Don't remove other volume layers when opening volume annotation

.circleci/config.yml

@@ -292,6 +292,10 @@ workflows:
   version: 2
   circleci_build:
     jobs:
+      - nightly:
+          filters:
+            tags:
+              only: /.*/
       - build_test_deploy:
           filters:
             tags:

CHANGELOG.unreleased.md

@@ -18,6 +18,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Changed
 - When creating a new annotation with a volume layer (without fallback) for a dataset which has an existing segmentation layer, the original segmentation layer is still listed (and viewable) in the left sidebar. Earlier versions simply hid the original segmentation layer. [#6186](https://github.com/scalableminds/webknossos/pull/6186)
 - Changing the visibility of a layer within an annotation does not change the visibility of the layer when viewing the corresponding dataset. [#6186](https://github.com/scalableminds/webknossos/pull/6186)
+- While viewing tracings in read-only mode, the options to manipulate the tracing are now disabled. This leads to less confusion as previously the input was silently discarded. [#6140](https://github.com/scalableminds/webknossos/pull/6140).
 - Changed default of `dynamicSpaceDirection` property to false to avoid confusion. [#6162](https://github.com/scalableminds/webknossos/pull/6162)
 - Changed the internal protocol for requesting image data. The zoomStep parameter has been replaced by mag. This increases the datastore API version to 2.0 [#6159](https://github.com/scalableminds/webknossos/pull/6159)
 - In annotation list in dashboard, replaced the non-standard word “Trace” by “Open”. [#6191](https://github.com/scalableminds/webknossos/pull/6191)

frontend/javascripts/admin/admin_rest_api.ts

@@ -1237,7 +1237,7 @@ export function updateDatasetConfiguration(
   datasetId: APIDatasetId,
   datasetConfig: PartialDatasetConfiguration,
   options: RequestOptions = {},
-): Record<string, any> {
+): Promise<Record<string, any>> {
   return Request.sendJSONReceiveJSON(
     `/api/dataSetConfigurations/${datasetId.owningOrganization}/${datasetId.name}`,
     { ...options, method: "PUT", data: datasetConfig },
@@ -1616,7 +1616,7 @@ export function getUserConfiguration(): Promise<UserConfiguration> {
 
 export function updateUserConfiguration(
   userConfiguration: Record<string, any>,
-): Record<string, any> {
+): Promise<Record<string, any>> {
   return Request.sendJSONReceiveJSON("/api/user/userConfiguration", {
     method: "PUT",
     data: userConfiguration,

frontend/javascripts/oxalis/model/sagas/settings_saga.ts

@@ -118,7 +118,7 @@ function* showUserSettingToast(action: UpdateUserSettingAction): Saga<void> {
 export default function* watchPushSettingsAsync(): Saga<void> {
   const action = yield* take("INITIALIZE_SETTINGS");
   if (action.type !== "INITIALIZE_SETTINGS") {
-    throw new Error("Unexpected action. Satisfy flow.");
+    throw new Error("Unexpected action. Satisfy typescript.");
   }
 
   const { originalDatasetSettings } = action;

frontend/javascripts/oxalis/model_initialization.ts

@@ -488,16 +488,9 @@ function setupLayerForVolumeTracing(
   tracings: Array<ServerVolumeTracing>,
 ): Array<APIDataLayer> {
   // This method adds/merges the segmentation layers of the tracing into the dataset layers.
-  // This is done by
-  // 1) removing all segmentation data layers (gathered in newLayers)
-  // 2) appending new tracing layers (using the original layers for fallback information)
+
   const originalLayers = dataset.dataSource.dataLayers;
-  // Remove other segmentation layers, since we are adding new ones.
-  // This is a temporary workaround. Even though we support multiple segmentation
-  // layers, we cannot render both at the same time. Hiding the existing segmentation
-  // layer would be good, but this information is stored per dataset and not per annotation
-  // currently. Also, see https://github.com/scalableminds/webknossos/issues/5695
-  const newLayers = originalLayers.slice(); // .filter((layer) => layer.category !== "segmentation");
+  const newLayers = originalLayers.slice();
 
   for (const tracing of tracings) {
     // The tracing always contains the layer information for the user segmentation.

frontend/javascripts/test/backend-snapshot-tests/teamstructure.e2e.ts

@@ -39,7 +39,7 @@ user_A, user_B, user_C, user_D, user_E
  */
 // Teams
 test("teams_userDefault", async (t) => {
-  await setCurrToken(tokenUserA);
+  setCurrToken(tokenUserA);
 
   const teams = _.sortBy(await api.getTeams(), (team) => team.name);
 
@@ -50,15 +50,15 @@ test("teams_userDefault", async (t) => {
   t.is(teams.length, 4);
 });
 test("teams_user_D", async (t) => {
-  await setCurrToken(tokenUserD);
+  setCurrToken(tokenUserD);
 
   const teams = _.sortBy(await api.getTeams(), (team) => team.name);
 
   t.is(teams[0].name, "team_X2");
   t.is(teams.length, 1);
 });
 test("teams_user_E", async (t) => {
-  await setCurrToken(tokenUserE);
+  setCurrToken(tokenUserE);
 
   const teams = _.sortBy(await api.getTeams(), (team) => team.name);
 
@@ -67,15 +67,15 @@ test("teams_user_E", async (t) => {
 });
 test("teams_delete_user_D", async (t) => {
   // the teamManager is not allowed to delete the team
-  await setCurrToken(tokenUserD);
+  setCurrToken(tokenUserD);
   t.plan(1);
   await api.deleteTeam("69882b370d889b84020efd4f").catch((err) => {
     t.is(err.messages[0].error, "Access denied. Only admin users can execute this operation.");
   });
 });
 test("teams_create_user_D", async (t) => {
   // the teamManager is not allowed to create a new team
-  await setCurrToken(tokenUserD);
+  setCurrToken(tokenUserD);
   t.plan(1);
   const newTeam = {
     name: "test-team-name",
@@ -86,51 +86,51 @@ test("teams_create_user_D", async (t) => {
 });
 // TaskTypes
 test("taskTypes_userDefault", async (t) => {
-  await setCurrToken(tokenUserA);
+  setCurrToken(tokenUserA);
 
   const taskTypes = _.sortBy(await api.getTaskTypes(), (taskType) => taskType.id);
 
   t.is(taskTypes[0].description, "Check those cells out!");
   t.is(taskTypes.length, 2);
 });
 test("taskTypes_user_D", async (t) => {
-  await setCurrToken(tokenUserD);
+  setCurrToken(tokenUserD);
 
   const taskTypes = _.sortBy(await api.getTaskTypes(), (taskType) => taskType.id);
 
   t.is(taskTypes.length, 1);
 });
 test("taskTypes_user_E", async (t) => {
-  await setCurrToken(tokenUserE);
+  setCurrToken(tokenUserE);
 
   const taskTypes = _.sortBy(await api.getTaskTypes(), (taskType) => taskType.id);
 
   t.is(taskTypes.length, 0);
 });
 // Tasks
 test("tasks_user_D", async (t) => {
-  await setCurrToken(tokenUserD);
+  setCurrToken(tokenUserD);
   t.plan(1);
   await api.getTask("58135c192faeb34c0081c058").catch((err) => {
     t.is(err.messages[0].error, "Task couldn’t be found");
   });
 });
 test("tasks_user_E", async (t) => {
-  await setCurrToken(tokenUserE);
+  setCurrToken(tokenUserE);
   t.plan(1);
   await api.getTask("58135c192faeb34c0081c058").catch((err) => {
     t.is(err.messages[0].error, "Task couldn’t be found");
   });
 });
 test("tasks_user_C", async (t) => {
-  await setCurrToken(tokenUserC);
+  setCurrToken(tokenUserC);
   const task = await api.getTask("58135c192faeb34c0081c058");
   t.is(task.id, "58135c192faeb34c0081c058");
 });
 // User
 test("user_user_B", async (t) => {
   // teamMng are not allowed to de-/activate a user (if they are not an admin)
-  await setCurrToken(tokenUserB);
+  setCurrToken(tokenUserB);
   t.plan(2);
   const userIdC = "770b9f4d2a7c0e4d008da6ef";
   const user = await api.getUser(userIdC);
@@ -145,7 +145,7 @@ test("user_user_B", async (t) => {
 // Project
 test("project_user_B", async (t) => {
   // teamMng are not allowed to delete a project (if they are not an admin and they are not the owner)
-  await setCurrToken(tokenUserE);
+  setCurrToken(tokenUserE);
   t.plan(1);
   const projectId = "58135bfd2faeb3190181c057";
   await api.deleteProject(projectId).catch((err) => {

frontend/javascripts/test/puppeteer/dataset_rendering.screenshot.ts

@@ -8,6 +8,7 @@ import type { Browser } from "puppeteer";
 import puppeteer from "puppeteer";
 import { compareScreenshot, isPixelEquivalent } from "./screenshot_helpers";
 import {
+  screenshotAnnotation,
   screenshotDataset,
   screenshotDatasetWithMapping,
   screenshotDatasetWithMappingLink,
@@ -39,8 +40,8 @@ if (!process.env.URL) {
 }
 
 console.log(`[Info] Executing tests on URL ${URL}.`);
-// Ava's recommendation for Flow types
-// https://github.com/avajs/ava/blob/master/docs/recipes/flow.md#typing-tcontext
+// Ava's recommendation for Typescript types
+// https://github.com/avajs/ava/blob/main/docs/recipes/typescript.md#typing-tcontext
 const test: TestInterface<{
   browser: Browser;
 }> = anyTest as any;
@@ -89,6 +90,14 @@ const datasetNames = [
   "Multi-Channel-Test",
   "connectome_file_test_dataset",
 ];
+
+type DatasetName = string;
+type FallbackLayerName = string | null;
+const annotationSpecs: Array<[DatasetName, FallbackLayerName]> = [
+  ["ROI2017_wkw_fallback", "segmentation"],
+  ["ROI2017_wkw_fallback", null],
+];
+
 const viewOverrides: Record<string, string> = {
   "2017-05-31_mSEM_scMS109_bk_100um_v01-aniso": "4608,4543,386,0,4.00",
   ROI2017_wkw_fallback: "535,536,600,0,1.18",
@@ -182,6 +191,51 @@ datasetNames.map(async (datasetName) => {
     );
   });
 });
+
+annotationSpecs.map(async (annotationSpec) => {
+  const [datasetName, fallbackLayerName] = annotationSpec;
+
+  test.serial.only(
+    `It should render an annotation for ${datasetName} with fallback_layer=${fallbackLayerName} correctly`,
+    async (t) => {
+      console.log(
+        `It should render an annotation for ${datasetName} with fallback_layer=${fallbackLayerName} correctly`,
+      );
+      await withRetry(
+        3,
+        async () => {
+          const datasetId = {
+            name: datasetName,
+            owningOrganization: "sample_organization",
+          };
+          const { screenshot, width, height } = await screenshotAnnotation(
+            await getNewPage(t.context.browser),
+            URL,
+            datasetId,
+            fallbackLayerName,
+            viewOverrides[datasetName],
+            datasetConfigOverrides[datasetName],
+          );
+          const changedPixels = await compareScreenshot(
+            screenshot,
+            width,
+            height,
+            BASE_PATH,
+            `annotation_${datasetName}_${fallbackLayerName}`,
+          );
+          return isPixelEquivalent(changedPixels, width, height);
+        },
+        (condition) => {
+          t.true(
+            condition,
+            `Dataset with name: "${datasetName}" does not look the same, see ${datasetName}.diff.png for the difference and ${datasetName}.new.png for the new screenshot.`,
+          );
+        },
+      );
+    },
+  );
+});
+
 test.serial("it should render a dataset with mappings correctly", async (t) => {
   const datasetName = "ROI2017_wkw";
   const mappingName = "astrocyte";
@@ -299,7 +353,6 @@ test.serial(
           name: datasetName,
           owningOrganization: "sample_organization",
         };
-        // @ts-expect-error ts-migrate(2554) FIXME: Expected 5 arguments, but got 4.
         const { screenshot, width, height } = await screenshotDataset(
           await getNewPage(t.context.browser),
           URL,