Merge branch 'master' into special-files

Author: frcroth

.dependency-cruiser.js

@@ -203,10 +203,10 @@ module.exports = {
       comment: "",
       severity: "warn",
       from: {
-        path: "^(frontend/javascripts/oxalis/model/accessors/).*[.]ts$",
+        path: "^(frontend/javascripts/viewer/model/accessors/).*[.]ts$",
       },
       to: {
-        path: "^(frontend/javascripts/oxalis/model/sagas/).*[.]ts$",
+        path: "^(frontend/javascripts/viewer/model/sagas/).*[.]ts$",
         reachable: true,
       },
     },

CHANGELOG.unreleased.md

@@ -11,19 +11,24 @@ 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)
 
 ### Fixed
 - 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)
+- 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

@@ -11,5 +11,6 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 ### Postgres Evolutions:
 
 - [131-more-indices-on-users.sql](conf/evolutions/131-more-indices-on-users.sql)
-- [132-special-files.sql](conf/evolutions/132-special-files.sql)
+- [132-remove-stored-meshes.sql](conf/evolutions/132-remove-stored-meshes.sql)
+- [133-special-files.sql](conf/evolutions/133-special-files.sql)
 

app/controllers/MeshController.scala

@@ -1,10 +1,10 @@
 {
   "$schema": "./node_modules/@biomejs/biome/configuration_schema.json",
-  "organizeImports": { 
-    "enabled": true,  
+  "organizeImports": {
+    "enabled": true,
     "ignore": [
       "frontend/javascripts/test/*",
-      "frontend/javascripts/oxalis/model/helpers/shader_editor.ts"
+      "frontend/javascripts/viewer/model/helpers/shader_editor.ts"
     ]
   },
   "linter": {
@@ -100,10 +100,12 @@
   },
   "overrides": [
     {
-      "include": ["**/package.json"],
+      "include": [
+        "**/package.json"
+      ],
       "formatter": {
         "lineWidth": 1
       }
     }
   ]
-}
+}

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;

biome.json

@@ -1,6 +1,6 @@
 START TRANSACTION;
 
-do $$ begin ASSERT (select schemaVersion from webknossos.releaseInformation) = 131, 'Previous schema version mismatch'; end; $$ LANGUAGE plpgsql;
+do $$ begin ASSERT (select schemaVersion from webknossos.releaseInformation) = 132, 'Previous schema version mismatch'; end; $$ LANGUAGE plpgsql;
 
 CREATE TABLE webknossos.dataset_layer_special_files(
    _dataset TEXT CONSTRAINT _dataset_objectId CHECK (_dataset ~ '^[0-9a-f]{24}$') NOT NULL,
@@ -9,6 +9,6 @@ CREATE TABLE webknossos.dataset_layer_special_files(
    type TEXT NOT NULL
 );
 
-UPDATE webknossos.releaseInformation SET schemaVersion = 132;
+UPDATE webknossos.releaseInformation SET schemaVersion = 133;
 
 COMMIT TRANSACTION;

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

@@ -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-special-files.sql renamed to conf/evolutions/133-special-files.sql

@@ -1,9 +1,9 @@
 START TRANSACTION;
 
-do $$ begin ASSERT (select schemaVersion from webknossos.releaseInformation) = 132, 'Previous schema version mismatch'; end; $$ LANGUAGE plpgsql;
+do $$ begin ASSERT (select schemaVersion from webknossos.releaseInformation) = 133, 'Previous schema version mismatch'; end; $$ LANGUAGE plpgsql;
 
 DROP TABLE IF EXISTS webknossos.dataset_layer_special_files;
 
-UPDATE webknossos.releaseInformation SET schemaVersion = 131;
+UPDATE webknossos.releaseInformation SET schemaVersion = 132;
 
 COMMIT TRANSACTION;