Merge branch 'master' into docs_lili

* master:
  fix docs formatting
  Remove experimental auto brush feature (#6107)
  Fix markdown issues in docs (#6105)
  Unify long-running RPC timeouts (#6103)
  Disallow deactivating users with active tasks (#6099)
  Add remote origin headers also in error case (#6098)
  Linking layers during upload no longer restricted to public datasets (#6097)
  Fix layer headers layout (#6087)
  Fix more docs links (#6095)
  Update datasets.md (#6094)
  More PR feedback for Docs (#6091)
  Updates to wK Docs (#5995)
  Connectome Tab (#5894)
  Fix duplicating annotations via toggling show archived annotations button and fix downsample modal rendering errors (#6058)

.circleci/slack-notification.sh

@@ -16,7 +16,8 @@ if [ "${CIRCLE_BRANCH}" == "master" ] ; then
     author=${author/tmbo/<@tmbo>}
     author=${author/valentin-pinkau/<@valentin>}
     author=${author/youri-k/<@youri>}
-    author=${author/Dagobert42/<@Arthur Hilbert>}
+    author=${author/Dagobert42/<@Arthur>}
+    author=${author/leowe/<@leowe>}
     channel="webknossos-bots"
     commitmsg="$(git log --format=%s -n 1)"
     pullregex="(.*)#([0-9]+)(.*)"

CHANGELOG.released.md

@@ -7,6 +7,39 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 For upgrade instructions, please check the [migration guide](MIGRATIONS.released.md).
 
+## [22.04.0](https://github.com/scalableminds/webknossos/releases/tag/22.04.0) - 2022-03-22
+[Commits](https://github.com/scalableminds/webknossos/compare/22.03.0...22.04.0)
+
+### Highlights
+- The visible meshes are now included in the link copied from the "Share" modal or the "Share" button next to the dataset position. They are automatically loaded for users that open the shared link. [#5993](https://github.com/scalableminds/webknossos/pull/5993)
+- Added a new "Connectome Tab" which can be used to explore connectomes by visualizing neurites and their synaptic connections. Connectome files need to be placed in a `connectomes` folder inside of the respective segmentation layer. It is possible to craft links that automatically load specific agglomerates and their synapses when openend. For more information refer to https://docs.webknossos.org/webknossos/sharing.html#sharing-link-format. [#5894](https://github.com/scalableminds/webknossos/pull/5894)
+
+### Added
+- Added a context-menu option when right-clicking on skeleton trees to hide/show all other trees but the selected one. Great for inspecting a single tree in isolation. Identical to keyboard shortcut "2". [#6102](https://github.com/scalableminds/webknossos/pull/6102)
+- Added support for reading Zarr image data. [#6019](https://github.com/scalableminds/webknossos/pull/6019)
+
+### Changed
+- The maximum brush size now depends on the available magnifications. Consequentially, one can use a larger brush size when the magnifications of a volume layer are restricted. [#6066](https://github.com/scalableminds/webknossos/pull/6066)
+- Improved stability and speed of volume annotations when annotating large areas. [#6055](https://github.com/scalableminds/webknossos/pull/6055)
+- In dataset upload, linking layers of existing datasets is no longer restricted to public datasets. [#6097](https://github.com/scalableminds/webknossos/pull/6097)
+- Deactivating users with currently active tasks is no longer allowed. [#6099](https://github.com/scalableminds/webknossos/pull/6099)
+
+### Fixed
+- Fixed a bug that led to crashing the layer settings once the icon for the downsample modal was clicked. [#6058](https://github.com/scalableminds/webknossos/pull/6058)
+- Fixed a bug where toggling between not archived and archived annotations in the "My Annotation" of the dashboard led to inconsistent states and duplicates of annotations. [#6058](https://github.com/scalableminds/webknossos/pull/6058)
+- Fixed a bug where deactivated users would still be listed as allowed to access the datasets of their team. [#6070](https://github.com/scalableminds/webknossos/pull/6070)
+- Fixed occasionally "disappearing" data. [#6055](https://github.com/scalableminds/webknossos/pull/6055)
+- Fixed a bug where remote-origin headers were omitted in error case. [#6098](https://github.com/scalableminds/webknossos/pull/6098)
+- Increased the timeouts for some internal operations like downsampling volume annotations. [#6103](https://github.com/scalableminds/webknossos/pull/6103)
+- Fixed a bug where there was a suggested change in the `datasource-config.json` was shown for resolution `1` instead of `[1,1,1]` or vice-versa. [#6104](https://github.com/scalableminds/webknossos/pull/6104)
+
+### Removed
+- The previously disabled Import Skeleton Button has been removed. The functionality is available via the context menu for datasets with active ID mappings. [#6073](https://github.com/scalableminds/webknossos/pull/6073)
+- Removes experimental (and hidden) automatic brushing feature. Consequentially, the corresponding feature flag `autoBrushReadyDatasets` is not used, anymore. [#6107](https://github.com/scalableminds/webknossos/pull/6107)
+
+### Breaking Changes
+
+
 ## [22.03.0](https://github.com/scalableminds/webknossos/releases/tag/22.03.0) - 2022-02-21
 [Commits](https://github.com/scalableminds/webknossos/compare/22.02.0...22.03.0)
 

CHANGELOG.unreleased.md

@@ -8,23 +8,15 @@ and this project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MIC
 For upgrade instructions, please check the [migration guide](MIGRATIONS.released.md).
 
 ## Unreleased
-[Commits](https://github.com/scalableminds/webknossos/compare/release-YY.MM...HEAD)
+[Commits](https://github.com/scalableminds/webknossos/compare/22.04.0...HEAD)
 
 ### Added
-- The visible meshes are now included in the link copied from the "Share" modal or the "Share" button next to the dataset position. They are automatically loaded for users that open the shared link. [#5993](https://github.com/scalableminds/webknossos/pull/5993)
-- Added a new "Connectome Tab" which can be used to explore connectomes by visualizing neurites and their synaptic connections. Connectome files need to be placed in a `connectomes` folder inside of the respective segmentation layer. It is possible to craft links that automatically load specific agglomerates and their synapses when openend. For more information refer to https://docs.webknossos.org/webknossos/sharing.html#sharing-link-format. [#5894](https://github.com/scalableminds/webknossos/pull/5894)
 
 ### Changed
-- The maximum brush size now depends on the available magnifications. Consequentially, one can use a larger brush size when the magnifications of a volume layer are restricted. [#6066](https://github.com/scalableminds/webknossos/pull/6066)
-- Improved stability and speed of volume annotations when annotating large areas. [#6055](https://github.com/scalableminds/webknossos/pull/6055)
 
 ### Fixed
-- Fixed a bug that led to crashing the layer settings once the icon for the downsample modal was clicked. [#6058](https://github.com/scalableminds/webknossos/pull/6058)
-- Fixed a bug where toggling between not archived and archived annotations in the "My Annotation" of the dashboard led to inconsistent states and duplicates of annotations. [#6058](https://github.com/scalableminds/webknossos/pull/6058)
-- Fixed a bug where deactivated users would still be listed as allowed to access the datasets of their team. [#6070](https://github.com/scalableminds/webknossos/pull/6070)
-- Fix occasionally "disappearing" data. [#6055](https://github.com/scalableminds/webknossos/pull/6055)
+- Fixed a bug that led to an error when drag-'n-dropping an empty volume annotation in the dataset view. [#6116](https://github.com/scalableminds/webknossos/pull/6116)
 
 ### Removed
-- The previously disabled Import Skeleton Button has been removed. The functionality is available via the context menu for datasets with active ID mappings. [#6073](https://github.com/scalableminds/webknossos/pull/6073)
 
 ### Breaking Changes

Dockerfile

@@ -1,6 +1,6 @@
 FROM openjdk:8-jdk
 RUN apt-get update \
-  && apt-get -y install postgresql-client \
+  && apt-get -y install libblosc1 postgresql-client \
   && rm -rf /var/lib/apt/lists/*
 
 RUN mkdir -p /webknossos

MIGRATIONS.released.md

@@ -5,6 +5,9 @@ See `MIGRATIONS.unreleased.md` for the changes which are not yet part of an offi
 This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 
+## [22.04.0](https://github.com/scalableminds/webknossos/releases/tag/22.04.0) - 2022-03-22
+[Commits](https://github.com/scalableminds/webknossos/compare/22.03.0...22.04.0)
+
 ## [22.03.0](https://github.com/scalableminds/webknossos/releases/tag/22.03.0) - 2022-02-21
 [Commits](https://github.com/scalableminds/webknossos/compare/22.02.0...22.03.0)
 - The config field `googleAnalytics.trackingId` needs to be changed to [GA4 measurement id](https://support.google.com/analytics/answer/10089681), if used.

MIGRATIONS.unreleased.md

@@ -6,6 +6,6 @@ This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 
 ## Unreleased
-[Commits](https://github.com/scalableminds/webknossos/compare/release-YY.MM...HEAD)
+[Commits](https://github.com/scalableminds/webknossos/compare/22.04.0...HEAD)
 
 ### Postgres Evolutions:

README.md

@@ -72,26 +72,34 @@ For non-localhost deployments, check out the [installation guide in the document
 * [sbt](http://www.scala-sbt.org/)
 * [PostgreSQL 10+](https://www.postgresql.org/)
 * [Redis 5+](https://redis.io/)
+* [Blosc](https://github.com/Blosc/c-blosc)
 * [node.js 12+](http://nodejs.org/download/)
 * [yarn package manager](https://yarnpkg.com/)
 * [git](http://git-scm.com/downloads)
 
-### OS X
-If you are using OS X try using this awesome installer:
-https://gist.github.com/normanrz/9128496
-
-Or install Java manually and run:
-
+### MacOS
 ```bash
+# webKnossos needs to be run from x86_64 environment (only applicable for arm64-based Macs)
+arch -x86_64 /bin/zsh
+
 # Install Homebrew package manager
-/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
+/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
 
 # Install git, node.js, postgres, sbt, gfind, gsed
-brew install git node postgresql sbt findutils coreutils gnu-sed redis
-npm install -g yarn
-
-# Start postgres
+brew install openjdk@8 openssl git node postgresql sbt findutils coreutils gnu-sed redis yarn
+
+# Set env variables for openjdk and openssl
+# You probably want to add these lines manually to avoid conflicts in your zshrc
+echo 'if [ $(arch) = "i386" ]; then' >> ~/.zshrc
+echo '  export PATH="/usr/local/opt/openjdk@8/bin:$PATH"' >> ~/.zshrc
+echo '  export PATH="/usr/local/opt/openssl/bin:$PATH"' >> ~/.zshrc
+echo '  export LDFLAGS="-L/usr/local/opt/openssl/lib"' >> ~/.zshrc
+echo '  export CPPFLAGS="-I/usr/local/opt/openssl/include"' >> ~/.zshrc
+echo 'fi' >> ~/.zshrc
+
+# Start postgres and redis
 brew services start postgresql
+brew services start redis
 
 # Create PostgreSQL user
 createdb
@@ -102,8 +110,12 @@ psql -c "GRANT ALL PRIVILEGES ON DATABASE webknossos TO postgres;"
 
 # Checkout the webKnossos git repository
 git clone [email protected]:scalableminds/webknossos.git
+
+
 ```
 
+Note: On arm64-based Macs (e.g. M1), you need to run webKnossos in an x86_64 environment (Rosetta 2). In case you accidentally started webKnossos in an arm64 environment, it is advisable to delete several caches `~/.m2`, `~/ivy2`, `~/.sbt`, `~/.yarn-cache` and run `./clean`. Since Postgres and Redis are isolated processes, they can be run either from arm64 or x86_64 environments.
+
 
 ### Ubuntu 20.04 LTS
 
@@ -118,7 +130,7 @@ 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 nodejs git postgresql postgresql-client scala sbt openjdk-8-jdk yarn redis-server build-essential
+sudo apt install -y nodejs git postgresql postgresql-client scala sbt openjdk-8-jdk yarn redis-server build-essential libblosc1
 
 # Assign a password to PostgreSQL user
 sudo -u postgres psql -c "ALTER USER postgres WITH ENCRYPTED PASSWORD 'postgres';"

app/controllers/Application.scala

@@ -3,7 +3,6 @@ package controllers
 import com.mohiva.play.silhouette.api.Silhouette
 import com.scalableminds.util.accesscontext.DBAccessContext
 import com.scalableminds.util.tools.{Fox, FoxImplicits}
-import com.scalableminds.webknossos.datastore.rpc.RPC
 import com.typesafe.config.ConfigRenderOptions
 import io.swagger.annotations.{Api, ApiOperation, ApiResponse, ApiResponses}
 import javax.inject.Inject
@@ -23,8 +22,7 @@ class Application @Inject()(multiUserDAO: MultiUserDAO,
                             releaseInformationDAO: ReleaseInformationDAO,
                             conf: WkConf,
                             storeModules: StoreModules,
-                            sil: Silhouette[WkEnv],
-                            rpc: RPC)(implicit ec: ExecutionContext, bodyParsers: PlayBodyParsers)
+                            sil: Silhouette[WkEnv])(implicit ec: ExecutionContext, bodyParsers: PlayBodyParsers)
     extends Controller {
 
   @ApiOperation(value = "Information about the version of webKnossos")

app/controllers/Controller.scala

@@ -4,7 +4,6 @@ import com.mohiva.play.silhouette.api.actions.{SecuredRequest, UserAwareRequest}
 import com.scalableminds.util.accesscontext.{AuthorizedAccessContext, DBAccessContext}
 import com.scalableminds.util.mvc.ExtendedController
 import com.scalableminds.util.tools.Fox
-import com.scalableminds.webknossos.datastore.controllers.ValidationHelpers
 import com.typesafe.scalalogging.LazyLogging
 import models.user.User
 import oxalis.security.{UserAwareRequestLogging, WkEnv}
@@ -17,7 +16,6 @@ import scala.concurrent.ExecutionContext
 trait Controller
     extends InjectedController
     with ExtendedController
-    with ValidationHelpers
     with UserAwareRequestLogging
     with I18nSupport
     with LazyLogging {