Merge branch 'master' into delete-workflow-reports

Author: frcroth

CHANGELOG.unreleased.md

@@ -26,6 +26,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Admins can now see and cancel all jobs. The owner of the job is shown in the job list. [#8112](https://github.com/scalableminds/webknossos/pull/8112)
 - Migrated nightly screenshot tests from CircleCI to GitHub actions. [#8134](https://github.com/scalableminds/webknossos/pull/8134)
 - Migrated nightly screenshot tests for wk.org from CircleCI to GitHub actions. [#8135](https://github.com/scalableminds/webknossos/pull/8135)
+- Thumbnails for datasets now use the selected mapping from the view configuration if available. [#8157](https://github.com/scalableminds/webknossos/pull/8157)
 
 ### Fixed
 - Fixed a bug during dataset upload in case the configured `datastore.baseFolder` is an absolute path. [#8098](https://github.com/scalableminds/webknossos/pull/8098) [#8103](https://github.com/scalableminds/webknossos/pull/8103)
@@ -36,6 +37,8 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed sorting of mags in outbound zarr streaming. [#8125](https://github.com/scalableminds/webknossos/pull/8125)
 - Fixed a bug where you could not create annotations for public datasets of other organizations. [#8107](https://github.com/scalableminds/webknossos/pull/8107)
 - Users without edit permissions to a dataset can no longer delete sharing tokens via the API. [#8083](https://github.com/scalableminds/webknossos/issues/8083)
+- Fixed downloading task annotations of teams you are not in, when accessing directly via URI. [#8155](https://github.com/scalableminds/webknossos/pull/8155)
+- Deleting a bounding box is now possible independently of a visible segmentation layer. [#8164](https://github.com/scalableminds/webknossos/pull/8164)
 
 ### Removed
 

DEV_INSTALL.md

@@ -44,7 +44,7 @@ arch -x86_64 /bin/zsh
 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
 
 # Install git, node.js, postgres, sbt, gfind, gsed, draco
-brew install openjdk draco openssl git node postgresql sbt findutils coreutils gnu-sed redis yarn c-blosc brotli wget
+brew install openjdk draco openssl git node postgresql sbt findutils coreutils gnu-sed redis c-blosc brotli wget
 
 # Set env variables for openjdk and openssl
 # You probably want to add these lines manually to avoid conflicts in your zshrc
@@ -84,12 +84,8 @@ source ~/.bashrc
 nvm install 18
 nvm use 18
 
-# Adding repositories for yarn
-curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | sudo apt-key add -
-echo "deb https://dl.yarnpkg.com/debian/ stable main" | sudo tee /etc/apt/sources.list.d/yarn.list
-
 sudo apt update
-sudo apt install -y git postgresql postgresql-client unzip zip yarn redis-server build-essential libblosc1 libbrotli1 libdraco-dev cmake
+sudo apt install -y git postgresql postgresql-client unzip zip redis-server build-essential libblosc1 libbrotli1 libdraco-dev cmake
 
  # Install sdkman, java, scala and sbt
 curl -s "https://get.sdkman.io" | bash
@@ -132,8 +128,10 @@ On older Ubuntu distributions: Please make sure to have the correct versions of
 ### node.js & yarn
 
 * Install node from [http://nodejs.org/download/](http://nodejs.org/download/)
-* node version **16 to 18 is required**
-* Install yarn package manager: `npm install -g yarn`
+* node version **18 is required**
+* Use `corepack` to install `yarn`
+* `corepack enable`&& `yarn install`
+
 
 ## Run locally
 

app/controllers/AnnotationIOController.scala

@@ -457,7 +457,7 @@ class AnnotationIOController @Inject()(
             tracingStoreClient.getSkeletonTracing(skeletonAnnotationLayer, skeletonVersion)
         } ?~> "annotation.download.fetchSkeletonLayer.failed"
         user <- userService.findOneCached(annotation._user)(GlobalAccessContext) ?~> "annotation.download.findUser.failed"
-        taskOpt <- Fox.runOptional(annotation._task)(taskDAO.findOne)
+        taskOpt <- Fox.runOptional(annotation._task)(taskDAO.findOne(_)(GlobalAccessContext)) ?~> "task.notFound"
         nmlStream = nmlWriter.toNmlStream(
           name,
           fetchedSkeletonLayers ::: fetchedVolumeLayers,

app/models/dataset/ThumbnailService.scala

@@ -14,7 +14,7 @@ import models.configuration.DatasetConfigurationService
 import net.liftweb.common.Full
 import play.api.http.Status.NOT_FOUND
 import play.api.i18n.{Messages, MessagesProvider}
-import play.api.libs.json.JsArray
+import play.api.libs.json.{JsArray, JsObject}
 import utils.ObjectId
 import utils.sql.{SimpleSQLDAO, SqlClient}
 
@@ -74,39 +74,41 @@ class ThumbnailService @Inject()(datasetService: DatasetService,
       viewConfiguration <- datasetConfigurationService.getDatasetViewConfigurationForDataset(List.empty,
                                                                                              datasetName,
                                                                                              organizationId)(ctx)
-      (mag1BoundingBox, mag, intensityRangeOpt, colorSettingsOpt) = selectParameters(viewConfiguration,
-                                                                                     usableDataSource,
-                                                                                     layerName,
-                                                                                     layer,
-                                                                                     width,
-                                                                                     height)
+      (mag1BoundingBox, mag, intensityRangeOpt, colorSettingsOpt, mapping) = selectParameters(viewConfiguration,
+                                                                                              usableDataSource,
+                                                                                              layerName,
+                                                                                              layer,
+                                                                                              width,
+                                                                                              height,
+                                                                                              mappingName)
       client <- datasetService.clientFor(dataset)
       image <- client.getDataLayerThumbnail(organizationId,
                                             dataset,
                                             layerName,
                                             mag1BoundingBox,
                                             mag,
-                                            mappingName,
+                                            mapping,
                                             intensityRangeOpt,
                                             colorSettingsOpt)
       _ <- thumbnailDAO.upsertThumbnail(dataset._id,
                                         layerName,
                                         width,
                                         height,
-                                        mappingName,
+                                        mapping,
                                         image,
                                         jpegMimeType,
                                         mag,
                                         mag1BoundingBox)
     } yield image
 
-  private def selectParameters(
-      viewConfiguration: DatasetViewConfiguration,
-      usableDataSource: GenericDataSource[DataLayerLike],
-      layerName: String,
-      layer: DataLayerLike,
-      targetMagWidth: Int,
-      targetMagHeigt: Int): (BoundingBox, Vec3Int, Option[(Double, Double)], Option[ThumbnailColorSettings]) = {
+  private def selectParameters(viewConfiguration: DatasetViewConfiguration,
+                               usableDataSource: GenericDataSource[DataLayerLike],
+                               layerName: String,
+                               layer: DataLayerLike,
+                               targetMagWidth: Int,
+                               targetMagHeigt: Int,
+                               mappingName: Option[String])
+    : (BoundingBox, Vec3Int, Option[(Double, Double)], Option[ThumbnailColorSettings], Option[String]) = {
     val configuredCenterOpt =
       viewConfiguration.get("position").flatMap(jsValue => JsonHelper.jsResultToOpt(jsValue.validate[Vec3Int]))
     val centerOpt =
@@ -124,7 +126,13 @@ class ThumbnailService @Inject()(datasetService: DatasetService,
     val x = center.x - mag1Width / 2
     val y = center.y - mag1Height / 2
     val z = center.z
-    (BoundingBox(Vec3Int(x, y, z), mag1Width, mag1Height, 1), mag, intensityRangeOpt, colorSettingsOpt)
+
+    val mappingNameResult = mappingName.orElse(readMappingName(viewConfiguration, layerName))
+    (BoundingBox(Vec3Int(x, y, z), mag1Width, mag1Height, 1),
+     mag,
+     intensityRangeOpt,
+     colorSettingsOpt,
+     mappingNameResult)
   }
 
   private def readIntensityRange(viewConfiguration: DatasetViewConfiguration,
@@ -147,6 +155,13 @@ class ThumbnailService @Inject()(datasetService: DatasetService,
       b <- colorArray(2).validate[Int].asOpt
     } yield ThumbnailColorSettings(Color(r / 255d, g / 255d, b / 255d, 0), isInverted)
 
+  private def readMappingName(viewConfiguration: DatasetViewConfiguration, layerName: String): Option[String] =
+    for {
+      layersJsValue <- viewConfiguration.get("layers")
+      mapping <- (layersJsValue \ layerName \ "mapping").validate[JsObject].asOpt
+      mappingName <- mapping("name").validate[String].asOpt
+    } yield mappingName
+
   private def magForZoom(dataLayer: DataLayerLike, zoom: Double): Vec3Int =
     dataLayer.resolutions.minBy(r => Math.abs(r.maxDim - zoom))
 

docs/volume_annotation/import_export.md

@@ -6,3 +6,11 @@ To import a volume annotation, ensure it is in the correct format (WKW or Zarr)
 To export (download) an annotation, go to **Menu > Download**. From there, select the data you want to download and choose the desired format (WKW, Zarr). Alternatively, you can open your annotation dashboard and click **Download** next to the annotation.
 
 ![youtube-video](https://www.youtube.com/embed/l8ZacNqvMzI)
+
+## Merging volume annotation with fallback data
+
+After finishing the annotation of a volume layer with a fallback layer, the combined state of these layers can be materialized into a new dataset. For this, go to the layer settings in the left border tab. On the top right of the volume layer is the following button:
+
+![Icon to open the materialize volume annotation modal](../images/materialize_volume_annotation_icon.jpg)
+
+This button opens up a modal that starts a long-running job which will materialize the volume annotation.

docs/volume_annotation/index.md

@@ -10,11 +10,3 @@ WEBKNOSSOS supports volume/segmentation annotations. This annotation type lets y
 
 Watch this tutorial to get started: 
 ![youtube-video](https://www.youtube.com/embed/iw2C7XB6wP4?start=120)
-
-## Merging volume annotation with fallback data
-
-After finishing the annotation of a volume layer with a fallback layer, the combined state of these layers can be materialized into a new dataset. For this, go to the layer settings in the left border tab. On the top right of the volume layer is the following button:
-
-![Icon to open the materialize volume annotation modal](../images/materialize_volume_annotation_icon.jpg)
-
-This button opens up a modal that starts a long-running job which will materialize the volume annotation.

frontend/javascripts/oxalis/view/components/setting_input_views.tsx

@@ -554,7 +554,6 @@ class UserBoundingBoxInput extends React.PureComponent<UserBoundingBoxInputProps
       isLockedByOwner,
       isOwner,
     );
-    const isDeleteEnabled = !disabled && this.props.visibleSegmentationLayer != null;
 
     const getContextMenu = () => {
       const items: MenuProps["items"] = [
@@ -590,13 +589,13 @@ class UserBoundingBoxInput extends React.PureComponent<UserBoundingBoxInputProps
         },
         {
           key: "delete",
-          label: isDeleteEnabled ? (
+          label: !disabled ? (
             deleteButton
           ) : (
             <FastTooltip title={editingDisallowedExplanation}>{deleteButton}</FastTooltip>
           ),
           onClick: onDelete,
-          disabled: !isDeleteEnabled,
+          disabled,
         },
       ];