Tiff Export Job

CHANGELOG.unreleased.md

@@ -13,6 +13,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Added
 - Added CTRL+Scroll for zooming, which enables pinch-to-zoom on some trackpads. [#5224](https://github.com/scalableminds/webknossos/pull/5224)
 - The time spent on a project is now displayed in the project list. [#5209](https://github.com/scalableminds/webknossos/pull/5209)
+- Added the possibility to export binary data as tiff (if long-runnings jobs are enabled). [#5195](https://github.com/scalableminds/webknossos/pull/5195)
 
 ### Changed
 -

app/controllers/JobsController.scala

@@ -1,6 +1,10 @@
 package controllers
 
+import java.nio.file.{Files, Paths}
+import java.util.Date
+
 import com.mohiva.play.silhouette.api.Silhouette
+import com.scalableminds.util.geometry.BoundingBox
 import com.scalableminds.util.tools.{Fox, FoxImplicits}
 import com.scalableminds.webknossos.datastore.rpc.{RPC, RPCRequest}
 import com.scalableminds.webknossos.schema.Tables.{Jobs, JobsRow}
@@ -91,7 +95,7 @@ class JobService @Inject()(wkConf: WkConf, jobDAO: JobDAO, rpc: RPC, analyticsSe
     } else {
       val updateResult = for {
         _ <- Fox.successful(celeryInfosLastUpdated = System.currentTimeMillis())
-        celeryInfoJson <- flowerRpc("/api/tasks").getWithJsonResponse[JsObject]
+        celeryInfoJson <- flowerRpc("/api/tasks?offset=0").getWithJsonResponse[JsObject]
         celeryInfoMap <- celeryInfoJson
           .validate[Map[String, JsObject]] ?~> "Could not validate celery response as json map"
         _ <- Fox.serialCombined(celeryInfoMap.keys.toList)(jobId =>
@@ -131,6 +135,13 @@ class JobService @Inject()(wkConf: WkConf, jobDAO: JobDAO, rpc: RPC, analyticsSe
 
   private def flowerRpc(route: String): RPCRequest =
     rpc(wkConf.Jobs.Flower.uri + route).withBasicAuth(wkConf.Jobs.Flower.username, wkConf.Jobs.Flower.password)
+
+  def assertTiffExportBoundingBoxLimits(bbox: String): Fox[Unit] =
+    for {
+      boundingBox <- BoundingBox.fromForm(bbox).toFox
+      _ <- bool2Fox(boundingBox.volume <= wkConf.Features.exportTiffMaxVolumeMVx * 1024 * 1024) ?~> "job.export.tiff.volumeExceeded"
+      _ <- bool2Fox(boundingBox.dimensions.maxDim <= wkConf.Features.exportTiffMaxEdgeLengthVx) ?~> "job.export.tiff.edgeLengthExceeded"
+    } yield ()
 }
 
 class JobsController @Inject()(jobDAO: JobDAO,
@@ -171,4 +182,38 @@ class JobsController @Inject()(jobDAO: JobDAO,
       } yield Ok(js)
     }
 
+  def runTiffExportJob(organizationName: String,
+                       dataSetName: String,
+                       layerName: String,
+                       bbox: String): Action[AnyContent] =
+    sil.SecuredAction.async { implicit request =>
+      for {
+        organization <- organizationDAO.findOneByName(organizationName) ?~> Messages("organization.notFound",
+                                                                                     organizationName)
+        _ <- bool2Fox(request.identity._organization == organization._id) ~> FORBIDDEN
+        _ <- jobService.assertTiffExportBoundingBoxLimits(bbox)
+        command = "export_tiff"
+        exportFileName = s"${formatDateForFilename(new Date())}__${dataSetName}__${layerName}.zip"
+        commandArgs = Json.obj(
+          "kwargs" -> Json.obj("organization_name" -> organizationName,
+                               "dataset_name" -> dataSetName,
+                               "layer_name" -> layerName,
+                               "bbox" -> bbox,
+                               "export_file_name" -> exportFileName))
+        job <- jobService.runJob(command, commandArgs, request.identity) ?~> "job.couldNotRunTiffExport"
+        js <- jobService.publicWrites(job)
+      } yield Ok(js)
+    }
+
+  def downloadExport(jobId: String, exportFileName: String): Action[AnyContent] =
+    sil.SecuredAction.async { implicit request =>
+      for {
+        jobIdValidated <- ObjectId.parse(jobId)
+        job <- jobDAO.findOne(jobIdValidated)
+        organization <- organizationDAO.findOne(request.identity._organization)
+        filePath = Paths.get("binaryData", organization.name, ".export", job.celeryJobId, exportFileName)
+        _ <- bool2Fox(Files.exists(filePath)) ?~> "job.export.fileNotFound"
+      } yield Ok.sendPath(filePath, inline = false)
+    }
+
 }

app/utils/WkConf.scala

@@ -100,6 +100,8 @@ class WkConf @Inject()(configuration: Configuration) extends ConfigReader {
     val taskReopenAllowed: FiniteDuration = get[Int]("features.taskReopenAllowedInSeconds") seconds
     val allowDeleteDatasets: Boolean = get[Boolean]("features.allowDeleteDatasets")
     val publicDemoDatasetUrl: String = get[String]("features.publicDemoDatasetUrl")
+    val exportTiffMaxVolumeMVx: Long = get[Long]("features.exportTiffMaxVolumeMVx")
+    val exportTiffMaxEdgeLengthVx: Long = get[Long]("features.exportTiffMaxEdgeLengthVx")
   }
 
   object BackendAnalytics {

conf/application.conf

@@ -87,6 +87,8 @@ features {
   # If isDemoInstance == false, `/view` is appended to the URL so that it's opened in view mode (since the user might not
   # have an account).
   publicDemoDatasetUrl = "https://webknossos.org/datasets/scalable_minds/l4dense_motta_et_al_demo"
+  exportTiffMaxVolumeMVx = 1024
+  exportTiffMaxEdgeLengthVx = 8192
 }
 
 tracingstore {

conf/messages

@@ -313,7 +313,11 @@ initialData.organizationsNotEmpty=There are already organizations present in the
 
 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.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.volumeExceeded = The volume of the selected bounding box is too large.
+job.export.tiff.edgeLengthExceeded = An edge length of the selected bounding box is too large.
 
 agglomerateSkeleton.failed=Could not generate agglomerate skeleton.