Avoid errors on zarr dataset settings page

CHANGELOG.unreleased.md

@@ -20,6 +20,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Fixed
 - Fixed several deprecation warning for using antd's Tabs.TabPane components. [#7469]
 - Fixed problems when requests for loading data failed (could impact volume data consistency and rendering). [#7477](https://github.com/scalableminds/webknossos/pull/7477)
+- The settings page for non-wkw datasets no longer shows a wall of non-applying errors. [#7475](https://github.com/scalableminds/webknossos/pull/7475)
 
 ### Removed
 

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

@@ -80,7 +80,7 @@ object BoundingBox {
     "\\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)
+    BoundingBox(Vec3Int.zeros, 0, 0, 0)
 
   def fromLiteral(s: String): Option[BoundingBox] =
     s match {
@@ -111,7 +111,7 @@ object BoundingBox {
       case head :: tail =>
         tail.foldLeft(head)(_ union _)
       case _ =>
-        BoundingBox(Vec3Int(0, 0, 0), 0, 0, 0)
+        BoundingBox.empty
     }
 
   def intersection(bbs: List[BoundingBox]): Option[BoundingBox] =

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

@@ -103,6 +103,8 @@ object Vec3Double {
 
   def ones: Vec3Double = Vec3Double(1.0, 1.0, 1.0)
 
+  def zeros: Vec3Double = Vec3Double(0.0, 0.0, 0.0)
+
   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/io/PathUtils.scala

@@ -50,11 +50,11 @@ trait PathUtils extends LazyLogging {
     else
       None
 
-  def listDirectoryEntries[A](directory: Path,
-                              maxDepth: Int,
-                              dropCount: Int,
-                              silent: Boolean,
-                              filters: (Path => Boolean)*)(f: Iterator[Path] => Box[A]): Box[A] =
+  private def listDirectoryEntries[A](directory: Path,
+                                      maxDepth: Int,
+                                      dropCount: Int,
+                                      silent: Boolean,
+                                      filters: (Path => Boolean)*)(f: Iterator[Path] => Box[A]): Box[A] =
     try {
       val directoryStream = Files.walk(directory, maxDepth, FileVisitOption.FOLLOW_LINKS)
       val r = f(directoryStream.iterator().asScala.drop(dropCount).filter(d => filters.forall(_(d))))
@@ -82,6 +82,9 @@ trait PathUtils extends LazyLogging {
         Failure(errorMsg)
     }
 
+  def containsFile(directory: Path, maxDepth: Int, silent: Boolean, filters: (Path => Boolean)*): Box[Boolean] =
+    listDirectoryEntries(directory, maxDepth, dropCount = 0, silent, filters :+ fileFilter _: _*)(r => Full(r.nonEmpty))
+
   def listDirectories(directory: Path, silent: Boolean, filters: (Path => Boolean)*): Box[List[Path]] =
     listDirectoryEntries(directory, 1, 1, silent, filters :+ directoryFilter _: _*)(r => Full(r.toList))
 

webknossos-datastore/app/com/scalableminds/webknossos/datastore/controllers/DataSourceController.scala

@@ -253,8 +253,8 @@ Expects:
     }
 
   @ApiOperation(hidden = true, value = "")
-  def explore(token: Option[String], organizationName: String, dataSetName: String): Action[AnyContent] = Action.async {
-    implicit request =>
+  def suggestDatasourceJson(token: Option[String], organizationName: String, dataSetName: String): Action[AnyContent] =
+    Action.async { implicit request =>
       accessTokenService.validateAccessForSyncBlock(
         UserAccessRequest.writeDataSource(DataSourceId(dataSetName, organizationName)),
         urlOrHeaderToken(token, request)) {
@@ -280,7 +280,7 @@ Expects:
             ))
         }
       }
-  }
+    }
 
   @ApiOperation(hidden = true, value = "")
   def listMappings(

webknossos-datastore/app/com/scalableminds/webknossos/datastore/helpers/SkeletonElementDefaults.scala

@@ -9,8 +9,8 @@ object SkeletonTracingDefaults extends ProtoGeometryImplicits {
   private def createdTimestamp = System.currentTimeMillis()
   private val boundingBox = None
   private val activeNodeId = None
-  val editPosition: Vec3Int = Vec3Int(0, 0, 0)
-  val editRotation: Vec3Double = Vec3Double(0, 0, 0)
+  val editPosition: Vec3Int = Vec3Int.zeros
+  val editRotation: Vec3Double = Vec3Double.zeros
   val zoomLevel: Double = 2.0
   private val version = 0
   private val userBoundingBox = None
@@ -30,8 +30,8 @@ object SkeletonTracingDefaults extends ProtoGeometryImplicits {
 
 object NodeDefaults extends ProtoGeometryImplicits {
   val id: Int = 0
-  val rotation: Vec3Double = Vec3Double(0, 0, 0)
-  val position: Vec3Int = Vec3Int(0, 0, 0)
+  val rotation: Vec3Double = Vec3Double.zeros
+  val position: Vec3Int = Vec3Int.zeros
   val radius: Float = 1.0f
   val viewport: Int = 1
   val resolution: Int = 1

webknossos-datastore/app/com/scalableminds/webknossos/datastore/models/requests/DataServiceRequests.scala

@@ -21,7 +21,7 @@ case class DataServiceDataRequest(
     dataLayerMapping: Option[String],
     cuboid: Cuboid,
     settings: DataServiceRequestSettings,
-    subsamplingStrides: Vec3Int = Vec3Int(1, 1, 1) // if > 1, skip voxels when loading (used for adhoc mesh generation)
+    subsamplingStrides: Vec3Int = Vec3Int.ones // if > 1, skip voxels when loading (used for adhoc mesh generation)
 )
 
 case class DataReadInstruction(

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/BinaryDataService.scala

@@ -40,7 +40,7 @@ class BinaryDataService(val dataBaseDir: Path,
 
     if (!request.cuboid.hasValidDimensions) {
       Fox.failure("Invalid cuboid dimensions (must be > 0 and <= 512).")
-    } else if (request.cuboid.isSingleBucket(DataLayer.bucketLength) && request.subsamplingStrides == Vec3Int(1, 1, 1)) {
+    } else if (request.cuboid.isSingleBucket(DataLayer.bucketLength) && request.subsamplingStrides == Vec3Int.ones) {
       bucketQueue.headOption.toFox.flatMap { bucket =>
         handleBucketRequest(request, bucket.copy(additionalCoordinates = request.settings.additionalCoordinates))
       }

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/DataFinder.scala

@@ -17,7 +17,7 @@ trait DataFinder {
       val voxelOffset = scaledX + scaledY + scaledZ
       if (data.slice(voxelOffset, voxelOffset + bytesPerElement).exists(_ != 0)) return Vec3Int(x, y, z)
     }
-    Vec3Int(0, 0, 0)
+    Vec3Int.zeros
   }
 
   def getPositionOfNonZeroData(data: Array[Byte],

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/DataSourceImporter.scala

@@ -1,7 +1,6 @@
 package com.scalableminds.webknossos.datastore.services
 
 import java.nio.file.Path
-
 import com.scalableminds.util.geometry.{Vec3Double, Vec3Int}
 import com.scalableminds.util.io.PathUtils
 import com.scalableminds.webknossos.datastore.dataformats.MappingProvider
@@ -28,6 +27,11 @@ trait DataSourceImporter {
   protected def exploreLayer(name: String, baseDir: Path, previous: Option[DataLayer])(
       implicit report: DataSourceImportReport[Path]): Box[DataLayer]
 
+  private def wkwFileFilter(path: Path): Boolean = path.getFileName.toString.toLowerCase().endsWith(".wkw")
+
+  def looksLikeWKWDataSource(baseDir: Path): Box[Boolean] =
+    PathUtils.containsFile(baseDir, maxDepth = 3, silent = true, filters = wkwFileFilter)
+
   def exploreDataSource(id: DataSourceId,
                         baseDir: Path,
                         previous: Option[DataSource],
@@ -40,10 +44,18 @@ trait DataSourceImporter {
       }
       GenericDataSource(id,
                         layers,
-                        previous.map(_.scale).getOrElse(Vec3Double(0, 0, 0)),
+                        previous.map(_.scale).getOrElse(Vec3Double.zeros),
                         previous.flatMap(_.defaultViewConfiguration))
     }
 
+  def dummyDataSource(id: DataSourceId,
+                      previous: Option[DataSource],
+                      report: DataSourceImportReport[Path]): Box[DataSource] = {
+    report.warning(_ =>
+      "Automatic suggestions for the datasource-properties.json are not available since the dataset is not in WKW format.")
+    previous.orElse(Some(GenericDataSource(id, List.empty, Vec3Double.zeros)))
+  }
+
   protected def guessLayerCategory(layerName: String, elementClass: ElementClass.Value)(
       implicit report: DataSourceImportReport[Path]): Category.Value = {
     val ColorRx = ".*color.*".r

webknossos-datastore/app/com/scalableminds/webknossos/datastore/services/DataSourceService.scala

@@ -116,7 +116,9 @@ class DataSourceService @Inject()(
     val path = dataBaseDir.resolve(id.team).resolve(id.name)
     val report = DataSourceImportReport[Path](dataBaseDir.relativize(path))
     for {
-      dataSource <- WKWDataFormat.exploreDataSource(id, path, previous, report)
+      looksLikeWKWDataSource <- WKWDataFormat.looksLikeWKWDataSource(path)
+      dataSource <- if (looksLikeWKWDataSource) WKWDataFormat.exploreDataSource(id, path, previous, report)
+      else WKWDataFormat.dummyDataSource(id, previous, report)
     } yield (dataSource, report.messages.toList)
   }
 

webknossos-datastore/conf/com.scalableminds.webknossos.datastore.routes

@@ -82,7 +82,7 @@ GET           /datasets/:organizationName/:dataSetName/readInboxDataSourceLike
 GET           /datasets/:organizationName/:dataSetName/readInboxDataSource                                                                    @com.scalableminds.webknossos.datastore.controllers.DataSourceController.read(token: Option[String], organizationName: String, dataSetName: String, returnFormatLike: Boolean ?= false)
 POST          /datasets/:organizationName/:dataSetName                                                                                        @com.scalableminds.webknossos.datastore.controllers.DataSourceController.update(token: Option[String], organizationName: String, dataSetName: String)
 PUT           /datasets/:organizationName/:dataSetName                                                                                        @com.scalableminds.webknossos.datastore.controllers.DataSourceController.add(token: Option[String], organizationName: String, dataSetName: String, folderId: Option[String])
-GET           /datasets/:organizationName/:dataSetName                                                                                        @com.scalableminds.webknossos.datastore.controllers.DataSourceController.explore(token: Option[String], organizationName: String, dataSetName: String)
+GET           /datasets/:organizationName/:dataSetName                                                                                        @com.scalableminds.webknossos.datastore.controllers.DataSourceController.suggestDatasourceJson(token: Option[String], organizationName: String, dataSetName: String)
 DELETE        /datasets/:organizationName/:dataSetName/deleteOnDisk                                                                           @com.scalableminds.webknossos.datastore.controllers.DataSourceController.deleteOnDisk(token: Option[String], organizationName: String, dataSetName: String)
 
 # Actions

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

@@ -298,7 +298,7 @@ class VolumeTracingController @Inject()(
       for {
         positionOpt <- tracingService.findData(tracingId)
       } yield {
-        Ok(Json.obj("position" -> positionOpt, "resolution" -> positionOpt.map(_ => Vec3Int(1, 1, 1))))
+        Ok(Json.obj("position" -> positionOpt, "resolution" -> positionOpt.map(_ => Vec3Int.ones)))
       }
     }
   }

webknossos-tracingstore/app/com/scalableminds/webknossos/tracingstore/tracings/volume/VolumeTracingLayer.scala

@@ -114,7 +114,7 @@ case class VolumeTracingLayer(
   def bucketProvider: AbstractVolumeTracingBucketProvider = volumeBucketProvider
 
   override val resolutions: List[Vec3Int] =
-    if (volumeResolutions.nonEmpty) volumeResolutions else List(Vec3Int(1, 1, 1))
+    if (volumeResolutions.nonEmpty) volumeResolutions else List(Vec3Int.ones)
 
   override def containsResolution(resolution: Vec3Int) =
     true // allow requesting buckets of all resolutions. database takes care of missing.