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This commit is contained in:
Dannon Baker
2019-04-30 16:41:42 -04:00
parent ce85dbc906
commit 78d0c1eb31
130 changed files with 505 additions and 505 deletions
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client/galaxy/scripts/admin.toolshed.js
+1 -1
View File
@@ -55,7 +55,7 @@ var GalaxyAdminToolshedApp = Backbone.View.extend({
},
initialize: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.admintoolshedapp = this;
this.admin_toolshed_router = new AdminToolshedRouter();
client/galaxy/scripts/app/galaxy.js
+2 -2
View File
@@ -53,7 +53,7 @@ GalaxyApp.prototype._init = function(options, bootstrapped) {
// Patch if this galaxy instance is replacing an existing one
// _patchGalaxy depends on options.patchExisting
// TODO: rethink this behavior
let existingGalaxy = getGalaxyInstance();
const existingGalaxy = getGalaxyInstance();
if (existingGalaxy) {
self._patchGalaxy(existingGalaxy);
}
@@ -212,7 +212,7 @@ GalaxyApp.prototype._initUserLocale = function _initUserLocale(options) {
? "__root"
: (navigator.language || navigator.userLanguage || "__root").toLowerCase();
let locale = user_locale || global_locale || nav_locale;
const locale = user_locale || global_locale || nav_locale;
sessionStorage.setItem("currentLocale", locale);
};
client/galaxy/scripts/app/singleton.js
+3 -3
View File
@@ -9,7 +9,7 @@ import { serverPath } from "utils/serverPath";
export function setGalaxyInstance(factory) {
console.warn("setGalaxyInstance", serverPath());
let storage = getStorage();
const storage = getStorage();
let newInstance = factory(GalaxyApp);
if (!(newInstance instanceof GalaxyApp)) {
newInstance = new GalaxyApp(newInstance);
@@ -24,12 +24,12 @@ export function setGalaxyInstance(factory) {
}
export function getGalaxyInstance() {
let storage = getStorage();
const storage = getStorage();
return storage._galaxyInstance;
}
export function galaxyIsInitialized() {
let instance = getGalaxyInstance();
const instance = getGalaxyInstance();
return instance !== null;
}
client/galaxy/scripts/bundleEntries.js
+3 -3
View File
@@ -54,14 +54,14 @@ export function library(options) {
}
export function multiHistory(options) {
let histories = new HistoryCollection([], {
const histories = new HistoryCollection([], {
includeDeleted: options.includingDeleted,
order: options.order,
limitOnFirstFetch: options.limit,
limitPerFetch: options.limit,
currentHistoryId: options.current_history_id
});
let multipanel = new MultiPanel.MultiPanelColumns({
const multipanel = new MultiPanel.MultiPanelColumns({
el: $("#center").get(0),
histories: histories
});
@@ -88,7 +88,7 @@ export function chart(options) {
return new Client(options);
}
export let chartUtilities = {
export const chartUtilities = {
Datasets: Datasets,
Jobs: Jobs,
Series: Series
client/galaxy/scripts/components/DataDialog/model.js
+1 -1
View File
@@ -10,7 +10,7 @@ export class Model {
if (!this.multiple) {
this.values = {};
}
let key = record && record.id;
const key = record && record.id;
if (key) {
if (!this.values[key]) {
this.values[key] = record;
client/galaxy/scripts/components/DataDialog/services.js
+5 -5
View File
@@ -12,7 +12,7 @@ export class Services {
axios
.get(url)
.then(response => {
let items = this.getItems(response.data);
const items = this.getItems(response.data);
resolve(items);
})
.catch(e => {
@@ -27,10 +27,10 @@ export class Services {
/** Returns the formatted results **/
getItems(data) {
let items = [];
let stack = [data];
const items = [];
const stack = [data];
while (stack.length > 0) {
let root = stack.pop();
const root = stack.pop();
if (Array.isArray(root)) {
root.forEach(element => {
stack.push(element);
@@ -40,7 +40,7 @@ export class Services {
} else if (root.object) {
stack.push(root.object);
} else {
let record = this.getRecord(root);
const record = this.getRecord(root);
if (record) {
items.push(record);
}
client/galaxy/scripts/components/DataDialog/utilities.js
+1 -1
View File
@@ -11,7 +11,7 @@ export class UrlTracker {
this.navigation.push(url);
} else {
this.navigation.pop();
let navigationLength = this.navigation.length;
const navigationLength = this.navigation.length;
if (navigationLength > 0) {
url = this.navigation[navigationLength - 1];
} else {
client/galaxy/scripts/components/Masthead/initMasthead.js
+1 -1
View File
@@ -7,7 +7,7 @@ import Masthead from "components/Masthead";
export function initMasthead(config, container) {
console.log("initMasthead");
let Component = Vue.extend(Masthead);
const Component = Vue.extend(Masthead);
return new Component({
props: Object.keys(config),
propsData: config,
client/galaxy/scripts/components/Tags/backboneTagService.js
+2 -2
View File
@@ -12,7 +12,7 @@ export class BackboneTagService extends TagService {
}
async save(rawTag) {
let tag = createTag(rawTag);
const tag = createTag(rawTag);
if (!tag.valid) {
throw new Error("Invalid tag");
}
@@ -27,7 +27,7 @@ export class BackboneTagService extends TagService {
}
async delete(rawTag) {
let tag = createTag(rawTag);
const tag = createTag(rawTag);
let tags = new Set(this.model.attributes.tags);
tags.delete(tag.text);
client/galaxy/scripts/components/Tags/model.js
+4 -4
View File
@@ -21,9 +21,9 @@ function TagModel(props = {}) {
enumerable: true,
get: function() {
if (this.text.startsWith("name:")) {
let { primary, contrasting, darker } = keyedColorScheme(this.text);
const { primary, contrasting, darker } = keyedColorScheme(this.text);
let styles = {
const styles = {
"background-color": primary,
color: contrasting,
"border-color": darker
@@ -82,7 +82,7 @@ export function createTag(data) {
// Returns tags in "newTags" that aren't present in "existingTags"
export const diffTags = (newTags, existingTags) => {
let newModels = newTags.map(createTag);
let existingModels = existingTags.map(createTag);
const newModels = newTags.map(createTag);
const existingModels = existingTags.map(createTag);
return newModels.filter(tag => !existingModels.some(st => st.equals(tag)));
};
client/galaxy/scripts/components/Tags/mounts.js
+11 -11
View File
@@ -14,17 +14,17 @@ import { BackboneTagService } from "./backboneTagService";
* by the tagging_common.mako file
*/
export const mountMakoTags = (options = {}, el) => {
let { id, itemClass, tags = [], disabled = false, context = "unspecified" } = options;
const { id, itemClass, tags = [], disabled = false, context = "unspecified" } = options;
let propData = {
const propData = {
storeKey: `${itemClass}-${id}`,
tagService: new TagService({ id, itemClass, context }),
tags,
disabled
};
let fn = mountVueComponent(Tags);
let vm = fn(propData, el);
const fn = mountVueComponent(Tags);
const vm = fn(propData, el);
vm.$on("tag-click", makoClickHandler(options, vm));
return vm;
};
@@ -40,15 +40,15 @@ const makoClickHandler = (options, vm) =>
return;
}
let { tagClickFn = "none", clickUrl } = options;
const { tagClickFn = "none", clickUrl } = options;
switch (tagClickFn) {
// I made this match the existing behavior, but I am not clear on
// the reason why this link redirects to a raw json page
case "community_tag_click":
if (undefined !== clickUrl) {
let suffix = tag.value ? `:${tag.value}` : "";
let href = `${clickUrl}?f-tags=${tag.text}${suffix}`;
const suffix = tag.value ? `:${tag.value}` : "";
const href = `${clickUrl}?f-tags=${tag.text}${suffix}`;
redirectToUrl(href);
}
break;
@@ -63,22 +63,22 @@ const makoClickHandler = (options, vm) =>
* Mount function when a backbone model is provided.
*/
export const mountModelTags = (options = {}, el) => {
let { model, disabled = false, context = "unspecified" } = options;
const { model, disabled = false, context = "unspecified" } = options;
if (!model) {
console.warn("Missing model in mountModelTags");
return;
}
let { id, model_class: itemClass, tags = [] } = model.attributes;
const { id, model_class: itemClass, tags = [] } = model.attributes;
let propData = {
const propData = {
storeKey: `${itemClass}-${id}`,
tagService: new BackboneTagService({ id, itemClass, context, model }),
tags,
disabled
};
let fn = mountVueComponent(Tags);
const fn = mountVueComponent(Tags);
return fn(propData, el);
};
client/galaxy/scripts/components/Tags/tagService.js
+11 -11
View File
@@ -52,13 +52,13 @@ export class TagService {
* @returns Promise yielding new tag model
*/
async save(rawTag) {
let { id, itemClass, context } = this;
let tag = createTag(rawTag);
const { id, itemClass, context } = this;
const tag = createTag(rawTag);
if (!tag.valid) {
throw new Error("Invalid tag");
}
let url = `/tag/add_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&new_tag=${tag.text}`;
let response = await axios.get(url);
const url = `/tag/add_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&new_tag=${tag.text}`;
const response = await axios.get(url);
if (response.status !== 200) {
throw new Error(`Unable to save tag: ${tag}`);
}
@@ -71,10 +71,10 @@ export class TagService {
* @returns Promise yielding deleted tag model
*/
async delete(rawTag) {
let { id, itemClass, context } = this;
let tag = createTag(rawTag);
let url = `/tag/remove_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&tag_name=${tag.text}`;
let response = await axios.get(url);
const { id, itemClass, context } = this;
const tag = createTag(rawTag);
const url = `/tag/remove_tag_async?item_id=${id}&item_class=${itemClass}&context=${context}&tag_name=${tag.text}`;
const response = await axios.get(url);
if (response.status !== 200) {
throw new Error(`Unable to delete tag: ${tag}`);
}
@@ -87,9 +87,9 @@ export class TagService {
* @returns Promise yielding an array of tag models
*/
async autocomplete(searchText) {
let { id, itemClass } = this;
let url = `/tag/tag_autocomplete_data?item_id=${id}&item_class=${itemClass}&q=${searchText}`;
let response = await axios.get(url);
const { id, itemClass } = this;
const url = `/tag/tag_autocomplete_data?item_id=${id}&item_class=${itemClass}&q=${searchText}`;
const response = await axios.get(url);
if (response.status !== 200) {
throw new Error(`Unable to retrieve autocomplete tags for search string: ${searchText}`);
}
client/galaxy/scripts/components/admin/AdminServices.js
+3 -3
View File
@@ -2,16 +2,16 @@ import { getAppRoot } from "onload/loadConfig";
import axios from "axios";
export function getErrorStack() {
let url = `${getAppRoot()}api/tools/error_stack`;
const url = `${getAppRoot()}api/tools/error_stack`;
return axios.get(url);
}
export function getDisplayApplications() {
let url = `${getAppRoot()}api/display_applications`;
const url = `${getAppRoot()}api/display_applications`;
return axios.get(url);
}
export function reloadDisplayApplications(ids) {
let url = `${getAppRoot()}api/display_applications/reload`;
const url = `${getAppRoot()}api/display_applications/reload`;
return axios.post(url, { ids: ids });
}
client/galaxy/scripts/entry/admin/AdminRouter.js
+9 -9
View File
@@ -15,7 +15,7 @@ import DisplayApplications from "components/admin/DisplayApplications.vue";
import Vue from "vue";
export const getAdminRouter = (Galaxy, options) => {
let galaxyRoot = getAppRoot();
const galaxyRoot = getAppRoot();
return Router.extend({
routes: {
@@ -38,7 +38,7 @@ export const getAdminRouter = (Galaxy, options) => {
},
authenticate: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
return Galaxy.user && Galaxy.user.id && Galaxy.user.get("is_admin");
},
@@ -57,8 +57,8 @@ export const getAdminRouter = (Galaxy, options) => {
},
show_users_create: function() {
let instance = Vue.extend(Register);
let vm = document.createElement("div");
const instance = Vue.extend(Register);
const vm = document.createElement("div");
this.page.display(vm);
new instance({
propsData: {
@@ -91,7 +91,7 @@ export const getAdminRouter = (Galaxy, options) => {
},
_show_grid_view: function(urlSuffix) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.page.display(
new GridView({
url_base: `${galaxyRoot}${urlSuffix}`,
@@ -101,8 +101,8 @@ export const getAdminRouter = (Galaxy, options) => {
},
_display_vue_helper: function(component, props) {
let instance = Vue.extend(component);
let vm = document.createElement("div");
const instance = Vue.extend(component);
const vm = document.createElement("div");
this.page.display(vm);
new instance(props).$mount(vm);
},
@@ -124,9 +124,9 @@ export const getAdminRouter = (Galaxy, options) => {
},
show_data_manager: function(path) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
console.log("show_data_manager");
let vueMount = document.createElement("div");
const vueMount = document.createElement("div");
this.page.display(vueMount);
// always set the route back to the base, i.e.
// `${galaxyRoot}admin/data_manager`
client/galaxy/scripts/entry/admin/index.js
+1 -1
View File
@@ -11,7 +11,7 @@ addInitialization((Galaxy, { options }) => {
active_view: "admin"
});
let pageOptions = Object.assign({}, options, {
const pageOptions = Object.assign({}, options, {
Left: AdminPanel,
Router: getAdminRouter(Galaxy, options)
});
client/galaxy/scripts/entry/analysis/AnalysisRouter.js
+7 -7
View File
@@ -78,13 +78,13 @@ export const getAnalysisRouter = Galaxy =>
require_login: ["show_user", "show_user_form", "show_workflows"],
authenticate: function(args, name) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
return (Galaxy.user && Galaxy.user.id) || this.require_login.indexOf(name) == -1;
},
_display_vue_helper: function(component, props) {
let instance = Vue.extend(component);
let vm = document.createElement("div");
const instance = Vue.extend(component);
const vm = document.createElement("div");
this.page.display(vm);
new instance(props).$mount(vm);
},
@@ -102,7 +102,7 @@ export const getAnalysisRouter = Galaxy =>
},
show_user_form: function(form_id) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var model = new UserPreferences.Model({
user_id: Galaxy.params.id
});
@@ -165,14 +165,14 @@ export const getAnalysisRouter = Galaxy =>
},
show_history_structure: function() {
let displayStructureInstance = Vue.extend(DisplayStructure);
let vm = document.createElement("div");
const displayStructureInstance = Vue.extend(DisplayStructure);
const vm = document.createElement("div");
this.page.display(vm);
new displayStructureInstance({ propsData: { id: QueryStringParsing.get(" id: ") } }).$mount(vm);
},
show_histories: function(action_id) {
let view = new HistoryList.View({ action_id: action_id });
const view = new HistoryList.View({ action_id: action_id });
this.page.display(view);
},
client/galaxy/scripts/entry/analysis/index.js
+1 -1
View File
@@ -7,7 +7,7 @@ import Page from "layout/page";
addInitialization((Galaxy, { options = {} }) => {
console.log("Analysis custom page setup");
let pageOptions = Object.assign({}, options, {
const pageOptions = Object.assign({}, options, {
config: Object.assign({}, options.config, {
hide_panels: Galaxy.params.hide_panels,
hide_masthead: Galaxy.params.hide_masthead
client/galaxy/scripts/entry/panels/tool-panel.js
+5 -5
View File
@@ -11,8 +11,8 @@ import Buttons from "mvc/ui/ui-buttons";
var ToolPanel = Backbone.View.extend({
initialize: function(page, options) {
let Galaxy = getGalaxyInstance();
let appRoot = getAppRoot();
const Galaxy = getGalaxyInstance();
const appRoot = getAppRoot();
// access configuration options
var config = options.config;
@@ -96,7 +96,7 @@ var ToolPanel = Backbone.View.extend({
/** build a link to one tool */
_templateTool: function(tool) {
let appRoot = getAppRoot();
const appRoot = getAppRoot();
return `<div class="toolTitle">
<a href="${appRoot}${tool.href}" target="galaxy_main">
${tool.title}
@@ -106,7 +106,7 @@ var ToolPanel = Backbone.View.extend({
/** build a link to 'All Workflows' */
_templateAllWorkflow: function(tool) {
let appRoot = getAppRoot();
const appRoot = getAppRoot();
return `<div class="toolTitle">
<a href="${appRoot}${tool.href}">
${tool.title}
@@ -116,7 +116,7 @@ var ToolPanel = Backbone.View.extend({
/** build links to workflows in toolpanel */
_templateWorkflowLink: function(wf) {
let appRoot = getAppRoot();
const appRoot = getAppRoot();
return `<div class="toolTitle">
<a class="${wf.cls}" href="${appRoot}${wf.href}">
${_.escape(wf.title)}
client/galaxy/scripts/galaxy.library.js
+1 -1
View File
@@ -110,7 +110,7 @@ var GalaxyLibrary = Backbone.View.extend({
initialize: function() {
// This should go upstream in the js app once available
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.config.ga_code) {
((i, s, o, g, r, a, m) => {
i["GoogleAnalyticsObject"] = r;
client/galaxy/scripts/galaxy.pages.js
+3 -3
View File
@@ -327,7 +327,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
url_base: item_info.list_ajax_url,
embedded: true
});
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.modal.show({
title: `Insert Link to ${item_info.singular}`,
body: $("<div/>")
@@ -416,11 +416,11 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
break;
}
let grid = new GridView({
const grid = new GridView({
url_base: item_info.list_ajax_url,
embedded: true
});
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.modal.show({
title: `Insert Link to ${item_info.singular}`,
body: $("<div/>")
client/galaxy/scripts/layout/communication-server-view.js
+1 -1
View File
@@ -13,7 +13,7 @@ export var CommunicationServerView = Backbone.View.extend({
/** makes bootstrap modal and iframe inside it */
makeModalIframe: function(e) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// make modal
var host = Galaxy.config.communication_server_host;
client/galaxy/scripts/layout/data.js
+4 -4
View File
@@ -10,8 +10,8 @@ export default class Data {
* @param {function} callback - Result function called with selection
*/
dialog(callback, options = {}) {
let galaxy = getGalaxyInstance();
let host = `${window.location.protocol}//${window.location.hostname}:${window.location.port}`;
const galaxy = getGalaxyInstance();
const host = `${window.location.protocol}//${window.location.hostname}:${window.location.port}`;
Object.assign(options, {
callback: callback,
history: galaxy.currHistoryPanel && galaxy.currHistoryPanel.model.id,
@@ -30,8 +30,8 @@ export default class Data {
* Creates a history dataset by submitting an upload request
*/
create(options) {
let Galaxy = getGalaxyInstance();
let history_panel = Galaxy.currHistoryPanel;
const Galaxy = getGalaxyInstance();
const history_panel = Galaxy.currHistoryPanel;
let history_id = options.history_id;
if (!history_id && history_panel) {
history_id = history_panel.model.get("id");
client/galaxy/scripts/layout/masthead.js
+1 -1
View File
@@ -8,7 +8,7 @@ import { getGalaxyInstance } from "app";
/** Masthead **/
var View = Backbone.View.extend({
initialize: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var self = this;
this.options = options;
client/galaxy/scripts/layout/menu.js
+7 -7
View File
@@ -11,9 +11,9 @@ import Webhooks from "mvc/webhooks";
import Utils from "utils/utils";
function logoutClick() {
let galaxy = getGalaxyInstance();
let session_csrf_token = galaxy.session_csrf_token;
let url = `${galaxy.root}user/logout?session_csrf_token=${session_csrf_token}`;
const galaxy = getGalaxyInstance();
const session_csrf_token = galaxy.session_csrf_token;
const url = `${galaxy.root}user/logout?session_csrf_token=${session_csrf_token}`;
axios.get(url).then(() => {
if (galaxy.user) {
galaxy.user.clearSessionStorage();
@@ -33,7 +33,7 @@ var Collection = Backbone.Collection.extend({
options = options || {};
this.reset();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
//
// Chat server tab
@@ -141,7 +141,7 @@ var Collection = Backbone.Collection.extend({
};
// Galaxy.page is undefined for data libraries, workflows pages
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.page) {
Galaxy.page.masthead.collection.add(obj);
} else if (Galaxy.masthead) {
@@ -403,7 +403,7 @@ var Tab = Backbone.View.extend({
if (options.onclick) {
options.onclick();
} else {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (options.target == "__use_router__" && typeof Galaxy.page != "undefined") {
Galaxy.page.router.executeUseRouter(options.url);
} else {
@@ -442,7 +442,7 @@ var Tab = Backbone.View.extend({
if (model.get("onclick")) {
model.get("onclick")();
} else {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (model.attributes.target == "__use_router__" && typeof Galaxy.page != "undefined") {
Galaxy.page.router.executeUseRouter(model.attributes.url);
} else {
client/galaxy/scripts/layout/page.js
+2 -2
View File
@@ -27,7 +27,7 @@ var View = Backbone.View.extend({
});
// attach global objects, build mastheads
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.modal = this.modal = new Modal.View();
Galaxy.router = this.router = options.Router && new options.Router(self, options);
Galaxy.data = this.data = new Data(this);
@@ -190,7 +190,7 @@ var View = Backbone.View.extend({
/** Check if the communication server is online and show the icon otherwise hide the icon */
_checkCommunicationServerOnline: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var host = Galaxy.config.communication_server_host;
var port = Galaxy.config.communication_server_port;
var preferences = Galaxy.user.attributes.preferences;
client/galaxy/scripts/layout/panel.js
+1 -1
View File
@@ -231,7 +231,7 @@ var CenterPanel = Backbone.View.extend({
/** Display a view in the center panel, hide iframe */
display: function(view) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
let contentWindow = this.$frame[0].contentWindow || {};
let message;
try {
client/galaxy/scripts/layout/router.js
+4 -4
View File
@@ -14,7 +14,7 @@ var Router = Backbone.Router.extend({
},
executeUseRouter: function(url) {
let prefix = getAppRoot();
const prefix = getAppRoot();
if (url.startsWith(prefix)) {
url = url.replace(prefix, "/");
}
@@ -28,9 +28,9 @@ var Router = Backbone.Router.extend({
.toString(36)
.substr(2);
url += url.indexOf("?") == -1 ? "?" : "&";
let bustParam = $.param(data, true);
const bustParam = $.param(data, true);
url += bustParam;
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.params = data;
this.navigate(url, { trigger: true });
window.history.replaceState(window.history.state, "", window.location.pathname.replace(bustParam, ""));
@@ -38,7 +38,7 @@ var Router = Backbone.Router.extend({
/** override to parse query string into obj and send to each route */
execute: function(callback, args, name) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.debug("router execute:", callback, args, name);
var queryObj = QUERY_STRING.parse(args.pop());
args.push(queryObj);
client/galaxy/scripts/layout/scratchbook.js
+1 -1
View File
@@ -74,7 +74,7 @@ export default Backbone.View.extend({
addDataset: function(dataset_id) {
var self = this;
var current_dataset = null;
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy && Galaxy.currHistoryPanel) {
var history_id = Galaxy.currHistoryPanel.collection.historyId;
this.history_cache[history_id] = {
client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
+4 -4
View File
@@ -28,14 +28,14 @@ var ControlledFetchCollection = Backbone.Collection.extend({
*/
fetch: function(options) {
options = this._buildFetchOptions(options);
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.debug("fetch options:", options);
return Backbone.Collection.prototype.fetch.call(this, options);
},
/** build ajax data/parameters from options */
_buildFetchOptions: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// note: we normally want options passed in to override the defaults built here
// so most of these fns will generate defaults
@@ -271,7 +271,7 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
/** fetch the first 'page' of data */
fetchFirst: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.debug("ControlledFetchCollection.fetchFirst:", options);
options = options ? _.clone(options) : {};
this.allFetched = false;
@@ -286,7 +286,7 @@ var InfinitelyScrollingCollection = ControlledFetchCollection.extend({
/** fetch the next page of data */
fetchMore: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.debug("ControlledFetchCollection.fetchMore:", options);
options = _.clone(options || {});
client/galaxy/scripts/mvc/collection/collection-view-edit.js
+6 -6
View File
@@ -49,7 +49,7 @@ var CollectionViewEdit = _super.extend(
}
// anon users shouldn't have access to any of the following
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (!Galaxy.user || Galaxy.user.isAnonymous()) {
return;
}
@@ -78,22 +78,22 @@ var CollectionViewEdit = _super.extend(
}
});
let el = $where.find(".tags-display")[0];
let propsData = {
const el = $where.find(".tags-display")[0];
const propsData = {
model: this.model,
disabled: false,
context: "collection-view-edit"
};
let vm = mountModelTags(propsData, el);
const vm = mountModelTags(propsData, el);
let toggleEditor = () => {
const toggleEditor = () => {
$(vm.$el).toggleClass("active");
this.tagsEditorShown = $(vm.$el).hasClass("active");
};
if (this.tagsEditorShown) {
let editorIsOpen = $(vm.$el).hasClass("active");
const editorIsOpen = $(vm.$el).hasClass("active");
if (!editorIsOpen) {
toggleEditor();
}
client/galaxy/scripts/mvc/collection/list-collection-creator.js
+1 -1
View File
@@ -1011,7 +1011,7 @@ var ListCollectionCreator = Backbone.View.extend(BASE_MVC.LoggableMixin)
const collectionCreatorModalSetup = function _collectionCreatorModalSetup(options) {
const deferred = jQuery.Deferred();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
const modal = Galaxy.modal || new UI_MODAL.View();
const creatorOptions = _.defaults(options || {}, {
client/galaxy/scripts/mvc/dataset/data.js
+1 -1
View File
@@ -405,7 +405,7 @@ var TabularButtonTracksterView = Backbone.View.extend({
// backbone initialize
initialize: function(options) {
// check if environment is available
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// link galaxy modal or create one
if (Galaxy && Galaxy.modal) {
client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
+2 -2
View File
@@ -12,7 +12,7 @@ import Form from "mvc/form/form-view";
var View = Backbone.View.extend({
initialize: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.setElement("<div/>");
this.model = new Backbone.Model({
dataset_id: Galaxy.params.dataset_id
@@ -214,7 +214,7 @@ var View = Backbone.View.extend({
/** reload Galaxy's history after updating dataset's attributes */
_reloadHistory: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy) {
Galaxy.currHistoryPanel.loadCurrentHistory();
}
client/galaxy/scripts/mvc/dataset/dataset-error.js
+3 -3
View File
@@ -11,7 +11,7 @@ import Form from "mvc/form/form-view";
/** Dataset edit attributes view */
var View = Backbone.View.extend({
initialize: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.setElement("<div/>");
this.model = new Backbone.Model({
dataset_id: Galaxy.params.dataset_id
@@ -132,7 +132,7 @@ var View = Backbone.View.extend({
var message = "<h3>Error Details</h3>";
if (job_messages) {
message += "<p>Execution resulted in the following messages:</p>";
for (let job_message of job_messages) {
for (const job_message of job_messages) {
message += `<p><pre>${_.escape(job_message["desc"])}</pre></p>`;
}
}
@@ -172,7 +172,7 @@ var View = Backbone.View.extend({
/** Convert tab template */
_getBugFormTemplate: function(dataset, job) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var inputs = [
{
help: _l("Your email address"),
client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
+13 -13
View File
@@ -63,7 +63,7 @@ var DatasetListItemEdit = _super.extend(
faIcon: "fa-pencil",
classes: "edit-btn",
onclick: function(ev) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.router) {
ev.preventDefault();
Galaxy.router.push("datasets/edit", {
@@ -164,7 +164,7 @@ var DatasetListItemEdit = _super.extend(
});
};
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.user.id === null) {
return null;
}
@@ -226,7 +226,7 @@ var DatasetListItemEdit = _super.extend(
classes: "report-error-btn",
faIcon: "fa-bug",
onclick: function(ev) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.router) {
ev.preventDefault();
Galaxy.router.push("datasets/error", {
@@ -248,7 +248,7 @@ var DatasetListItemEdit = _super.extend(
target: this.linkTarget,
faIcon: "fa-refresh",
onclick: function(ev) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.router) {
ev.preventDefault();
Galaxy.router.push("/", {
@@ -273,15 +273,15 @@ var DatasetListItemEdit = _super.extend(
}
if (visualizations.length >= 1) {
let dsid = this.model.get("id");
let url = getAppRoot() + "visualizations?dataset_id=" + dsid;
const dsid = this.model.get("id");
const url = getAppRoot() + "visualizations?dataset_id=" + dsid;
return faIconButton({
title: _l("Visualize this data"),
href: url,
classes: "visualization-link",
faIcon: "fa-bar-chart-o",
onclick: ev => {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.frame && Galaxy.frame.active) {
ev.preventDefault();
Galaxy.frame.add({ url: url, title: "Visualization" });
@@ -303,24 +303,24 @@ var DatasetListItemEdit = _super.extend(
return;
}
let el = $where.find(".tags-display")[0];
const el = $where.find(".tags-display")[0];
let propsData = {
const propsData = {
model: this.model,
disabled: false,
context: "dataset-li-edit"
};
let vm = mountModelTags(propsData, el);
const vm = mountModelTags(propsData, el);
// tag icon button open/closes
let activator = faIconButton({
const activator = faIconButton({
title: _l("Edit dataset tags"),
classes: "tag-btn",
faIcon: "fa-tags"
}).appendTo($where.find(".actions .right"));
let toggleEditor = () => {
const toggleEditor = () => {
$(vm.$el).toggleClass("active");
this.tagsEditorShown = $(vm.$el).hasClass("active");
};
@@ -328,7 +328,7 @@ var DatasetListItemEdit = _super.extend(
activator.on("click", toggleEditor);
if (this.tagsEditorShown) {
let editorIsOpen = $(vm.$el).hasClass("active");
const editorIsOpen = $(vm.$el).hasClass("active");
if (!editorIsOpen) {
toggleEditor();
}
client/galaxy/scripts/mvc/dataset/dataset-li.js
+6 -6
View File
@@ -45,15 +45,15 @@ export var DatasetListItemView = _super.extend(
// mount new vue component for tags
render: function() {
let result = _super.prototype.render.apply(this, arguments);
const result = _super.prototype.render.apply(this, arguments);
this._mountVueNametags();
return result;
},
_mountVueNametags: function() {
let container = this.$(".nametags")[0];
let { id, model_class, tags } = this.model.attributes;
let storeKey = `${model_class}-${id}`;
const container = this.$(".nametags")[0];
const { id, model_class, tags } = this.model.attributes;
const storeKey = `${model_class}-${id}`;
mountNametags({ storeKey, tags }, container);
},
@@ -181,7 +181,7 @@ export var DatasetListItemView = _super.extend(
// add frame manager option onclick event
var self = this;
displayBtnData.onclick = ev => {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.frame && Galaxy.frame.active) {
// Add dataset to frames.
Galaxy.frame.addDataset(self.model.get("id"));
@@ -279,7 +279,7 @@ export var DatasetListItemView = _super.extend(
target: this.linkTarget,
faIcon: "fa-info-circle",
onclick: function(ev) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.frame && Galaxy.frame.active) {
Galaxy.frame.add({
title: _l("Dataset details"),
client/galaxy/scripts/mvc/form/form-data.js
+1 -1
View File
@@ -214,7 +214,7 @@ export var visitInputs = (inputs, callback, prefix, context) => {
}
});
for (var key in inputs) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var node = inputs[key];
node.name = node.name || key;
var name = prefix ? `${prefix}|${node.name}` : node.name;
client/galaxy/scripts/mvc/form/form-parameters.js
+1 -1
View File
@@ -42,7 +42,7 @@ export default Backbone.Model.extend({
/** Returns an input field for a given field type */
create: function(input_def) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var fieldClass = this.types[input_def.type];
var field = typeof this[fieldClass] === "function" ? this[fieldClass].call(this, input_def) : null;
if (!field) {
client/galaxy/scripts/mvc/form/form-repeat.js
+2 -2
View File
@@ -42,7 +42,7 @@ export var View = Backbone.View.extend({
/** Add new repeat block */
add: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (!options.id || this.list[options.id]) {
Galaxy.emit.debug("form-repeat::add()", "Duplicate or invalid repeat block id.");
return;
@@ -75,7 +75,7 @@ export var View = Backbone.View.extend({
/** Delete repeat block */
del: function(id) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (!this.list[id]) {
Galaxy.emit.debug("form-repeat::del()", "Invalid repeat block id.");
return;
client/galaxy/scripts/mvc/form/form-view.js
+2 -2
View File
@@ -33,7 +33,7 @@ export default Backbone.View.extend({
if (field.update) {
field.update(node);
field.trigger("change");
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.emit.debug("form-view::update()", `Updating input: ${input_id}`);
}
});
@@ -157,7 +157,7 @@ export default Backbone.View.extend({
message: options.message
});
}
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.emit.debug("form-view::initialize()", "Completed");
}
});
client/galaxy/scripts/mvc/grid/grid-shared.js
+1 -1
View File
@@ -10,7 +10,7 @@ import LoadingIndicator from "ui/loading-indicator";
var View = Backbone.View.extend({
initialize: function(options) {
var self = this;
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
LoadingIndicator.markViewAsLoading(this);
this.model = new Backbone.Model(options);
this.item = this.model.get("item");
client/galaxy/scripts/mvc/grid/grid-template.js
+12 -12
View File
@@ -67,7 +67,7 @@ export default {
'<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li>' +
'<div popupmenu="popup-global-actions">';
}
for (let action of options.global_actions) {
for (const action of options.global_actions) {
tmpl += `<li><a class="action-button use-target" target="${action.target}" href="${
action.url_args
}" onclick="return false;" >${action.label}</a></li>`;
@@ -106,7 +106,7 @@ export default {
}
// create header elements
for (let column of options.columns) {
for (const column of options.columns) {
if (column.visible) {
tmpl += `<th id="${column.key}-header">`;
if (column.sortable) {
@@ -140,7 +140,7 @@ export default {
}
// create rows
for (let item of options.items) {
for (const item of options.items) {
// Tag current
tmpl += "<tr ";
if (options.current_item_id == item.id) {
@@ -156,7 +156,7 @@ export default {
}
// Data columns
for (let column of options.columns) {
for (const column of options.columns) {
if (column.visible) {
// Nowrap
var nowrap = "";
@@ -302,7 +302,7 @@ export default {
`;
// configure buttons for operations
for (let operation of options.operations) {
for (const operation of options.operations) {
if (operation.allow_multiple) {
tmpl += `<input type="button" value="${
operation.label
@@ -316,7 +316,7 @@ export default {
// count global operations
var found_global = false;
for (let operation of options.operations) {
for (const operation of options.operations) {
if (operation.global_operation) {
found_global = true;
break;
@@ -326,7 +326,7 @@ export default {
// add global operations
if (found_global) {
tmpl += "<tr>" + '<td colspan="100">';
for (let operation of options.operations) {
for (const operation of options.operations) {
if (operation.global_operation) {
tmpl += `<a class="action-button" href="${operation.global_operation}">${operation.label}</a>`;
}
@@ -368,7 +368,7 @@ export default {
// identify columns with advanced filtering
var show_advanced_search_link = false;
for (let column of options.columns) {
for (const column of options.columns) {
if (column.filterable == "advanced") {
var column_key = column.key;
var f_key = filters[column_key];
@@ -392,7 +392,7 @@ export default {
var tmpl = `<div id="standard-search" style="display: ${standard_search_display};"><table><tr><td style="padding: 0;"><table>`;
// add standard filters
for (let column of options.columns) {
for (const column of options.columns) {
if (column.filterable == "standard") {
tmpl += this.grid_column_filter(options, column);
}
@@ -415,7 +415,7 @@ export default {
tmpl += `<div id="advanced-search" style="display: ${advanced_search_display}; margin-top: 5px;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>`;
// add advanced filters
for (let column of options.columns) {
for (const column of options.columns) {
if (column.filterable == "advanced") {
tmpl += this.grid_column_filter(options, column);
}
@@ -448,7 +448,7 @@ export default {
if (column.is_text) {
tmpl += `<form class="text-filter-form" column_key="${column_key}" action="${options.url}" method="get" >`;
// Carry forward filtering criteria with hidden inputs.
for (let column of options.columns) {
for (const column of options.columns) {
var filter_value = filters[column.key];
if (filter_value) {
if (filter_value != "All") {
@@ -480,7 +480,7 @@ export default {
// multiple filter values
if (type == "array") {
for (let i in column_filter) {
for (const i in column_filter) {
// copy filters and remove entry
var params = column_filter;
params = params.slice(i);
client/galaxy/scripts/mvc/grid/grid-view.js
+2 -2
View File
@@ -34,7 +34,7 @@ export default Backbone.View.extend({
store.watch(
state => state.gridSearch.searchTags,
newTags => {
let tagArray = Array.from(newTags);
const tagArray = Array.from(newTags);
self.grid.add_filter("tags", tagArray, false);
self.openAdvancedSearch();
self.render_filter_button("tags", tagArray);
@@ -84,7 +84,7 @@ export default Backbone.View.extend({
handle_refresh: function(refresh_frames) {
if (refresh_frames) {
if ($.inArray("history", refresh_frames) > -1) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy && Galaxy.currHistoryPanel) {
Galaxy.currHistoryPanel.loadCurrentHistory();
}
client/galaxy/scripts/mvc/history/copy-dialog.js
+2 -2
View File
@@ -141,7 +141,7 @@ var CopyDialog = {
}
var originalClosingCallback = options.closing_callback;
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
modal.show(
_.extend(options, {
title: this.title({ name: history.get("name") }),
@@ -229,7 +229,7 @@ var ImportDialog = _.extend({}, CopyDialog, {
* {String} allDatasets default initial checked radio button: 'copy-all' or 'copy-non-deleted',
*/
var historyCopyDialog = (history, options) => {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
options = options || {};
// create our own modal if Galaxy doesn't have one (mako tab without use_panels)
var modal = Galaxy.modal || new MODAL.View({});
client/galaxy/scripts/mvc/history/hdca-li.js
+4 -4
View File
@@ -14,7 +14,7 @@ var HDCAListItemView = _super.extend(
className: `${_super.prototype.className} history-content`,
render: function() {
let result = _super.prototype.render.apply(this, arguments);
const result = _super.prototype.render.apply(this, arguments);
this._mountNametags("initialize");
return result;
},
@@ -36,10 +36,10 @@ var HDCAListItemView = _super.extend(
},
_mountNametags(context) {
let container = this.$el.find(".nametags")[0];
const container = this.$el.find(".nametags")[0];
if (container) {
let { id, model_class, tags } = this.model.attributes;
let storeKey = `${model_class}-${id}`;
const { id, model_class, tags } = this.model.attributes;
const storeKey = `${model_class}-${id}`;
mountNametags({ storeKey, tags }, container);
}
},
client/galaxy/scripts/mvc/history/history-contents.js
+1 -1
View File
@@ -394,7 +394,7 @@ export var HistoryContents = _super.extend(BASE_MVC.LoggableMixin).extend({
progressivelyFetchDetails: function(options) {
// TODO: only fetch tags and annotations if specifically requested
options = options || {};
let deferred = jQuery.Deferred();
const deferred = jQuery.Deferred();
this._recursivelyFetch(
options,
HDA_MODEL.HistoryDatasetAssociation.prototype.searchAttributes.join(","),
client/galaxy/scripts/mvc/history/history-list.js
+3 -3
View File
@@ -32,7 +32,7 @@ var HistoryGridView = GridView.extend({
options.success = req => {
const contentsStates = req.contents_states;
let stateHtml = "";
for (let state of ["ok", "running", "queued", "new", "error"]) {
for (const state of ["ok", "running", "queued", "new", "error"]) {
const stateCount = contentsStates[state];
if (stateCount) {
stateHtml += `<div class="count-box state-color-${state}" title="Datasets in ${state} state">${stateCount}</div> `;
@@ -67,7 +67,7 @@ var HistoryGridView = GridView.extend({
})
.done(() => {
historyCopyDialog(history, {}).done(() => {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy && Galaxy.currHistoryPanel) {
Galaxy.currHistoryPanel.loadCurrentHistory();
}
@@ -89,7 +89,7 @@ var HistoryGridView = GridView.extend({
var View = Backbone.View.extend({
title: _l("Histories"),
initialize: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
LoadingIndicator.markViewAsLoading(this);
if (options.action_id == "list_published") {
client/galaxy/scripts/mvc/history/history-model.js
+1 -1
View File
@@ -138,7 +138,7 @@ export var History = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
* Note: that this will return false for an anon user even if the history is theirs.
*/
ownedByCurrUser: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// no currUser
if (!Galaxy || !Galaxy.user) {
return false;
client/galaxy/scripts/mvc/history/history-view-edit-current.js
+4 -4
View File
@@ -117,7 +117,7 @@ var CurrentHistoryView = _super.extend(
/** loads a history & contents w/ details and makes them the current history */
switchToHistory: function(historyId, attributes) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.user.isAnonymous()) {
this.trigger("error", _l("You must be logged in to switch histories"), _l("Anonymous user"));
return $.when();
@@ -129,7 +129,7 @@ var CurrentHistoryView = _super.extend(
/** creates a new history on the server and sets it as the user's current history */
createNewHistory: function(attributes) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.user.isAnonymous()) {
this.trigger("error", _l("You must be logged in to create histories"), _l("Anonymous user"));
return $.when();
@@ -344,7 +344,7 @@ var CurrentHistoryView = _super.extend(
events: _.extend(_.clone(_super.prototype.events), {
// the two links in the empty message
"click .uploader-link": function(ev) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.upload.show(ev);
},
"click .get-data-link": function(ev) {
@@ -384,7 +384,7 @@ var CurrentHistoryView = _super.extend(
// when the center panel is given a new view, clear the current indicator
"center-panel:load": function(view) {
try {
let hdaId = view.model.attributes.dataset_id || null;
const hdaId = view.model.attributes.dataset_id || null;
if (hdaId === null) {
throw "Invalid id";
}
client/galaxy/scripts/mvc/history/history-view-edit.js
+5 -5
View File
@@ -155,18 +155,18 @@ var HistoryViewEdit = _super.extend(
/** render the tags sub-view controller */
_renderTags: function($where) {
let el = $where.find(".controls .tags-display")[0];
const el = $where.find(".controls .tags-display")[0];
let propsData = {
const propsData = {
model: this.model,
disabled: false,
context: "history-view-edit"
};
let vm = mountModelTags(propsData, el);
const vm = mountModelTags(propsData, el);
// tag icon button open/closes
let activator = faIconButton({
const activator = faIconButton({
title: _l("Edit history tags"),
classes: "history-tag-btn",
faIcon: "fa-tags",
@@ -283,7 +283,7 @@ var HistoryViewEdit = _super.extend(
var xhr = jQuery.ajax(options);
xhr.done((message, status, responseObj) => {
for (let updated of message) {
for (const updated of message) {
const typeId = updated.history_content_type + "-" + updated.id;
actionModels[typeId].set(updated);
}
client/galaxy/scripts/mvc/history/history-view.js
+5 -5
View File
@@ -635,7 +635,7 @@ export function historyEntry(options) {
$("#switch").click(function() {
//##HACK:ity hack hack
//##TODO: remove when out of iframe
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var hview = Galaxy.currHistoryPanel ? Galaxy.currHistoryPanel : null;
if (hview) {
hview.switchToHistory("${ history[ 'id' ] }");
@@ -649,12 +649,12 @@ export function historyEntry(options) {
$("#center").addClass("flex-vertical-container");
}
let viewClass = options.userIsOwner ? HistoryViewEdit.HistoryViewEdit : HistoryView.HistoryView;
let history = new History(options.historyJSON);
const viewClass = options.userIsOwner ? HistoryViewEdit.HistoryViewEdit : HistoryView.HistoryView;
const history = new History(options.historyJSON);
// attach the copy dialog to the import button now that we have a history
$("#import").click(function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
HistoryCopyDialog(history, {
useImport: true,
// use default datasets option to match the toggle-deleted button
@@ -668,7 +668,7 @@ export function historyEntry(options) {
});
});
let historyView = new viewClass({
const historyView = new viewClass({
el: $("#history-" + options.historyJSON.id),
className: viewClass.prototype.className + " wide",
$scrollContainer: options.hasMasthead
client/galaxy/scripts/mvc/history/multi-panel.js
+1 -1
View File
@@ -473,7 +473,7 @@ var MultiPanelColumns = Backbone.View.extend(baseMVC.LoggableMixin).extend({
/** create a column and its panel and set up any listeners to them */
createColumn: function createColumn(history, options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// options passed can be re-used, so extend them before adding the model to prevent pollution for the next
options = _.extend({}, options, {
model: history,
client/galaxy/scripts/mvc/history/options-menu.js
+11 -11
View File
@@ -31,7 +31,7 @@ var menu = [
{
html: _l("Copy History"),
func: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
historyCopyDialog(Galaxy.currHistoryPanel.model).done(() => {
Galaxy.currHistoryPanel.loadCurrentHistory();
});
@@ -40,7 +40,7 @@ var menu = [
{
html: _l("Share or Publish"),
func: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
Galaxy.router.push(`/histories/sharing?id=${Galaxy.currHistoryPanel.model.id}`);
}
@@ -50,7 +50,7 @@ var menu = [
html: _l("Show Structure"),
anon: true,
func: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
Galaxy.router.push("/histories/show_structure");
}
@@ -64,7 +64,7 @@ var menu = [
html: _l("Delete"),
anon: true,
func: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy && Galaxy.currHistoryPanel && confirm(_l("Really delete the current history?"))) {
Galaxy.currHistoryPanel.model._delete().done(() => {
Galaxy.currHistoryPanel.loadCurrentHistory();
@@ -77,7 +77,7 @@ var menu = [
purge: true,
anon: true,
func: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (
Galaxy &&
Galaxy.currHistoryPanel &&
@@ -93,7 +93,7 @@ var menu = [
html: _l("Make Data Private"),
anon: true,
func: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (
Galaxy &&
Galaxy.currHistoryPanel &&
@@ -121,7 +121,7 @@ var menu = [
{
html: _l("Dataset Security"),
func: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
Galaxy.router.push(`/histories/permissions?id=${Galaxy.currHistoryPanel.model.id}`);
}
@@ -135,7 +135,7 @@ var menu = [
{
html: _l("Collapse Expanded Datasets"),
func: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy && Galaxy.currHistoryPanel) {
Galaxy.currHistoryPanel.collapseAll();
}
@@ -145,7 +145,7 @@ var menu = [
html: _l("Unhide Hidden Datasets"),
anon: true,
func: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// TODO: Deprecate this functionality and replace with group dataset selector and action combination
if (Galaxy && Galaxy.currHistoryPanel && confirm(_l("Really unhide all hidden datasets?"))) {
$.post(`${getAppRoot()}history/adjust_hidden`, { user_action: "unhide" }, () => {
@@ -158,7 +158,7 @@ var menu = [
html: _l("Delete Hidden Datasets"),
anon: true,
func: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// TODO: Deprecate this functionality and replace with group dataset selector and action combination
if (Galaxy && Galaxy.currHistoryPanel && confirm(_l("Really delete all hidden datasets?"))) {
$.post(`${getAppRoot()}history/adjust_hidden`, { user_action: "delete" }, () => {
@@ -183,7 +183,7 @@ var menu = [
html: _l("Export Tool Citations"),
anon: true,
func: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
Galaxy.router.push(`/histories/citations?id=${Galaxy.currHistoryPanel.model.id}`);
}
client/galaxy/scripts/mvc/library/library-dataset-view.js
+5 -5
View File
@@ -67,7 +67,7 @@ var LibraryDatasetView = Backbone.View.extend({
},
fetchDataset: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.options = _.extend(this.options, options);
this.model = new mod_library_model.Item({
id: this.options.id
@@ -184,7 +184,7 @@ var LibraryDatasetView = Backbone.View.extend({
importIntoHistory: function() {
this.refreshUserHistoriesList(self => {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var template = self.templateBulkImportInModal();
self.modal = Galaxy.modal;
self.modal.show({
@@ -255,7 +255,7 @@ var LibraryDatasetView = Backbone.View.extend({
},
processImportToHistory: function(history_id) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var historyItem = new mod_library_model.HistoryItem();
historyItem.url = `${historyItem.urlRoot + history_id}/contents`;
// set the used history as current so user will see the last one
@@ -285,7 +285,7 @@ var LibraryDatasetView = Backbone.View.extend({
},
showPermissions: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var template = this.templateDatasetPermissions();
var self = this;
this.options = _.extend(this.options, options);
@@ -400,7 +400,7 @@ var LibraryDatasetView = Backbone.View.extend({
},
detectDatatype: function(options) {
let ld = this.model;
const ld = this.model;
ld.set("file_ext", "auto");
this._submitModification(ld);
},
client/galaxy/scripts/mvc/library/library-folder-view.js
+2 -2
View File
@@ -26,7 +26,7 @@ var FolderView = Backbone.View.extend({
},
fetchFolder: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.options = _.extend(this.options, options);
this.model = new mod_library_model.FolderAsModel({
id: this.options.id
@@ -57,7 +57,7 @@ var FolderView = Backbone.View.extend({
},
showPermissions: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.options = _.extend(this.options, options);
$(".tooltip").remove();
client/galaxy/scripts/mvc/library/library-folderlist-view.js
+4 -4
View File
@@ -77,7 +77,7 @@ var FolderListView = Backbone.View.extend({
self.render();
},
error: function(model, response) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (typeof response.responseJSON !== "undefined") {
Toast.error(`${response.responseJSON.err_msg} Click this to go back.`, "", {
onclick: function() {
@@ -141,7 +141,7 @@ var FolderListView = Backbone.View.extend({
},
paginate: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.options = _.extend(this.options, options);
if (this.options.show_page === null || this.options.show_page < 1) {
@@ -181,7 +181,7 @@ var FolderListView = Backbone.View.extend({
* be added to the view's collection.
*/
addAll: function(models) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
_.each(models, model => {
Galaxy.libraries.folderListView.collection.add(model, {
current_sort_order: false
@@ -198,7 +198,7 @@ var FolderListView = Backbone.View.extend({
* and that event will be bound on all subviews.
*/
postRender: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var fetched_metadata = this.folderContainer.attributes.metadata;
fetched_metadata.contains_file_or_folder =
typeof this.collection.findWhere({ type: "file" }) !== "undefined" ||
client/galaxy/scripts/mvc/library/library-folderrow-view.js
+5 -5
View File
@@ -36,7 +36,7 @@ var FolderRowView = Backbone.View.extend({
this.options = _.extend(this.options, options);
var folder_item = this.options.model;
var template = null;
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (folder_item.get("type") === "folder" || folder_item.get("model_class") === "LibraryFolder") {
this.options.type = "folder";
@@ -105,14 +105,14 @@ var FolderRowView = Backbone.View.extend({
/* Show the page with dataset details. */
showDatasetDetails: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({ id: this.id });
},
/* Undelete the dataset on server and render the row again. */
undeleteDataset: function(event) {
$(".tooltip").hide();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var that = this;
var dataset_id = $(event.target)
.closest("tr")
@@ -144,7 +144,7 @@ var FolderRowView = Backbone.View.extend({
/* Undelete the folder on server and render the row again. */
undeleteFolder: function(event) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
$(".tooltip").hide();
var folder_id = $(event.target)
.closest("tr")
@@ -182,7 +182,7 @@ var FolderRowView = Backbone.View.extend({
},
saveModifications: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var folder = Galaxy.libraries.folderListView.collection.get(this.$el.data("id"));
var is_changed = false;
var new_name = this.$el.find(".input_folder_name").val();
client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+50 -50
View File
@@ -78,7 +78,7 @@ var FolderToolbarView = Backbone.View.extend({
render: function(options) {
this.options = _.extend(this.options, options);
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var toolbar_template = this.templateToolBar();
var template_defaults = {
id: this.options.id,
@@ -107,7 +107,7 @@ var FolderToolbarView = Backbone.View.extend({
*/
renderPaginator: function(options) {
this.options = _.extend(this.options, options);
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var paginator_template = this.templatePaginator();
$("body")
.find(".folder-paginator")
@@ -125,7 +125,7 @@ var FolderToolbarView = Backbone.View.extend({
configureElements: function(options) {
this.options = _.extend(this.options, options);
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (this.options.can_add_library_item === true) {
$(".add-library-items").show();
@@ -155,7 +155,7 @@ var FolderToolbarView = Backbone.View.extend({
createFolderFromModal: function(event) {
event.preventDefault();
event.stopPropagation();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var template = this.templateNewFolderInModal();
this.modal = Galaxy.modal;
this.modal.show({
@@ -174,7 +174,7 @@ var FolderToolbarView = Backbone.View.extend({
},
createNewFolderEvent: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var folderDetails = this.serializeNewFolder();
if (this.validateNewFolder(folderDetails)) {
var folder = new mod_library_model.FolderAsModel();
@@ -222,7 +222,7 @@ var FolderToolbarView = Backbone.View.extend({
importToHistoryModal: function(e) {
e.preventDefault();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var $checkedValues = this.findCheckedRows();
var template = this.templateImportIntoHistoryModal();
if ($checkedValues.length === 0) {
@@ -296,8 +296,8 @@ var FolderToolbarView = Backbone.View.extend({
var items_to_import = [];
// prepare the dataset objects to be imported
for (let i = checked_items.dataset_ids.length - 1; i >= 0; i--) {
let library_dataset_id = checked_items.dataset_ids[i];
let historyItem = new mod_library_model.HistoryItem();
const library_dataset_id = checked_items.dataset_ids[i];
const historyItem = new mod_library_model.HistoryItem();
historyItem.url = `${historyItem.urlRoot + history_id}/contents`;
historyItem.content = library_dataset_id;
historyItem.source = "library";
@@ -305,8 +305,8 @@ var FolderToolbarView = Backbone.View.extend({
}
// prepare the folder objects to be imported
for (let i = checked_items.folder_ids.length - 1; i >= 0; i--) {
let library_folder_id = checked_items.folder_ids[i];
let historyItem = new mod_library_model.HistoryItem();
const library_folder_id = checked_items.folder_ids[i];
const historyItem = new mod_library_model.HistoryItem();
historyItem.url = `${historyItem.urlRoot + history_id}/contents`;
historyItem.content = library_folder_id;
historyItem.source = "library_folder";
@@ -373,7 +373,7 @@ var FolderToolbarView = Backbone.View.extend({
},
addFilesFromHistoryModal: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.histories = new mod_library_model.GalaxyHistories();
this.histories
.fetch()
@@ -416,7 +416,7 @@ var FolderToolbarView = Backbone.View.extend({
* Create modal for importing from Galaxy path.
*/
importFilesFromPathModal: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.modal = Galaxy.modal;
var template_modal = this.templateImportPathModal();
this.modal.show({
@@ -450,7 +450,7 @@ var FolderToolbarView = Backbone.View.extend({
url: `${getAppRoot()}api/datatypes?extension_only=False`,
success: datatypes => {
this.list_extensions = [];
for (let key in datatypes) {
for (const key in datatypes) {
this.list_extensions.push({
id: datatypes[key].extension,
text: datatypes[key].extension,
@@ -467,7 +467,7 @@ var FolderToolbarView = Backbone.View.extend({
url: `${getAppRoot()}api/genomes`,
success: genomes => {
this.list_genomes = [];
for (let key in genomes) {
for (const key in genomes) {
this.list_genomes.push({
id: genomes[key][1],
text: genomes[key][0]
@@ -480,7 +480,7 @@ var FolderToolbarView = Backbone.View.extend({
},
renderSelectBoxes: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// This won't work properly unlesss we already have the data fetched.
// See this.fetchExtAndGenomes()
this.select_genome = new mod_select.View({
@@ -503,7 +503,7 @@ var FolderToolbarView = Backbone.View.extend({
*/
importFilesFromGalaxyFolderModal: function(options) {
var template_modal = this.templateBrowserModal();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.modal = Galaxy.modal;
this.modal.show({
closing_events: true,
@@ -650,7 +650,7 @@ var FolderToolbarView = Backbone.View.extend({
* @param {int} length The number of items in the chain call.
*/
initChainCallControl: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var template;
switch (options.action) {
case "adding_datasets":
@@ -719,7 +719,7 @@ var FolderToolbarView = Backbone.View.extend({
action: "adding_datasets"
});
if (selection_type === "folder") {
let full_source = `${options.source}_folder`;
const full_source = `${options.source}_folder`;
this.chainCallImportingFolders({
paths: paths,
preserve_dirs: preserve_dirs,
@@ -732,7 +732,7 @@ var FolderToolbarView = Backbone.View.extend({
tag_using_filenames: tag_using_filenames
});
} else if (selection_type === "file") {
let full_source = `${options.source}_file`;
const full_source = `${options.source}_file`;
this.chainCallImportingUserdirFiles({
paths: paths,
file_type: file_type,
@@ -827,7 +827,7 @@ var FolderToolbarView = Backbone.View.extend({
* @param {str} history_name name of the history to import to
*/
chainCallImportingIntoHistory: function(history_item_set, history_name) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var popped_item = history_item_set.pop();
if (typeof popped_item == "undefined") {
if (this.options.chain_call_control.failed_number === 0) {
@@ -878,8 +878,8 @@ var FolderToolbarView = Backbone.View.extend({
* @param {boolean} tag_using_filenames add tags to datasets using names of files
*/
chainCallImportingUserdirFiles: function(options) {
let Galaxy = getGalaxyInstance();
let popped_item = options.paths.pop();
const Galaxy = getGalaxyInstance();
const popped_item = options.paths.pop();
if (typeof popped_item === "undefined") {
if (this.options.chain_call_control.failed_number === 0) {
Toast.success("Selected files imported into the current folder");
@@ -889,8 +889,8 @@ var FolderToolbarView = Backbone.View.extend({
}
return true;
}
let post_url = `${getAppRoot()}api/libraries/datasets`;
let post_data = {
const post_url = `${getAppRoot()}api/libraries/datasets`;
const post_data = {
encoded_folder_id: this.id,
source: options.source,
path: popped_item,
@@ -901,7 +901,7 @@ var FolderToolbarView = Backbone.View.extend({
dbkey: options.dbkey,
tag_using_filenames: options.tag_using_filenames
};
let promise = $.when($.post(post_url, post_data));
const promise = $.when($.post(post_url, post_data));
promise
.done(response => {
this.updateProgress();
@@ -927,9 +927,9 @@ var FolderToolbarView = Backbone.View.extend({
* @param {boolean} tag_using_filenames add tags to datasets using names of files
*/
chainCallImportingFolders: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// TODO need to check which paths to call
let popped_item = options.paths.pop();
const popped_item = options.paths.pop();
if (typeof popped_item == "undefined") {
if (this.options.chain_call_control.failed_number === 0) {
Toast.success("Selected folders and their contents imported into the current folder.");
@@ -940,8 +940,8 @@ var FolderToolbarView = Backbone.View.extend({
}
return true;
}
let post_url = `${getAppRoot()}api/libraries/datasets`;
let post_data = {
const post_url = `${getAppRoot()}api/libraries/datasets`;
const post_data = {
encoded_folder_id: this.id,
source: options.source,
path: popped_item,
@@ -953,7 +953,7 @@ var FolderToolbarView = Backbone.View.extend({
dbkey: options.dbkey,
tag_using_filenames: options.tag_using_filenames
};
let promise = $.when($.post(post_url, post_data));
const promise = $.when($.post(post_url, post_data));
promise
.done(response => {
this.updateProgress();
@@ -972,7 +972,7 @@ var FolderToolbarView = Backbone.View.extend({
* @param {array} hdas_set array of empty hda objects
*/
chainCallAddingHdas: function(hdas_set) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.added_hdas = new mod_library_model.Folder();
var popped_item = hdas_set.pop();
if (typeof popped_item == "undefined") {
@@ -1011,7 +1011,7 @@ var FolderToolbarView = Backbone.View.extend({
* @param {array} lddas_set array of lddas to delete
*/
chainCallDeletingItems: function(items_to_delete) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.deleted_items = new mod_library_model.Folder();
var item_to_delete = items_to_delete.pop();
if (typeof item_to_delete === "undefined") {
@@ -1060,7 +1060,7 @@ var FolderToolbarView = Backbone.View.extend({
* Handles the click on 'show deleted' checkbox
*/
checkIncludeDeleted: function(event) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (event.target.checked) {
Galaxy.libraries.folderListView.fetchFolder({
include_deleted: true
@@ -1076,7 +1076,7 @@ var FolderToolbarView = Backbone.View.extend({
* Delete the selected items. Atomic. One by one.
*/
deleteSelectedItems: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var dataset_ids = [];
var folder_ids = [];
var $checkedValues = this.findCheckedRows();
@@ -1138,7 +1138,7 @@ var FolderToolbarView = Backbone.View.extend({
},
showLocInfo: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var library = null;
if (Galaxy.libraries.libraryListView !== null) {
library = Galaxy.libraries.libraryListView.collection.get(this.options.parent_library_id);
@@ -1163,7 +1163,7 @@ var FolderToolbarView = Backbone.View.extend({
},
showLocInfoModal: function(library) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var template = this.templateLocInfoInModal();
this.modal = Galaxy.modal;
this.modal.show({
@@ -1179,7 +1179,7 @@ var FolderToolbarView = Backbone.View.extend({
},
showImportModal: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
switch (options.source) {
case "history":
this.addFilesFromHistoryModal();
@@ -1209,7 +1209,7 @@ var FolderToolbarView = Backbone.View.extend({
*/
showPageSizePrompt: function(e) {
e.preventDefault();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var folder_page_size = prompt(
"How many items per page do you want to see?",
Galaxy.libraries.preferences.get("folder_page_size")
@@ -1248,7 +1248,7 @@ var FolderToolbarView = Backbone.View.extend({
showCollectionSelect: function(e) {
e.preventDefault();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var checked_items = this.findCheckedItems();
var template = this.templateCollectionSelectModal();
this.modal = Galaxy.modal;
@@ -1317,13 +1317,13 @@ var FolderToolbarView = Backbone.View.extend({
* The code below overwrites the id with ldda_id for this reason.
*/
showCollectionBuilder: function(checked_items) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
let collection_elements = [];
let elements_source = this.modal.$('input[type="radio"]:checked').val();
const elements_source = this.modal.$('input[type="radio"]:checked').val();
if (elements_source === "selection") {
for (let i = checked_items.length - 1; i >= 0; i--) {
let collection_item = {};
let dataset = Galaxy.libraries.folderListView.folder_container.get("folder").get(checked_items[i]);
const collection_item = {};
const dataset = Galaxy.libraries.folderListView.folder_container.get("folder").get(checked_items[i]);
collection_item.id = dataset.get("ldda_id");
collection_item.name = dataset.get("name");
collection_item.deleted = dataset.get("deleted");
@@ -1331,13 +1331,13 @@ var FolderToolbarView = Backbone.View.extend({
collection_elements.push(collection_item);
}
} else if (elements_source === "folder") {
let all_datasets = Galaxy.libraries.folderListView.folder_container.get("folder").where({ type: "file" });
const all_datasets = Galaxy.libraries.folderListView.folder_container.get("folder").where({ type: "file" });
collection_elements = new Backbone.Collection(all_datasets).toJSON();
for (var i = collection_elements.length - 1; i >= 0; i--) {
collection_elements[i].id = collection_elements[i].ldda_id;
}
}
let new_history_name = this.modal.$("input[name=history_name]").val();
const new_history_name = this.modal.$("input[name=history_name]").val();
if (new_history_name !== "") {
this.createNewHistory(new_history_name)
.done(new_history => {
@@ -1348,14 +1348,14 @@ var FolderToolbarView = Backbone.View.extend({
Toast.error("An error occurred.");
});
} else {
let selected_history_id = this.select_collection_history.value();
let selected_history_name = this.select_collection_history.text();
const selected_history_id = this.select_collection_history.value();
const selected_history_name = this.select_collection_history.text();
this.collectionImport(collection_elements, selected_history_id, selected_history_name);
}
},
collectionImport: function(collection_elements, history_id, history_name) {
let modal_title = `Creating Collection in ${history_name}`;
const modal_title = `Creating Collection in ${history_name}`;
let creator_class;
let creationFn;
if (this.collectionType === "list") {
@@ -1388,7 +1388,7 @@ var FolderToolbarView = Backbone.View.extend({
creator_class
);
} else if (this.collectionType === "list:paired") {
let elements = collection_elements.map(element => ({
const elements = collection_elements.map(element => ({
id: element.id,
name: element.name,
src: "ldda"
@@ -1410,7 +1410,7 @@ var FolderToolbarView = Backbone.View.extend({
},
createHDCA: function(elementIdentifiers, collectionType, name, hideSourceItems, history_id, options) {
let hdca = new HDCA_MODEL.HistoryDatasetCollection({
const hdca = new HDCA_MODEL.HistoryDatasetCollection({
history_content_type: "dataset_collection",
collection_type: collectionType,
history_id: history_id,
client/galaxy/scripts/mvc/library/library-library-view.js
+2 -2
View File
@@ -38,7 +38,7 @@ var LibraryView = Backbone.View.extend({
}
},
error: function(model, response) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (typeof response.responseJSON !== "undefined") {
Toast.error(`${response.responseJSON.err_msg} Click this to go back.`, "", {
onclick: function() {
@@ -68,7 +68,7 @@ var LibraryView = Backbone.View.extend({
}
}
var is_admin = false;
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.user) {
is_admin = Galaxy.user.isAdmin();
}
client/galaxy/scripts/mvc/library/library-librarylist-view.js
+3 -3
View File
@@ -51,7 +51,7 @@ var LibraryListView = Backbone.View.extend({
* or render an empty list in case no data is given.
*/
render: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.options = _.extend(this.options, options);
this.setElement("#libraries_element");
var template = this.templateLibraryList();
@@ -182,7 +182,7 @@ var LibraryListView = Backbone.View.extend({
* @return {[type]} [description]
*/
sort_clicked: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.libraries.preferences.get("sort_order") === "asc") {
Galaxy.libraries.preferences.set({ sort_order: "desc" });
} else {
@@ -196,7 +196,7 @@ var LibraryListView = Backbone.View.extend({
* Currently supports only sorting by name.
*/
sortLibraries: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.libraries.preferences.get("sort_by") === "name") {
if (Galaxy.libraries.preferences.get("sort_order") === "asc") {
this.collection.sortLibraries("name", "asc");
client/galaxy/scripts/mvc/library/library-libraryrow-view.js
+4 -4
View File
@@ -32,7 +32,7 @@ var LibraryRowView = Backbone.View.extend({
render: function(library) {
if (typeof library === "undefined") {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
console.log(library);
}
@@ -122,7 +122,7 @@ var LibraryRowView = Backbone.View.extend({
},
save_library_modification: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
var is_changed = false;
@@ -174,7 +174,7 @@ var LibraryRowView = Backbone.View.extend({
},
delete_library: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
var row_view = this;
// mark the library deleted
@@ -204,7 +204,7 @@ var LibraryRowView = Backbone.View.extend({
},
undelete_library: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var library = Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));
var row_view = this;
client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
+8 -8
View File
@@ -31,7 +31,7 @@ var LibraryToolbarView = Backbone.View.extend({
},
render: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var toolbar_template = this.templateToolBar();
var is_admin = false;
var is_anonym = true;
@@ -52,7 +52,7 @@ var LibraryToolbarView = Backbone.View.extend({
* Renders the element that shows pages into its div within the toolbar.
*/
renderPaginator: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.options = _.extend(this.options, options);
var paginator_template = this.templatePaginator();
this.$el.find(".library-paginator").html(
@@ -73,7 +73,7 @@ var LibraryToolbarView = Backbone.View.extend({
createLibraryFromModal: function(event) {
event.preventDefault();
event.stopPropagation();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var self = this;
this.modal = Galaxy.modal;
this.modal.show({
@@ -95,7 +95,7 @@ var LibraryToolbarView = Backbone.View.extend({
* Create the new library using the API asynchronously.
*/
createNewLibrary: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var libraryDetails = this.serializeNewLibrary();
if (this.validateNewLibrary(libraryDetails)) {
var library = new mod_library_model.Library();
@@ -127,7 +127,7 @@ var LibraryToolbarView = Backbone.View.extend({
*/
showPageSizePrompt: function(e) {
e.preventDefault();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var library_page_size = prompt(
"How many libraries per page do you want to see?",
Galaxy.libraries.preferences.get("library_page_size")
@@ -171,7 +171,7 @@ var LibraryToolbarView = Backbone.View.extend({
* Include or exclude deleted libraries in the view.
*/
includeDeletedChecked: function(event) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (event.target.checked) {
Galaxy.libraries.preferences.set({ with_deleted: true });
Galaxy.libraries.libraryListView.fetchDeleted();
@@ -185,7 +185,7 @@ var LibraryToolbarView = Backbone.View.extend({
* Include or exclude restricted libraries in the view.
*/
excludeRestrictedChecked: function(event) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (event.target.checked) {
Galaxy.libraries.preferences.set({ without_restricted: true });
} else {
@@ -199,7 +199,7 @@ var LibraryToolbarView = Backbone.View.extend({
* to query the collection of libraries.
*/
searchLibraries: function(event) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var search_term = $(".library-search-input").val();
this.options.search_term = search_term;
Galaxy.libraries.libraryListView.searchLibraries(search_term);
client/galaxy/scripts/mvc/library/library-model.js
+1 -1
View File
@@ -91,7 +91,7 @@ var FolderContainer = Backbone.Model.extend({
id: "unknown"
},
parse: function(obj) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// empty the collection
this.get("folder").reset();
// response is not a simple array, it contains metadata
client/galaxy/scripts/mvc/rules/rule-definitions.js
+4 -4
View File
@@ -18,7 +18,7 @@ const multiColumnsToString = function(targetColumns, colHeaders) {
const removeColumns = function(columns, targetColumns) {
const newColumns = [];
for (let index in columns) {
for (const index in columns) {
if (targetColumns.indexOf(index) === -1) {
newColumns.push(columns[index]);
}
@@ -223,7 +223,7 @@ const RULES = {
const tags = sources[index]["tags"];
tags.sort();
let groupTagValue = rule.default_value;
for (let index in tags) {
for (const index in tags) {
const tag = tags[index];
if (tag.indexOf(groupTagPrefix) == 0) {
groupTagValue = tag.substr(groupTagPrefix.length);
@@ -402,7 +402,7 @@ const RULES = {
const targets = rule.target_columns;
function newRow(row) {
const newRow = [];
for (let index in row) {
for (const index in row) {
if (targets.indexOf(parseInt(index)) == -1) {
newRow.push(row[index]);
}
@@ -862,7 +862,7 @@ const colHeadersFor = function(data, columns) {
};
const applyRules = function(data, sources, columns, rules, headersPerRule = []) {
let colHeadersPerRule = Array.from(headersPerRule);
const colHeadersPerRule = Array.from(headersPerRule);
let hasRuleError = false;
for (var ruleIndex in rules) {
const ruleHeaders = colHeadersFor(data, columns);
client/galaxy/scripts/mvc/tag.js
+2 -2
View File
@@ -142,7 +142,7 @@ var TagsEditor = Backbone.View.extend(baseMVC.LoggableMixin)
/** @returns {String[]} all tags used by the current user */
_getTagsUsed: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var self = this;
return _.map(Galaxy.user.get("tags_used"), self._nameToHash);
},
@@ -168,7 +168,7 @@ var TagsEditor = Backbone.View.extend(baseMVC.LoggableMixin)
* @param {String} newTag the tag to add to the list of used
*/
_addNewTagToTagsUsed: function(newTag) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var tagsUsed = Galaxy.user.get("tags_used");
if (!_.contains(tagsUsed, newTag)) {
tagsUsed.push(newTag);
client/galaxy/scripts/mvc/tool/tool-form-base.js
+5 -5
View File
@@ -17,7 +17,7 @@ import axios from "axios";
export default FormBase.extend({
initialize: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var self = this;
this.deferred = new Deferred();
FormBase.prototype.initialize.call(this, options);
@@ -60,7 +60,7 @@ export default FormBase.extend({
this.$el.off().hide();
this.deferred.execute(() => {
FormBase.prototype.remove.call(self);
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.emit.debug("tool-form-base::_destroy()", "Destroy view.");
});
},
@@ -75,7 +75,7 @@ export default FormBase.extend({
`<b>${options.name}</b> ${options.description} (Galaxy Version ${options.version})`,
operations: !options.hide_operations && this._operations(),
onchange: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
self.deferred.reset();
self.deferred.execute(process => {
self.model.get("postchange")(process, self);
@@ -114,10 +114,10 @@ export default FormBase.extend({
_operations: function() {
var self = this;
var options = this.model.attributes;
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// Buttons for adding and removing favorite.
let in_favorites = Galaxy.user.getFavorites().tools.indexOf(options.id) >= 0;
const in_favorites = Galaxy.user.getFavorites().tools.indexOf(options.id) >= 0;
var favorite_button = new Ui.Button({
icon: "fa-star-o",
title: options.narrow ? null : "Favorite",
client/galaxy/scripts/mvc/tool/tool-form-composite.js
+8 -8
View File
@@ -17,7 +17,7 @@ import WorkflowIcons from "mvc/workflow/workflow-icons";
var View = Backbone.View.extend({
initialize: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.modal = Galaxy.modal || new Modal.View();
this.model = (options && options.model) || new Backbone.Model(options);
this.deferred = new Deferred();
@@ -39,7 +39,7 @@ var View = Backbone.View.extend({
/** Configures form/step options for each workflow step */
_configure: function() {
var self = this;
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.forms = [];
this.steps = [];
this.links = [];
@@ -336,7 +336,7 @@ var View = Backbone.View.extend({
/** Render job caching option */
_renderUseCachedJob: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var extra_user_preferences = {};
if (Galaxy.user.attributes.preferences && "extra_user_preferences" in Galaxy.user.attributes.preferences) {
extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences);
@@ -370,7 +370,7 @@ var View = Backbone.View.extend({
/** Render step */
_renderStep: function(step) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var self = this;
var form = null;
this.deferred.execute(promise => {
@@ -529,7 +529,7 @@ var View = Backbone.View.extend({
/** Refresh the history after job submission while form is shown */
_refreshHistory: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var self = this;
var history = Galaxy && Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model;
if (this._refresh_history) {
@@ -561,7 +561,7 @@ var View = Backbone.View.extend({
/** Validate and submit workflow */
_submit: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var self = this;
var history_form_data = this.history_form.data.create();
var job_def = {
@@ -716,13 +716,13 @@ var View = Backbone.View.extend({
/** Templates */
_templateSuccess: function(response) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if ($.isArray(response) && response.length > 0) {
let timesExecuted = "";
// Default destination blurb, used for a single execution, same history.
let destinationBlurb =
"You can check the status of queued jobs and view the resulting data by refreshing the History pane, if this has not already happened automatically.";
let newHistoryTarget =
const newHistoryTarget =
(response[0].history_id &&
Galaxy.currHistoryPanel &&
Galaxy.currHistoryPanel.model.id != response[0].history_id) ||
client/galaxy/scripts/mvc/tool/tool-form.js
+16 -16
View File
@@ -14,8 +14,8 @@ import Webhooks from "mvc/webhooks";
var View = Backbone.View.extend({
initialize: function(options) {
let Galaxy = getGalaxyInstance();
let self = this;
const Galaxy = getGalaxyInstance();
const self = this;
this.modal = Galaxy.modal || new Modal.View();
this.form = new ToolFormBase(
Utils.merge(
@@ -166,7 +166,7 @@ var View = Backbone.View.extend({
}
// Job Re-use Options
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var extra_user_preferences = {};
if (Galaxy.user.attributes.preferences && "extra_user_preferences" in Galaxy.user.attributes.preferences) {
extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences);
@@ -194,10 +194,10 @@ var View = Backbone.View.extend({
* @param{function} callback - Called when request has completed
*/
submit: function(options, callback) {
let Galaxy = getGalaxyInstance();
let history_id = Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;
let self = this;
let job_def = {
const Galaxy = getGalaxyInstance();
const history_id = Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;
const self = this;
const job_def = {
history_id: history_id,
tool_id: options.id,
tool_version: options.version,
@@ -210,7 +210,7 @@ var View = Backbone.View.extend({
return;
}
if (options.action !== `${getAppRoot()}tool_runner/index`) {
let $f = $("<form/>").attr({
const $f = $("<form/>").attr({
action: options.action,
method: options.method,
enctype: options.enctype
@@ -249,8 +249,8 @@ var View = Backbone.View.extend({
Galaxy.emit.debug("tool-form::submit", "Submission failed.", response);
let input_found = false;
if (response && response.err_data) {
let error_messages = self.form.data.matchResponse(response.err_data);
for (let input_id in error_messages) {
const error_messages = self.form.data.matchResponse(response.err_data);
for (const input_id in error_messages) {
self.form.highlight(input_id, error_messages[input_id]);
input_found = true;
break;
@@ -275,7 +275,7 @@ var View = Backbone.View.extend({
* @param{dict} job_def - Job execution dictionary
*/
validate: function(job_def) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var job_inputs = job_def.inputs;
var batch_n = -1;
var batch_src = null;
@@ -330,10 +330,10 @@ var View = Backbone.View.extend({
_getInputs: function(job_def) {
var inputs = [];
var index = {};
for (let i in job_def.inputs) {
let input = job_def.inputs[i];
for (const i in job_def.inputs) {
const input = job_def.inputs[i];
if (input && $.isArray(input.values)) {
for (let j of input.values) {
for (const j of input.values) {
if (j.src && !index[j.id]) {
inputs.push(j);
index[j.id] = true;
@@ -351,8 +351,8 @@ var View = Backbone.View.extend({
});
if (list.length > 0) {
blurb += `<p>${title}:</p>`;
for (let item of list) {
let rowString = max > 0 ? `${item.hid}: ${_.escape(item.name)}` : "...";
for (const item of list) {
const rowString = max > 0 ? `${item.hid}: ${_.escape(item.name)}` : "...";
blurb += `<p class="messagerow">
<b>${rowString}</b>
</p>`;
client/galaxy/scripts/mvc/tool/tool-genomespace.js
+1 -1
View File
@@ -4,7 +4,7 @@ import { getGalaxyInstance } from "app";
// tool form templates
export default {
openFileBrowser: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var GS_UI_URL = Galaxy.config.genomespace_ui_url;
var GS_UPLOAD_URL = `${GS_UI_URL}upload/loadUrlToGenomespace.html?getLocation=true`;
client/galaxy/scripts/mvc/tool/tools.js
+7 -7
View File
@@ -367,7 +367,7 @@ var ToolSearch = Backbone.Model.extend({
* Do the search and update the results.
*/
do_search: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var query = this.attributes.query;
// If query is too short, do not search.
@@ -436,20 +436,20 @@ var ToolPanel = Backbone.Model.extend({
var // Helper to recursively parse tool panel.
parse_elt = elt_dict => {
let type = elt_dict.model_class;
const type = elt_dict.model_class;
// There are many types of tools; for now, anything that ends in 'Tool'
// and is not a ExpressionTool is treated as a generic tool.
if (type.indexOf("Tool") === type.length - 4) {
let tool = self.attributes.tools.get(elt_dict.id);
const tool = self.attributes.tools.get(elt_dict.id);
if (type === 'ExpressionTool') {
tool.hide();
}
return tool;
} else if (type === "ToolSection") {
// Parse elements.
let elems = _.map(elt_dict.elems, parse_elt).filter(el => el.is_visible());
const elems = _.map(elt_dict.elems, parse_elt).filter(el => el.is_visible());
elt_dict.elems = elems;
let section = new ToolSection(elt_dict);
const section = new ToolSection(elt_dict);
if (elems.length == 0) {
section.hide();
}
@@ -537,7 +537,7 @@ var ToolLinkView = BaseView.extend({
if (this.model.id === "upload1") {
$link.find("a").on("click", e => {
e.preventDefault();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.upload.show();
});
} else if (formStyle === "regular") {
@@ -545,7 +545,7 @@ var ToolLinkView = BaseView.extend({
var self = this;
$link.find("a").on("click", e => {
e.preventDefault();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.router.push("/", {
tool_id: self.model.id,
version: self.model.get("version")
client/galaxy/scripts/mvc/toolshed/repository-view.js
+1 -1
View File
@@ -376,7 +376,7 @@ var ToolShedRepositoryView = Backbone.View.extend({
toolTPSSelectionEvents: function() {
$(".tool_panel_section_picker").on("change", ev => {
let element = $(ev.target);
const element = $(ev.target);
var new_value = element.find("option:selected").val();
var default_tps = $("#tool_panel_section_select")
.find("option:selected")
client/galaxy/scripts/mvc/tours.js
+3 -3
View File
@@ -12,7 +12,7 @@ import { getAppRoot } from "onload/loadConfig";
import "libs/bootstrap-tour";
// bootstrap-tour configures a window.Tour object; keep a local ref.
let Tour = window.Tour;
const Tour = window.Tour;
// For buttons to show, we need to add them to bootstrap/popper's sanitizing filters.
$.fn.tooltip.Constructor.Default.whiteList.button = ["data-role"];
@@ -206,10 +206,10 @@ export var ToursView = Backbone.View.extend({
});
export function giveTourWithData(data) {
let hookedTourData = hooked_tour_from_data(data);
const hookedTourData = hooked_tour_from_data(data);
window.sessionStorage.setItem("activeGalaxyTour", JSON.stringify(data));
// Store tour steps in sessionStorage to easily persist w/o hackery.
let tour = new Tour(_.extend({ steps: hookedTourData.steps }, tour_opts));
const tour = new Tour(_.extend({ steps: hookedTourData.steps }, tour_opts));
// Always clean restart, since this is a new, explicit execution.
tour.init();
tour.goTo(0);
client/galaxy/scripts/mvc/ui/error-modal.js
+3 -3
View File
@@ -35,7 +35,7 @@ var DETAILS_MSG = _l("The following information can assist the developers in fin
/** private helper that builds the modal and handles adding details */
function _errorModal(message, title, details) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
// create and return the modal, adding details button only if needed
Galaxy.modal.show({
title: title,
@@ -75,7 +75,7 @@ function errorModal(message, title, details) {
return;
}
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
message = _l(message);
title = _l(title) || _l("Error:");
if (Galaxy && Galaxy.modal) {
@@ -113,7 +113,7 @@ function ajaxErrorModal(model, xhr, options, message, title) {
/** build details which may help debugging the ajax call */
function _ajaxDetails(model, xhr, options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
return {
//TODO: still can't manage Raven id
raven: _.result(window.Raven, "lastEventId"),
client/galaxy/scripts/mvc/ui/ui-frames.js
+1 -1
View File
@@ -156,7 +156,7 @@ var View = Backbone.View.extend({
* argument that is the frame's content DOM element
*/
add: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (this.frame_counter >= this.options.frame_max) {
Galaxy.modal.show({
title: _l("Warning"),
client/galaxy/scripts/mvc/ui/ui-misc.js
+7 -7
View File
@@ -257,13 +257,13 @@ export var Upload = Backbone.View.extend({
* what we need where we need it, allowing for better package optimization.
*/
export let Button = Buttons.Button;
export let ButtonCheck = Buttons.ButtonCheck;
export let ButtonMenu = Buttons.ButtonMenu;
export let ButtonLink = Buttons.ButtonLink;
export let Checkbox = Options.Checkbox;
export let RadioButton = Options.RadioButton;
export let Radio = Options.Radio;
export const Button = Buttons.Button;
export const ButtonCheck = Buttons.ButtonCheck;
export const ButtonMenu = Buttons.ButtonMenu;
export const ButtonLink = Buttons.ButtonLink;
export const Checkbox = Options.Checkbox;
export const RadioButton = Options.RadioButton;
export const Radio = Options.Radio;
export { Select, Slider, Drilldown };
export default {
client/galaxy/scripts/mvc/ui/ui-popover.js
+2 -2
View File
@@ -21,7 +21,7 @@ export default Backbone.View.extend({
* Show popover
*/
show: function($content) {
let btn = "<i class='fa fa-times-circle'/>";
const btn = "<i class='fa fa-times-circle'/>";
$(this.$target).popover({
title: `${this.options.title} ${btn}`,
placement: this.options.placement,
@@ -33,7 +33,7 @@ export default Backbone.View.extend({
// add event to hide if click is outside of popup and not on container
var self = this;
let $popover = $(this.$target.data("bs.popover").tip);
const $popover = $(this.$target.data("bs.popover").tip);
$popover.find(".popover-header > i").on("click", () => this.hide());
$("body").on(`mousedown.${this.uid}`, e => {
if (!$($popover).is(e.target) && $($popover).has(e.target).length === 0) {
client/galaxy/scripts/mvc/ui/ui-rules-edit.js
+2 -2
View File
@@ -72,7 +72,7 @@ var View = Backbone.View.extend({
_showRuleEditor: function(elements) {
const elementsType = "collection_contents";
const importType = "collections";
let value = this._value;
const value = this._value;
const options = {
saveRulesFn: rules => this._handleRulesSave(rules),
initialRules: value
@@ -142,7 +142,7 @@ var View = Backbone.View.extend({
} else if (value.mapping.length === 0) {
message = "No collection identifiers defined, specify at least one collection identifier.";
} else {
for (let rule of value.rules) {
for (const rule of value.rules) {
if (rule.error) {
message = "One or more rules in error.";
break;
client/galaxy/scripts/mvc/ui/ui-select-content.js
+26 -26
View File
@@ -157,7 +157,7 @@ var View = Backbone.View.extend({
};
// add drag-drop event handlers
let element = this.$el.get(0);
const element = this.$el.get(0);
element.addEventListener("dragenter", e => {
this.lastenter = e.target;
self.$el.addClass("ui-dragover");
@@ -171,7 +171,7 @@ var View = Backbone.View.extend({
element.addEventListener("drop", e => {
e.preventDefault();
try {
let drop_data = JSON.parse(e.dataTransfer.getData("text"))[0];
const drop_data = JSON.parse(e.dataTransfer.getData("text"))[0];
this._handleDropValues(drop_data);
} catch (e) {
this._handleDropStatus("danger");
@@ -223,19 +223,19 @@ var View = Backbone.View.extend({
/** Return the currently selected dataset values */
value: function(new_value) {
let galaxy = getGalaxyInstance();
const galaxy = getGalaxyInstance();
new_value !== undefined && this.model.set("value", new_value);
let current = this.model.get("current");
const current = this.model.get("current");
if (this.config[current]) {
let id_list = this.fields[current].value();
if (id_list !== null) {
id_list = $.isArray(id_list) ? id_list : [id_list];
if (id_list.length > 0) {
let result = this._batch({ values: [] });
for (let i in id_list) {
let details = this.cache[`${id_list[i]}_${this.config[current].src}`];
const result = this._batch({ values: [] });
for (const i in id_list) {
const details = this.cache[`${id_list[i]}_${this.config[current].src}`];
if (details) {
let unpatchedValue = this._unpatchValue(details);
const unpatchedValue = this._unpatchValue(details);
result.values.push(unpatchedValue);
} else {
galaxy.emit.debug(
@@ -259,7 +259,7 @@ var View = Backbone.View.extend({
_changeCurrent: function() {
var self = this;
_.each(this.fields, (field, i) => {
let cnf = self.config[i];
const cnf = self.config[i];
if (self.model.get("current") == i) {
field.$el.show();
_.each(self.$batch, ($batchfield, batchmode) => {
@@ -288,8 +288,8 @@ var View = Backbone.View.extend({
/** Change of type */
_changeType: function() {
let self = this;
let galaxy = getGalaxyInstance();
const self = this;
const galaxy = getGalaxyInstance();
// identify selector type identifier i.e. [ flavor ]_[ type ]_[ multiple ]
var config_id =
@@ -347,8 +347,8 @@ var View = Backbone.View.extend({
tooltip: "Browse Datasets",
cls: "ml-2",
onclick: () => {
let current = this.model.get("current");
let cnf = this.config[current];
const current = this.model.get("current");
const cnf = this.config[current];
galaxy.data.dialog(
response => {
this._handleDropValues(response, false);
@@ -363,7 +363,7 @@ var View = Backbone.View.extend({
});
// append views
let $fields = $("<div/>").addClass("w-100");
const $fields = $("<div/>").addClass("w-100");
this.$el
.empty()
.addClass("d-flex flex-row")
@@ -458,7 +458,7 @@ var View = Backbone.View.extend({
/** Restores original value e.g. after patching library datasets **/
_unpatchValue: function(v) {
if (v.origin) {
let d = Object.assign({}, v);
const d = Object.assign({}, v);
d.id = d.id.substr(d.origin.length);
d.src = d.origin;
return d;
@@ -468,20 +468,20 @@ var View = Backbone.View.extend({
/** Add values from drag/drop */
_handleDropValues: function(drop_data, drop_partial = true) {
let self = this;
let data = this.model.get("data");
let current = this.model.get("current");
let config = this.config[current];
let field = this.fields[current];
const self = this;
const data = this.model.get("data");
const current = this.model.get("current");
const config = this.config[current];
const field = this.fields[current];
if (data) {
let values = $.isArray(drop_data) ? drop_data : [drop_data];
const values = $.isArray(drop_data) ? drop_data : [drop_data];
if (values.length > 0) {
let data_changed = false;
_.each(values, v => {
self._patchValue(v);
let new_id = v.id;
let new_src = (v.src = this._getSource(v));
let new_value = { id: new_id, src: new_src };
const new_id = v.id;
const new_src = (v.src = this._getSource(v));
const new_value = { id: new_id, src: new_src };
if (!_.findWhere(data[new_src], new_value)) {
data_changed = true;
data[new_src].push({
@@ -498,8 +498,8 @@ var View = Backbone.View.extend({
if (data_changed) {
this._changeData();
}
let first_id = values[0].id;
let first_src = values[0].src;
const first_id = values[0].id;
const first_src = values[0].src;
if (config.src == first_src && drop_partial) {
var current_value = field.value();
if (current_value && config.multiple) {
client/galaxy/scripts/mvc/ui/ui-select-default.js
+2 -2
View File
@@ -165,7 +165,7 @@ var View = Backbone.View.extend({
this.data2 = [];
this.data2index = {};
_.each(this.data, (option, index) => {
let d = {
const d = {
order: index,
id: option.value,
text: option.label,
@@ -201,7 +201,7 @@ var View = Backbone.View.extend({
},
formatResult: result => {
let extraTagWarning = "";
let filteredTags = _.filter(result.tags, t => this.matched_tags.hasOwnProperty(t));
const filteredTags = _.filter(result.tags, t => this.matched_tags.hasOwnProperty(t));
if (filteredTags.length > 5) {
extraTagWarning = `&nbsp;<div class="label label-warning">${filteredTags.length -
5} more tags</div>`;
client/galaxy/scripts/mvc/ui/ui-select.js
+2 -2
View File
@@ -153,11 +153,11 @@ var View = Backbone.View.extend({
if (!this.options.multiple) {
if (this.select_data) {
this.select_data.map(value => {
let mx = this.options.maximumTextLength + 3;
const mx = this.options.maximumTextLength + 3;
if (value.text && value.text.length > mx) {
let pos = value.text.indexOf(`(${value.id})`);
pos = pos != -1 && pos < mx ? pos : mx;
let sub = value.text.substring(0, pos).replace(/[ .]*$/, "");
const sub = value.text.substring(0, pos).replace(/[ .]*$/, "");
value.text = `${sub}...(${value.id})`;
}
});
client/galaxy/scripts/mvc/ui/ui-slider.js
+5 -5
View File
@@ -107,9 +107,9 @@ var View = Backbone.View.extend({
/** Set and return the current value */
value: function(new_val) {
if (new_val !== undefined) {
let options = this.model.attributes;
let original_val = new_val;
let is_value = new_val !== null && new_val !== "" && !this._isParameter(new_val);
const options = this.model.attributes;
const original_val = new_val;
const is_value = new_val !== null && new_val !== "" && !this._isParameter(new_val);
if (is_value) {
if (isNaN(new_val)) {
new_val = 0;
@@ -127,8 +127,8 @@ var View = Backbone.View.extend({
this.model.set("value", new_val);
this.model.trigger("change");
options.onchange(new_val);
let has_changed = is_value && parseInt(original_val) !== parseInt(new_val);
let message = has_changed ? "This value was invalid or out-of-range. It has been auto-corrected." : null;
const has_changed = is_value && parseInt(original_val) !== parseInt(new_val);
const message = has_changed ? "This value was invalid or out-of-range. It has been auto-corrected." : null;
this.model.trigger("error", message);
}
return this.model.get("value");
client/galaxy/scripts/mvc/upload/collection/collection-view.js
+2 -2
View File
@@ -248,7 +248,7 @@ export default Backbone.View.extend({
this.counter.announce--;
this.counter.success++;
this._updateScreen();
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
Galaxy.currHistoryPanel.refreshContents();
},
@@ -276,7 +276,7 @@ export default Backbone.View.extend({
},
_eventBuild: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var allHids = [];
_.forEach(this.collection.models, upload => {
allHids.push.apply(allHids, upload.get("hids"));
client/galaxy/scripts/mvc/upload/collection/rules-input-view.js
+4 -4
View File
@@ -78,14 +78,14 @@ export default Backbone.View.extend({
_renderSelectedType: function() {
const selectionType = this.selectionType;
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (selectionType == "dataset") {
if (!this.datasetSelectorView) {
this.selectedDatasetId = null;
const history = Galaxy && Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model;
const historyContentModels = history.contents.models;
const options = [];
for (let historyContentModel of historyContentModels) {
for (const historyContentModel of historyContentModels) {
const attr = historyContentModel.attributes;
if (attr.history_content_type !== "dataset") {
continue;
@@ -113,7 +113,7 @@ export default Backbone.View.extend({
},
_onDataset: function(selectedDatasetId) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.selectedDatasetId = selectedDatasetId;
if (!selectedDatasetId) {
this._setPreview("");
@@ -146,7 +146,7 @@ export default Backbone.View.extend({
_buildSelection: function(content) {
const selectionType = this.selectionType;
const selection = {};
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (selectionType == "dataset" || selectionType == "paste") {
selection.selectionType = "raw";
selection.content = content;
client/galaxy/scripts/mvc/upload/composite/composite-view.js
+1 -1
View File
@@ -160,7 +160,7 @@ export default Backbone.View.extend({
/** Refresh success state */
_eventSuccess: function(message) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.collection.each(it => {
it.set("status", "success");
});
client/galaxy/scripts/mvc/upload/default/default-row.js
+1 -1
View File
@@ -84,7 +84,7 @@ export default Backbone.View.extend({
// handle extension info popover
this.$(".upload-extension-info")
.on("click", e => {
let upload_ext = this.upload_extension;
const upload_ext = this.upload_extension;
if (upload_ext) {
if (upload_ext.extension_popup.visible) {
upload_ext.extension_popup.hide();
client/galaxy/scripts/mvc/upload/default/default-view.js
+2 -2
View File
@@ -260,7 +260,7 @@ export default Backbone.View.extend({
/** Success */
_eventSuccess: function(index, message) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var it = this.collection.get(index);
it.set({ percentage: 100, status: "success" });
this.ui_button.model.set("percentage", this._uploadPercentage(100, it.get("file_size")));
@@ -373,7 +373,7 @@ export default Backbone.View.extend({
this._uploadFtp();
// queue remaining files
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.uploadbox.start({
id: Galaxy.user.id,
chunk_upload_size: this.app.options.chunk_upload_size
client/galaxy/scripts/mvc/upload/upload-ftp.js
+1 -1
View File
@@ -27,7 +27,7 @@ export default Backbone.View.extend({
}).set(options);
this.collection = this.model.get("collection");
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy.config.enable_oidc) {
this.model.set("help_text", this.model.get("help_text") + this.model.get("oidc_text"));
}
client/galaxy/scripts/mvc/upload/upload-settings.js
+1 -1
View File
@@ -40,7 +40,7 @@ export default Backbone.View.extend({
var $checkbox = $("<div/>")
.addClass(`upload-${parameter.id} fa`)
.addClass((self.model.get(parameter.id) && self.options.class_check) || self.options.class_uncheck);
let $row = $("<tr/>")
const $row = $("<tr/>")
.append($("<td/>").append($checkbox))
.append($("<td/>").append(parameter.title))
.on("click", () => {
client/galaxy/scripts/mvc/upload/upload-view.js
+2 -2
View File
@@ -65,7 +65,7 @@ export default Backbone.View.extend({
/** Show/hide upload dialog */
show: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var self = this;
if (!Galaxy.currHistoryPanel || !Galaxy.currHistoryPanel.model) {
window.setTimeout(() => {
@@ -114,7 +114,7 @@ export default Backbone.View.extend({
/** Refresh user and current history */
currentHistory: function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
return this.current_user && Galaxy.currHistoryPanel.model.get("id");
},
client/galaxy/scripts/mvc/user/user-custom-builds.js
+1 -1
View File
@@ -19,7 +19,7 @@ var Collection = Backbone.Collection.extend({
var View = Backbone.View.extend({
initialize: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var self = this;
this.active_tab = "user";
var history_id = Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;
client/galaxy/scripts/mvc/user/user-model.js
+3 -3
View File
@@ -55,13 +55,13 @@ var User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(
},
updatePreferences: function(name, new_value) {
let preferences = this.get("preferences");
const preferences = this.get("preferences");
preferences[name] = JSON.stringify(new_value);
this.preferences = preferences;
},
getFavorites: function() {
let preferences = this.get("preferences");
const preferences = this.get("preferences");
if (preferences && preferences.favorites) {
return JSON.parse(preferences.favorites);
} else {
@@ -72,7 +72,7 @@ var User = Backbone.Model.extend(baseMVC.LoggableMixin).extend(
},
updateFavorites: function(object_type, new_favorites) {
let favorites = this.getFavorites();
const favorites = this.getFavorites();
favorites[object_type] = new_favorites[object_type];
this.updatePreferences("favorites", favorites);
},
client/galaxy/scripts/mvc/user/user-preferences.js
+3 -3
View File
@@ -12,7 +12,7 @@ import QueryStringParsing from "utils/query-string-parsing";
/** Contains descriptive dictionaries describing user forms */
var Model = Backbone.Model.extend({
initialize: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
options = options || {};
options.user_id = options.user_id || Galaxy.user.id;
this.set({
@@ -151,7 +151,7 @@ var View = Backbone.View.extend({
render: function() {
var self = this;
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var config = Galaxy.config;
$.getJSON(`${getAppRoot()}api/users/${Galaxy.user.id}`, data => {
self.$preferences = $("<div/>")
@@ -215,7 +215,7 @@ var View = Backbone.View.extend({
},
_templateFooter: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
return `<p class="mt-2">You are using <strong>${
options.nice_total_disk_usage
}</strong> of disk space in this Galaxy instance. ${
client/galaxy/scripts/mvc/visualization/chart/chart-client.js
+2 -2
View File
@@ -12,7 +12,7 @@ import Menu from "mvc/visualization/chart/views/menu";
export default Backbone.View.extend({
initialize: function(options) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
this.modal = Galaxy && Galaxy.modal ? Galaxy.modal : new Modal.View();
this.setElement(
$("<div/>")
@@ -45,7 +45,7 @@ export default Backbone.View.extend({
this.chart.trigger("redraw");
})
.fail(response => {
let message = response.responseJSON && response.responseJSON.err_msg;
const message = response.responseJSON && response.responseJSON.err_msg;
this.errormessage = message || "Import failed for unkown reason.";
});
}
client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js
+3 -3
View File
@@ -12,7 +12,7 @@ function createPNG(options) {
}
function _downloadData(imageData, filename) {
let link = document.createElement("a");
const link = document.createElement("a");
link.download = filename;
link.href = imageData;
link.click();
@@ -47,7 +47,7 @@ function _toImage($el, x_offset, y_offset, newContext) {
/** Convert canvas to png */
function _canvas2png(options) {
let $canvas = options.$el.find(".charts-viewer-canvas");
const $canvas = options.$el.find(".charts-viewer-canvas");
try {
if ($canvas.width() !== 0 && $canvas.height() !== 0) {
var newCanvas = document.createElement("canvas");
@@ -91,7 +91,7 @@ function _svg2png(options) {
source.src = "data:image/svg+xml;base64," + window.btoa(xml.string);
source.onload = function() {
context.drawImage(source, 0, 0, canvas.width, canvas.height);
let imageData = canvas.toDataURL("image/png");
const imageData = canvas.toDataURL("image/png");
_downloadPNGData(imageData, options.title);
$container.remove();
};
client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
+3 -3
View File
@@ -86,9 +86,9 @@ var request = function(options) {
for (let i = 0; i < results.length; i++) {
results[i] = [];
}
for (let i in response.data) {
for (const i in response.data) {
var row = response.data[i];
for (let j in row) {
for (const j in row) {
var v = row[j];
if (v !== undefined && v != 2147483647 && j < column_length) {
results[j].push(v);
@@ -96,7 +96,7 @@ var request = function(options) {
}
}
console.debug("tabular-datasets::_fetch() - Fetching complete.");
for (let i in results) {
for (const i in results) {
var column = column_list[i];
var block_id = _block_id(dataset_id, column);
_cache[block_id] = results[i];
client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
+1 -1
View File
@@ -142,7 +142,7 @@ var wait = function(chart, success, error) {
/** Refresh history panel */
var refreshHdas = function() {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
if (Galaxy && Galaxy.currHistoryPanel) {
Galaxy.currHistoryPanel.refreshContents();
}
client/galaxy/scripts/mvc/visualization/chart/utilities/series.js
+10 -10
View File
@@ -5,8 +5,8 @@ import * as d3 from "d3";
function getDomains(groups, keys) {
function _apply(operator, key) {
let value;
for (let group_index in groups) {
let value_sub = d3[operator](groups[group_index].values, function(d) {
for (const group_index in groups) {
const value_sub = d3[operator](groups[group_index].values, function(d) {
return d[key];
});
value = value === undefined ? value_sub : Math[operator](value, value_sub);
@@ -34,11 +34,11 @@ function makeSeries(groups, keys) {
var point = [];
if (keys) {
for (var key_index in keys) {
let column_index = keys[key_index];
const column_index = keys[key_index];
point.push(group.values[value_index][column_index]);
}
} else {
for (let column_index in group.values[value_index]) {
for (const column_index in group.values[value_index]) {
point.push(group.values[value_index][column_index]);
}
}
@@ -109,12 +109,12 @@ function makeUniqueCategories(groups, with_index) {
}
}
// convert group values into category indeces
for (let i in groups) {
let group = groups[i];
for (let j in group.values) {
let value_dict = group.values[j];
for (let key in categories) {
let value = String(value_dict[key]);
for (const i in groups) {
const group = groups[i];
for (const j in group.values) {
const value_dict = group.values[j];
for (const key in categories) {
const value = String(value_dict[key]);
value_dict[key] = categories[key][value];
}
}
client/galaxy/scripts/mvc/visualization/chart/views/menu.js
+1 -1
View File
@@ -124,7 +124,7 @@ export default Backbone.View.extend({
});
this.buttons = [this.left_button, this.right_button, this.execute_button, this.export_button, this.save_button];
this.setElement("<div/>");
for (let b of this.buttons) {
for (const b of this.buttons) {
this.$el.append(b.$el);
}
this.listenTo(this.model, "change", () => this.render());
client/galaxy/scripts/mvc/webhooks.js
+1 -1
View File
@@ -54,7 +54,7 @@ const load = options => {
function filterType(data, type) {
return data.models.filter(item => {
let itype = item.get("type");
const itype = item.get("type");
if (itype) {
return itype.indexOf(type) !== -1;
} else {
client/galaxy/scripts/mvc/workflow/workflow-forms.js
+6 -6
View File
@@ -56,7 +56,7 @@ var Tool = Backbone.View.extend({
form.model.get("postchange")(process, form);
},
postchange: function(process, form) {
let Galaxy = getGalaxyInstance();
const Galaxy = getGalaxyInstance();
var options = form.model.attributes;
var current_state = {
tool_id: options.id,
@@ -201,7 +201,7 @@ function _visit(head, head_list, output_id, options) {
function _makeRenameHelp(name_labels) {
let help_section = `This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables/">here</a> for more information. Valid input variables are:`;
let li = `
const li = `
<ul>
${name_labels
.map(
@@ -224,10 +224,10 @@ function _makeSection(output_id, label, options) {
var node = options.node;
var workflow = options.workflow;
for (let key in datatypes) {
for (const key in datatypes) {
extensions.push({ 0: datatypes[key], 1: datatypes[key] });
}
for (let key in node.input_terminals) {
for (const key in node.input_terminals) {
name_label_map.push({ name: node.input_terminals[key].name, label: node.input_terminals[key].label });
}
var rename_help = _makeRenameHelp(name_label_map);
@@ -379,8 +379,8 @@ function _addSections(form) {
help:
"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."
});
for (let output_id in node.output_terminals) {
let label = node.output_terminals[output_id].label || output_id;
for (const output_id in node.output_terminals) {
const label = node.output_terminals[output_id].label || output_id;
inputs.push(_makeSection(output_id, label, options));
}
}

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