Change parameter precedence when creating task from base (#6249)

* Change parameter precedence when creating task from base

* pass new arguments to duplicate call in tracingstore

* changelog

CHANGELOG.unreleased.md

@@ -15,6 +15,7 @@ Added a warning for when the resolution in the XY viewport on z=1-downsampled da
 
 ### Changed
 - For the api routes that return annotation info objects, the user field was renamed to owner. User still exists as an alias, but will be removed in a future release. [#6250](https://github.com/scalableminds/webknossos/pull/6250)
+- When creating a task from a base annotation, the starting position/rotation and bounding box as specified during task creation are now used and overwrite the ones from the original base annotation. [#6249](https://github.com/scalableminds/webknossos/pull/6249)
 
 
 ### Fixed

app/models/annotation/WKRemoteTracingStoreClient.scala

@@ -2,7 +2,7 @@ package models.annotation
 
 import java.io.File
 
-import com.scalableminds.util.geometry.BoundingBox
+import com.scalableminds.util.geometry.{BoundingBox, Vec3Double, Vec3Int}
 import com.scalableminds.util.io.ZipIO
 import com.scalableminds.util.tools.Fox
 import com.scalableminds.util.tools.Fox.bool2Fox
@@ -78,26 +78,38 @@ class WKRemoteTracingStoreClient(tracingStore: TracingStore, dataSet: DataSet, r
 
   def duplicateSkeletonTracing(skeletonTracingId: String,
                                versionString: Option[String] = None,
-                               isFromTask: Boolean = false): Fox[String] = {
+                               isFromTask: Boolean = false,
+                               editPosition: Option[Vec3Int] = None,
+                               editRotation: Option[Vec3Double] = None,
+                               boundingBox: Option[BoundingBox] = None): Fox[String] = {
     logger.debug("Called to duplicate SkeletonTracing." + baseInfo)
     rpc(s"${tracingStore.url}/tracings/skeleton/$skeletonTracingId/duplicate").withLongTimeout
       .addQueryString("token" -> RpcTokenHolder.webKnossosToken)
       .addQueryStringOptional("version", versionString)
+      .addQueryStringOptional("editPosition", editPosition.map(_.toUriLiteral))
+      .addQueryStringOptional("editRotation", editRotation.map(_.toUriLiteral))
+      .addQueryStringOptional("boundingBox", boundingBox.map(_.toLiteral))
       .addQueryString("fromTask" -> isFromTask.toString)
       .postWithJsonResponse[String]
   }
 
   def duplicateVolumeTracing(volumeTracingId: String,
-                             fromTask: Boolean = false,
+                             isFromTask: Boolean = false,
                              dataSetBoundingBox: Option[BoundingBox] = None,
                              resolutionRestrictions: ResolutionRestrictions = ResolutionRestrictions.empty,
-                             downsample: Boolean = false): Fox[String] = {
+                             downsample: Boolean = false,
+                             editPosition: Option[Vec3Int] = None,
+                             editRotation: Option[Vec3Double] = None,
+                             boundingBox: Option[BoundingBox] = None): Fox[String] = {
     logger.debug("Called to duplicate VolumeTracing." + baseInfo)
     rpc(s"${tracingStore.url}/tracings/volume/$volumeTracingId/duplicate").withLongTimeout
       .addQueryString("token" -> RpcTokenHolder.webKnossosToken)
-      .addQueryString("fromTask" -> fromTask.toString)
+      .addQueryString("fromTask" -> isFromTask.toString)
       .addQueryStringOptional("minResolution", resolutionRestrictions.minStr)
       .addQueryStringOptional("maxResolution", resolutionRestrictions.maxStr)
+      .addQueryStringOptional("editPosition", editPosition.map(_.toUriLiteral))
+      .addQueryStringOptional("editRotation", editRotation.map(_.toUriLiteral))
+      .addQueryStringOptional("boundingBox", boundingBox.map(_.toLiteral))
       .addQueryString("downsample" -> downsample.toString)
       .postJsonWithJsonResponse[Option[BoundingBox], String](dataSetBoundingBox)
   }

app/models/job/Job.scala

@@ -361,7 +361,7 @@ class JobService @Inject()(wkConf: WkConf,
 
   def assertTiffExportBoundingBoxLimits(bbox: String): Fox[Unit] =
     for {
-      boundingBox <- BoundingBox.createFrom(bbox).toFox ?~> "job.export.tiff.invalidBoundingBox"
+      boundingBox <- BoundingBox.fromLiteral(bbox).toFox ?~> "job.export.tiff.invalidBoundingBox"
       _ <- bool2Fox(boundingBox.volume <= wkConf.Features.exportTiffMaxVolumeMVx * 1024 * 1024) ?~> "job.export.tiff.volumeExceeded"
       _ <- bool2Fox(boundingBox.dimensions.maxDim <= wkConf.Features.exportTiffMaxEdgeLengthVx) ?~> "job.export.tiff.edgeLengthExceeded"
     } yield ()

app/models/task/TaskCreationService.scala

@@ -123,7 +123,12 @@ class TaskCreationService @Inject()(taskTypeService: TaskTypeService,
     for {
       baseSkeletonTracingIdOpt <- baseAnnotation.skeletonTracingId
       newTracingId <- baseSkeletonTracingIdOpt
-        .map(id => tracingStoreClient.duplicateSkeletonTracing(id))
+        .map(
+          id =>
+            tracingStoreClient.duplicateSkeletonTracing(id,
+                                                        editPosition = Some(params.editPosition),
+                                                        editRotation = Some(params.editRotation),
+                                                        boundingBox = params.boundingBox))
         .getOrElse(
           tracingStoreClient.saveSkeletonTracing(
             annotationService.createSkeletonTracingBase(

util/src/main/scala/com/scalableminds/util/geometry/BoundingBox.scala

@@ -1,6 +1,6 @@
 package com.scalableminds.util.geometry
 
-import net.liftweb.common.{Box, Empty, Full}
+import net.liftweb.common.Full
 
 case class BoundingBox(topLeft: Vec3Int, width: Int, height: Int, depth: Int) {
 
@@ -41,20 +41,21 @@ case class BoundingBox(topLeft: Vec3Int, width: Int, height: Int, depth: Int) {
   def dimensions: Vec3Int =
     Vec3Int(width, height, depth)
 
+  def toLiteral: String = f"${topLeft.x},${topLeft.y},${topLeft.z},$width,$height,$depth"
 }
 
 object BoundingBox {
 
   import play.api.libs.json._
 
-  private val formRx = "\\s*([0-9]+),\\s*([0-9]+),\\s*([0-9]+)\\s*,\\s*([0-9]+),\\s*([0-9]+),\\s*([0-9]+)\\s*".r
+  private val literalPattern = "\\s*([0-9]+),\\s*([0-9]+),\\s*([0-9]+)\\s*,\\s*([0-9]+),\\s*([0-9]+),\\s*([0-9]+)\\s*".r
 
   def empty: BoundingBox =
     BoundingBox(Vec3Int(0, 0, 0), 0, 0, 0)
 
-  def createFrom(s: String): Box[BoundingBox] =
+  def fromLiteral(s: String): Option[BoundingBox] =
     s match {
-      case formRx(minX, minY, minZ, width, height, depth) =>
+      case literalPattern(minX, minY, minZ, width, height, depth) =>
         try {
           Full(
             BoundingBox(
@@ -64,12 +65,18 @@ object BoundingBox {
               Integer.parseInt(depth)
             ))
         } catch {
-          case _: NumberFormatException => Empty
+          case _: NumberFormatException => None
         }
       case _ =>
-        Empty
+        None
     }
 
+  def fromSQL(ints: List[Int]): Option[BoundingBox] =
+    if (ints.length == 6)
+      Some(BoundingBox(Vec3Int(ints(0), ints(1), ints(2)), ints(3), ints(4), ints(5)))
+    else
+      None
+
   def combine(bbs: List[BoundingBox]): BoundingBox =
     bbs match {
       case head :: tail =>
@@ -78,27 +85,5 @@ object BoundingBox {
         BoundingBox(Vec3Int(0, 0, 0), 0, 0, 0)
     }
 
-  def createFrom(bbox: List[List[Int]]): Box[BoundingBox] =
-    if (bbox.size < 3 || bbox(0).size < 2 || bbox(1).size < 2 || bbox(2).size < 2)
-      Empty
-    else
-      Full(
-        BoundingBox(Vec3Int(bbox(0)(0), bbox(1)(0), bbox(2)(0)),
-                    bbox(0)(1) - bbox(0)(0),
-                    bbox(1)(1) - bbox(1)(0),
-                    bbox(2)(1) - bbox(2)(0)))
-
-  def createFrom(topLeft: Vec3Int, bottomRight: Vec3Int): Box[BoundingBox] =
-    if (topLeft <= bottomRight)
-      Full(BoundingBox(topLeft, bottomRight.x - topLeft.x, bottomRight.y - topLeft.y, bottomRight.z - topLeft.z))
-    else
-      Empty
-
-  def fromSQL(ints: List[Int]): Option[BoundingBox] =
-    if (ints.length == 6)
-      Some(BoundingBox(Vec3Int(ints(0), ints(1), ints(2)), ints(3), ints(4), ints(5)))
-    else
-      None
-
-  implicit val boundingBoxFormat: OFormat[BoundingBox] = Json.format[BoundingBox]
+  implicit val jsonFormat: OFormat[BoundingBox] = Json.format[BoundingBox]
 }

util/src/main/scala/com/scalableminds/util/geometry/Vec3Double.scala

@@ -67,6 +67,8 @@ case class Vec3Double(x: Double, y: Double, z: Double) {
   def isStrictlyPositive: Boolean = x > 0 && y > 0 && z > 0
 
   override def toString = s"($x, $y, $z)"
+
+  def toUriLiteral: String = s"$x,$y,$z"
 }
 
 object Vec3Double {
@@ -88,6 +90,13 @@ object Vec3Double {
   def fromList(l: List[Double]): Option[Vec3Double] =
     fromArray(l.toArray)
 
+  def fromUriLiteral(s: String): Option[Vec3Double] =
+    try {
+      fromArray(s.trim.split(",").map(java.lang.Double.parseDouble))
+    } catch {
+      case _: NumberFormatException => None
+    }
+
   implicit object Vector3DReads extends Format[Vec3Double] {
     def reads(json: JsValue): JsResult[Vec3Double] = json match {
       case JsArray(ts) if ts.size == 3 =>

util/src/main/scala/com/scalableminds/util/geometry/Vec3Int.scala

@@ -22,20 +22,22 @@ case class Vec3Int(x: Int, y: Int, z: Int) {
   def toMagLiteral(allowScalar: Boolean = false): String =
     if (allowScalar && isIsotropic) s"$x" else s"$x-$y-$z"
 
-  def toList = List(x, y, z)
+  def toUriLiteral: String = s"$x,$y,$z"
 
-  def move(dx: Int, dy: Int, dz: Int) =
+  def toList: List[Int] = List(x, y, z)
+
+  def move(dx: Int, dy: Int, dz: Int): Vec3Int =
     Vec3Int(x + dx, y + dy, z + dz)
 
   def move(other: Vec3Int): Vec3Int =
     move(other.x, other.y, other.z)
 
-  def negate = Vec3Int(-x, -y, -z)
+  def negate: Vec3Int = Vec3Int(-x, -y, -z)
 
-  def to(bottomRight: Vec3Int) =
+  def to(bottomRight: Vec3Int): Seq[Vec3Int] =
     range(bottomRight, _ to _)
 
-  def until(bottomRight: Vec3Int) =
+  def until(bottomRight: Vec3Int): Seq[Vec3Int] =
     range(bottomRight, _ until _)
 
   def maxDim: Int = Math.max(Math.max(x, y), z)
@@ -52,28 +54,40 @@ case class Vec3Int(x: Int, y: Int, z: Int) {
 
 object Vec3Int {
   private val magLiteralRegex = """(\d+)-(\d+)-(\d+)""".r
+  private val uriLiteralRegex = """(\d+),(\d+),(\d+)""".r
 
   def fromMagLiteral(s: String, allowScalar: Boolean = false): Option[Vec3Int] =
     s.toIntOpt match {
       case Some(scalar) if allowScalar => Some(Vec3Int.full(scalar))
       case _ =>
         s match {
           case magLiteralRegex(x, y, z) =>
-            Some(Vec3Int(Integer.parseInt(x), Integer.parseInt(y), Integer.parseInt(z)))
+            try {
+              Some(Vec3Int(Integer.parseInt(x), Integer.parseInt(y), Integer.parseInt(z)))
+            } catch {
+              case _: NumberFormatException => None
+            }
           case _ =>
             None
         }
     }
 
-  def fromArray[T <% Int](array: Array[T]) =
-    if (array.size >= 3)
-      Some(Vec3Int(array(0), array(1), array(2)))
+  def fromUriLiteral(s: String): Option[Vec3Int] = s match {
+    case uriLiteralRegex(x, y, z) =>
+      try {
+        Some(Vec3Int(Integer.parseInt(x), Integer.parseInt(y), Integer.parseInt(z)))
+      } catch {
+        case _: NumberFormatException => None
+      }
+    case _ => None
+  }
+
+  def fromList(l: List[Int]): Option[Vec3Int] =
+    if (l.length >= 3)
+      Some(Vec3Int(l.head, l(1), l(2)))
     else
       None
 
-  def fromList(l: List[Int]) =
-    fromArray(l.toArray)
-
   def full(i: Int): Vec3Int = Vec3Int(i, i, i)
 
   implicit object Vec3IntReads extends Reads[Vec3Int] {

webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/controllers/SkeletonTracingController.scala

@@ -1,11 +1,13 @@
 package com.scalableminds.webknossos.tracingstore.controllers
 
 import com.google.inject.Inject
+import com.scalableminds.util.geometry.{BoundingBox, Vec3Double, Vec3Int}
+import com.scalableminds.util.tools.Fox
 import com.scalableminds.webknossos.datastore.SkeletonTracing.{SkeletonTracing, SkeletonTracingOpt, SkeletonTracings}
 import com.scalableminds.webknossos.datastore.services.UserAccessRequest
 import com.scalableminds.webknossos.tracingstore.slacknotification.TSSlackNotificationService
 import com.scalableminds.webknossos.tracingstore.tracings.skeleton._
-import com.scalableminds.webknossos.tracingstore.{TracingStoreAccessTokenService, TSRemoteWebKnossosClient}
+import com.scalableminds.webknossos.tracingstore.{TSRemoteWebKnossosClient, TracingStoreAccessTokenService}
 import play.api.i18n.Messages
 import play.api.libs.json.Json
 import play.api.mvc.{Action, AnyContent, PlayBodyParsers}
@@ -48,13 +50,23 @@ class SkeletonTracingController @Inject()(val tracingService: SkeletonTracingSer
   def duplicate(token: Option[String],
                 tracingId: String,
                 version: Option[Long],
-                fromTask: Option[Boolean]): Action[AnyContent] =
+                fromTask: Option[Boolean],
+                editPosition: Option[String],
+                editRotation: Option[String],
+                boundingBox: Option[String]): Action[AnyContent] =
     Action.async { implicit request =>
       log() {
         accessTokenService.validateAccess(UserAccessRequest.webknossos, token) {
           for {
             tracing <- tracingService.find(tracingId, version, applyUpdates = true) ?~> Messages("tracing.notFound")
-            newId <- tracingService.duplicate(tracing, fromTask.getOrElse(false))
+            editPositionParsed <- Fox.runOptional(editPosition)(Vec3Int.fromUriLiteral)
+            editRotationParsed <- Fox.runOptional(editRotation)(Vec3Double.fromUriLiteral)
+            boundingBoxParsed <- Fox.runOptional(boundingBox)(BoundingBox.fromLiteral)
+            newId <- tracingService.duplicate(tracing,
+                                              fromTask.getOrElse(false),
+                                              editPositionParsed,
+                                              editRotationParsed,
+                                              boundingBoxParsed)
           } yield {
             Ok(Json.toJson(newId))
           }

webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/controllers/VolumeTracingController.scala

@@ -1,23 +1,23 @@
 package com.scalableminds.webknossos.tracingstore.controllers
 
-import akka.http.caching.LfuCache
-import akka.http.caching.scaladsl.{Cache, CachingSettings}
-
 import java.io.File
 import java.nio.{ByteBuffer, ByteOrder}
+
+import akka.http.caching.LfuCache
+import akka.http.caching.scaladsl.{Cache, CachingSettings}
 import akka.stream.scaladsl.Source
 import com.google.inject.Inject
 import com.scalableminds.util.geometry.{BoundingBox, Vec3Double, Vec3Int}
 import com.scalableminds.util.tools.ExtendedTypes.ExtendedString
 import com.scalableminds.util.tools.Fox
-import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, DataSourceId, ElementClass}
-import com.scalableminds.webknossos.datastore.models.{WebKnossosDataRequest, WebKnossosIsosurfaceRequest}
-import com.scalableminds.webknossos.datastore.services.UserAccessRequest
 import com.scalableminds.webknossos.datastore.VolumeTracing.{VolumeTracing, VolumeTracingOpt, VolumeTracings}
 import com.scalableminds.webknossos.datastore.dataformats.zarr.ZarrCoordinatesParser
 import com.scalableminds.webknossos.datastore.helpers.ProtoGeometryImplicits
 import com.scalableminds.webknossos.datastore.jzarr.{ArrayOrder, OmeNgffHeader, ZarrHeader}
+import com.scalableminds.webknossos.datastore.models.datasource.{DataLayer, ElementClass}
+import com.scalableminds.webknossos.datastore.models.{WebKnossosDataRequest, WebKnossosIsosurfaceRequest}
 import com.scalableminds.webknossos.datastore.rpc.RPC
+import com.scalableminds.webknossos.datastore.services.UserAccessRequest
 import com.scalableminds.webknossos.tracingstore.slacknotification.TSSlackNotificationService
 import com.scalableminds.webknossos.tracingstore.tracings.volume.{ResolutionRestrictions, VolumeTracingService}
 import com.scalableminds.webknossos.tracingstore.{
@@ -159,19 +159,28 @@ class VolumeTracingController @Inject()(
                 fromTask: Option[Boolean],
                 minResolution: Option[Int],
                 maxResolution: Option[Int],
-                downsample: Option[Boolean]): Action[AnyContent] = Action.async { implicit request =>
+                downsample: Option[Boolean],
+                editPosition: Option[String],
+                editRotation: Option[String],
+                boundingBox: Option[String]): Action[AnyContent] = Action.async { implicit request =>
     log() {
       logTime(slackNotificationService.noticeSlowRequest) {
         accessTokenService.validateAccess(UserAccessRequest.webknossos, token) {
           for {
             tracing <- tracingService.find(tracingId) ?~> Messages("tracing.notFound")
             dataSetBoundingBox = request.body.asJson.flatMap(_.validateOpt[BoundingBox].asOpt.flatten)
             resolutionRestrictions = ResolutionRestrictions(minResolution, maxResolution)
+            editPositionParsed <- Fox.runOptional(editPosition)(Vec3Int.fromUriLiteral)
+            editRotationParsed <- Fox.runOptional(editRotation)(Vec3Double.fromUriLiteral)
+            boundingBoxParsed <- Fox.runOptional(boundingBox)(BoundingBox.fromLiteral)
             (newId, newTracing) <- tracingService.duplicate(tracingId,
                                                             tracing,
                                                             fromTask.getOrElse(false),
                                                             dataSetBoundingBox,
-                                                            resolutionRestrictions)
+                                                            resolutionRestrictions,
+                                                            editPositionParsed,
+                                                            editRotationParsed,
+                                                            boundingBoxParsed)
             _ <- Fox.runIfOptionTrue(downsample)(tracingService.downsample(newId, newTracing))
           } yield Ok(Json.toJson(newId))
         }