adapt code to work with some server side json property renamings, dis…

…tinguish between tracingId and annotationId, fix unit tests (#1759)

app/assets/javascripts/oxalis/api/api_latest.js

@@ -234,9 +234,9 @@ class TracingApi {
    */
   async finishAndGetNextTask() {
     const state = Store.getState();
-    const { tracingType, tracingId } = state.tracing;
+    const { tracingType, annotationId } = state.tracing;
     const task = state.task;
-    const finishUrl = `/annotations/${tracingType}/${tracingId}/finish`;
+    const finishUrl = `/annotations/${tracingType}/${annotationId}/finish`;
     const requestTaskUrl = "/user/tasks/request";
 
     await Model.save();
@@ -277,12 +277,12 @@ class TracingApi {
    */
   async restart(
     newTracingType: SkeletonTracingTypeTracingType,
-    newTracingId: string,
+    newAnnotationId: string,
     newControlMode: ControlModeType,
   ) {
     Store.dispatch(restartSagaAction());
     UrlManager.reset();
-    await Model.fetch(newTracingType, newTracingId, newControlMode, false);
+    await Model.fetch(newTracingType, newAnnotationId, newControlMode, false);
     Store.dispatch(wkReadyAction());
     UrlManager.updateUnthrottled(true);
   }

app/assets/javascripts/oxalis/controller.js

@@ -39,7 +39,7 @@ import type { OxalisState, SkeletonTracingTypeTracingType } from "oxalis/store";
 class Controller extends React.PureComponent {
   props: {
     initialTracingType: SkeletonTracingTypeTracingType,
-    initialTracingId: string,
+    initialAnnotationId: string,
     initialControlmode: ControlModeType,
     // Delivered by connect()
     viewMode: ModeType,
@@ -84,7 +84,7 @@ class Controller extends React.PureComponent {
 
     Model.fetch(
       this.props.initialTracingType,
-      this.props.initialTracingId,
+      this.props.initialAnnotationId,
       this.props.initialControlmode,
       true,
     )

app/assets/javascripts/oxalis/controller/url_manager.js

@@ -126,24 +126,28 @@ class UrlManager {
     }
 
     getActiveNode(tracing).map(node => state.push(node.id));
-    const newBaseUrl = updateTypeAndId(this.baseUrl, tracing.tracingType, tracing.tracingId);
+    const newBaseUrl = updateTypeAndId(this.baseUrl, tracing.tracingType, tracing.annotationId);
     return `${newBaseUrl}#${state.join(",")}`;
   }
 }
 
-export function updateTypeAndId(baseUrl: string, tracingType: string, tracingId: string): string {
+export function updateTypeAndId(
+  baseUrl: string,
+  tracingType: string,
+  annotationId: string,
+): string {
   // Update the baseUrl with a potentially new tracing id and or tracing type.
   // There are two possible routes (annotations or datasets) which will be handled
   // both here. Chaining the replace function is possible, since they are mutually
   // exclusive and thus can't apply both simultaneously.
   return baseUrl
     .replace(
       /^(.*\/annotations)\/(.*?)\/([^/]*)(\/?.*)$/,
-      (all, base, type, id, rest) => `${base}/${tracingType}/${tracingId}${rest}`,
+      (all, base, type, id, rest) => `${base}/${tracingType}/${annotationId}${rest}`,
     )
     .replace(
       /^(.*\/datasets)\/([^/]*)(\/.*)$/,
-      (all, base, id, rest) => `${base}/${tracingId}${rest}`,
+      (all, base, id, rest) => `${base}/${annotationId}${rest}`,
     );
 }
 

app/assets/javascripts/oxalis/model.js

@@ -54,7 +54,7 @@ import update from "immutability-helper";
 import UrlManager from "oxalis/controller/url_manager";
 
 type ServerSkeletonTracingTreeType = {
-  id: number,
+  treeId: number,
   color: ?Vector3,
   name: string,
   timestamp: number,
@@ -65,11 +65,12 @@ type ServerSkeletonTracingTreeType = {
 };
 
 export type ServerSkeletonTracingType = {
-  activeNode?: number,
+  activeNodeId?: number,
   boundingBox?: BoundingBoxObjectType,
-  customLayers: Array<Object>,
+  customLayers?: Array<Object>,
   editPosition: Vector3,
   editRotation: Vector3,
+  id: string,
   trees: Array<ServerSkeletonTracingTreeType>,
   version: number,
   zoomLevel: number,
@@ -78,9 +79,10 @@ export type ServerSkeletonTracingType = {
 export type ServerVolumeTracingType = {
   activeCell?: number,
   boundingBox?: BoundingBoxObjectType,
-  customLayers: Array<Object>,
+  customLayers?: Array<Object>,
   editPosition: Vector3,
   editRotation: Vector3,
+  id: string,
   nextCell: ?number,
   version: number,
   zoomLevel: number,
@@ -133,7 +135,7 @@ export class OxalisModel {
 
   async fetch(
     tracingType: SkeletonTracingTypeTracingType,
-    tracingId: string,
+    annotationId: string,
     controlMode: ControlModeType,
     initialFetch: boolean,
   ) {
@@ -144,9 +146,9 @@ export class OxalisModel {
       // Include /readOnly part whenever it is in the pathname
       const isReadOnly = window.location.pathname.endsWith("/readOnly");
       const readOnlyPart = isReadOnly ? "readOnly/" : "";
-      infoUrl = `/annotations/${tracingType}/${tracingId}/${readOnlyPart}info`;
+      infoUrl = `/annotations/${tracingType}/${annotationId}/${readOnlyPart}info`;
     } else {
-      infoUrl = `/annotations/${tracingType}/${tracingId}/info`;
+      infoUrl = `/annotations/${tracingType}/${annotationId}/info`;
     }
 
     const annotation: ServerAnnotationType = await Request.receiveJSON(infoUrl);
@@ -160,7 +162,7 @@ export class OxalisModel {
     } else if (!dataset) {
       error = "Selected dataset doesn't exist";
     } else if (!dataset.dataSource.dataLayers) {
-      const datasetName = dataset.dataSource.id.name;
+      const datasetName = annotation.dataSetName;
       if (datasetName) {
         error = `Please, double check if you have the dataset '${datasetName}' imported.`;
       } else {
@@ -238,7 +240,7 @@ export class OxalisModel {
     const { allowedModes, preferredMode } = this.determineAllowedModes(annotation.settings);
     _.extend(annotation.settings, { allowedModes, preferredMode });
 
-    const isVolume = annotation.settings.allowedModes.includes("volume");
+    const isVolume = annotation.content.typ === "volume";
     const controlMode = Store.getState().temporaryConfiguration.controlMode;
     if (controlMode === ControlModeEnum.TRACE) {
       if (isVolume) {
@@ -259,7 +261,7 @@ export class OxalisModel {
 
     if (initialFetch) {
       // TODO remove default value
-      Store.dispatch(setZoomStepAction(tracing.zoomLevel || 2));
+      Store.dispatch(setZoomStepAction(tracing.zoomLevel != null ? tracing.zoomLevel : 2));
     }
 
     // Initialize 'flight', 'oblique' or 'orthogonal'/'volume' mode

app/assets/javascripts/oxalis/model/actions/save_actions.js

@@ -4,6 +4,7 @@
  * save_actions.js
  * @flow
  */
+import Date from "libs/date";
 import type { UpdateAction } from "oxalis/model/sagas/update_actions";
 
 type PushSaveQueueActionType = {

app/assets/javascripts/oxalis/model/reducers/readonlytracing_reducer.js

@@ -15,11 +15,12 @@ function ReadOnlyTracingReducer(state: OxalisState, action: ActionType): OxalisS
       );
 
       const readonlyTracing: ReadOnlyTracingType = {
+        annotationId: action.annotation.id,
         type: "readonly",
         restrictions,
         name: action.annotation.name,
         tracingType: "View",
-        tracingId: action.annotation.id,
+        tracingId: action.tracing.id,
         version: action.tracing.version,
         boundingBox: convertBoundingBox(action.tracing.boundingBox),
       };

app/assets/javascripts/oxalis/model/reducers/skeletontracing_reducer.js

@@ -45,16 +45,15 @@ function SkeletonTracingReducer(state: OxalisState, action: ActionType): OxalisS
       const trees = _.keyBy(
         action.tracing.trees.map(tree =>
           update(tree, {
-            treeId: { $set: tree.id },
             nodes: { $set: _.keyBy(tree.nodes, "id") },
-            color: { $set: tree.color || ColorGenerator.distinctColorForId(tree.id) },
+            color: { $set: tree.color || ColorGenerator.distinctColorForId(tree.treeId) },
             isVisible: { $set: true },
           }),
         ),
-        "id",
+        "treeId",
       );
 
-      const activeNodeIdMaybe = Maybe.fromNullable(action.tracing.activeNode);
+      const activeNodeIdMaybe = Maybe.fromNullable(action.tracing.activeNodeId);
       let cachedMaxNodeId = _.max(_.flatMap(trees, __ => _.map(__.nodes, node => node.id)));
       cachedMaxNodeId = cachedMaxNodeId != null ? cachedMaxNodeId : Constants.MIN_NODE_ID - 1;
 
@@ -87,6 +86,7 @@ function SkeletonTracingReducer(state: OxalisState, action: ActionType): OxalisS
       const activeTreeId = Utils.toNullable(activeTreeIdMaybe);
 
       const skeletonTracing: SkeletonTracingType = {
+        annotationId: action.annotation.id,
         type: "skeleton",
         activeNodeId,
         cachedMaxNodeId,
@@ -95,7 +95,7 @@ function SkeletonTracingReducer(state: OxalisState, action: ActionType): OxalisS
         trees,
         name: action.annotation.name,
         tracingType: action.annotation.typ,
-        tracingId: action.annotation.id,
+        tracingId: action.tracing.id,
         version: action.tracing.version,
         boundingBox: convertBoundingBox(action.tracing.boundingBox),
       };

app/assets/javascripts/oxalis/model/reducers/volumetracing_reducer.js

@@ -34,6 +34,7 @@ function VolumeTracingReducer(state: OxalisState, action: VolumeTracingActionTyp
       }
 
       const volumeTracing: VolumeTracingType = {
+        annotationId: action.annotation.id,
         type: "volume",
         activeCellId: 0,
         lastCentroid: null,
@@ -44,7 +45,7 @@ function VolumeTracingReducer(state: OxalisState, action: VolumeTracingActionTyp
         volumeTraceOrMoveMode: Constants.VOLUME_MODE_MOVE,
         name: action.annotation.name,
         tracingType: action.annotation.typ,
-        tracingId: action.annotation.id,
+        tracingId: action.tracing.id,
         version: action.tracing.version,
         boundingBox: convertBoundingBox(action.tracing.boundingBox),
       };

app/assets/javascripts/oxalis/model/sagas/annotation_saga.js

@@ -4,7 +4,7 @@ import Request from "libs/request";
 
 export function* pushTracingNameAsync(): Generator<*, *, *> {
   const tracing = yield select(state => state.tracing);
-  const url = `/annotations/${tracing.tracingType}/${tracing.tracingId}/name`;
+  const url = `/annotations/${tracing.tracingType}/${tracing.annotationId}/name`;
   yield [
     call(Request.sendJSONReceiveJSON, url, {
       data: { name: tracing.name },

app/assets/javascripts/oxalis/model/sagas/save_saga.js

@@ -57,14 +57,19 @@ export function* pushAnnotationAsync(): Generator<*, *, *> {
 export function* sendRequestToServer(timestamp: number = Date.now()): Generator<*, *, *> {
   const batch = yield select(state => state.save.queue);
   let compactBatch = compactUpdateActions(batch);
-  const { version, tracingType, tracingId } = yield select(state => state.tracing);
+  const { version, type, tracingId } = yield select(state => state.tracing);
+  const dataStoreUrl = yield select(state => state.dataset.dataStore.url);
   compactBatch = addVersionNumbers(compactBatch, version);
   try {
-    yield call(Request.sendJSONReceiveJSON, `/annotations/${tracingType}/${tracingId}`, {
-      method: "PUT",
-      headers: { "X-Date": timestamp },
-      data: compactBatch,
-    });
+    yield call(
+      Request.sendJSONReceiveJSON,
+      `${dataStoreUrl}/data/tracings/${type}/${tracingId}/update`,
+      {
+        method: "POST",
+        headers: { "X-Date": timestamp },
+        data: compactBatch,
+      },
+    );
     yield put(setVersionNumberAction(version + compactBatch.length));
     yield put(setLastSaveTimestampAction());
     yield put(shiftSaveQueueAction(batch.length));
@@ -227,13 +232,14 @@ function compactDeletedTrees(updateActions: Array<UpdateAction>) {
   const deletedTreeIds = updateActions
     .filter(ua => ua.name === "deleteTree")
     .map(ua => (ua.name === "deleteTree" ? ua.value.id : -1));
-  _.remove(
+  return _.filter(
     updateActions,
     ua =>
-      (ua.name === "deleteNode" || ua.name === "deleteEdge") &&
-      deletedTreeIds.includes(ua.value.treeId),
+      !(
+        (ua.name === "deleteNode" || ua.name === "deleteEdge") &&
+        deletedTreeIds.includes(ua.value.treeId)
+      ),
   );
-  return updateActions;
 }
 
 export function compactUpdateActions(

app/assets/javascripts/oxalis/store.js

@@ -160,6 +160,7 @@ export type SkeletonTracingTypeTracingType = $Keys<typeof SkeletonTracingTypeTra
 export type VolumeTracingTypeTracingType = SkeletonTracingTypeTracingType;
 
 export type SkeletonTracingType = {
+  +annotationId: string,
   +type: "skeleton",
   +trees: TreeMapType,
   +name: string,
@@ -174,6 +175,7 @@ export type SkeletonTracingType = {
 };
 
 export type VolumeTracingType = {
+  +annotationId: string,
   +type: "volume",
   +name: string,
   +version: number,
@@ -190,6 +192,7 @@ export type VolumeTracingType = {
 };
 
 export type ReadOnlyTracingType = {
+  +annotationId: string,
   +type: "readonly",
   +name: string,
   +version: number,
@@ -273,7 +276,7 @@ export type SaveQueueEntryType = {
   version: number,
   timestamp: number,
   actions: Array<UpdateAction>,
-}
+};
 
 export type SaveStateType = {
   +isBusy: boolean,
@@ -392,6 +395,8 @@ export const defaultState: OxalisState = {
     dataLayers: [],
   },
   tracing: {
+    annotationId: "",
+    boundingBox: null,
     type: "skeleton",
     trees: {},
     name: "",

app/assets/javascripts/oxalis/view/action-bar/dataset_actions_view.js

@@ -56,14 +56,14 @@ class DatasetActionsView extends PureComponent {
   handleCopyToAccount = async (event: SyntheticInputEvent) => {
     event.target.blur();
     const url = `/annotations/${this.props.tracing.tracingType}/${this.props.tracing
-      .tracingId}/duplicate`;
+      .annotationId}/duplicate`;
     app.router.loadURL(url);
   };
 
   handleFinish = async (event: SyntheticInputEvent) => {
     event.target.blur();
     const url = `/annotations/${this.props.tracing.tracingType}/${this.props.tracing
-      .tracingId}/finishAndRedirect`;
+      .annotationId}/finishAndRedirect`;
     await this.handleSave();
     if (confirm(messages["finish.confirm"])) {
       app.router.loadURL(url);