Merge branch 'master' into expand-parent-tree

Author: knollengewaechs

.github/ISSUE_TEMPLATE/config.yml

@@ -1 +1 @@
-blank_issues_enabled: false
+blank_issues_enabled: true

CHANGELOG.unreleased.md

@@ -11,21 +11,28 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 [Commits](https://github.com/scalableminds/webknossos/compare/25.05.0...HEAD)
 
 ### Added
+- Meshes of Neuroglancer Precomputed Datasets can now be viewed. [#8236](https://github.com/scalableminds/webknossos/pull/8236)
 - Added the possibility to join an organization without requiring a paid user slot in case an organization already pays for the same user. Such a user is called a "Guest User". [#8502](https://github.com/scalableminds/webknossos/pull/8502)
+- Added that "Create Animation" jobs will now use the correct semgent colors for rendering meshes. [#8605](https://github.com/scalableminds/webknossos/pull/8605) 
 
 ### Changed
 - Remove `data.maybe` dependency and replaced with regular Typescript types. [#8563](https://github.com/scalableminds/webknossos/pull/8563)
 - Updated `View Modes` documentation page with links for mouse and keyboard shortcuts. [#8582](https://github.com/scalableminds/webknossos/pull/8582)
 - Renamed the button to view the compound annotation of all tasks of a tasktype to be more descriptive. [#8565](https://github.com/scalableminds/webknossos/pull/8565)
-- Replaced fixed threshold of 40 meshes by a dynamic limit based on the number of triangles in the mesh for the "Create Animation" job. [#8588](https://github.com/scalableminds/webknossos/pull/8588) 
+- Replaced fixed threshold of 40 meshes by a dynamic limit based on the number of triangles in the mesh for the "Create Animation" job. [#8588](https://github.com/scalableminds/webknossos/pull/8588)
 - Replaced Redux selector `useSelector((state: OxalisState) => ...)` with a typed `useWkSelector(state => ...)` shorthand. [#8591](https://github.com/scalableminds/webknossos/pull/8591)
 - Renamed `OxalisState`, `OxalisApplication`, and `OxalisApi` to their respective `Webknossos{State, API, Application}` equivalent [#8591](https://github.com/scalableminds/webknossos/pull/8591)
 - Renamed `frontend/javascripts/oxalis` to `frontend/javascripts/viewer`. [#8601](https://github.com/scalableminds/webknossos/pull/8601)
+- When loading data from a data layer that has data stored beyond the bounding box specified in the datasource-properties.json, data outside of the bounding box is now zeroed. (the layer is “clipped”). [#8551](https://github.com/scalableminds/webknossos/pull/8551)
+- Updated to Typescript from version `5.5` to `5.8`. [#8613](https://github.com/scalableminds/webknossos/pull/8613)
+- Updated Voxelytics log streaming to also include the `log_path` attribute. [#8615](https://github.com/scalableminds/webknossos/pull/8615)
 
 ### Fixed
 - When selecting a skeleton node in a viewport, its tree is focused and scrolled to in the skeleton tab, even if its parent group was collapsed before. [#8585](https://github.com/scalableminds/webknossos/pull/8585)
 - Fixed that layer bounding boxes were sometimes colored green even though this should only happen for tasks. [#8535](https://github.com/scalableminds/webknossos/pull/8535)
 - Fixed that annotations could not be opened anymore (caused by #8535). [#8599](https://github.com/scalableminds/webknossos/pull/8599)
+- The guest tag is now also shown for guest admin users. [#8612](https://github.com/scalableminds/webknossos/pull/8612)
+- Fixed a rare bug where segment bounding box would not be displayed correctly, with the request potentially even crashing the server. [#8590](https://github.com/scalableminds/webknossos/pull/8590)
 
 ### Removed
 

MIGRATIONS.unreleased.md

@@ -9,4 +9,6 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 [Commits](https://github.com/scalableminds/webknossos/compare/25.05.0...HEAD)
 
 ### Postgres Evolutions:
+
 - [131-more-indices-on-users.sql](conf/evolutions/131-more-indices-on-users.sql)
+- [132-remove-stored-meshes.sql](conf/evolutions/132-remove-stored-meshes.sql)

app/controllers/AuthenticationController.scala

@@ -580,15 +580,14 @@ class AuthenticationController @Inject()(
       }
     }
 
-  private def validateNameAndEmail(firstName: String,
-                                   lastName: String,
-                                   email: String): Fox[(String, String, String, List[String])] = {
+  private def validateNameAndEmail(firstName: String, lastName: String, email: String)(
+      implicit messages: Messages): Fox[(String, String, String, List[String])] = {
     var (errors, fN, lN) = normalizeName(firstName, lastName)
     for {
       nameEmailError: (String, String, String,
       List[String]) <- multiUserDAO.findOneByEmail(email.toLowerCase)(GlobalAccessContext).shiftBox.flatMap {
         case Full(_) =>
-          errors ::= "user.email.alreadyInUse"
+          errors ::= Messages("user.email.alreadyInUse")
           Fox.successful(("", "", "", errors))
         case Empty =>
           if (errors.nonEmpty) {

app/controllers/MeshController.scala

@@ -220,7 +220,8 @@ class LokiClient @Inject()(wkConf: WkConf, rpc: RPC, val actorSystem: ActorSyste
                         "thread_name" -> (entry \ "vx" \ "thread_name").as[String],
                         "vx_version" -> (entry \ "vx" \ "version").as[String],
                         "user" -> (entry \ "vx" \ "user").as[String],
-                        "pgid" -> (entry \ "vx" \ "process_group_id").as[Long].toString
+                        "pgid" -> (entry \ "vx" \ "process_group_id").as[Long].toString,
+                        "log_path" -> (entry \ "vx" \ "log_path").as[String]
                       ))
                   ).toFox
                 } yield

app/models/mesh/Mesh.scala

@@ -0,0 +1,6 @@
+do $$ begin ASSERT (select schemaVersion from webknossos.releaseInformation) = 131, 'Previous schema version mismatch'; end; $$ LANGUAGE plpgsql;
+
+DROP VIEW webknossos.meshes_;
+DROP TABLE webknossos.meshes;
+
+UPDATE webknossos.releaseInformation SET schemaVersion = 132;

app/models/voxelytics/LokiClient.scala

@@ -0,0 +1,19 @@
+do $$ begin ASSERT (select schemaVersion from webknossos.releaseInformation) = 132, 'Previous schema version mismatch'; end; $$ LANGUAGE plpgsql;
+
+
+CREATE TABLE webknossos.meshes(
+  _id TEXT CONSTRAINT _id_objectId CHECK (_id ~ '^[0-9a-f]{24}$') PRIMARY KEY,
+  _annotation TEXT CONSTRAINT _annotation_objectId CHECK (_annotation ~ '^[0-9a-f]{24}$') NOT NULL,
+  description TEXT NOT NULL DEFAULT '',
+  position webknossos.VECTOR3 NOT NULL,
+  data TEXT,
+  created TIMESTAMPTZ NOT NULL DEFAULT NOW(),
+  isDeleted BOOLEAN NOT NULL DEFAULT false
+);
+
+CREATE VIEW webknossos.meshes_ AS SELECT * FROM webknossos.meshes WHERE NOT isDeleted;
+
+ALTER TABLE webknossos.meshes
+  ADD CONSTRAINT annotation_ref FOREIGN KEY(_annotation) REFERENCES webknossos.annotations(_id) DEFERRABLE;
+
+UPDATE webknossos.releaseInformation SET schemaVersion = 131;

conf/evolutions/132-remove-stored-meshes.sql

@@ -260,19 +260,9 @@ annotation.editableMapping.getAgglomerateGraph.failed=Could not look up an agglo
 annotation.editableMapping.getAgglomerateIdsForSegments.failed=Could not look up agglomerate ids for requested segments.
 annotation.duplicate.failed=Failed to duplicate annotation
 
-mesh.notFound=Mesh could not be found
-mesh.write.failed=Failed to convert mesh info to json
-mesh.create.failed=Failed to save mesh info
-mesh.update.failed=Failed to update mesh info
-mesh.data.get.failed=Failed to load mesh raw data
-mesh.data.read.failed=Failed to convert mesh raw data for saving
-mesh.data.save.failed=Failed to save mesh raw data
-mesh.delete.failed=Failed to delete mesh
-mesh.file.load.failed=Failed to load mesh for segment {0}
 mesh.file.listChunks.failed=Failed to load chunk list for segment {0} from mesh file “{1}”
 mesh.file.loadChunk.failed=Failed to load mesh chunk for segment
 mesh.file.open.failed=Failed to open mesh file for reading
-mesh.file.readData.failed=Failed to read data from mesh file
 mesh.file.readEncoding.failed=Failed to read encoding from mesh file
 
 task.create.noTasks=Zero tasks were requested