO.findOneByName(dataStoreName)
+      _ <- workerDAO.findOneByDataStore(dataStoreName)
+    } yield ()
+
   def assertTiffExportBoundingBoxLimits(bbox: String): Fox[Unit] =
     for {
       boundingBox <- BoundingBox.fromLiteral(bbox).toFox ?~> "job.export.tiff.invalidBoundingBox"

app/models/job/Worker.scala

@@ -1,22 +1,21 @@
 package models.job
 
 import akka.actor.ActorSystem
-import com.scalableminds.util.accesscontext.{DBAccessContext, GlobalAccessContext}
+import com.scalableminds.util.accesscontext.GlobalAccessContext
 import com.scalableminds.util.mvc.Formatter
 import com.scalableminds.util.tools.Fox
 import com.scalableminds.webknossos.datastore.helpers.IntervalScheduler
 import com.scalableminds.webknossos.schema.Tables._
 import com.typesafe.scalalogging.LazyLogging
 import models.binary.DataStoreDAO
-
-import javax.inject.Inject
 import oxalis.telemetry.SlackNotificationService
 import play.api.inject.ApplicationLifecycle
 import play.api.libs.json.{JsObject, Json}
 import slick.jdbc.PostgresProfile.api._
 import slick.lifted.Rep
 import utils.{ObjectId, SQLClient, SQLDAO, WkConf}
 
+import javax.inject.Inject
 import scala.concurrent.ExecutionContext
 import scala.concurrent.duration._
 
@@ -83,12 +82,6 @@ class WorkerService @Inject()(conf: WkConf, dataStoreDAO: DataStoreDAO, workerDA
       "lastHeartBeatIsRecent" -> lastHeartBeatIsRecent(worker)
     )
 
-  def assertDataStoreHasWorkers(dataStoreName: String)(implicit ctx: DBAccessContext): Fox[Unit] =
-    for {
-      _ <- dataStoreDAO.findOneByName(dataStoreName)
-      _ <- workerDAO.findOneByDataStore(dataStoreName) ?~> "jobs.noWorkerForDatastore"
-    } yield ()
-
 }
 
 class WorkerLivenessService @Inject()(workerService: WorkerService,

conf/messages

@@ -265,7 +265,7 @@ 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 annotation.
 job.disabled = Long-running jobs are not enabled for this webKnossos instance.
-jobs.worker.notFound = Could not find this worker in the database.
+job.worker.notFound = Could not find this worker in the database.
 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
 job.export.tiff.volumeExceeded = The volume of the selected bounding box is too large.
@@ -275,6 +275,7 @@ job.inferNeurons.notAllowed.organization = Currently neuron inferral is only all
 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.
+job.noWorkerForDatastore = Processing jobs are not available for the datastore this dataset belongs to.
 
 voxelytics.disabled = Voxelytics workflow reporting and logging are not enabled for this webKnossos instance.
 voxelytics.runNotFound = Workflow runs not found

conf/webknossos.latest.routes

@@ -86,7 +86,7 @@ GET           /datastores
 PUT           /datastores/:name/datasource                                              controllers.WKRemoteDataStoreController.updateOne(name: String, key: String)
 PUT           /datastores/:name/datasources                                             controllers.WKRemoteDataStoreController.updateAll(name: String, key: String)
 PATCH         /datastores/:name/status                                                  controllers.WKRemoteDataStoreController.statusUpdate(name: String, key: String)
-POST          /datastores/:name/verifyUpload                                            controllers.WKRemoteDataStoreController.validateDataSetUpload(name: String, key: String, token: String)
+POST          /datastores/:name/reserveUpload                                           controllers.WKRemoteDataStoreController.reserveDataSetUpload(name: String, key: String, token: String)
 POST          /datastores/:name/reportDatasetUpload                                     controllers.WKRemoteDataStoreController.reportDatasetUpload(name: String, key: String, token: String, dataSetName: String, dataSetSizeBytes: Long)
 POST          /datastores/:name/deleteDataset                                           controllers.WKRemoteDataStoreController.deleteDataset(name: String, key: String)
 GET           /datastores/:name/jobExportProperties                                     controllers.WKRemoteDataStoreController.jobExportProperties(name: String, key: String, jobId: String)
@@ -226,7 +226,7 @@ GET           /time/user/:userId
 GET           /jobs/request                                                             controllers.WKRemoteWorkerController.requestJobs(key: String)
 GET           /jobs                                                                     controllers.JobsController.list
 GET           /jobs/status                                                              controllers.JobsController.status
-POST          /jobs/run/convertToWkw/:organizationName/:dataSetName                     controllers.JobsController.runConvertToWkwJob(organizationName: String, dataSetName: String, scale: String, dataStoreName: String)
+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/inferNuclei/:organizationName/:dataSetName                      controllers.JobsController.runInferNucleiJob(organizationName: String, dataSetName: String, layerName: String, newDatasetName: String)

frontend/javascripts/admin/admin_rest_api.ts

@@ -1072,10 +1072,9 @@ export async function startConvertToWkwJob(
   datasetName: string,
   organizationName: string,
   scale: Vector3,
-  datastoreName: string,
 ): Promise<APIJob> {
   return Request.receiveJSON(
-    `/api/jobs/run/convertToWkw/${organizationName}/${datasetName}?scale=${scale.toString()}&dataStoreName=${datastoreName}`,
+    `/api/jobs/run/convertToWkw/${organizationName}/${datasetName}?scale=${scale.toString()}`,
     {
       method: "POST",
     },

frontend/javascripts/admin/dataset/dataset_upload_view.tsx

@@ -310,7 +310,6 @@ class DatasetUploadView extends React.Component<PropsWithFormAndRouter, State> {
                   formValues.name,
                   activeUser.organization,
                   formValues.scale,
-                  datastore.name,
                 );
               } catch (error) {
                 maybeError = error;

frontend/javascripts/oxalis/controller/scene_controller.ts

@@ -392,13 +392,11 @@ class SceneController {
     const taskBoundingBox = getSomeTracing(state.tracing).boundingBox;
     this.buildTaskingBoundingBox(taskBoundingBox);
 
-    if (state.tracing.volumes.length > 0) {
-      this.contour = new ContourGeometry();
-      this.contour.getMeshes().forEach((mesh) => this.annotationToolsGeometryGroup.add(mesh));
+    this.contour = new ContourGeometry();
+    this.contour.getMeshes().forEach((mesh) => this.annotationToolsGeometryGroup.add(mesh));
 
-      this.quickSelectGeometry = new QuickSelectGeometry();
-      this.annotationToolsGeometryGroup.add(this.quickSelectGeometry.getMeshGroup());
-    }
+    this.quickSelectGeometry = new QuickSelectGeometry();
+    this.annotationToolsGeometryGroup.add(this.quickSelectGeometry.getMeshGroup());
 
     if (state.tracing.skeleton != null) {
       this.addSkeleton((_state) => getSkeletonTracing(_state.tracing), true);