Merge branch 'master' into remove-returns

CHANGELOG.unreleased.md

@@ -11,16 +11,19 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 [Commits](https://github.com/scalableminds/webknossos/compare/24.11.1...HEAD)
 
 ### Added
+- When exploring remote URIs pasted from Neuroglancer, the format prefixes like `precomputed://` are now ignored, so users don’t have to remove them. [#8195](https://github.com/scalableminds/webknossos/pull/8195)
 
 ### Changed
 - Reading image files on datastore filesystem is now done asynchronously. [#8126](https://github.com/scalableminds/webknossos/pull/8126)
 - Improved error messages for starting jobs on datasets from other organizations. [#8181](https://github.com/scalableminds/webknossos/pull/8181)
+- Removed bounding box size restriction for inferral jobs for super users. [#8200](https://github.com/scalableminds/webknossos/pull/8200)
 
 ### Fixed
 - 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
+- Removed Google Analytics integration. [#8201](https://github.com/scalableminds/webknossos/pull/8201)
 
 ### Breaking Changes

MIGRATIONS.unreleased.md

@@ -8,4 +8,6 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 ## Unreleased
 [Commits](https://github.com/scalableminds/webknossos/compare/24.11.1...HEAD)
 
+- The config option `googleAnalytics.trackingId` is no longer used and can be removed. [#8201](https://github.com/scalableminds/webknossos/pull/8201)
+
 ### Postgres Evolutions:

app/controllers/AnnotationController.scala

@@ -545,8 +545,7 @@ class AnnotationController @Inject()(
         annotationInfos <- annotationDAO.findAllListableExplorationals(
           isFinished,
           None,
-          isForOwnDashboard = true,
-          AnnotationType.Explorational,
+          filterOwnedOrShared = true,
           limit.getOrElse(annotationService.DefaultAnnotationListLimit),
           pageNumber.getOrElse(0)
         )

app/controllers/InitialDataController.scala

@@ -5,6 +5,7 @@ import com.scalableminds.util.accesscontext.GlobalAccessContext
 import com.scalableminds.util.time.Instant
 import com.scalableminds.util.tools.{Fox, FoxImplicits}
 import com.typesafe.scalalogging.LazyLogging
+import models.aimodels.{AiModel, AiModelCategory, AiModelDAO}
 import models.annotation.{TracingStore, TracingStoreDAO}
 import models.dataset._
 import models.folder.{Folder, FolderDAO, FolderService}
@@ -42,6 +43,7 @@ class InitialDataService @Inject()(userService: UserService,
                                    taskTypeDAO: TaskTypeDAO,
                                    dataStoreDAO: DataStoreDAO,
                                    folderDAO: FolderDAO,
+                                   aiModelDAO: AiModelDAO,
                                    folderService: FolderService,
                                    tracingStoreDAO: TracingStoreDAO,
                                    teamDAO: TeamDAO,
@@ -139,6 +141,19 @@ Samplecountry
     Some(
       "This is a wonderful dummy publication, it has authors, it has a link, it has a doi number, those could go here.\nLorem [ipsum](https://github.com/scalableminds/webknossos) dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua.")
   )
+  private val defaultDataStore =
+    DataStore(conf.Datastore.name, conf.Http.uri, conf.Datastore.publicUri.getOrElse(conf.Http.uri), conf.Datastore.key)
+  private val defaultAiModel = AiModel(
+    ObjectId("66544a56d20000af0e42ba0f"),
+    defaultOrganization._id,
+    defaultDataStore.name,
+    defaultUser._id,
+    None,
+    List.empty,
+    "sample_ai_model",
+    Some("Works if model files are manually placed at binaryData/sample_organization/66544a56d20000af0e42ba0f/"),
+    Some(AiModelCategory.em_neurons)
+  )
 
   def insert: Fox[Unit] =
     for {
@@ -158,6 +173,7 @@ Samplecountry
       _ <- insertTaskType()
       _ <- insertProject()
       _ <- insertPublication()
+      _ <- insertAiModel()
     } yield ()
 
   private def assertInitialDataEnabled: Fox[Unit] =
@@ -266,16 +282,18 @@ Samplecountry
     } else Fox.successful(())
   }
 
+  private def insertAiModel(): Fox[Unit] = aiModelDAO.findAll.flatMap { aiModels =>
+    if (aiModels.isEmpty) {
+      aiModelDAO.insertOne(defaultAiModel)
+    } else Fox.successful(())
+  }
+
   def insertLocalDataStoreIfEnabled(): Fox[Unit] =
     if (storeModules.localDataStoreEnabled) {
       dataStoreDAO.findOneByUrl(conf.Http.uri).futureBox.flatMap { maybeStore =>
         if (maybeStore.isEmpty) {
           logger.info("Inserting local datastore")
-          dataStoreDAO.insertOne(
-            DataStore(conf.Datastore.name,
-                      conf.Http.uri,
-                      conf.Datastore.publicUri.getOrElse(conf.Http.uri),
-                      conf.Datastore.key))
+          dataStoreDAO.insertOne(defaultDataStore)
         } else Fox.successful(())
       }
     } else Fox.successful(())

app/controllers/UserController.scala

@@ -63,8 +63,7 @@ class UserController @Inject()(userService: UserService,
         annotations <- annotationDAO.findAllListableExplorationals(
           isFinished,
           Some(request.identity._id),
-          isForOwnDashboard = true,
-          AnnotationType.Explorational,
+          filterOwnedOrShared = true,
           limit.getOrElse(annotationService.DefaultAnnotationListLimit),
           pageNumber.getOrElse(0)
         )
@@ -118,8 +117,7 @@ class UserController @Inject()(userService: UserService,
         annotations <- annotationDAO.findAllListableExplorationals(
           isFinished,
           Some(userIdValidated),
-          isForOwnDashboard = false,
-          AnnotationType.Explorational,
+          filterOwnedOrShared = false,
           limit.getOrElse(annotationService.DefaultAnnotationListLimit),
           pageNumber.getOrElse(0)
         )

app/models/annotation/Annotation.scala

@@ -359,20 +359,34 @@ class AnnotationDAO @Inject()(sqlClient: SqlClient, annotationLayerDAO: Annotati
     // format: on
   }
 
+  /**
+    * Find all annotations which are listable by the user specified in 'forUser'
+    *
+    * @param isFinished
+    * If set to `true`, only finished annotations are returned. If set to `false`, only active annotations are returned.
+    * If set to `None`, all non-cancelled annotations are returned.
+    * @param forUser
+    * If set, only annotations of this user are returned. If not set, all annotations are returned.
+    * @param filterOwnedOrShared
+    * If `true`, the function lists only annotations owned by the user or explicitly shared with them (used for the
+    * user's own dashboard). If `false`, it lists all annotations the viewer is allowed to see.
+    * @param limit
+    * The maximum number of annotations to return.
+    * @param pageNumber
+    * The page number to return. The first page is 0.
+    */
   def findAllListableExplorationals(
       isFinished: Option[Boolean],
       forUser: Option[ObjectId],
-      // In dashboard, list only own + explicitly shared annotations. When listing those of another user, list all of their annotations the viewer is allowed to see
-      isForOwnDashboard: Boolean,
-      typ: AnnotationType,
+      filterOwnedOrShared: Boolean,
       limit: Int,
       pageNumber: Int = 0)(implicit ctx: DBAccessContext): Fox[List[AnnotationCompactInfo]] =
     for {
-      accessQuery <- if (isForOwnDashboard) accessQueryFromAccessQWithPrefix(listAccessQ, q"a.")
+      accessQuery <- if (filterOwnedOrShared) accessQueryFromAccessQWithPrefix(listAccessQ, q"a.")
       else accessQueryFromAccessQWithPrefix(readAccessQWithPrefix, q"a.")
       stateQuery = getStateQuery(isFinished)
       userQuery = forUser.map(u => q"a._user = $u").getOrElse(q"TRUE")
-      typQuery = q"a.typ = $typ"
+      typQuery = q"a.typ = ${AnnotationType.Explorational}"
 
       query = q"""WITH
                     -- teams_agg is extracted to avoid left-join fanout.

app/utils/WkConf.scala

@@ -200,10 +200,6 @@ class WkConf @Inject()(configuration: Configuration) extends ConfigReader with L
     val environment: String = get[String]("airbrake.environment")
   }
 
-  object GoogleAnalytics {
-    val trackingId: String = get[String]("googleAnalytics.trackingId")
-  }
-
   object SlackNotifications {
     val uri: String = get[String]("slackNotifications.uri")
     val verboseLoggingEnabled: Boolean = get[Boolean]("slackNotifications.verboseLoggingEnabled")
@@ -259,7 +255,6 @@ class WkConf @Inject()(configuration: Configuration) extends ConfigReader with L
       Silhouette,
       Jobs,
       Airbrake,
-      GoogleAnalytics,
       BackendAnalytics,
       Slick,
       Voxelytics,

app/views/main.scala.html

@@ -6,9 +6,6 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=no" />
     <meta name="commit-hash" content="@(webknossos.BuildInfo.commitHash)" />
     <meta name="selected-theme" content="@(selectedTheme)" />
-    @if(conf.GoogleAnalytics.trackingId.nonEmpty) {
-    <meta name="google-analytics-tracking-id" content="@(conf.GoogleAnalytics.trackingId)" />
-    }
     <title>@(conf.WebKnossos.tabTitle)</title>
     @openGraphTitle.map { ogt =>
     <meta property="og:title" content="@ogt" />
@@ -52,25 +49,5 @@
   </head>
   <body>
     <main id="main-container"></main>
-
-    @if(conf.GoogleAnalytics.trackingId.nonEmpty) {
-    <script
-      async
-      src="https://www.googletagmanager.com/gtag/js?id=@(conf.GoogleAnalytics.trackingId)"
-    ></script>
-    <script>
-      const metaElement = document.querySelector("meta[name='google-analytics-tracking-id']");
-      const googleAnalyticsTrackingId = metaElement ? metaElement.getAttribute("content") : null;
-      window.dataLayer = window.dataLayer || [];
-      function gtag() {
-        dataLayer.push(arguments);
-      }
-      gtag("js", new Date());
-      gtag("config", googleAnalyticsTrackingId, {
-        anonymize_ip: true,
-        cookie_expires: 0,
-      });
-    </script>
-    }
   </body>
 </html>

conf/application.conf

@@ -293,9 +293,6 @@ airbrake {
   projectID = "insert-valid-projectID-here"
 }
 
-# Front-end analytics
-googleAnalytics.trackingId = ""
-
 # Slack notification
 slackNotifications {
   uri = ""

frontend/javascripts/admin/dataset/dataset_add_remote_view.tsx

@@ -483,6 +483,15 @@ function AddRemoteLayer({
   };
 
   function validateUrls(userInput: string) {
+    const removePrefix = (value: string, prefix: string) =>
+      value.startsWith(prefix) ? value.slice(prefix.length) : value;
+
+    // If pasted from neuroglancer, uris have these prefixes even before the protocol. The backend ignores them.
+    userInput = removePrefix(userInput, "zarr://");
+    userInput = removePrefix(userInput, "zarr3://");
+    userInput = removePrefix(userInput, "n5://");
+    userInput = removePrefix(userInput, "precomputed://");
+
     if (userInput.startsWith("https://") || userInput.startsWith("http://")) {
       setSelectedProtocol("https");
     } else if (userInput.startsWith("s3://")) {

frontend/javascripts/admin/dataset/dataset_upload_view.tsx

@@ -54,7 +54,6 @@ import {
 import Toast from "libs/toast";
 import * as Utils from "libs/utils";
 import messages from "messages";
-import { trackAction } from "oxalis/model/helpers/analytics";
 import Zip from "libs/zipjs_wrapper";
 import {
   AllowedTeamsFormItem,
@@ -350,7 +349,6 @@ class DatasetUploadView extends React.Component<PropsWithFormAndRouter, State> {
       });
       finishDatasetUpload(datastoreUrl, uploadInfo).then(
         async () => {
-          trackAction("Upload dataset");
           Toast.success(messages["dataset.upload_success"]);
           let maybeError;
 

frontend/javascripts/dashboard/advanced_dataset/dataset_table.tsx

@@ -14,7 +14,6 @@ import type {
 } from "types/api_flow_types";
 import type { DatasetFilteringMode } from "dashboard/dataset_view";
 import { stringToColor } from "libs/format_utils";
-import { trackAction } from "oxalis/model/helpers/analytics";
 import CategorizationLabel from "oxalis/view/components/categorization_label";
 import DatasetActionView, {
   getDatasetActionContextMenu,
@@ -791,7 +790,6 @@ export function DatasetTags({
       };
     }
 
-    trackAction("Edit dataset tag");
     updateDataset(dataset, updater);
   };
 

frontend/javascripts/dashboard/dataset/dataset_settings_view.tsx

@@ -32,7 +32,6 @@ import {
   updateDatasetPartial,
 } from "admin/admin_rest_api";
 import { handleGenericError } from "libs/error_handling";
-import { trackAction } from "oxalis/model/helpers/analytics";
 import Toast from "libs/toast";
 import messages from "messages";
 import features from "features";
@@ -390,7 +389,6 @@ class DatasetSettingsView extends React.PureComponent<PropsWithFormAndRouter, St
       }
     }
 
-    trackAction(`Dataset ${verb}`);
     this.props.onComplete();
   };
 

frontend/javascripts/dashboard/explorative_annotations_view.tsx

@@ -60,7 +60,6 @@ import Store from "oxalis/store";
 import Toast from "libs/toast";
 import * as Utils from "libs/utils";
 import messages from "messages";
-import { trackAction } from "oxalis/model/helpers/analytics";
 import TextWithDescription from "components/text_with_description";
 import { getVolumeDescriptors } from "oxalis/model/accessors/volumetracing_accessor";
 import { RenderToPortal } from "oxalis/view/layouting/portal_utils";
@@ -289,7 +288,6 @@ class ExplorativeAnnotationsView extends React.PureComponent<Props, State> {
       const newTracing = await editLockedState(tracing.id, tracing.typ, locked);
       Toast.success(messages["annotation.was_edited"]);
       this.updateTracingInLocalState(tracing, (_t) => newTracing);
-      trackAction("Lock/Unlock explorative annotation");
     } catch (error) {
       handleGenericError(error as Error, "Could not update the annotation lock state.");
     }
@@ -475,7 +473,6 @@ class ExplorativeAnnotationsView extends React.PureComponent<Props, State> {
           editAnnotation(newAnnotation.id, newAnnotation.typ, {
             tags: newAnnotation.tags,
           });
-          trackAction("Edit annotation tag");
         }
 
         return newAnnotation;
@@ -699,7 +696,7 @@ class ExplorativeAnnotationsView extends React.PureComponent<Props, State> {
               </div>
               <div className="flex-container">
                 <div className="flex-item" style={{ flexGrow: 0 }}>
-                  {teamTags.length > 0 ? <TeamOutlined /> : null}
+                  {teamTags.length > 0 ? <TeamOutlined className="icon-margin-right" /> : null}
                 </div>
                 <div className="flex-item">{teamTags}</div>
               </div>

frontend/javascripts/main.tsx

@@ -6,7 +6,6 @@ import UnthrottledStore, { startSagas } from "oxalis/store";
 import { message } from "antd";
 
 import { getActiveUser, checkAnyOrganizationExists, getOrganization } from "admin/admin_rest_api";
-import { googleAnalyticsLogClicks } from "oxalis/model/helpers/analytics";
 import { load as loadFeatureToggles } from "features";
 import { setActiveUserAction } from "oxalis/model/actions/user_actions";
 import { setHasOrganizationsAction, setThemeAction } from "oxalis/model/actions/ui_actions";
@@ -97,7 +96,6 @@ document.addEventListener("DOMContentLoaded", async () => {
     throwAssertions: false,
   });
   message.config({ top: 30 });
-  document.addEventListener("click", googleAnalyticsLogClicks);
   checkBrowserFeatures();
   await Promise.all([loadFeatureToggles(), loadActiveUser(), loadHasOrganizations()]);
   await Promise.all([loadOrganization()]);

frontend/javascripts/navbar.tsx

@@ -45,7 +45,6 @@ import {
   sendAnalyticsEvent,
 } from "admin/admin_rest_api";
 import { logoutUserAction, setActiveUserAction } from "oxalis/model/actions/user_actions";
-import { trackVersion } from "oxalis/model/helpers/analytics";
 import { useFetch, useInterval } from "libs/react_helpers";
 import LoginForm from "admin/auth/login_form";
 import Request from "libs/request";
@@ -739,13 +738,9 @@ function AnonymousAvatar() {
   );
 }
 
-async function getAndTrackVersion(dontTrack: boolean = false) {
+async function getVersion() {
   const buildInfo = await getBuildInfo();
-  const { version } = buildInfo.webknossos;
-  if (dontTrack) {
-    trackVersion(version);
-  }
-  return version;
+  return buildInfo.webknossos.version;
 }
 
 function AnnotationLockedByUserTag({
@@ -831,15 +826,15 @@ function Navbar({
     location.href = "/";
   };
 
-  const version = useFetch(getAndTrackVersion, null, []);
+  const version = useFetch(getVersion, null, []);
   const [isHelpMenuOpen, setIsHelpMenuOpen] = useState(false);
   const [polledVersion, setPolledVersion] = useState<string | null>(null);
   const [isHelpModalOpen, setIsHelpModalOpen] = useState(false);
 
   useInterval(
     async () => {
       if (isHelpMenuOpen) {
-        setPolledVersion(await getAndTrackVersion(true));
+        setPolledVersion(await getVersion());
       }
     },
     2000,