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

…ct-task-create * 'master' of github.com:scalableminds/webknossos: (167 commits) Enable interpolation setting in volume mode (#2089) allow admins to administrate datasets fix compilation update libs remove jsRoutes from tests apply PR feedback (#1957) removed github conf fixed lint make flow happy fix merge conflicts in frontend Changed schema after tests #2055 merge master. TODO: fix flow errors, test volume fallback layer remove obsolete version field from annotation (only tracings are versioned now) Further implementation of PR review advices #2055 Implemented first part of review comments #2055 remove obsolete todo log time for the user who sent the updates, not for the annotation owner use new libs version update libs version disable e2e tests ...
scalableminds · Nov 3, 2017 · a86af13 · a86af13
2 parents 073657f + b7b91b3
commit a86af13
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Showing 233 changed files with 13,061 additions and 22,809 deletions.
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -32,9 +32,9 @@ wrap(repo: "scalableminds/webknossos") {
     sh "docker-compose run frontend-linting"
     sh "docker-compose run frontend-flow"
     sh "docker-compose run frontend-tests"
-    retry (3) {
-      sh "docker-compose run e2e-tests"
-    }
+//    retry (3) {
+//      sh "docker-compose run e2e-tests"
+//    }
     sh """
       DOCKER_TAG=${env.BRANCH_NAME}__${env.BUILD_NUMBER} docker-compose up webknossos &
       sleep 10

diff --git a/app/Global.scala b/app/Global.scala
@@ -33,8 +33,8 @@ object Global extends GlobalSettings with LazyLogging{
       InitialData.insert(conf)
     }
 
-    CleanUpService.register("deletion of expired dataTokens", DataToken.expirationTime){
-      DataTokenDAO.removeExpiredTokens()(GlobalAccessContext).map(r => s"deleted ${r.n}")
+    CleanUpService.register("deletion of expired dataTokens", UserToken.expirationTime) {
+      UserTokenDAO.removeExpiredTokens()(GlobalAccessContext).map(r => s"deleted ${r.n}")
     }
 
     CleanUpService.register("deletion of openAssignments with zero instances", OpenAssignment.pruningInterval) {

diff --git a/app/assets/javascripts/admin/admin_rest_api.js b/app/assets/javascripts/admin/admin_rest_api.js
@@ -209,6 +209,35 @@ export async function deleteProject(projectName: string): Promise<void> {
   });
 }
 
+// ### Do with userToken
+
+let tokenRequestPromise;
+function requestUserToken(): Promise<string> {
+  if (tokenRequestPromise) {
+    return tokenRequestPromise;
+  }
+
+  tokenRequestPromise = Request.receiveJSON("/api/userToken/generate").then(tokenObj => {
+    tokenRequestPromise = null;
+    return tokenObj.token;
+  });
+
+  return tokenRequestPromise;
+}
+
+let tokenPromise;
+export async function doWithToken<T>(fn: (token: string) => Promise<T>): Promise<*> {
+  if (!tokenPromise) tokenPromise = requestUserToken();
+  return tokenPromise.then(fn).catch(error => {
+    if (error.status === 403) {
+      console.warn("Token expired. Requesting new token...");
+      tokenPromise = requestUserToken();
+      return doWithToken(fn);
+    }
+    throw error;
+  });
+}
+
 export async function createProject(project: APIProjectType): Promise<APIProjectType> {
   const transformedProject = Object.assign({}, project, {
     expectedTime: Utils.minutesToMilliseconds(project.expectedTime),
@@ -282,29 +311,22 @@ export async function getTasks(queryObject: QueryObjectType): Promise<Array<APIT
 }
 
 // TODO fix return types
-export async function createTask(task: NewTaskType): Promise<*> {
-  return Request.sendJSONReceiveJSON("/api/tasks?type=default", {
-    data: task,
+export async function createTasks(tasks: Array<NewTaskType>): Promise<Array<*>> {
+  return Request.sendJSONReceiveJSON("/api/tasks", {
+    data: tasks,
   });
 }
 
 // TODO fix return types
 export async function createTaskFromNML(task: NewTaskType): Promise<*> {
-  return Request.sendMultipartFormReceiveJSON("/api/tasks?type=nml", {
+  return Request.sendMultipartFormReceiveJSON("/api/tasks/createFromFile", {
     data: {
       nmlFile: task.nmlFile,
       formJSON: JSON.stringify(task),
     },
   });
 }
 
-// TODO fix return types
-export async function createTasksFromBulk(tasks: Array<NewTaskType>): Promise<*> {
-  return Request.sendJSONReceiveJSON("/api/tasks?type=bulk", {
-    data: tasks,
-  });
-}
-
 export async function getTask(taskId: string): Promise<APITaskType> {
   const task = await Request.receiveJSON(`/api/tasks/${taskId}`);
   return transformTask(task);
@@ -361,11 +383,12 @@ export async function addNDStoreDataset(
 }
 
 export async function addDataset(datatsetConfig: DatasetConfigType): Promise<APIAnnotationType> {
-  const response = await Request.receiveJSON("/api/dataToken/generate");
-  return Request.sendMultipartFormReceiveJSON(`/data/datasets?token=${response.token}`, {
-    data: datatsetConfig,
-    host: datatsetConfig.datastore,
-  });
+  return doWithToken(token =>
+    Request.sendMultipartFormReceiveJSON(`/data/datasets?token=${token}`, {
+      data: datatsetConfig,
+      host: datatsetConfig.datastore,
+    }),
+  );
 }
 
 // #### Datastores

diff --git a/app/assets/javascripts/admin/api_flow_types.js b/app/assets/javascripts/admin/api_flow_types.js
@@ -2,6 +2,7 @@
  * api_flow_types.js
  * @flow
  */
+import type { SkeletonTracingStatsType } from "oxalis/model/accessors/skeletontracing_accessor";
 import type { Vector3, Vector6 } from "oxalis/constants";
 import type { DataLayerType, SettingsType, BoundingBoxObjectType } from "oxalis/store";
 
@@ -19,6 +20,7 @@ export type APIDataStoreType = {
   +name: string,
   +url: string,
   +typ: "webknossos-store" | "nd-store",
+  +accessToken?: string,
 };
 
 export type APIDatasetType = {
@@ -27,13 +29,20 @@ export type APIDatasetType = {
   +dataStore: APIDataStoreType,
   +sourceType: "wkw" | "knossos",
   +owningTeam: "Connectomics department",
+};
+
+export type APIDatasetType = {
   +allowedTeams: Array<string>,
-  +isActive: boolean,
-  +accessToken: null,
-  +isPublic: boolean,
-  +description: ?string,
   +created: number,
+  +dataSource: APIDataSourceType,
+  +dataStore: APIDataStoreType,
+  +description: ?string,
+  +isActive: boolean,
   +isEditable: boolean,
+  +isPublic: boolean,
+  +name: string,
+  +owningTeam: "Connectomics department",
+  +sourceType: "wkw" | "knossos",
 };
 
 export type APIRoleType = { +name: string };
@@ -43,7 +52,7 @@ export type APITeamRoleType = {
   +role: APIRoleType,
 };
 
-type ExperienceMapType = { +[string]: number };
+export type ExperienceMapType = { +[string]: number };
 
 export type APIUserType = {
   +email: string,
@@ -66,37 +75,34 @@ export type APITeamType = {
   +roles: Array<APIRoleType>,
 };
 
-export type APIAnnotationType = {
-  +version: number,
-  +user: {
-    +id: string,
-    +email: string,
-    +firstName: string,
-    +lastName: string,
-    +isAnonymous: boolean,
-    +teams: Array<APITeamRoleType>,
-  },
-  +modified: string,
-  +stateLabel: string,
-  +state: { +isAssigned: boolean, +isFinished: boolean, +isInProgress: boolean },
-  +id: string,
-  +name: string,
-  +typ: string,
-  +stats: { +numberOfNodes: number, +numberOfEdges: number, +numberOfTrees: number },
-  +restrictions: {
-    +allowAccess: boolean,
-    +allowUpdate: boolean,
-    +allowFinish: boolean,
-    +allowDownload: boolean,
-  },
-  +formattedHash: string,
-  +downloadUrl: string,
-  +contentType: string,
-  +dataSetName: string,
-  +tracingTime: null,
-  +tags: Array<string>,
+export type APIRestrictionsType = {
+  +allowAccess: boolean,
+  +allowUpdate: boolean,
+  +allowFinish: boolean,
+  +allowDownload: boolean,
+};
+
+export type APIAllowedModeType = "orthogonal" | "oblique" | "flight" | "volume";
+
+export type APISettingsType = {
+  +advancedOptionsAllowed: boolean,
+  +allowedModes: Array<APIAllowedModeType>,
+  +preferredMode: APIAllowedModeType,
+  +branchPointsAllowed: boolean,
+  +somaClickingAllowed: boolean,
 };
 
+export const APITracingTypeTracingEnum = {
+  Explorational: "Explorational",
+  Task: "Task",
+  View: "View",
+  CompoundTask: "CompoundTask",
+  CompoundProject: "CompoundProject",
+  CompoundTaskType: "CompoundTaskType",
+};
+
+export type APITracingTypeTracingType = $Keys<typeof APITracingTypeTracingEnum>;
+
 export type APITaskTypeType = {
   +id: string,
   +summary: string,
@@ -107,30 +113,23 @@ export type APITaskTypeType = {
 
 export type TaskStatusType = { +open: number, +inProgress: number, +completed: number };
 
-export type APITaskWithAnnotationType = {
+export type APIScriptType = {
   +id: string,
-  +team: string,
-  +formattedHash: string,
-  +projectName: string,
-  +type: APITaskTypeType,
-  +dataSet: string,
-  +editPosition: Vector3,
-  +editRotation: Vector3,
-  +boundingBox: null,
-  +neededExperience: ExperienceMapType,
-  +created: string,
-  +status: TaskStatusType,
-  +script: null,
-  +tracingTime: null,
-  +creationInfo: null,
-  +annotation: APIAnnotationType,
+  +name: string,
+  +owner: APIUserType,
+  +gist: string,
 };
 
-export type APIScriptType = {
+export type APIProjectType = {
   +id: string,
   +name: string,
+  +team: string,
   +owner: APIUserType,
-  +gist: string,
+  +priority: number,
+  +paused: boolean,
+  +expectedTime: number,
+  +assignmentConfiguration: { location: "webknossos" | "mturk" },
+  +numberOfOpenAssignments: number,
 };
 
 export type APITaskType = {
@@ -156,16 +155,51 @@ export type APITaskType = {
   +directLinks?: Array<string>,
 };
 
-export type APIProjectType = {
+export type APIAnnotationType = {
+  +content: {
+    +id: string,
+    +typ: string,
+  },
+  +dataSetName: string,
+  +dataStore: APIDataStoreType,
+  +description: string,
+  +formattedHash: string,
+  +modified: string,
   +id: string,
+  +isPublic: boolean,
   +name: string,
+  +restrictions: APIRestrictionsType,
+  +settings: APISettingsType,
+  +state: {
+    +isAssigned: boolean,
+    +isFinished: boolean,
+    +isInProgress: boolean,
+  },
+  +stats: SkeletonTracingStatsType,
+  +tags: Array<string>,
+  +task: APITaskType,
+  +tracingTime: number,
+  +typ: APITracingTypeTracingType,
+  +user?: APIUserType,
+};
+
+export type APITaskWithAnnotationType = {
+  +id: string,
   +team: string,
-  +owner: APIUserType,
-  +priority: number,
-  +paused: boolean,
-  +expectedTime: number,
-  +assignmentConfiguration: { location: "webknossos" | "mturk" },
-  +numberOfOpenAssignments: number,
+  +formattedHash: string,
+  +projectName: string,
+  +type: APITaskTypeType,
+  +dataSet: string,
+  +editPosition: Vector3,
+  +editRotation: Vector3,
+  +boundingBox: null,
+  +neededExperience: ExperienceMapType,
+  +created: string,
+  +status: TaskStatusType,
+  +script: null,
+  +tracingTime: null,
+  +creationInfo: null,
+  +annotation: APIAnnotationType,
 };
 
 export type APIDatastoreType = {
@@ -187,3 +221,5 @@ export type DatasetConfigType = {
   +datastore: string,
   +zipFile: File,
 };
+
+export default {};
diff --git a/app/assets/javascripts/admin/views/project/project_list_view.js b/app/assets/javascripts/admin/views/project/project_list_view.js
@@ -183,7 +183,7 @@ class ProjectListView extends React.PureComponent<{}, State> {
                 render={(__, project: APIProjectType) => (
                   <span>
                     <a
-                      href={`/annotations/CompoundProject/${project.name}`}
+                      href={`/annotations/CompoundProject/${project.id}`}
                       title="View all Finished Tracings"
                     >
                       <Icon type="eye-o" />View
@@ -215,7 +215,7 @@ class ProjectListView extends React.PureComponent<{}, State> {
                       </div>
                     )}
                     <a
-                      href={`/api/projects/${project.name}/download`}
+                      href={`/annotations/CompoundProject/${project.id}/download`}
                       title="Download all Finished Tracings"
                     >
                       <Icon type="download" />Download