Merged dev

.gitignore

@@ -127,9 +127,6 @@ client/**/jsconfig.json
 # Jars
 tool-data/shared/jars/
 
-# CSS build artifacts.
-sprite-*.scss
-
 # JS, Local node_modules, and bower_components directories
 static/maps
 static/plugins
@@ -147,9 +144,13 @@ doc/source/api/api.rst
 doc/source/api/ts_api.rst
 doc/source/dev/schema.rst
 
+# webpack stats
+client/webpack-stats.json
+
 # Misc
 *.orig
 .DS_Store
 *.rej
 *~
 .idea
+.vscode

client/.babelrc

@@ -1,14 +1,12 @@
 {
-  "presets": [
-    ["@babel/preset-env", { "modules": false }]
-  ],
-  "plugins": [
-    "transform-vue-template", 
-    "@babel/plugin-syntax-dynamic-import"
-  ],
-  "ignore": [
-    "i18n.js",
-    "utils/localization.js",
-    "nls/*"
-  ]
+    "presets": [
+        [
+            "@babel/preset-env",
+            {
+                "modules": false
+            }
+        ]
+    ],
+    "plugins": ["transform-vue-template", "@babel/plugin-syntax-dynamic-import"],
+    "ignore": ["i18n.js", "utils/localization.js", "nls/*"]
 }

client/galaxy/scripts/apps/admin.js

@@ -1,9 +1,9 @@
-import * as Backbone from "backbone";
-import * as _ from "underscore";
+/* global Galaxy */
+/* global $ */
+/* global _ */
+
 import _l from "utils/localization";
-import jQuery from "jquery";
-var $ = jQuery;
-import GalaxyApp from "galaxy";
+import { GalaxyApp } from "galaxy";
 import AdminPanel from "./panels/admin-panel";
 import FormWrapper from "mvc/form/form-wrapper";
 import GridView from "mvc/grid/grid-view";
@@ -15,10 +15,8 @@ import DataTables from "components/admin/DataTables.vue";
 import DataTypes from "components/admin/DataTypes.vue";
 import Vue from "vue";
 
-/* global Galaxy */
-
 window.app = function app(options, bootstrapped) {
-    window.Galaxy = new GalaxyApp.GalaxyApp(options, bootstrapped);
+    window.Galaxy = new GalaxyApp(options, bootstrapped);
     Galaxy.debug("admin app");
 
     /** Routes */
@@ -105,17 +103,17 @@ window.app = function app(options, bootstrapped) {
                 })
             );
         },
-
+        _display_vue_helper: function(component, props) {
+            let instance = Vue.extend(component);
+            let vm = document.createElement("div");
+            this.page.display(vm);
+            new instance(props).$mount(vm);
+        },
         show_data_tables: function() {
-            var vueMount = document.createElement("div");
-            this.page.display(vueMount);
-            new Vue(DataTables).$mount(vueMount);
+            this._display_vue_helper(DataTables);
         },
-
         show_data_types: function() {
-            var vueMount = document.createElement("div");
-            this.page.display(vueMount);
-            new Vue(DataTypes).$mount(vueMount);
+            this._display_vue_helper(DataTypes);
         },
 
         show_forms: function() {

client/galaxy/scripts/apps/analysis.js

@@ -1,8 +1,6 @@
-import $ from "jquery";
-import "bootstrap";
-import * as _ from "underscore";
+/* global Galaxy, $, _ */
+import { GalaxyApp } from "galaxy";
 import decodeUriComponent from "decode-uri-component";
-import GalaxyApp from "galaxy";
 import Router from "layout/router";
 import ToolPanel from "./panels/tool-panel";
 import HistoryPanel from "./panels/history-panel";
@@ -31,8 +29,6 @@ import Citations from "components/Citations.vue";
 import DisplayStructure from "components/DisplayStructured.vue";
 import Vue from "vue";
 
-/* global Galaxy */
-
 /** define the 'Analyze Data'/analysis/main/home page for Galaxy
  *  * has a masthead
  *  * a left tool menu to allow the user to load tools in the center panel
@@ -45,7 +41,7 @@ import Vue from "vue";
  *      * etc.
  */
 window.app = function app(options, bootstrapped) {
-    window.Galaxy = new GalaxyApp.GalaxyApp(options, bootstrapped);
+    window.Galaxy = new GalaxyApp(options, bootstrapped);
     Galaxy.debug("analysis app");
 
     /** Routes */
@@ -90,6 +86,13 @@ window.app = function app(options, bootstrapped) {
             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");
+            this.page.display(vm);
+            new instance(props).$mount(vm);
+        },
+
         show_tours: function(tour_id) {
             if (tour_id) {
                 Tours.giveTourById(tour_id);
@@ -150,10 +153,9 @@ window.app = function app(options, bootstrapped) {
                 new GridView({
                     url_base: `${Galaxy.root}workflow/list_published`,
                     active_tab: "shared",
-                    url_data:
-                        {
-                            'f-username': ( userFilter == null ) ? "" : userFilter
-                        }
+                    url_data: {
+                        "f-username": userFilter == null ? "" : userFilter
+                    }
                 })
             );
         },
@@ -206,10 +208,7 @@ window.app = function app(options, bootstrapped) {
         },
 
         show_histories_import: function() {
-            var historyImportInstance = Vue.extend(HistoryImport);
-            var vm = document.createElement("div");
-            this.page.display(vm);
-            new historyImportInstance().$mount(vm);
+            this._display_vue_helper(HistoryImport);
         },
 
         show_histories_permissions: function() {

client/galaxy/scripts/apps/chart.js

@@ -1,20 +1,19 @@
-import * as _ from "libs/underscore";
+/**
+ * These props are being exported with extended.js now since
+ * extended is exposing its props on window via the expose-loader
+ */
+
 import Client from "mvc/visualization/chart/chart-client";
 import Datasets from "mvc/visualization/chart/utilities/datasets";
 import Series from "mvc/visualization/chart/utilities/series";
 import Jobs from "mvc/visualization/chart/utilities/jobs";
 
-window.bundleEntries = window.bundleEntries || {};
+export function chart(options) {
+    return new Client(options);
+}
 
-export const bundleEntries = {
-    chart: function(options) {
-        return new Client(options);
-    },
-    chartUtilities: {
-        Datasets: Datasets,
-        Jobs: Jobs,
-        Series: Series
-    }
+export let chartUtilities = {
+    Datasets: Datasets,
+    Jobs: Jobs,
+    Series: Series
 };
-
-_.extend(window.bundleEntries, bundleEntries);

client/galaxy/scripts/apps/extended.js

@@ -1,40 +1,43 @@
-import $ from "jquery";
+/* global Galaxy, $ */
 import "bootstrap";
-import GalaxyApp from "galaxy";
+export { GalaxyApp } from "galaxy";
 import WorkflowView from "mvc/workflow/workflow-view";
-import Trackster from "viz/trackster";
+import { TracksterUIView } from "viz/trackster";
+export { TracksterUI } from "viz/trackster";
 import Circster from "viz/circster";
-import Phyloviz from "viz/phyloviz";
-import Sweepster from "viz/sweepster";
+export { PhylovizView as phyloviz } from "viz/phyloviz";
+export { SweepsterVisualization, SweepsterVisualizationView } from "viz/sweepster";
 import GalaxyLibrary from "galaxy.library";
 import AdminToolshed from "admin.toolshed";
 import Masthead from "layout/masthead";
 import user from "mvc/user/user-model";
 import Modal from "mvc/ui/ui-modal";
-import pagesEditorOnload from "galaxy.pages";
-import Data from "mvc/dataset/data";
-import History from "mvc/history/history-model";
-import HistoryContents from "mvc/history/history-contents";
+export { default as pages } from "galaxy.pages";
+export { createTabularDatasetChunkedView } from "mvc/dataset/data";
+import { HistoryCollection } from "mvc/history/history-model";
+export { History } from "mvc/history/history-model";
+export { HistoryContents } from "mvc/history/history-contents";
 import MultiPanel from "mvc/history/multi-panel";
-import HistoryView from "mvc/history/history-view";
-import HistoryViewAnnotated from "mvc/history/history-view-annotated";
-import HistoryCopyDialog from "mvc/history/copy-dialog";
-import HDAListItemEdit from "mvc/history/hda-li-edit";
-import HDAModel from "mvc/history/hda-model";
+export { historyEntry as history } from "mvc/history/history-view";
+export { default as HistoryViewAnnotated } from "mvc/history/history-view-annotated";
+export { default as HistoryCopyDialog } from "mvc/history/copy-dialog";
+export { default as HDAListItemEdit } from "mvc/history/hda-li-edit";
+export { default as HDAModel } from "mvc/history/hda-model";
 import addLogging from "utils/add-logging";
-import LegacyGridView from "legacy/grid/grid-view";
-import * as run_stats from "reports/run_stats";
-import ToolshedGroups from "toolshed/toolshed.groups";
+export { default as LegacyGridView } from "legacy/grid/grid-view";
+export { create_chart, create_histogram } from "reports/run_stats";
+export { default as ToolshedGroups } from "toolshed/toolshed.groups";
 
-/* global Galaxy */
+export { chart, chartUtilities } from "./chart";
 
+// TODO: update this when galaxy singleton code is merged
 if (window.Galaxy && window.Galaxy.debug === undefined) {
     //TODO: (kind of a temporary hack?) Must have Galaxy.logging for some of the imports
     //here; remove when imports are all fixed.
     addLogging(window.Galaxy, "GalaxyApp");
 }
 
-export function mastheadEntry(options) {
+export function masthead(options) {
     if (!Galaxy.user) {
         Galaxy.user = new user.User(options.user_json);
     }
@@ -45,28 +48,28 @@ export function mastheadEntry(options) {
     }
 }
 
-export function adminToolshedEntry(options) {
+export function adminToolshed(options) {
     new AdminToolshed.GalaxyApp(options);
 }
 
-export function tracksterEntry(options) {
-    new Trackster.GalaxyApp(options);
+export function trackster(options) {
+    new TracksterUIView(options);
 }
 
-export function circsterEntry(options) {
+export function circster(options) {
     new Circster.GalaxyApp(options);
 }
 
-export function workflowEntry(options) {
+export function workflow(options) {
     new WorkflowView(options);
 }
 
-export function libraryEntry(options) {
+export function library(options) {
     new GalaxyLibrary.GalaxyApp(options);
 }
 
-export function multiHistoryEntry(options) {
-    let histories = new History.HistoryCollection([], {
+export function multiHistory(options) {
+    let histories = new HistoryCollection([], {
         includeDeleted: options.includingDeleted,
         order: options.order,
         limitOnFirstFetch: options.limit,
@@ -83,32 +86,3 @@ export function multiHistoryEntry(options) {
         multipanel.render(0);
     });
 }
-
-export const bundleEntries = {
-    library: libraryEntry,
-    masthead: mastheadEntry,
-    workflow: workflowEntry,
-    trackster: tracksterEntry,
-    circster: circsterEntry,
-    adminToolshed: adminToolshedEntry,
-    pages: pagesEditorOnload,
-    phyloviz: Phyloviz.PhylovizView,
-    createTabularDatasetChunkedView: Data.createTabularDatasetChunkedView,
-    multiHistory: multiHistoryEntry,
-    history: HistoryView.historyEntry,
-    History: History.History,
-    HistoryContents: HistoryContents.HistoryContents,
-    SweepsterVisualization: Sweepster.SweepsterVisualization,
-    SweepsterVisualizationView: Sweepster.SweepsterVisualizationView,
-    HistoryCopyDialog,
-    HistoryViewAnnotated,
-    Trackster,
-    HDAListItemEdit,
-    HDAModel,
-    GalaxyApp,
-    LegacyGridView,
-    run_stats,
-    ToolshedGroups
-};
-
-window.bundleEntries = bundleEntries;