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scalableminds · Nov 14, 2024 · 6bf39dd · 6bf39dd
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -118,6 +118,7 @@ jobs:
       - run:
           name: Run end-to-end tests
           command: |
+            mkdir -p binaryData/Organization_X && chmod 777 binaryData/Organization_X
             for i in {1..3}; do # retry
               .circleci/not-on-master.sh docker-compose run e2e-tests && s=0 && break || s=$?
             done

diff --git a/CHANGELOG.released.md b/CHANGELOG.released.md
@@ -7,6 +7,56 @@ 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).
 
+## [24.11.1](https://github.com/scalableminds/webknossos/releases/tag/24.11.1) - 2024-11-13
+[Commits](https://github.com/scalableminds/webknossos/compare/24.10.0...24.11.1)
+
+### Highlights
+- It is now possible to add metadata in annotations to Trees and Segments. [#7875](https://github.com/scalableminds/webknossos/pull/7875)
+- Added a button to the search popover in the skeleton and segment tab to select all matching non-group results. [#8123](https://github.com/scalableminds/webknossos/pull/8123)
+
+### Added
+- It is now possible to add metadata in annotations to Trees and Segments. [#7875](https://github.com/scalableminds/webknossos/pull/7875)
+- Added a summary row to the time tracking overview, where times and annotations/tasks are summed. [#8092](https://github.com/scalableminds/webknossos/pull/8092)
+- Most sliders have been improved: Wheeling above a slider now changes its value and double-clicking its knob resets it to its default value. [#8095](https://github.com/scalableminds/webknossos/pull/8095)
+- It is now possible to search for unnamed segments with the full default name instead of only their id. [#8133](https://github.com/scalableminds/webknossos/pull/8133)
+- Increased loading speed for precomputed meshes. [#8110](https://github.com/scalableminds/webknossos/pull/8110)
+- Added a button to the search popover in the skeleton and segment tab to select all matching non-group results. [#8123](https://github.com/scalableminds/webknossos/pull/8123)
+- Unified wording in UI and code: “Magnification”/“mag” is now used in place of “Resolution“ most of the time, compare [https://docs.webknossos.org/webknossos/terminology.html](terminology document). [#8111](https://github.com/scalableminds/webknossos/pull/8111)
+- Added support for adding remote OME-Zarr NGFF version 0.5 datasets. [#8122](https://github.com/scalableminds/webknossos/pull/8122)
+- Workflow reports may be deleted by superusers. [#8156](https://github.com/scalableminds/webknossos/pull/8156)
+
+### Changed
+- Some mesh-related actions were disabled in proofreading-mode when using meshfiles that were created for a mapping rather than an oversegmentation. [#8091](https://github.com/scalableminds/webknossos/pull/8091)
+- 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)
+- Fixed bbox export menu item [#8152](https://github.com/scalableminds/webknossos/pull/8152)
+- When trying to save an annotation opened via a link including a sharing token, the token is automatically discarded in case it is insufficient for update actions but the users token is. [#8139](https://github.com/scalableminds/webknossos/pull/8139)
+- Fix that scrolling in the trees and segments tab did not work while dragging. [#8162](https://github.com/scalableminds/webknossos/pull/8162)
+- Fixed that uploading a dataset which needs a conversion failed when the angstrom unit was configured for the conversion. [#8173](https://github.com/scalableminds/webknossos/pull/8173)
+- Fixed that the skeleton search did not automatically expand groups that contained the selected tree [#8129](https://github.com/scalableminds/webknossos/pull/8129)
+- Fixed interactions in the trees and segments tab like the search due to a bug introduced by [#8162](https://github.com/scalableminds/webknossos/pull/8162). [#8186](https://github.com/scalableminds/webknossos/pull/8186)
+- Fixed a bug that zarr streaming version 3 returned the shape of mag (1, 1, 1) / the finest mag for all mags. [#8116](https://github.com/scalableminds/webknossos/pull/8116)
+- 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)
+- Removed unnecessary scrollbars in skeleton tab that occurred especially after resizing. [#8148](https://github.com/scalableminds/webknossos/pull/8148)
+- Deleting a bounding box is now possible independently of a visible segmentation layer. [#8164](https://github.com/scalableminds/webknossos/pull/8164)
+- S3-compliant object storages can now be accessed via HTTPS. [#8167](https://github.com/scalableminds/webknossos/pull/8167)
+- Fixed that skeleton tree nodes were created with the wrong mag. [#8185](https://github.com/scalableminds/webknossos/pull/8185)
+- Fixed the expected type of a tree node received from the server. Fixes nml export to include the `inMag` field correctly. [#8187](https://github.com/scalableminds/webknossos/pull/8187)
+- Fixed a layout persistence bug leading to empty viewports, triggered when switching between orthogonal, flight, or oblique mode. [#8177](https://github.com/scalableminds/webknossos/pull/8177)
+
+### Removed
+
+### Breaking Changes
+
+
 ## [24.10.0](https://github.com/scalableminds/webknossos/releases/tag/24.10.0) - 2024-09-24
 [Commits](https://github.com/scalableminds/webknossos/compare/24.08.1...24.10.0)
 

diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -8,42 +8,18 @@ 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/24.10.0...HEAD)
+[Commits](https://github.com/scalableminds/webknossos/compare/24.11.1...HEAD)
 
 ### Added
-- It is now possible to add metadata in annotations to Trees and Segments. [#7875](https://github.com/scalableminds/webknossos/pull/7875)
-- Added a summary row to the time tracking overview, where times and annotations/tasks are summed. [#8092](https://github.com/scalableminds/webknossos/pull/8092)
-- Most sliders have been improved: Wheeling above a slider now changes its value and double-clicking its knob resets it to its default value. [#8095](https://github.com/scalableminds/webknossos/pull/8095)
-- It is now possible to search for unnamed segments with the full default name instead of only their id. [#8133](https://github.com/scalableminds/webknossos/pull/8133)
-- Increased loading speed for precomputed meshes. [#8110](https://github.com/scalableminds/webknossos/pull/8110)
-- Added a button to the search popover in the skeleton and segment tab to select all matching non-group results. [#8123](https://github.com/scalableminds/webknossos/pull/8123)
-- Unified wording in UI and code: “Magnification”/“mag” is now used in place of “Resolution“ most of the time, compare [https://docs.webknossos.org/webknossos/terminology.html](terminology document). [#8111](https://github.com/scalableminds/webknossos/pull/8111)
-- Added support for adding remote OME-Zarr NGFF version 0.5 datasets. [#8122](https://github.com/scalableminds/webknossos/pull/8122)
-- Workflow reports may be deleted by superusers. [#8156](https://github.com/scalableminds/webknossos/pull/8156)
 
 ### Changed
-- Some mesh-related actions were disabled in proofreading-mode when using meshfiles that were created for a mapping rather than an oversegmentation. [#8091](https://github.com/scalableminds/webknossos/pull/8091)
-- 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)
 - Renamed "resolution" to "magnification" in more places within the codebase, including local variables. [#8168](https://github.com/scalableminds/webknossos/pull/8168)
+- Reading image files on datastore filesystem is now done asynchronously. [#8126](https://github.com/scalableminds/webknossos/pull/8126)
 
 ### 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)
-- Fixed bbox export menu item [#8152](https://github.com/scalableminds/webknossos/pull/8152)
-- When trying to save an annotation opened via a link including a sharing token, the token is automatically discarded in case it is insufficient for update actions but the users token is. [#8139](https://github.com/scalableminds/webknossos/pull/8139)
-- Fix that scrolling in the trees and segments tab did not work while dragging. [#8162](https://github.com/scalableminds/webknossos/pull/8162) 
-- Fixed that uploading a dataset which needs a conversion failed when the angstrom unit was configured for the conversion. [#8173](https://github.com/scalableminds/webknossos/pull/8173)
-- Fixed that the skeleton search did not automatically expand groups that contained the selected tree [#8129](https://github.com/scalableminds/webknossos/pull/8129)
-- Fixed a bug that zarr streaming version 3 returned the shape of mag (1, 1, 1) / the finest mag for all mags. [#8116](https://github.com/scalableminds/webknossos/pull/8116)
-- 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)
-- Removed unnecessary scrollbars in skeleton tab that occurred especially after resizing. [#8148](https://github.com/scalableminds/webknossos/pull/8148)
-- Deleting a bounding box is now possible independently of a visible segmentation layer. [#8164](https://github.com/scalableminds/webknossos/pull/8164)
-- S3-compliant object storages can now be accessed via HTTPS. [#8167](https://github.com/scalableminds/webknossos/pull/8167)
+- Fix performance bottleneck when deleting a lot of trees at once. [#8176](https://github.com/scalableminds/webknossos/pull/8176)
+- Fix a bug when importing an NML with groups when only groups but no trees exist in an annotation. [#8176](https://github.com/scalableminds/webknossos/pull/8176)
+- Fix a bug where trying to delete a non-existing node (via the API, for example) would delete the whole active tree. [#8176](https://github.com/scalableminds/webknossos/pull/8176)
 
 ### Removed
 

diff --git a/MIGRATIONS.released.md b/MIGRATIONS.released.md
@@ -6,6 +6,16 @@ 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).
 
+## [24.11.1](https://github.com/scalableminds/webknossos/releases/tag/24.11.1) - 2024-11-13
+[Commits](https://github.com/scalableminds/webknossos/compare/24.10.0...24.11.1)
+
+### Postgres Evolutions:
+
+- [121-worker-name.sql](conf/evolutions/121-worker-name.sql)
+- [122-resolution-to-mag.sql](conf/evolutions/122-resolution-to-mag.sql)
+- [123-more-model-categories.sql](conf/evolutions/123-more-model-categories.sql)
+
+
 ## [24.10.0](https://github.com/scalableminds/webknossos/releases/tag/24.10.0) - 2024-09-24
 [Commits](https://github.com/scalableminds/webknossos/compare/24.08.1...24.10.0)
 

diff --git a/MIGRATIONS.unreleased.md b/MIGRATIONS.unreleased.md
@@ -6,10 +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/24.10.0...HEAD)
+[Commits](https://github.com/scalableminds/webknossos/compare/24.11.1...HEAD)
 
 ### Postgres Evolutions:
-
-- [121-worker-name.sql](conf/evolutions/121-worker-name.sql)
-- [122-resolution-to-mag.sql](conf/evolutions/122-resolution-to-mag.sql)
-- [123-more-model-categories.sql](conf/evolutions/123-more-model-categories.sql)
diff --git a/conf/application.conf b/conf/application.conf
@@ -125,7 +125,7 @@ webKnossos {
   securityTxt {
     enabled = true
     content ="""Contact: https://github.com/scalableminds/webknossos/security/advisories/new
-Expires: 2024-07-03T10:00:00.000Z
+Expires: 2025-07-03T10:00:00.000Z
 Preferred-Languages: en,de
     """
   }

diff --git a/conf/messages b/conf/messages
@@ -73,10 +73,6 @@ oidc.disabled=OIDC is disabled
 oidc.configuration.invalid=OIDC configuration is invalid
 oidc.authentication.failed=Failed to register / log in via Single-Sign-On (SSO with OIDC)
 
-braintracing.new=An account on braintracing.org was created for you. You can use the same credentials as on WEBKNOSSOS to login.
-braintracing.error=We could not automatically create an account for you on braintracing.org. Please do it on your own.
-braintracing.exists=Great, you already have an account on braintracing.org. Please double check that you have uploaded all requested information.
-
 dataset=Dataset
 dataset.notFound=Dataset {0} does not exist or could not be accessed
 dataset.notFoundConsiderLogin=Dataset {0} does not exist or could not be accessed. You may need to log in.

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -201,7 +201,7 @@ services:
           -Ddatastore.redis.address=redis
           -Ddatastore.watchFileSystem.enabled=false"
     volumes:
-      - ./binaryData/Connectomics department:/home/${USER_NAME:-sbt-user}/webknossos/binaryData/Organization_X
+      - ./binaryData/Organization_X:/home/${USER_NAME:-sbt-user}/webknossos/binaryData/Organization_X
 
   screenshot-tests:
     image: scalableminds/puppeteer:master

diff --git a/frontend/javascripts/libs/diffable_map.ts b/frontend/javascripts/libs/diffable_map.ts
@@ -54,7 +54,7 @@ class DiffableMap<K extends number, V> {
     if (value !== undefined) {
       return value;
     } else {
-      throw new Error("Get empty");
+      throw new Error(`Key '${key}' does not exist in diffable map.`);
     }
   }
 

diff --git a/frontend/javascripts/oxalis/model/accessors/skeletontracing_accessor.ts b/frontend/javascripts/oxalis/model/accessors/skeletontracing_accessor.ts
@@ -175,7 +175,7 @@ export function getNodeAndTree(
     let node = null;
 
     if (nodeId != null) {
-      node = tree.nodes.getOrThrow(nodeId);
+      node = tree.nodes.getNullable(nodeId);
     } else {
       const { activeNodeId } = skeletonTracing;
 

diff --git a/frontend/javascripts/oxalis/model/actions/skeletontracing_actions.tsx b/frontend/javascripts/oxalis/model/actions/skeletontracing_actions.tsx
@@ -39,6 +39,7 @@ type CreateTreeAction = ReturnType<typeof createTreeAction>;
 type SetEdgeVisibilityAction = ReturnType<typeof setTreeEdgeVisibilityAction>;
 type AddTreesAndGroupsAction = ReturnType<typeof addTreesAndGroupsAction>;
 type DeleteTreeAction = ReturnType<typeof deleteTreeAction>;
+type DeleteTreesAction = ReturnType<typeof deleteTreesAction>;
 type ResetSkeletonTracingAction = ReturnType<typeof resetSkeletonTracingAction>;
 type SetActiveTreeAction = ReturnType<typeof setActiveTreeAction>;
 type SetActiveTreeByNameAction = ReturnType<typeof setActiveTreeByNameAction>;
@@ -65,7 +66,11 @@ type UpdateNavigationListAction = ReturnType<typeof updateNavigationListAction>;
 export type LoadAgglomerateSkeletonAction = ReturnType<typeof loadAgglomerateSkeletonAction>;
 type NoAction = ReturnType<typeof noAction>;
 
-export type BatchableUpdateTreeAction = SetTreeGroupAction | DeleteTreeAction | SetTreeGroupsAction;
+export type BatchableUpdateTreeAction =
+  | SetTreeGroupAction
+  | DeleteTreeAction
+  | DeleteTreesAction
+  | SetTreeGroupsAction;
 export type BatchUpdateGroupsAndTreesAction = {
   type: "BATCH_UPDATE_GROUPS_AND_TREES";
   payload: BatchableUpdateTreeAction[];
@@ -93,6 +98,7 @@ export type SkeletonTracingAction =
   | SetEdgeVisibilityAction
   | AddTreesAndGroupsAction
   | DeleteTreeAction
+  | DeleteTreesAction
   | ResetSkeletonTracingAction
   | SetActiveTreeAction
   | SetActiveTreeByNameAction
@@ -139,6 +145,7 @@ export const SkeletonTracingSaveRelevantActions = [
   "SET_EDGES_ARE_VISIBLE",
   "ADD_TREES_AND_GROUPS",
   "DELETE_TREE",
+  "DELETE_TREES",
   "SET_ACTIVE_TREE",
   "SET_ACTIVE_TREE_BY_NAME",
   "SET_TREE_NAME",
@@ -337,6 +344,19 @@ export const deleteTreeAction = (treeId?: number, suppressActivatingNextNode: bo
     suppressActivatingNextNode,
   }) as const;
 
+export const deleteTreesAction = (treeIds: number[], suppressActivatingNextNode: boolean = false) =>
+  // If suppressActivatingNextNode is true, the trees will be deleted without activating
+  // another node (nor tree). Use this in cases where you want to avoid changing
+  // the active position (due to the auto-centering). One could also suppress the auto-centering
+  // behavior, but the semantics of changing the active node might also be confusing to the user
+  // (e.g., when proofreading). So, it might be clearer to not have an active node in the first
+  // place.
+  ({
+    type: "DELETE_TREES",
+    treeIds,
+    suppressActivatingNextNode,
+  }) as const;
+
 export const resetSkeletonTracingAction = () =>
   ({
     type: "RESET_SKELETON_TRACING",
@@ -555,11 +575,15 @@ export const deleteNodeAsUserAction = (
 
       return deleteNodeAction(node.id, tree.treeId);
     }) // If the tree is empty, it will be deleted
-    .getOrElse(deleteTreeAction(treeId));
+    .getOrElse(
+      getTree(skeletonTracing, treeId)
+        .map((tree) => (tree.nodes.size() === 0 ? deleteTreeAction(tree.treeId) : noAction()))
+        .getOrElse(noAction()),
+    );
 };
 
 // Let the user confirm the deletion of the initial node (node with id 1) of a task
-function confirmDeletingInitialNode(treeId?: number) {
+function confirmDeletingInitialNode(treeId: number) {
   Modal.confirm({
     title: messages["tracing.delete_tree_with_initial_node"],
     onOk: () => {
@@ -573,12 +597,15 @@ export const deleteTreeAsUserAction = (treeId?: number): NoAction => {
   const skeletonTracing = enforceSkeletonTracing(state.tracing);
   getTree(skeletonTracing, treeId).map((tree) => {
     if (state.task != null && tree.nodes.has(1)) {
-      confirmDeletingInitialNode(treeId);
+      confirmDeletingInitialNode(tree.treeId);
     } else if (state.userConfiguration.hideTreeRemovalWarning) {
-      Store.dispatch(deleteTreeAction(treeId));
+      Store.dispatch(deleteTreeAction(tree.treeId));
     } else {
       renderIndependently((destroy) => (
-        <RemoveTreeModal onOk={() => Store.dispatch(deleteTreeAction(treeId))} destroy={destroy} />
+        <RemoveTreeModal
+          onOk={() => Store.dispatch(deleteTreeAction(tree.treeId))}
+          destroy={destroy}
+        />
       ));
     }
   });