Merge branch 'master' of github.com:scalableminds/webknossos into ant…

…d-v4.24 * 'master' of github.com:scalableminds/webknossos: Implement http range requests for HttpsSeekableByteChannel (#6869) new GH action for adding issues to project board Fix links in Changelog (#6881) adds dedicated explore method for zarr datasets with a datasource-properties.json (#6879) Release 23.03.0 (#6880) Fix superUser being wrongly marked as organization owners (#6876) Followups for OME-TIFF export (#6874) Fix reload-precomputed-mesh functionality (#6875) Adds OME-TIFF export (#6838) Add evolutions 99,100 to migration guide (#6871) Add link to imprint and privacy to help menu (#6870) Annotation Locking Mechanism (#6819)
scalableminds · Mar 2, 2023 · 8320f9d · 8320f9d
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diff --git a/.github/workflows/assign_issue_project.yml b/.github/workflows/assign_issue_project.yml
@@ -1,46 +1,14 @@
 name: Auto Assign Issues to Project
-# From: https://www.cloudwithchris.com/blog/automate-adding-gh-issues-projects-beta/
 on:
   issues:
     types: [opened]
-env:
-  GITHUB_TOKEN: ${{ secrets.PROJECT_GITHUB_TOKEN }}
 
 jobs:
   assign_issue_to_project:
     runs-on: ubuntu-latest
     steps:
-      - name: Get project data
-        env:
-          ORGANIZATION: scalableminds
-          PROJECT_NUMBER: 6
-        run: |
-          gh api graphql -f query='
-            query($org: String!, $number: Int!) {
-              organization(login: $org){
-                projectNext(number: $number) {
-                  id
-                  fields(first:20) {
-                    nodes {
-                      id
-                      name
-                      settings
-                    }
-                  }
-                }
-              }
-            }' -f org=$ORGANIZATION -F number=$PROJECT_NUMBER > project_data.json
-          echo 'PROJECT_ID='$(jq '.data.organization.projectNext.id' project_data.json) >> $GITHUB_ENV
-                    
-      - name: Add issue to project
-        env:
-          ISSUE_ID: ${{ github.event.issue.node_id }}
-        run: |
-          item_id="$( gh api graphql -f query='
-            mutation($project:ID!, $issue:ID!) {
-              addProjectNextItem(input: {projectId: $project, contentId: $issue}) {
-                projectNextItem {
-                  id
-                }
-              }
-            }' -f project=$PROJECT_ID -f issue=$ISSUE_ID --jq '.data.addProjectNextItem.projectNextItem.id')"
+      - name: Add to GitHub projects
+        uses: actions/[email protected]
+        with:
+          project-url: https://github.com/orgs/scalableminds/projects/6
+          github-token: ${{ secrets.PROJECT_GITHUB_TOKEN }}
diff --git a/CHANGELOG.released.md b/CHANGELOG.released.md
@@ -7,6 +7,42 @@ 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).
 
+## [23.03.0](https://github.com/scalableminds/webknossos/releases/tag/23.03.0) - 2023-02-28
+[Commits](https://github.com/scalableminds/webknossos/compare/23.02.1...23.03.0)
+
+### Highlights
+- Remote datasets can now also be streamed from Google Cloud Storage URIs (`gs://`). [#6775](https://github.com/scalableminds/webknossos/pull/6775)
+- Remote volume datasets in the neuroglancer precomputed format can now be viewed in WEBKNOSSOS. [#6716](https://github.com/scalableminds/webknossos/pull/6716)
+- Added new mesh-related menu items to the context menu when a mesh is hovered in the 3d viewport. [#6813](https://github.com/scalableminds/webknossos/pull/6813)
+
+### Added
+- If an annotation that others are allowed to edit is opened, it will now be automatically locked. This prevents conflicts when multiple users try to edit it at the same time. [#6819](https://github.com/scalableminds/webknossos/pull/6819)
+- Highlight 'organization owner' in Admin>User page. [#6832](https://github.com/scalableminds/webknossos/pull/6832)
+- Added OME-TIFF export for bounding boxes. [#6838](https://github.com/scalableminds/webknossos/pull/6838) [#6874](https://github.com/scalableminds/webknossos/pull/6874)
+- Added functions to get and set segment colors to the frontend API (`api.data.{getSegmentColor,setSegmentColor}`). [#6853](https://github.com/scalableminds/webknossos/pull/6853)
+
+### Changed
+- Limit paid team sharing features to respective organization plans. [#6767](https://github.com/scalableminds/webknossos/pull/6776)
+- Rewrite the database tools in `tools/postgres` to JavaScript and adding support for non-default Postgres username-password combinations. [#6803](https://github.com/scalableminds/webknossos/pull/6803)
+- Added owner name to organization page. [#6811](https://github.com/scalableminds/webknossos/pull/6811)
+- Remove multiline <TextArea> support from <InputComponent>. [#6839](https://github.com/scalableminds/webknossos/pull/6839)
+- Improved the performance of the dataset table in the dashboard. [#6834](https://github.com/scalableminds/webknossos/pull/6834)
+- Updated the styling and background of login, password reset/change and sign up pages. [#6844](https://github.com/scalableminds/webknossos/pull/6844)
+- Replaced date handling and formatting library momentjs with dayjs. [#6849](https://github.com/scalableminds/webknossos/pull/6849)
+
+### Fixed
+- Fixed saving allowed teams in dataset settings. [#6817](https://github.com/scalableminds/webknossos/pull/6817)
+- Fixed log streaming in Voxelytics workflow reports. [#6828](https://github.com/scalableminds/webknossos/pull/6828) [#6831](https://github.com/scalableminds/webknossos/pull/6831)
+- Fixed some layouting issues with line breaks in segment list/dataset info tab. [#6799](https://github.com/scalableminds/webknossos/pull/6799)
+- Fixed basic auth for exploring remote http datasets. [#6866](https://github.com/scalableminds/webknossos/pull/6866)
+- Fixed the layouting in the connectome tab. [#6864](https://github.com/scalableminds/webknossos/pull/6864)
+- Fixed that the quick-select and floodfill tool didn't update the segment list. [#6867](https://github.com/scalableminds/webknossos/pull/6867)
+- Fixed deprecation warnings for antd' <Menu> component in Navbar. [#6860](https://github.com/scalableminds/webknossos/pull/6860)
+- Fixed that trying to reload a precomputed mesh via context menu could crash webKnossos. [#6875](https://github.com/scalableminds/webknossos/pull/6875)
+
+### Removed
+- Removed the old Datasets tab in favor of the Dataset Folders tab. [#6834](https://github.com/scalableminds/webknossos/pull/6834)
+
 ## [23.02.1](https://github.com/scalableminds/webknossos/releases/tag/23.02.1) - 2023-02-07
 [Commits](https://github.com/scalableminds/webknossos/compare/23.02.0...23.02.1)
 
@@ -498,7 +534,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 
 ### Breaking Change
 - When using the front-end API, functions that accept a layer name, such as `api.data.getDataValue`, won't interpret the name "segmentation" as the current volume tracing if it exists. Instead, "segmentation" can only be used if the current dataset has a layer which is named "segmentation". If you want to interact with the volume tracing layer, use `api.data.getVolumeTracingLayerIds()` instead. Also see `api.data.getSegmentationLayerNames` and `api.data.getVisibleSegmentationLayer`. [#5771](https://github.com/scalableminds/webknossos/pull/5771)
-- The datastore server routes `/datasets/reserveUpload` and `/datasets/finishUpload` now expect the additional field `layersToLink`, which should be an empty list by default. [#5863](https://github.com/scalableminds/webknossos/pull/5863
+- The datastore server routes `/datasets/reserveUpload` and `/datasets/finishUpload` now expect the additional field `layersToLink`, which should be an empty list by default. [#5863](https://github.com/scalableminds/webknossos/pull/5863)
 
 
 ## [21.11.2](https://github.com/scalableminds/webknossos/releases/tag/21.11.2) - 2021-12-21

diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md
@@ -8,36 +8,16 @@ 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/23.02.1...HEAD)
+[Commits](https://github.com/scalableminds/webknossos/compare/23.03.0...HEAD)
 
 ### Added
-- Remote datasets can now also be streamed from Google Cloud Storage URIs (`gs://`). [#6775](https://github.com/scalableminds/webknossos/pull/6775)
-- Remote volume datasets in the neuroglancer precomputed format can now be viewed in WEBKNOSSOS. [#6716](https://github.com/scalableminds/webknossos/pull/6716)
-- Added new mesh-related menu items to the context menu when a mesh is hovered in the 3d viewport. [#](https://github.com/scalableminds/webknossos/pull/6813)
-- Highlight 'organization owner' in Admin>User page. [#6832](https://github.com/scalableminds/webknossos/pull/6832)
-- Added functions to get and set segment colors to the frontend API (`api.data.{getSegmentColor,setSegmentColor}`). [#6853](https://github.com/scalableminds/webknossos/pull/6853)
-
+- Added support for remote Zarr datasets with a `datasource-properties.json` as created by the WEBKNOSSOS Python library. [#6879](https://github.com/scalableminds/webknossos/pull/6879)
 
 ### Changed
-- Limit paid team sharing features to respective organization plans. [#6767](https://github.com/scalableminds/webknossos/pull/6776)
-- Rewrite the database tools in `tools/postgres` to JavaScript and adding support for non-default Postgres username-password combinations. [#6803](https://github.com/scalableminds/webknossos/pull/6803)
-- Added owner name to organization page. [#6811](https://github.com/scalableminds/webknossos/pull/6811)
-- Remove multiline <TextArea> support from <InputComponent>. [#6839](https://github.com/scalableminds/webknossos/pull/6839)
-- Improved the performance of the dataset table in the dashboard. [#6834](https://github.com/scalableminds/webknossos/pull/6834)
-- Updated the styling and background of login, password reset/change and sign up pages. [#6844](https://github.com/scalableminds/webknossos/pull/6844)
-- Replaced date handling and formatting library momentjs with dayjs. [#6849](https://github.com/scalableminds/webknossos/pull/6849)
 - Upgraded antd UI library to v4.24.8 [#6865](https://github.com/scalableminds/webknossos/pull/6865)
 
 ### Fixed
-- Fixed saving allowed teams in dataset settings. [#6817](https://github.com/scalableminds/webknossos/pull/6817)
-- Fixed log streaming in Voxelytics workflow reports. [#6828](https://github.com/scalableminds/webknossos/pull/6828) [#6831](https://github.com/scalableminds/webknossos/pull/6831)
-- Fixed some layouting issues with line breaks in segment list/dataset info tab. [#6799](https://github.com/scalableminds/webknossos/pull/6799)
-- Fixed basic auth for exploring remote http datasets. [#6866](https://github.com/scalableminds/webknossos/pull/6866)
-- Fixed the layouting in the connectome tab. [#6864](https://github.com/scalableminds/webknossos/pull/6864)
-- Fixed that the quick-select and floodfill tool didn't update the segment list. [#6867](https://github.com/scalableminds/webknossos/pull/6867)
-- Fixed deprecation warnings for antd' <Menu> component in Navbar. [#6860](https://github.com/scalableminds/webknossos/pull/6860)
 
 ### Removed
-- Removed the old Datasets tab in favor of the Dataset Folders tab. [#6834](https://github.com/scalableminds/webknossos/pull/6834)
 
 ### Breaking Changes
diff --git a/DEV_INSTALL.md b/DEV_INSTALL.md
@@ -18,7 +18,7 @@ For non-localhost deployments, check out the [installation guide in the document
 
 ### Dependencies
 
-* [Oracle JDK 8 to 14](http://www.oracle.com/technetwork/java/javase/downloads/index.html) or [Open JDK 8 to 14](http://openjdk.java.net/) (full JDK, JRE is not enough)
+* [Oracle JDK 11 to 14](http://www.oracle.com/technetwork/java/javase/downloads/index.html) or [Open JDK 11 to 14](http://openjdk.java.net/) (full JDK, JRE is not enough)
 * [sbt](http://www.scala-sbt.org/)
 * [PostgreSQL 10+](https://www.postgresql.org/)
 * [Redis 5+](https://redis.io/)

diff --git a/MIGRATIONS.released.md b/MIGRATIONS.released.md
@@ -5,6 +5,18 @@ 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).
 
+## [23.03.0](https://github.com/scalableminds/webknossos/releases/tag/23.03.0) - 2023-02-28
+[Commits](https://github.com/scalableminds/webknossos/compare/23.02.1...23.03.0)
+
+- WEBKNOSSOS now requires Node.js not only for development and building, but also for execution. The prebuilt Docker images already contain this dependency. If you're using these, nothing needs to be changed. [#6803](https://github.com/scalableminds/webknossos/pull/6803)
+- Requires Voxelytics worker version 23.02.xx for long-running jobs. [#6838](https://github.com/scalableminds/webknossos/pull/6838)
+
+### Postgres Evolutions:
+
+- [099-rename-credential-types.sql](conf/evolutions/099-rename-credential-types.sql)
+- [100-annotation-mutexes.sql](conf/evolutions/100-annotation-mutexes.sql)
+
+
 ## [23.02.1](https://github.com/scalableminds/webknossos/releases/tag/23.02.1) - 2023-02-07
 [Commits](https://github.com/scalableminds/webknossos/compare/23.02.0...23.02.1)
 
@@ -517,4 +529,4 @@ No migrations necessary.
 
 
 ## [18.07.0](https://github.com/scalableminds/webknossos/releases/tag/18.07.0) - 2018-07-05
-First release
+First release
diff --git a/MIGRATIONS.unreleased.md b/MIGRATIONS.unreleased.md
@@ -6,8 +6,7 @@ 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/23.02.1...HEAD)
-
-- WEBKNOSSOS now requires Node.js not only for development and building, but also for execution. The prebuilt Docker images already contain this dependency. If you're using these, nothing needs to be changed. [#6803](https://github.com/scalableminds/webknossos/pull/6803)
+[Commits](https://github.com/scalableminds/webknossos/compare/23.03.0...HEAD)
+- WEBKNOSSOS now requires at least Java 11 (up from Java 8). [#6869](https://github.com/scalableminds/webknossos/pull/6869)
 
 ### Postgres Evolutions:
diff --git a/app/WebKnossosModule.scala b/app/WebKnossosModule.scala
@@ -1,7 +1,7 @@
 import com.google.inject.AbstractModule
 import controllers.InitialDataService
 import models.analytics.AnalyticsSessionService
-import models.annotation.AnnotationStore
+import models.annotation.{AnnotationMutexService, AnnotationStore}
 import models.binary.DataSetService
 import models.job.{JobService, WorkerLivenessService}
 import models.storage.UsedStorageService
@@ -26,6 +26,7 @@ class WebKnossosModule extends AbstractModule {
     bind(classOf[UserDataSetConfigurationDAO]).asEagerSingleton()
     bind(classOf[UserCache]).asEagerSingleton()
     bind(classOf[AnnotationStore]).asEagerSingleton()
+    bind(classOf[AnnotationMutexService]).asEagerSingleton()
     bind(classOf[DataSetService]).asEagerSingleton()
     bind(classOf[TimeSpanService]).asEagerSingleton()
     bind(classOf[TempFileService]).asEagerSingleton()

diff --git a/app/controllers/AnnotationController.scala b/app/controllers/AnnotationController.scala
@@ -22,7 +22,8 @@ import models.team.{TeamDAO, TeamService}
 import models.user.time._
 import models.user.{User, UserDAO, UserService}
 import oxalis.mail.{MailchimpClient, MailchimpTag}
-import oxalis.security.{URLSharing, WkEnv}
+import oxalis.security.{URLSharing, UserAwareRequestLogging, WkEnv}
+import oxalis.telemetry.SlackNotificationService
 import play.api.i18n.{Messages, MessagesProvider}
 import play.api.libs.json.Json.WithDefaultValues
 import play.api.libs.json._
@@ -54,6 +55,7 @@ class AnnotationController @Inject()(
     dataSetDAO: DataSetDAO,
     dataSetService: DataSetService,
     annotationService: AnnotationService,
+    annotationMutexService: AnnotationMutexService,
     userService: UserService,
     teamService: TeamService,
     projectDAO: ProjectDAO,
@@ -64,10 +66,12 @@ class AnnotationController @Inject()(
     provider: AnnotationInformationProvider,
     annotationRestrictionDefaults: AnnotationRestrictionDefaults,
     analyticsService: AnalyticsService,
+    slackNotificationService: SlackNotificationService,
     mailchimpClient: MailchimpClient,
     conf: WkConf,
     sil: Silhouette[WkEnv])(implicit ec: ExecutionContext, bodyParsers: PlayBodyParsers)
     extends Controller
+    with UserAwareRequestLogging
     with FoxImplicits {
 
   implicit val timeout: Timeout = Timeout(5 seconds)
@@ -559,6 +563,7 @@ class AnnotationController @Inject()(
     sil.SecuredAction.async { implicit request =>
       for {
         annotation <- provider.provideAnnotation(typ, id, request.identity)
+        _ <- bool2Fox(annotation.typ == AnnotationType.Explorational || annotation.typ == AnnotationType.Task) ?~> "annotation.othersMayEdit.onlyExplorationalOrTask"
         _ <- bool2Fox(annotation._user == request.identity._id) ?~> "notAllowed" ~> FORBIDDEN
         _ <- annotationDAO.updateOthersMayEdit(annotation._id, othersMayEdit)
       } yield Ok(Json.toJson(othersMayEdit))
@@ -601,4 +606,20 @@ class AnnotationController @Inject()(
       }
     } yield annotationLayer.copy(tracingId = newTracingId)
 
+  @ApiOperation(hidden = true, value = "")
+  def tryAcquiringAnnotationMutex(id: String): Action[AnyContent] =
+    sil.SecuredAction.async { implicit request =>
+      logTime(slackNotificationService.noticeSlowRequest, durationThreshold = 1 second) {
+        for {
+          idValidated <- ObjectId.fromString(id)
+          annotation <- provider.provideAnnotation(id, request.identity) ~> NOT_FOUND
+          _ <- bool2Fox(annotation.othersMayEdit) ?~> "notAllowed" ~> FORBIDDEN
+          restrictions <- provider.restrictionsFor(AnnotationIdentifier(annotation.typ, idValidated)) ?~> "restrictions.notFound" ~> NOT_FOUND
+          _ <- restrictions.allowUpdate(request.identity) ?~> "notAllowed" ~> FORBIDDEN
+          mutexResult <- annotationMutexService.tryAcquiringAnnotationMutex(annotation._id, request.identity._id) ?~> "annotation.mutex.failed"
+          resultJson <- annotationMutexService.publicWrites(mutexResult)
+        } yield Ok(resultJson)
+      }
+    }
+
 }