Merge branch 'clean-up-merge-modal' of github.com:scalableminds/webkn…

…ossos into chunk-save-actions

.eslintrc.json

@@ -39,6 +39,7 @@
     "react/jsx-filename-extension": "off",
     "react/no-multi-comp": "warn",
     "react/prop-types": "off",
+    "react/require-default-props": "off",
     "radix": "off",
     "no-bitwise": "off",
     "no-confusing-arrow": "off",

.flowconfig

@@ -16,6 +16,7 @@
 <PROJECT_ROOT>/node_modules/findup/
 <PROJECT_ROOT>/node_modules/documentation/
 <PROJECT_ROOT>/node_modules/flow-coverage-report/
+<PROJECT_ROOT>/.nyc_output
 
 [untyped]
 <PROJECT_ROOT>/node_modules/ava/

Dockerfile

@@ -15,4 +15,4 @@ RUN addgroup --system --gid 999 webknossos \
 
 USER webknossos
 
-ENTRYPOINT [ "bin/oxalis" ]
+ENTRYPOINT [ "bin/webknossos" ]

MIGRATIONS.md

@@ -4,13 +4,19 @@ All migrations of webknossos are documented in this file.
 This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 User-facing changes are documented in the [changelog](CHANGELOG.md).
 
-## [Unreleased]
+## Unreleased
+### Postgres Evolutions:
+- 
+
+## [18.08.0](https://github.com/scalableminds/webknossos/releases/tag/18.08.0) - 2018-07-23
 ### Postgres Evolutions:
 - [013-add-logoUrl.sql](conf/evolutions/013-add-logoUrl.sql)
 - [014-equalize-schema-and-evolutions.sql](conf/evolutions/014-equalize-schema-and-evolutions.sql)
 - [015-add-organization-displayname.sql](conf/evolutions/015-add-organization-displayname.sql)
 - To clean up half-deleted tasks as caused by [this bug](https://github.com/scalableminds/webknossos/issues/2873), run `update webknossos.annotations set isDeleted = true where _id in (select a._id from webknossos.annotations_ a join webknossos.tasks t on a._task = t._id where t.isDeleted and a.typ == 'Task')`
 - [016-add-schema-version.sql](conf/evolutions/016-add-schema-version.sql)
+- [017-add-organization-email.sql](conf/evolutions/017-add-organization-email.sql)
+- Add email addresses for notifications about new users and about task overtime to the `webknossos.organizations` entries in the Postgres database (previously in `application.conf` > `braintracing.newuserlist` and `braintracing.overTimeList`)
 
 ## [18.07.0](https://github.com/scalableminds/webknossos/releases/tag/18.07.0) - 2018-07-05
 First release

app/assets/javascripts/admin/statistic/project_progress_report_view.js

@@ -2,10 +2,10 @@
 import * as React from "react";
 import { Icon, Spin, Table, Card } from "antd";
 import Utils from "libs/utils";
-import FormatUtils from "libs/format_utils";
 import Loop from "components/loop";
 import { getProjectProgressReport } from "admin/admin_rest_api";
 import type { APIProjectProgressReportType, APITeamType } from "admin/api_flow_types";
+import FormattedDate from "components/formatted_date";
 import TeamSelectionForm from "./team_selection_form";
 
 const { Column, ColumnGroup } = Table;
@@ -69,7 +69,7 @@ class ProjectProgressReportView extends React.PureComponent<{}, State> {
       <div className="container">
         <Loop onTick={this.handleAutoReload} interval={RELOAD_INTERVAL} />
         <div className="pull-right">
-          {this.state.updatedAt != null ? FormatUtils.formatDate(this.state.updatedAt) : null}{" "}
+          {this.state.updatedAt != null ? <FormattedDate timestamp={this.state.updatedAt} /> : null}{" "}
           <Icon type="setting" onClick={this.handleOpenSettings} />
           <Icon type="reload" onClick={this.handleReload} />
         </div>

app/assets/javascripts/admin/task/task_annotation_view.js

@@ -3,7 +3,6 @@
 import { Dropdown, Menu, Icon, Modal } from "antd";
 import React from "react";
 import { connect } from "react-redux";
-import moment from "moment";
 import FormatUtils from "libs/format_utils";
 import {
   getAnnotationsForTask,
@@ -16,6 +15,7 @@ import messages from "messages";
 import TransferTaskModal from "dashboard/transfer_task_modal";
 import type { APIUserType, APITaskType, APIAnnotationType } from "admin/api_flow_types";
 import type { OxalisState } from "oxalis/store";
+import FormattedDate from "components/formatted_date";
 
 const { Item } = Menu;
 const { confirm } = Modal;
@@ -163,7 +163,9 @@ class TaskAnnotationView extends React.PureComponent<Props & StateProps, State>
               return (
                 <tr key={`${annotation.id}-tr`}>
                   <td>{userString}</td>
-                  <td>{moment(annotation.modified).format("YYYY-MM-DD HH:mm")}</td>
+                  <td>
+                    <FormattedDate timestamp={annotation.modified} />
+                  </td>
                   <td>
                     <span>
                       <Icon type="check-circle-o" />

app/assets/javascripts/admin/task/task_list_view.js

@@ -20,6 +20,7 @@ import type { APITaskType, APITaskTypeType } from "admin/api_flow_types";
 import type { QueryObjectType, TaskFormFieldValuesType } from "admin/task/task_search_form";
 import type { RouterHistory } from "react-router-dom";
 import { handleGenericError } from "libs/error_handling";
+import FormattedDate from "components/formatted_date";
 
 const { Column } = Table;
 const { Search, TextArea } = Input;
@@ -244,6 +245,7 @@ class TaskListView extends React.PureComponent<Props, State> {
               key="created"
               width={150}
               sorter={Utils.localeCompareBy(typeHint, "created")}
+              render={created => <FormattedDate timestamp={created} />}
             />
             <Column
               title="Stats"

app/assets/javascripts/components/file_upload.js

@@ -14,6 +14,15 @@ type Props = {
   onUploading?: Function,
 };
 
+export function readFileAsText(file: File): Promise<string> {
+  return new Promise((resolve, reject) => {
+    const reader = new FileReader();
+    reader.onerror = reject;
+    reader.onload = () => resolve(reader.result.toString());
+    reader.readAsText(file);
+  });
+}
+
 class FileUpload extends React.PureComponent<Props> {
   fileInput: ?HTMLInputElement;
 
@@ -32,10 +41,7 @@ class FileUpload extends React.PureComponent<Props> {
         data: { [this.props.name]: files },
       }).then(successCallback, errorCallback);
     } else {
-      const reader = new FileReader();
-      reader.onerror = errorCallback;
-      reader.onload = () => successCallback(reader.result);
-      reader.readAsText(files[0]);
+      readFileAsText(files[0]).then(successCallback, errorCallback);
     }
   };
 

app/assets/javascripts/components/formatted_date.js

@@ -0,0 +1,38 @@
+// @flow
+import * as React from "react";
+import moment from "moment";
+import { Tooltip } from "antd";
+
+const defaultTimeFormat = "YYYY-MM-DD HH:mm";
+
+/**
+ * Return current date and time. Please only use this function if you need
+ * a pure string representation. In all other cases, please prefer the
+ * <FormattedDate /> component below.
+ */
+export function formatDateInLocalTimeZone(date?: number = Date.now()): string {
+  return moment(date).format(defaultTimeFormat);
+}
+
+export default function FormattedDate({
+  timestamp,
+  format,
+}: {
+  timestamp: string | number,
+  format?: string,
+}) {
+  const _moment = moment.utc(timestamp);
+  const _format = format || defaultTimeFormat;
+  return (
+    <Tooltip
+      title={
+        <span>
+          The displayed time refers to your local timezone. In UTC, the time is:{" "}
+          {_moment.format(_format)}
+        </span>
+      }
+    >
+      {_moment.local().format(_format)}
+    </Tooltip>
+  );
+}

app/assets/javascripts/dashboard/advanced_dataset/advanced_dataset_view.js

@@ -11,6 +11,7 @@ import type { DatasetType } from "dashboard/dataset_view";
 import type { APITeamType } from "admin/api_flow_types";
 import dice from "dice-coefficient";
 import _ from "lodash";
+import FormattedDate from "components/formatted_date";
 
 const { Column } = Table;
 
@@ -120,9 +121,9 @@ class AdvancedDatasetView extends React.PureComponent<Props, State> {
             title="Creation Date"
             dataIndex="created"
             key="created"
-            sorter={Utils.localeCompareBy(typeHint, "formattedCreated")}
+            sorter={Utils.compareBy(typeHint, "created")}
             sortOrder={sortedInfo.columnKey === "created" && sortedInfo.order}
-            render={(__, dataset: DatasetType) => dataset.formattedCreated}
+            render={created => <FormattedDate timestamp={created} />}
           />
           <Column
             title="Scale"

app/assets/javascripts/dashboard/dashboard_task_list_view.js

@@ -9,7 +9,6 @@ import { AsyncButton } from "components/async_clickables";
 import { Button, Modal, Tag, Icon, Card, Row, Col, List } from "antd";
 import Markdown from "react-remarkable";
 import Utils from "libs/utils";
-import moment from "moment";
 import Toast from "libs/toast";
 import messages from "messages";
 import TransferTaskModal from "dashboard/transfer_task_modal";
@@ -32,6 +31,7 @@ import type {
 } from "admin/api_flow_types";
 import type { OxalisState } from "oxalis/store";
 import type { RouterHistory } from "react-router-dom";
+import FormattedDate from "components/formatted_date";
 
 const typeHint: APITaskWithAnnotationType[] = [];
 
@@ -322,9 +322,9 @@ class DashboardTaskListView extends React.PureComponent<Props, State> {
 
     const TaskCardTitle = ({ task }) => (
       <React.Fragment>
-        <span style={{ marginRight: 8 }}>{`${task.type.summary} (${moment(task.created).format(
-          "YYYY-MM-DD HH:mm",
-        )}) `}</span>
+        <span style={{ marginRight: 8 }}>
+          {task.type.summary} (<FormattedDate timestamp={task.created} />)
+        </span>
         {task.type.settings.allowedModes.map(mode => <Tag key={mode}>{mode}</Tag>)}
       </React.Fragment>
     );

app/assets/javascripts/dashboard/dataset_view.js

@@ -4,7 +4,6 @@ import _ from "lodash";
 import * as React from "react";
 import { Link, withRouter } from "react-router-dom";
 import Utils from "libs/utils";
-import moment from "moment";
 import { Spin, Input, Button } from "antd";
 import AdvancedDatasetView from "dashboard/advanced_dataset/advanced_dataset_view";
 import GalleryDatasetView from "dashboard/gallery_dataset_view";
@@ -26,7 +25,6 @@ type Props = {
 export type DatasetType = APIDatasetType & {
   hasSegmentation: boolean,
   thumbnailURL: string,
-  formattedCreated: string,
 };
 
 type State = {
@@ -57,7 +55,6 @@ export function transformDatasets(datasets: Array<APIDatasetType>): Array<Datase
           layer => layer.category === "segmentation",
         ),
         thumbnailURL: createThumbnailURL(dataset.name, dataset.dataSource.dataLayers),
-        formattedCreated: moment(dataset.created).format("YYYY-MM-DD HH:mm"),
       }),
     ),
     "created",

app/assets/javascripts/dashboard/explorative_annotations_view.js

@@ -27,6 +27,7 @@ import {
 } from "admin/admin_rest_api";
 import type { RouterHistory } from "react-router-dom";
 import { handleGenericError } from "libs/error_handling";
+import FormattedDate from "components/formatted_date";
 
 const { Column } = Table;
 const { Search } = Input;
@@ -417,6 +418,7 @@ class ExplorativeAnnotationsView extends React.PureComponent<Props, State> {
           title="Modification Date"
           dataIndex="modified"
           sorter={Utils.localeCompareBy(typeHint, "modified")}
+          render={modified => <FormattedDate timestamp={modified} />}
         />
         <Column
           title="Actions"

app/assets/javascripts/dashboard/gallery_dataset_view.js

@@ -75,17 +75,14 @@ class GalleryDatasetView extends React.PureComponent<Props, State> {
       .entries()
       .map(([organization, datasets]) =>
         // Sort each group of datasets
-        [
-          organization,
-          datasets.sort(Utils.localeCompareBy(([]: DatasetType[]), "formattedCreated", false)),
-        ],
+        [organization, datasets.sort(Utils.localeCompareBy(([]: DatasetType[]), "created", false))],
       )
       .value()
       .sort(
         // Sort groups by creation date of first dataset
         Utils.localeCompareBy(
           ([]: DatasetType[]),
-          ([_organization, datasets]) => datasets[0].formattedCreated,
+          ([_organization, datasets]) => datasets[0].created,
           false,
         ),
       );

app/assets/javascripts/libs/format_utils.js

@@ -36,13 +36,6 @@ class FormatUtils {
     }
     return text;
   }
-
-  /**
-   * Return current date and time
-   */
-  static formatDate(date?: number = Date.now()): string {
-    return moment(date).format("YYYY-MM-DD HH:mm");
-  }
 }
 
 export default FormatUtils;

app/assets/javascripts/libs/utils.js

@@ -503,6 +503,28 @@ const Utils = {
     // Big endian
     return [a, b, g, r];
   },
+
+  async promiseAllWithErrors<T>(
+    promises: Array<Promise<T>>,
+  ): Promise<{ successes: Array<T>, errors: Array<Error> }> {
+    const successOrErrorObjects = await Promise.all(promises.map(p => p.catch(error => error)));
+    return successOrErrorObjects.reduce(
+      ({ successes, errors }, successOrError) => {
+        if (successOrError instanceof Error) {
+          return {
+            successes,
+            errors: errors.concat([successOrError]),
+          };
+        } else {
+          return {
+            successes: successes.concat([successOrError]),
+            errors,
+          };
+        }
+      },
+      { successes: [], errors: [] },
+    );
+  },
 };
 
 export default Utils;

app/assets/javascripts/messages.js

@@ -48,6 +48,8 @@ In order to restore the current window, a reload is necessary.`,
   "tracing.delete_tree_with_initial_node":
     "This tree contains the initial node. Do you really want to delete the whole tree?",
   "tracing.merged": "Merging successfully done",
+  "tracing.merged_with_redirect":
+    "Merging successfully done. You will be redirected to the new annotation.",
   "tracing.tree_viewer_no_cyclic_trees":
     "Cyclic trees are not supported by the abstract tree viewer.",
   "tracing.changed_move_value": "The move value was changed to: ",
@@ -148,6 +150,9 @@ In order to restore the current window, a reload is necessary.`,
     "NML contains <edge ...> with same source and target id: Edge",
   "nml.tree_not_connected": "NML contains tree that is not fully connected: Tree with id",
   "nml.different_dataset": "Imported NML was originally for a different dataset.",
+  "merge.different_dataset":
+    "The merge cannot be executed, because the underlying datasets are not the same.",
+  "merge.volume_unsupported": "Merging is not supported for volume tracings.",
   "users.is_admin":
     "At least one of the selected users is an admin of this organization and already has access to all teams. No team assignments are necessary for this user.",
   "users.grant_admin_rights_title": "Do you really want to grant admin rights?",

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

@@ -17,6 +17,7 @@ import {
   setActiveNodeAction,
   createCommentAction,
   deleteNodeAction,
+  deleteTreeAction,
   setNodeRadiusAction,
   setTreeNameAction,
 } from "oxalis/model/actions/skeletontracing_actions";
@@ -161,6 +162,11 @@ class TracingApi {
     Store.dispatch(deleteNodeAction(nodeId, treeId));
   }
 
+  deleteTree(treeId: number) {
+    assertSkeleton(Store.getState().tracing);
+    Store.dispatch(deleteTreeAction(treeId));
+  }
+
   /**
    * Sets the comment for a node.
    *

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

@@ -10,6 +10,7 @@ import type { ViewModeActionType } from "oxalis/model/actions/view_mode_actions"
 import type { AnnotationActionTypes } from "oxalis/model/actions/annotation_actions";
 import type { FlycamActionType } from "oxalis/model/actions/flycam_actions";
 import type { UserActionType } from "oxalis/model/actions/user_actions";
+import type { UiActionType } from "oxalis/model/actions/ui_actions";
 
 export type ActionType =
   | SkeletonTracingActionType
@@ -20,7 +21,8 @@ export type ActionType =
   | ViewModeActionType
   | AnnotationActionTypes
   | FlycamActionType
-  | UserActionType;
+  | UserActionType
+  | UiActionType;
 
 export const wkReadyAction = () => ({
   type: "WK_READY",

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

@@ -0,0 +1,16 @@
+// @flow
+/* eslint-disable import/prefer-default-export */
+
+type SetDropzoneModalVisibilityActionType = {
+  type: "SET_DROPZONE_MODAL_VISIBILITY_ACTION_TYPE",
+  visible: boolean,
+};
+
+export type UiActionType = SetDropzoneModalVisibilityActionType;
+
+export const setDropzoneModalVisibilityAction = (
+  visible: boolean,
+): SetDropzoneModalVisibilityActionType => ({
+  type: "SET_DROPZONE_MODAL_VISIBILITY_ACTION_TYPE",
+  visible,
+});