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

…pdown-menu

* 'master' of github.com:scalableminds/webknossos:
  Avoid SQL error when fetching view config for zero-layer dataset (#6912)
  Fix date formatting for VX reports (#6908)
  Fix rare crash when viewing shared annotation (#6892)
  Slim down view mode dropdown by using icons (#6900)
  Logging on password reset/change (#6901)
  When merging volume tracings, also merge segment lists (#6882)
  avoid spinner when switching tabs in dashboard (#6894)

CHANGELOG.unreleased.md

@@ -15,9 +15,14 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 
 ### Changed
 - Upgraded antd UI library to v4.24.8 [#6865](https://github.com/scalableminds/webknossos/pull/6865)
+- The view mode dropdown was slimmed down by using icons to make the toolbar more space efficient. [#6900](https://github.com/scalableminds/webknossos/pull/6900)
 
 ### Fixed
 - Fixed a bug where N5 datasets reading with end-chunks that have a chunk size differing from the metadata-supplied chunk size would fail for some areas. [#6890](https://github.com/scalableminds/webknossos/pull/6890)
+- Fixed potential crash when trying to edit certain annotation properties of a shared annotation. [#6892](https://github.com/scalableminds/webknossos/pull/6892)
+- Fixed a bug where merging multiple volume annotations would result in inconsistent segment lists. [#6882](https://github.com/scalableminds/webknossos/pull/6882)
+- Fixed a bug where uploading multiple annotations with volume layers at once would fail. [#6882](https://github.com/scalableminds/webknossos/pull/6882)
+- Fixed a bug where dates were formatted incorrectly in Voxelytics reports. [#6908](https://github.com/scalableminds/webknossos/pull/6908)
 - Fix antd deprecation warning for Dropdown menus. [#6898](https://github.com/scalableminds/webknossos/pull/6898)
 
 ### Removed

app/controllers/AnnotationIOController.scala

@@ -23,7 +23,7 @@ import com.scalableminds.webknossos.datastore.models.datasource.{
   SegmentationLayer
 }
 import com.scalableminds.webknossos.tracingstore.tracings.TracingType
-import com.scalableminds.webknossos.tracingstore.tracings.volume.VolumeTracingDefaults
+import com.scalableminds.webknossos.tracingstore.tracings.volume.{VolumeTracingDefaults, VolumeTracingDownsampling}
 import com.typesafe.scalalogging.LazyLogging
 import io.swagger.annotations._
 
@@ -280,7 +280,9 @@ Expects:
       fallbackLayer = fallbackLayerOpt.map(_.name),
       largestSegmentId =
         annotationService.combineLargestSegmentIdsByPrecedence(volumeTracing.largestSegmentId,
-                                                               fallbackLayerOpt.map(_.largestSegmentId))
+                                                               fallbackLayerOpt.map(_.largestSegmentId)),
+      resolutions =
+        VolumeTracingDownsampling.resolutionsForVolumeTracing(dataSource, fallbackLayerOpt).map(vec3IntToProto)
     )
   }
 

app/controllers/AuthenticationController.scala

@@ -394,6 +394,7 @@ class AuthenticationController @Inject()(
         bearerTokenAuthenticatorService.userForToken(passwords.token.trim).futureBox.flatMap {
           case Full(user) =>
             for {
+              - <- Fox.successful(logger.info(s"Multiuser ${user._multiUser} reset their password."))
               _ <- multiUserDAO.updatePasswordInfo(user._multiUser, passwordHasher.hash(passwords.password1))(
                 GlobalAccessContext)
               _ <- bearerTokenAuthenticatorService.remove(passwords.token.trim)
@@ -420,6 +421,7 @@ class AuthenticationController @Inject()(
                   Future.successful(NotFound(Messages("error.noUser")))
                 case Some(user) =>
                   for {
+                    - <- Fox.successful(logger.info(s"Multiuser ${user._multiUser} changed their password."))
                     _ <- multiUserDAO.updatePasswordInfo(user._multiUser, passwordHasher.hash(passwords.password1))
                     _ <- combinedAuthenticatorService.discard(request.authenticator, Ok)
                     userEmail <- userService.emailFor(user)

app/controllers/JobsController.scala

@@ -272,9 +272,10 @@ class JobsController @Inject()(jobDAO: JobDAO,
     sil.SecuredAction.async { implicit request =>
       log(Some(slackNotificationService.noticeFailedJobRequest)) {
         for {
-          organization <- organizationDAO.findOneByName(organizationName) ?~> Messages("organization.notFound",
-                                                                                       organizationName)
-          _ <- bool2Fox(request.identity._organization == organization._id) ?~> "job.applyMergerMode.notAllowed.organization" ~> FORBIDDEN
+          organization <- organizationDAO.findOneByName(organizationName)(GlobalAccessContext) ?~> Messages(
+            "organization.notFound",
+            organizationName)
+          _ <- bool2Fox(request.identity._organization == organization._id) ?~> "job.materializeVolumeAnnotation.notAllowed.organization" ~> FORBIDDEN
           dataSet <- dataSetDAO.findOneByNameAndOrganization(dataSetName, organization._id) ?~> Messages(
             "dataSet.notFound",
             dataSetName) ~> NOT_FOUND

app/models/user/User.scala

@@ -417,14 +417,18 @@ class UserDataSetLayerConfigurationDAO @Inject()(sqlClient: SqlClient, userDAO:
   def findAllByLayerNameForUserAndDataset(layerNames: List[String],
                                           userId: ObjectId,
                                           dataSetId: ObjectId): Fox[Map[String, LayerViewConfiguration]] =
-    for {
-      rows <- run(q"""select layerName, viewConfiguration
+    if (layerNames.isEmpty) {
+      Fox.successful(Map.empty[String, LayerViewConfiguration])
+    } else {
+      for {
+        rows <- run(q"""select layerName, viewConfiguration
                       from webknossos.user_dataSetLayerConfigurations
                       where _dataset = $dataSetId
                       and _user = $userId
                       and layerName in ${SqlToken.tupleFromList(layerNames)}""".as[(String, String)])
-      parsed = rows.flatMap(t => Json.parse(t._2).asOpt[LayerViewConfiguration].map((t._1, _)))
-    } yield parsed.toMap
+        parsed = rows.flatMap(t => Json.parse(t._2).asOpt[LayerViewConfiguration].map((t._1, _)))
+      } yield parsed.toMap
+    }
 
   def updateDatasetConfigurationForUserAndDatasetAndLayer(
       userId: ObjectId,

conf/messages

@@ -292,7 +292,7 @@ job.inferNuclei.notAllowed.organization = Currently nuclei inferral is only allo
 job.inferNeurons.notAllowed.organization = Currently neuron inferral is only allowed for datasets of your own organization.
 job.meshFile.notAllowed.organization = Calculating mesh files is only allowed for datasets of your own organization.
 job.globalizeFloodfill.notAllowed.organization = Globalizing floodfills is only allowed for datasets of your own organization.
-job.applyMergerMode.notAllowed.organization = Applying merger mode tracings is only allowed for datasets of your own organization.
+job.materializeVolumeAnnotation.notAllowed.organization = Materializing volume annotations is only allowed for datasets of your own organization.
 job.noWorkerForDatastore = Processing jobs are not available for the datastore this dataset belongs to.
 
 voxelytics.disabled = Voxelytics workflow reporting and logging are not enabled for this WEBKNOSSOS instance.

frontend/javascripts/admin/admin_rest_api.ts

@@ -2053,6 +2053,8 @@ export async function getPricingPlanStatus(): Promise<APIPricingPlanStatus> {
   return Request.receiveJSON("/api/pricing/status");
 }
 
+export const cachedGetPricingPlanStatus = _.memoize(getPricingPlanStatus);
+
 // ### BuildInfo webknossos
 export function getBuildInfo(): Promise<APIBuildInfo> {
   return Request.receiveJSON("/api/buildinfo", {

frontend/javascripts/dashboard/dashboard_view.tsx

@@ -11,7 +11,7 @@ import type { APIOrganization, APIPricingPlanStatus, APIUser } from "types/api_f
 import type { OxalisState } from "oxalis/store";
 import { enforceActiveUser } from "oxalis/model/accessors/user_accessor";
 import {
-  getPricingPlanStatus,
+  cachedGetPricingPlanStatus,
   getUser,
   updateNovelUserExperienceInfos,
 } from "admin/admin_rest_api";
@@ -120,7 +120,10 @@ class DashboardView extends PureComponent<PropsWithRouter, State> {
     const user =
       this.props.userId != null ? await getUser(this.props.userId) : this.props.activeUser;
 
-    const pricingPlanStatus = await getPricingPlanStatus();
+    // Use a cached version of this route to avoid that a tab switch in the dashboard
+    // causes a whole-page spinner. Since the different tabs are controlled by the
+    // router, the DashboardView re-mounts.
+    const pricingPlanStatus = await cachedGetPricingPlanStatus();
 
     this.setState({
       user,

frontend/javascripts/libs/format_utils.ts

@@ -7,6 +7,7 @@ import dayjs from "dayjs";
 import duration from "dayjs/plugin/duration";
 import updateLocale from "dayjs/plugin/updateLocale";
 import relativeTime from "dayjs/plugin/relativeTime";
+import localizedFormat from "dayjs/plugin/localizedFormat";
 import calendar from "dayjs/plugin/calendar";
 import utc from "dayjs/plugin/utc";
 import weekday from "dayjs/plugin/weekday";
@@ -22,6 +23,7 @@ dayjs.extend(utc);
 dayjs.extend(calendar);
 dayjs.extend(weekday);
 dayjs.extend(localeData);
+dayjs.extend(localizedFormat);
 dayjs.updateLocale("en", {
   weekStart: 1,
   calendar: {

frontend/javascripts/oxalis/model/accessors/annotation_accessor.ts

@@ -0,0 +1,13 @@
+import type { OxalisState } from "oxalis/store";
+
+export function mayEditAnnotationProperties(state: OxalisState) {
+  const { owner, restrictions } = state.tracing;
+  const activeUser = state.activeUser;
+
+  return !!(
+    restrictions.allowUpdate &&
+    restrictions.allowSave &&
+    activeUser &&
+    owner?.id === activeUser.id
+  );
+}

frontend/javascripts/oxalis/model/sagas/annotation_saga.tsx

@@ -20,7 +20,6 @@ import {
 import type { Saga } from "oxalis/model/sagas/effect-generators";
 import {
   takeLatest,
-  select,
   take,
   retry,
   delay,
@@ -31,6 +30,7 @@ import {
   cancel,
   cancelled,
 } from "typed-redux-saga";
+import { select } from "oxalis/model/sagas/effect-generators";
 import { getMappingInfo } from "oxalis/model/accessors/dataset_accessor";
 import { getRequestLogZoomStep } from "oxalis/model/accessors/flycam_accessor";
 import { Model } from "oxalis/singletons";
@@ -40,14 +40,17 @@ import constants, { MappingStatusEnum } from "oxalis/constants";
 import messages from "messages";
 import { APIUserCompact } from "types/api_flow_types";
 import { Button } from "antd";
+import ErrorHandling from "libs/error_handling";
+import { mayEditAnnotationProperties } from "../accessors/annotation_accessor";
 
 /* Note that this must stay in sync with the back-end constant
   compare https://github.com/scalableminds/webknossos/issues/5223 */
 const MAX_MAG_FOR_AGGLOMERATE_MAPPING = 16;
-export function* pushAnnotationUpdateAsync() {
-  const tracing = yield* select((state) => state.tracing);
 
-  if (!tracing.restrictions.allowUpdate) {
+export function* pushAnnotationUpdateAsync(action: Action) {
+  const tracing = yield* select((state) => state.tracing);
+  const mayEdit = yield* select((state) => mayEditAnnotationProperties(state));
+  if (!mayEdit) {
     return;
   }
 
@@ -66,14 +69,30 @@ export function* pushAnnotationUpdateAsync() {
     description: tracing.description,
     viewConfiguration,
   };
-  yield* retry(
-    SETTINGS_MAX_RETRY_COUNT,
-    SETTINGS_RETRY_DELAY,
-    editAnnotation,
-    tracing.annotationId,
-    tracing.annotationType,
-    editObject,
-  );
+  try {
+    yield* retry(
+      SETTINGS_MAX_RETRY_COUNT,
+      SETTINGS_RETRY_DELAY,
+      editAnnotation,
+      tracing.annotationId,
+      tracing.annotationType,
+      editObject,
+    );
+  } catch (error) {
+    // If the annotation cannot be saved repeatedly (retries will continue for 5 minutes),
+    // we will only notify the user if the name, visibility or description could not be changed.
+    // Otherwise, we won't notify the user and won't let the sagas crash as the actual skeleton/volume
+    // tracings are handled separately.
+    console.error(error);
+    ErrorHandling.notify(error as Error);
+    if (
+      ["SET_ANNOTATION_NAME", "SET_ANNOTATION_VISIBILITY", "SET_ANNOTATION_DESCRIPTION"].includes(
+        action.type,
+      )
+    ) {
+      Toast.error("Could not update annotation property. Please try again.");
+    }
+  }
 }
 
 function* pushAnnotationLayerUpdateAsync(action: EditAnnotationLayerAction): Saga<void> {

frontend/javascripts/oxalis/model/sagas/effect-generators.ts

@@ -5,9 +5,12 @@ import { select as _select, take as _take } from "typed-redux-saga";
 import type { Channel } from "redux-saga";
 import { ActionPattern } from "redux-saga/effects";
 
-export function* select<T>(fn: (state: OxalisState) => T) {
-  const res: T = yield _select(fn);
-  return res;
+// Ensures that the type of state is known. Otherwise,
+// a statement such as
+//   const tracing = yield* select((state) => state.tracing);
+// would result in tracing being any.
+export function select<T>(fn: (state: OxalisState) => T) {
+  return _select(fn);
 }
 
 export function* take(

frontend/javascripts/oxalis/view/action-bar/dataset_position_view.tsx

@@ -24,6 +24,7 @@ type Props = {
 };
 const positionIconStyle: React.CSSProperties = {
   transform: "rotate(-45deg)",
+  marginRight: 0,
 };
 const warningColors: React.CSSProperties = {
   color: "rgb(255, 155, 85)",

frontend/javascripts/oxalis/view/action-bar/share_modal_view.tsx

@@ -46,6 +46,7 @@ import { makeComponentLazy } from "libs/react_helpers";
 import { AsyncButton } from "components/async_clickables";
 import { PricingEnforcedBlur } from "components/pricing_enforcers";
 import { PricingPlanEnum } from "admin/organization/pricing_plan_utils";
+import { mayEditAnnotationProperties } from "oxalis/model/accessors/annotation_accessor";
 
 const RadioGroup = Radio.Group;
 const sharingActiveNode = true;
@@ -181,11 +182,10 @@ function _ShareModalView(props: Props) {
   const [sharedTeams, setSharedTeams] = useState<APITeam[]>([]);
   const sharingToken = useDatasetSharingToken(dataset);
 
-  const { owner, othersMayEdit, restrictions } = tracing;
+  const { othersMayEdit } = tracing;
   const [newOthersMayEdit, setNewOthersMayEdit] = useState(othersMayEdit);
 
-  const hasUpdatePermissions =
-    restrictions.allowUpdate && restrictions.allowSave && activeUser && owner?.id === activeUser.id;
+  const hasUpdatePermissions = useSelector(mayEditAnnotationProperties);
   useEffect(() => setVisibility(annotationVisibility), [annotationVisibility]);
 
   const fetchAndSetSharedTeams = async () => {

frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx

@@ -1,4 +1,4 @@
-import { Select } from "antd";
+import { Button, Dropdown, MenuProps, Space } from "antd";
 import { connect } from "react-redux";
 import type { Dispatch } from "redux";
 import React, { PureComponent } from "react";
@@ -9,9 +9,9 @@ import {
 import type { OxalisState, AllowedMode } from "oxalis/store";
 import Store from "oxalis/store";
 import * as Utils from "libs/utils";
-import type { ViewMode } from "oxalis/constants";
+import { ViewMode, ViewModeValues } from "oxalis/constants";
 import constants from "oxalis/constants";
-const { Option } = Select;
+
 type StateProps = {
   viewMode: ViewMode;
   allowedModes: Array<AllowedMode>;
@@ -21,6 +21,17 @@ type DispatchProps = {
 };
 type Props = StateProps & DispatchProps;
 
+const VIEW_MODE_TO_ICON = {
+  [constants.MODE_PLANE_TRACING]: <i className="fas fa-th-large without-icon-margin" />,
+  [constants.MODE_ARBITRARY]: <i className="fas fa-globe without-icon-margin" />,
+  [constants.MODE_ARBITRARY_PLANE]: (
+    <i
+      className="fas fa-square-full without-icon-margin"
+      style={{ transform: "scale(0.8, 1) rotate(-45deg)" }}
+    />
+  ),
+};
+
 class ViewModesView extends PureComponent<Props, {}> {
   handleChange = (mode: ViewMode) => {
     // If we switch back from any arbitrary mode we stop recording.
@@ -51,24 +62,40 @@ class ViewModesView extends PureComponent<Props, {}> {
   }
 
   render() {
+    const handleMenuClick: MenuProps["onClick"] = (args) => {
+      if (ViewModeValues.includes(args.key as ViewMode)) {
+        this.handleChange(args.key as ViewMode);
+      }
+    };
+
+    const MENU_ITEMS: MenuProps["items"] = [
+      {
+        key: "1",
+        type: "group",
+        label: "Select View Mode",
+        children: ViewModeValues.map((mode) => ({
+          label: Utils.capitalize(mode),
+          key: mode,
+          disabled: this.isDisabled(mode),
+          icon: <span style={{ marginRight: 8 }}>{VIEW_MODE_TO_ICON[mode]}</span>,
+        })),
+      },
+    ];
+
+    const menuProps = {
+      items: MENU_ITEMS,
+      onClick: handleMenuClick,
+    };
+
     return (
-      <Select
-        value={this.props.viewMode}
-        style={{
-          width: 120,
-        }}
-        onChange={this.handleChange}
-      >
-        {[
-          constants.MODE_PLANE_TRACING,
-          constants.MODE_ARBITRARY,
-          constants.MODE_ARBITRARY_PLANE,
-        ].map((mode) => (
-          <Option key={mode} disabled={this.isDisabled(mode)} value={mode}>
-            {Utils.capitalize(mode)}
-          </Option>
-        ))}
-      </Select>
+      // The outer div is necessary for proper spacing.
+      <div>
+        <Dropdown menu={menuProps}>
+          <Button>
+            <Space>{VIEW_MODE_TO_ICON[this.props.viewMode]}</Space>
+          </Button>
+        </Dropdown>
+      </div>
     );
   }
 }