Merge branch 'dev' into remove_unused_workflow_endpoint

.travis.yml

@@ -16,6 +16,7 @@ env:
 matrix:
   allow_failures:
   - env: TOX_ENV=check-python-dependencies
+  - env: TOX_ENV=qunit
 
 addons:
   apt:

Makefile

@@ -138,6 +138,9 @@ client-watch: node-deps ## A useful target for parallel development building.
 	cd client && yarn run watch
 	@echo "Remember to 'make client' when finished developing!"
 
+client-test:
+	cd client && yarn run test
+
 charts: node-deps ## Rebuild charts
 	cd client && yarn run build-charts
 

client/galaxy/scripts/apps/admin-toolshed.js

@@ -0,0 +1,7 @@
+import AdminToolshed from "admin.toolshed";
+
+export function App(options) {
+    new AdminToolshed.GalaxyApp(options);
+}
+
+window.adminToolshedApp = App;

client/galaxy/scripts/apps/admin.js

@@ -9,6 +9,8 @@ import QueryStringParsing from "utils/query-string-parsing";
 import Router from "layout/router";
 import Utils from "utils/utils";
 import Page from "layout/page";
+import Vue from "libs/vue";
+import UserAPIKeys from "components/user_api_keys.vue";
 
 window.app = function app(options, bootstrapped) {
     window.Galaxy = new GalaxyApp.GalaxyApp(options, bootstrapped);
@@ -24,7 +26,8 @@ window.app = function app(options, bootstrapped) {
             "(/)admin(/)quotas": "show_quotas",
             "(/)admin(/)repositories": "show_repositories",
             "(/)admin(/)forms": "show_forms",
-            "(/)admin(/)form(/)(:form_id)": "show_form"
+            "(/)admin(/)form(/)(:form_id)": "show_form",
+            "(/)admin/api_keys": "show_user_api_keys"
         },
 
         authenticate: function(args, name) {
@@ -91,6 +94,12 @@ window.app = function app(options, bootstrapped) {
             );
         },
 
+        show_user_api_keys: function() {
+            var vuemount = document.createElement("div");
+            this.page.display(vuemount);
+            new Vue(UserAPIKeys).$mount(vuemount);
+        },
+
         show_forms: function() {
             this.page.display(
                 new GridView({

client/galaxy/scripts/apps/analysis.js

@@ -20,6 +20,8 @@ import Utils from "utils/utils";
 import Ui from "mvc/ui/ui-misc";
 import DatasetError from "mvc/dataset/dataset-error";
 import DatasetEditAttributes from "mvc/dataset/dataset-edit-attributes";
+import Citations from "components/citations.vue";
+import Vue from "libs/vue";
 
 /** define the 'Analyze Data'/analysis/main/home page for Galaxy
  *  * has a masthead
@@ -54,6 +56,7 @@ window.app = function app(options, bootstrapped) {
             "(/)workflows(/)list": "show_workflows",
             "(/)workflows/list_published(/)": "show_workflows_published",
             "(/)workflows/create(/)": "show_workflows_create",
+            "(/)histories(/)citations(/)": "show_history_citations",
             "(/)histories(/)rename(/)": "show_histories_rename",
             "(/)histories(/)permissions(/)": "show_histories_permissions",
             "(/)histories(/)(:action_id)": "show_histories",
@@ -120,6 +123,13 @@ window.app = function app(options, bootstrapped) {
             this.page.display(new HistoryList.View({ action_id: action_id }));
         },
 
+        show_history_citations: function() {
+            var citationInstance = Vue.extend(Citations);
+            var vm = document.createElement("div");
+            this.page.display(vm);
+            new citationInstance({ propsData: { id: QueryStringParsing.get("id"), source: "histories" } }).$mount(vm);
+        },
+
         show_histories_rename: function() {
             this.page.display(
                 new FormWrapper.View({
@@ -197,11 +207,10 @@ window.app = function app(options, bootstrapped) {
         },
 
         show_custom_builds: function() {
-            var self = this;
             var historyPanel = this.page.historyPanel.historyView;
             if (!historyPanel || !historyPanel.model || !historyPanel.model.id) {
                 window.setTimeout(() => {
-                    self.show_custom_builds();
+                    this.show_custom_builds();
                 }, 500);
                 return;
             }
@@ -257,20 +266,19 @@ window.app = function app(options, bootstrapped) {
 
         /** load workflow by its url in run mode */
         _loadWorkflow: function() {
-            var self = this;
             Utils.get({
                 url: `${Galaxy.root}api/workflows/${Utils.getQueryString("id")}/download?style=run`,
-                success: function(response) {
-                    self.page.display(new ToolFormComposite.View(response));
+                success: response => {
+                    this.page.display(new ToolFormComposite.View(response));
                 },
-                error: function(response) {
+                error: response => {
                     var error_msg = response.err_msg || "Error occurred while loading the resource.";
                     var options = {
                         message: error_msg,
                         status: "danger",
                         persistent: true
                     };
-                    self.page.display(new Ui.Message(options));
+                    this.page.display(new Ui.Message(options));
                 }
             });
         }

client/galaxy/scripts/apps/library.js

@@ -0,0 +1,7 @@
+import GalaxyLibrary from "galaxy.library";
+
+export function App(options) {
+    new GalaxyLibrary.GalaxyApp(options);
+}
+
+window.libraryApp = App;

client/galaxy/scripts/apps/masthead.js

@@ -0,0 +1,16 @@
+import Masthead from "layout/masthead";
+import user from "mvc/user/user-model";
+import Modal from "mvc/ui/ui-modal";
+
+export default function masthead(options) {
+    if (!Galaxy.user) {
+        Galaxy.user = new user.User(options.user_json);
+    }
+    if (!Galaxy.masthead) {
+        Galaxy.masthead = new Masthead.View(options);
+        Galaxy.modal = new Modal.View();
+        $("#masthead").replaceWith(Galaxy.masthead.render().$el);
+    }
+}
+
+window.masthead = masthead;

client/galaxy/scripts/apps/panels/admin-panel.js

@@ -69,7 +69,8 @@ var AdminPanel = Backbone.View.extend({
                     },
                     {
                         title: "API keys",
-                        url: "userskeys/all_users"
+                        url: "admin/api_keys",
+                        target: "__use_router__"
                     },
                     {
                         title: "Impersonate a user",

client/galaxy/scripts/apps/viz.js

@@ -0,0 +1,13 @@
+import Trackster from "viz/trackster";
+import Circster from "viz/circster";
+
+export function tracksterApp(options) {
+    new Trackster.GalaxyApp(options);
+}
+
+export function circsterApp(options) {
+    new Circster.GalaxyApp(options);
+}
+
+window.tracksterApp = tracksterApp;
+window.circsterApp = circsterApp;

client/galaxy/scripts/apps/workflow.js

@@ -0,0 +1,7 @@
+import WorkflowView from "mvc/workflow/workflow-view";
+
+export default function workflowApp(options) {
+    new WorkflowView(options);
+}
+
+window.workflowApp = workflowApp;

client/galaxy/scripts/components/citations.vue

@@ -0,0 +1,202 @@
+<template>
+    <div class="toolForm">
+        <div class="toolFormTitle">
+            Citations
+            <button v-if="viewRender" v-on:click="toggleViewRender" type="button" class="btn btn-xs" title="Show all in BibTeX format.">
+                <i class="fa fa-pencil-square-o"></i>
+                Show BibTeX
+            </button>
+            <button v-else type="button" v-on:click="toggleViewRender" class="btn btn-xs" title="Return to formatted citation list.">
+                <i class="fa fa-times"></i>
+                Hide BibTeX
+            </button>
+        </div>
+        <div class="citations-bibtex toolFormBody citation-padding">
+            <div v-if="source === 'histories'" class="infomessage">
+                When writing up your analysis, remember to include all references that should be cited in order
+                to completely describe your work. Also, please remember to <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.
+            </div>
+            <span v-if="viewRender" class="citations-formatted">
+                <p v-html="formattedReferences">
+                </p>
+            </span>
+            <textarea v-else class="citations-bibtex-text">
+                {{ content }}
+            </textarea>
+        </div>
+    </div>
+</template>
+<script>
+import axios from "axios";
+import * as bibtexParse from "libs/bibtexParse";
+import { convertLaTeX } from "latex-to-unicode-converter";
+import { stringifyLaTeX } from "latex-parser";
+
+export default {
+    props: {
+        source: {
+            type: String,
+            required: true
+        },
+        id: {
+            type: String,
+            required: true
+        },
+        viewRender: {
+            type: Boolean,
+            requried: false,
+            default: true
+        }
+    },
+    data() {
+        return {
+            citations: [],
+            content: "",
+            errors: []
+        };
+    },
+    computed: {
+        formattedReferences: function() {
+            return this.citations.reduce((a, b) => a.concat(`<p class="formatted-reference">${this.formattedReference(b)}</p>`), "");
+        }
+    },
+    created: function() {
+        axios
+            .get(`${Galaxy.root}api/${this.source}/${this.id}/citations`)
+            .then(response => {
+                this.content = "";
+                for (var rawCitation of response.data) {
+                    try {
+                        var citation = {
+                            fields: {},
+                            entryType: undefined
+                        };
+                        var parsed = bibtexParse.toJSON(rawCitation.content);
+                        if (parsed) {
+                            parsed = _.first(parsed);
+                            citation.entryType = parsed.entryType || undefined;
+                            for (var key in parsed.entryTags) {
+                                citation.fields[key.toLowerCase()] = parsed.entryTags[key];
+                            }
+                        }
+                        this.citations.push(citation);
+                        this.content += rawCitation.content;
+                    } catch (err) {
+                        console.warn("Error parsing bibtex: " + err);
+                    }
+                }
+            })
+            .catch(e => {
+                console.error(e);
+            });
+    },
+    methods: {
+        formattedReference: function(citation) {
+            var entryType = citation.entryType;
+            var fields = citation.fields;
+
+            var ref = "";
+            var authorsAndYear = `${this._asSentence(
+                (fields.author ? fields.author : "") + (fields.year ? ` (${fields.year})` : "")
+            )} `;
+            var title = fields.title || "";
+            var pages = fields.pages ? `pp. ${fields.pages}` : "";
+            var address = fields.address;
+            if (entryType == "article") {
+                var volume =
+                    (fields.volume ? fields.volume : "") +
+                    (fields.number ? ` (${fields.number})` : "") +
+                    (pages ? `, ${pages}` : "");
+                ref = `${authorsAndYear +
+                    this._asSentence(title) +
+                    (fields.journal ? `In <em>${fields.journal}, ` : "") +
+                    this._asSentence(volume) +
+                    this._asSentence(fields.address)}</em>`;
+            } else if (entryType == "inproceedings" || entryType == "proceedings") {
+                ref = `${authorsAndYear +
+                    this._asSentence(title) +
+                    (fields.booktitle ? `In <em>${fields.booktitle}, ` : "") +
+                    (pages ? pages : "") +
+                    (address ? `, ${address}` : "")}.</em>`;
+            } else if (entryType == "mastersthesis" || entryType == "phdthesis") {
+                ref =
+                    authorsAndYear +
+                    this._asSentence(title) +
+                    (fields.howpublished ? `${fields.howpublished}. ` : "") +
+                    (fields.note ? `${fields.note}.` : "");
+            } else if (entryType == "techreport") {
+                ref =
+                    authorsAndYear +
+                    this._asSentence(title) +
+                    this._asSentence(fields.institution) +
+                    this._asSentence(fields.number) +
+                    this._asSentence(fields.type);
+            } else if (entryType == "book" || entryType == "inbook" || entryType == "incollection") {
+                ref = `${authorsAndYear} ${this._formatBookInfo(fields)}`;
+            } else {
+                ref = `${authorsAndYear} ${this._asSentence(title)}${this._asSentence(
+                    fields.howpublished
+                )}${this._asSentence(fields.note)}`;
+            }
+            var doiUrl = "";
+            if (fields.doi) {
+                doiUrl = `http://dx.doi.org/${fields.doi}`;
+                ref += `[<a href="${doiUrl}" target="_blank">doi:${fields.doi}</a>]`;
+            }
+            var url = fields.url || doiUrl;
+            if (url) {
+                ref += `[<a href="${url}" target="_blank">Link</a>]`;
+            }
+            return convertLaTeX({ onError: (error, latex) => `{${stringifyLaTeX(latex)}}` }, ref);
+        },
+        _formatBookInfo: function(fields) {
+            var info = "";
+            if (fields.chapter) {
+                info += `${fields.chapter} in `;
+            }
+            if (fields.title) {
+                info += `<em>${fields.title}</em>`;
+            }
+            if (fields.editor) {
+                info += `, Edited by ${fields.editor}, `;
+            }
+            if (fields.publisher) {
+                info += `, ${fields.publisher}`;
+            }
+            if (fields.pages) {
+                info += `, pp. ${fields.pages}`;
+            }
+            if (fields.series) {
+                info += `, <em>${fields.series}</em>`;
+            }
+            if (fields.volume) {
+                info += `, Vol.${fields.volume}`;
+            }
+            if (fields.issn) {
+                info += `, ISBN: ${fields.issn}`;
+            }
+            return `${info}.`;
+        },
+        _asSentence: function(str) {
+            return str && str.trim() ? `${str}. ` : "";
+        },
+        toggleViewRender: function() {
+            this.viewRender = !this.viewRender;
+        }
+    }
+};
+</script>
+<style>
+.citations-formatted{
+    word-wrap: break-word;
+}
+
+.citations-bibtex-text{
+    width: 100%;
+    height: 500px;
+}
+
+.citation-padding{
+    padding:5px 10px;
+}
+</style>

client/galaxy/scripts/components/user_api_keys.vue

@@ -0,0 +1,68 @@
+<template>
+    <div id="form-userkeys" class="toolForm" v-cloak>
+        <div class="toolFormTitle">User Information</div>
+        <div v-if="users && users.length > 0">
+            <table class="grid">
+                <thead><th>Encoded UID</th><th>Email</th><th>API Key</th><th>Actions</th></thead>
+                <tbody>
+                    <tr v-for="user in users">
+                        <td>
+                            {{ user.uid }}
+                        </td>
+                        <td>
+                            {{ user.email }}
+                        </td>
+                        <td>
+                            {{ user.key }}
+                        </td>
+                        <td>
+                            <input type="button" value="Generate a new key now" v-on:click="generateKey( user.uid )" />
+                        </td>
+                    </tr>
+                </tbody>
+            </table>
+        </div>
+        <div v-else>
+            <div>No user information available</div>
+        </div>
+        <div style="clear: both"></div>
+    </div>
+</template>
+
+<script>
+import axios from "axios";
+
+export default {
+    data() {
+        return {
+            // Should really do something with errors here.  Eventually.
+            users: [],
+            errors: []
+        };
+    },
+    created: function() {
+        axios
+            .get(`${Galaxy.root}userskeys/all_users`)
+            .then(response => {
+                this.users = response.data;
+            })
+            .catch(e => {
+                this.errors.push(e);
+            });
+    },
+    methods: {
+        generateKey: function(id) {
+            axios
+                .get(`${Galaxy.root}userskeys/admin_api_keys`, { params: { uid: id } })
+                .then(response => {
+                    this.users = response.data;
+                })
+                .catch(e => {
+                    this.errors.push(e);
+                });
+        }
+    }
+};
+</script>
+<style>
+</style>

client/galaxy/scripts/galaxy.library.js

@@ -2,7 +2,6 @@
 // === MAIN GALAXY LIBRARY MODULE ====
 // MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
 
-import mod_masthead from "layout/masthead";
 import mod_utils from "utils/utils";
 import mod_toastr from "libs/toastr";
 import mod_baseMVC from "mvc/base-mvc";

client/galaxy/scripts/layout/panel.js

@@ -230,7 +230,7 @@ var CenterPanel = Backbone.View.extend({
             this.$panel
                 .empty()
                 .scrollTop(0)
-                .append(view.$el)
+                .append(view.$el || view)
                 .show();
             Galaxy.trigger("center-panel:load", view);
         }

client/galaxy/scripts/mvc/citation/citation-model.js

@@ -1,93 +0,0 @@
-import * as parseBibtex from "libs/bibtex";
-import baseMVC from "mvc/base-mvc";
-import _l from "utils/localization";
-
-/* global Backbone */
-
-_.extend(parseBibtex.ENTRY_TYPES_, {
-    online: 998, // Galaxy MOD: Handle @online entries for preprints.
-    data: 999 // Galaxy MOD: Handle @data citations coming from figshare.
-});
-
-var logNamespace = "citation";
-//==============================================================================
-/** @class model for tool citations.
- *  @name Citation
- *  @augments Backbone.Model
- */
-var Citation = Backbone.Model.extend(baseMVC.LoggableMixin).extend({
-    _logNamespace: logNamespace,
-
-    defaults: {
-        content: ""
-    },
-
-    initialize: function() {
-        var parsed;
-        try {
-            // TODO: to model.parse/.validate
-            parsed = parseBibtex(this.attributes.content);
-        } catch (err) {
-            return;
-        }
-        // bibtex returns successfully parsed in .entries and any parsing errors in .errors
-        if (parsed.errors.length) {
-            // the gen. form of these errors seems to be [ line, col, char, error message ]
-            var errors = parsed.errors.reduce((all, current) => `${all}; ${current}`);
-            // throw new Error( 'Error parsing bibtex: ' + errors );
-            this.log(`Error parsing bibtex: ${errors}`);
-        }
-
-        this._fields = {};
-        this.entry = _.first(parsed.entries);
-        if (this.entry) {
-            var rawFields = this.entry.Fields;
-            for (var key in rawFields) {
-                var value = rawFields[key];
-                var lowerKey = key.toLowerCase();
-                this._fields[lowerKey] = value;
-            }
-        }
-    },
-    entryType: function() {
-        return this.entry ? this.entry.EntryType : undefined;
-    },
-    fields: function() {
-        return this._fields;
-    }
-});
-
-//==============================================================================
-/** @class Backbone collection of citations.
- */
-var BaseCitationCollection = Backbone.Collection.extend(baseMVC.LoggableMixin).extend({
-    _logNamespace: logNamespace,
-
-    /** root api url */
-    urlRoot: `${Galaxy.root}api`,
-    partial: true, // Assume some tools in history/workflow may not be properly annotated yet.
-    model: Citation
-});
-
-var HistoryCitationCollection = BaseCitationCollection.extend({
-    /** complete api url */
-    url: function() {
-        return `${this.urlRoot}/histories/${this.history_id}/citations`;
-    }
-});
-
-var ToolCitationCollection = BaseCitationCollection.extend({
-    /** complete api url */
-    url: function() {
-        return `${this.urlRoot}/tools/${this.tool_id}/citations`;
-    },
-    partial: false // If a tool has citations, assume they are complete.
-});
-
-//==============================================================================
-
-export default {
-    Citation: Citation,
-    HistoryCitationCollection: HistoryCitationCollection,
-    ToolCitationCollection: ToolCitationCollection
-};

client/galaxy/scripts/mvc/citation/citation-view.js

@@ -1,189 +0,0 @@
-import baseMVC from "mvc/base-mvc";
-import citationModel from "mvc/citation/citation-model";
-import _l from "utils/localization";
-var CitationView = Backbone.View.extend({
-    tagName: "div",
-    className: "citations",
-    render: function() {
-        this.$el.append(`<p>${this.formattedReference()}</p>`);
-        return this;
-    },
-    formattedReference: function() {
-        var model = this.model;
-        var entryType = model.entryType();
-        var fields = model.fields();
-
-        var ref = "";
-        // Code inspired by...
-        // https://github.com/vkaravir/bib-publication-list/blob/master/src/bib-publication-list.js
-        var authorsAndYear = `${this._asSentence(
-            (fields.author ? fields.author : "") + (fields.year ? ` (${fields.year})` : "")
-        )} `;
-        var title = fields.title || "";
-        var pages = fields.pages ? `pp. ${fields.pages}` : "";
-        var address = fields.address;
-        if (entryType == "article") {
-            var volume =
-                (fields.volume ? fields.volume : "") +
-                (fields.number ? ` (${fields.number})` : "") +
-                (pages ? `, ${pages}` : "");
-            ref = `${authorsAndYear +
-                this._asSentence(title) +
-                (fields.journal ? `In <em>${fields.journal}, ` : "") +
-                this._asSentence(volume) +
-                this._asSentence(fields.address)}</em>`;
-        } else if (entryType == "inproceedings" || entryType == "proceedings") {
-            ref = `${authorsAndYear +
-                this._asSentence(title) +
-                (fields.booktitle ? `In <em>${fields.booktitle}, ` : "") +
-                (pages ? pages : "") +
-                (address ? `, ${address}` : "")}.</em>`;
-        } else if (entryType == "mastersthesis" || entryType == "phdthesis") {
-            ref =
-                authorsAndYear +
-                this._asSentence(title) +
-                (fields.howpublished ? `${fields.howpublished}. ` : "") +
-                (fields.note ? `${fields.note}.` : "");
-        } else if (entryType == "techreport") {
-            ref =
-                authorsAndYear +
-                this._asSentence(title) +
-                this._asSentence(fields.institution) +
-                this._asSentence(fields.number) +
-                this._asSentence(fields.type);
-        } else if (entryType == "book" || entryType == "inbook" || entryType == "incollection") {
-            ref = `${authorsAndYear} ${this._formatBookInfo(fields)}`;
-        } else {
-            ref = `${authorsAndYear} ${this._asSentence(title)}${this._asSentence(
-                fields.howpublished
-            )}${this._asSentence(fields.note)}`;
-        }
-        var doiUrl = "";
-        if (fields.doi) {
-            doiUrl = `http://dx.doi.org/${fields.doi}`;
-            ref += `[<a href="${doiUrl}" target="_blank">doi:${fields.doi}</a>]`;
-        }
-        var url = fields.url || doiUrl;
-        if (url) {
-            ref += `[<a href="${url}" target="_blank">Link</a>]`;
-        }
-        return ref;
-    },
-    _formatBookInfo: function(fields) {
-        var info = "";
-        if (fields.chapter) {
-            info += `${fields.chapter} in `;
-        }
-        if (fields.title) {
-            info += `<em>${fields.title}</em>`;
-        }
-        if (fields.editor) {
-            info += `, Edited by ${fields.editor}, `;
-        }
-        if (fields.publisher) {
-            info += `, ${fields.publisher}`;
-        }
-        if (fields.pages) {
-            info += `, pp. ${fields.pages}`;
-        }
-        if (fields.series) {
-            info += `, <em>${fields.series}</em>`;
-        }
-        if (fields.volume) {
-            info += `, Vol.${fields.volume}`;
-        }
-        if (fields.issn) {
-            info += `, ISBN: ${fields.issn}`;
-        }
-        return `${info}.`;
-    },
-    _asSentence: function(str) {
-        return str && str.trim() ? `${str}. ` : "";
-    }
-});
-
-var CitationListView = Backbone.View.extend({
-    el: "#citations",
-    /**
-     * Set up view.
-     */
-    initialize: function() {
-        this.listenTo(this.collection, "add", this.renderCitation);
-    },
-
-    events: {
-        "click .citations-to-bibtex": "showBibtex",
-        "click .citations-to-formatted": "showFormatted"
-    },
-
-    renderCitation: function(citation) {
-        var citationView = new CitationView({ model: citation });
-        this.$(".citations-formatted").append(citationView.render().el);
-        var rawTextarea = this.$(".citations-bibtex-text");
-        rawTextarea.val(`${rawTextarea.val()}\n\r${citation.attributes.content}`);
-    },
-
-    render: function() {
-        this.$el.html(this.citationsElement());
-        this.collection.each(function(item) {
-            this.renderCitation(item);
-        }, this);
-        this.showFormatted();
-    },
-
-    showBibtex: function() {
-        this.$(".citations-to-formatted").show();
-        this.$(".citations-to-bibtex").hide();
-        this.$(".citations-bibtex").show();
-        this.$(".citations-formatted").hide();
-        this.$(".citations-bibtex-text").select();
-    },
-
-    showFormatted: function() {
-        this.$(".citations-to-formatted").hide();
-        this.$(".citations-to-bibtex").show();
-        this.$(".citations-bibtex").hide();
-        this.$(".citations-formatted").show();
-    },
-
-    partialWarningElement: function() {
-        if (this.collection.partial) {
-            return [
-                '<div style="padding:5px 10px">',
-                "<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate",
-                " citations explicitly at this time. When writing up your analysis, please manually",
-                " review your histories and find all references",
-                " that should be cited in order to completely describe your work. Also, please remember to",
-                ' <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.',
-                "</div>"
-            ].join("");
-        } else {
-            return "";
-        }
-    },
-
-    citationsElement: function() {
-        return [
-            '<div class="toolForm">',
-            '<div class="toolFormTitle">',
-            _l("Citations"),
-            ' <button type="button" class="btn btn-xs citations-to-bibtex" title="Show all in BibTeX format."><i class="fa fa-pencil-square-o"></i> Show BibTeX</button>',
-            ' <button type="button" class="btn btn-xs citations-to-formatted" title="Return to formatted citation list."><i class="fa fa-times"></i> Hide BibTeX</button>',
-            "</div>",
-            '<div class="toolFormBody" style="padding:5px 10px">',
-            this.partialWarningElement(),
-            '<span class="citations-formatted" style="word-wrap: break-word;"></span>',
-            "</div>",
-            '<div class="citations-bibtex toolFormBody" style="padding:5px 10px">',
-            '<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',
-            "</div>",
-            "</div>"
-        ].join("");
-    }
-});
-
-//==============================================================================
-export default {
-    CitationView: CitationView,
-    CitationListView: CitationListView
-};

client/galaxy/scripts/mvc/history/options-menu.js

@@ -150,8 +150,12 @@ var menu = [
     },
     {
         html: _l("Export Tool Citations"),
-        href: "history/citations",
-        anon: true
+        anon: true,
+        func: function() {
+            if (Galaxy && Galaxy.currHistoryPanel && Galaxy.router) {
+                Galaxy.router.push(`/histories/citations?id=${Galaxy.currHistoryPanel.model.id}`);
+            }
+        }
     },
     {
         html: _l("Export History to File"),

client/galaxy/scripts/mvc/library/library-folderlist-view.js

@@ -1,9 +1,7 @@
-import mod_masthead from "layout/masthead";
-import mod_utils from "utils/utils";
 import mod_toastr from "libs/toastr";
 import mod_library_model from "mvc/library/library-model";
 import mod_library_folderrow_view from "mvc/library/library-folderrow-view";
-import mod_library_dataset_view from "mvc/library/library-dataset-view";
+
 var FolderListView = Backbone.View.extend({
     el: "#folder_items_element",
     // progress percentage

client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js

@@ -1,4 +1,3 @@
-import mod_masthead from "layout/masthead";
 import mod_utils from "utils/utils";
 import mod_toastr from "libs/toastr";
 import mod_library_model from "mvc/library/library-model";

client/galaxy/scripts/mvc/library/library-libraryrow-view.js

@@ -1,6 +1,4 @@
 // dependencies
-import mod_masthead from "layout/masthead";
-import mod_utils from "utils/utils";
 import mod_toastr from "libs/toastr";
 // galaxy library row view
 var LibraryRowView = Backbone.View.extend({

client/galaxy/scripts/mvc/tool/tool-form-base.js

@@ -5,8 +5,8 @@ import Utils from "utils/utils";
 import Deferred from "utils/deferred";
 import Ui from "mvc/ui/ui-misc";
 import FormBase from "mvc/form/form-view";
-import CitationModel from "mvc/citation/citation-model";
-import CitationView from "mvc/citation/citation-view";
+import Citations from "components/citations.vue";
+import Vue from "libs/vue";
 export default FormBase.extend({
     initialize: function(options) {
         var self = this;
@@ -225,16 +225,15 @@ export default FormBase.extend({
         var options = this.model.attributes;
         var $el = $("<div/>").append(this._templateHelp(options));
         if (options.citations) {
-            var $citations = $("<div/>");
-            var citations = new CitationModel.ToolCitationCollection();
-            citations.tool_id = options.id;
-            var citation_list_view = new CitationView.CitationListView({
-                el: $citations,
-                collection: citations
-            });
-            citation_list_view.render();
-            citations.fetch();
-            $el.append($citations);
+            var citationInstance = Vue.extend(Citations);
+            var vm = document.createElement("div");
+            $el.append(vm);
+            new citationInstance({
+                propsData: {
+                    id: options.id,
+                    source: "tools"
+                }
+            }).$mount(vm);
         }
         return $el;
     },

client/galaxy/scripts/mvc/workflow/workflow-forms.js

@@ -98,12 +98,14 @@ var Tool = Backbone.View.extend({
                         __class__: "RuntimeValue"
                     };
                     input.is_workflow =
-                        (input.options && input.options.length == 0) || ["integer", "float"].indexOf(input.type) != -1;
+                        (input.options && input.options.length === 0) || ["integer", "float"].indexOf(input.type) != -1;
                 }
             }
         });
         Utils.deepeach(options.inputs, input => {
-            input.type == "conditional" && (input.test_param.collapsible_value = undefined);
+            if (input.type === "conditional") {
+                input.test_param.collapsible_value = undefined;
+            }
         });
         _addSections(form);
         _addLabelAnnotation(form);
@@ -151,182 +153,186 @@ function _addLabelAnnotation(form) {
     });
 }
 
+/** Visit input nodes and enrich by name/value pairs from server data */
+function _visit(head, head_list, output_id, options) {
+    var post_job_actions = options.node.post_job_actions;
+    head_list = head_list || [];
+    head_list.push(head);
+    for (var i in head.inputs) {
+        var input = head.inputs[i];
+        var action = input.action;
+        if (action) {
+            input.name = `pja__${output_id}__${input.action}`;
+            if (input.pja_arg) {
+                input.name += `__${input.pja_arg}`;
+            }
+            if (input.payload) {
+                for (var p_id in input.payload) {
+                    input.payload[`${input.name}__${p_id}`] = input.payload[p_id];
+                    delete input.payload[p_id];
+                }
+            }
+            var d = post_job_actions[input.action + output_id];
+            if (d) {
+                for (var j in head_list) {
+                    head_list[j].expanded = true;
+                }
+                if (input.pja_arg) {
+                    input.value = (d.action_arguments && d.action_arguments[input.pja_arg]) || input.value;
+                } else {
+                    input.value = "true";
+                }
+            }
+        }
+        if (input.inputs) {
+            _visit(input, head_list.slice(0), output_id, options);
+        }
+    }
+}
+
+/** Builds sub section with step actions/annotation */
+function _makeSection(output_id, options) {
+    var extensions = [];
+    var input_terminal_names = [];
+    var datatypes = options.datatypes;
+    var node = options.node;
+    var workflow = options.workflow;
+
+    for (var key in datatypes) {
+        extensions.push({ 0: datatypes[key], 1: datatypes[key] });
+    }
+    for (key in node.input_terminals) {
+        input_terminal_names.push(node.input_terminals[key].name);
+    }
+    extensions.sort((a, b) => (a.label > b.label ? 1 : a.label < b.label ? -1 : 0));
+    extensions.unshift({
+        0: "Sequences",
+        1: "Sequences"
+    });
+    extensions.unshift({
+        0: "Roadmaps",
+        1: "Roadmaps"
+    });
+    extensions.unshift({
+        0: "Leave unchanged",
+        1: "__empty__"
+    });
+    var output;
+    var input_config = {
+        title: `Configure Output: '${output_id}'`,
+        type: "section",
+        flat: true,
+        inputs: [
+            {
+                label: "Label",
+                type: "text",
+                value: ((output = node.getWorkflowOutput(output_id)) && output.label) || "",
+                help: "This will provide a short name to describe the output - this must be unique across workflows.",
+                onchange: function(new_value) {
+                    workflow.attemptUpdateOutputLabel(node, output_id, new_value);
+                }
+            },
+            {
+                action: "RenameDatasetAction",
+                pja_arg: "newname",
+                label: "Rename dataset",
+                type: "text",
+                value: "",
+                ignore: "",
+                help: `This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables/">here</a> for more information. Valid inputs are: <strong>${input_terminal_names.join(
+                    ", "
+                )}</strong>.`
+            },
+            {
+                action: "ChangeDatatypeAction",
+                pja_arg: "newtype",
+                label: "Change datatype",
+                type: "select",
+                ignore: "__empty__",
+                value: "__empty__",
+                options: extensions,
+                help: "This action will change the datatype of the output to the indicated value."
+            },
+            {
+                action: "TagDatasetAction",
+                pja_arg: "tags",
+                label: "Add Tags",
+                type: "text",
+                value: "",
+                ignore: "",
+                help: "This action will set tags for the dataset."
+            },
+            {
+                action: "RemoveTagDatasetAction",
+                pja_arg: "tags",
+                label: "Remove Tags",
+                type: "text",
+                value: "",
+                ignore: "",
+                help: "This action will remove tags for the dataset."
+            },
+            {
+                title: "Assign columns",
+                type: "section",
+                flat: true,
+                inputs: [
+                    {
+                        action: "ColumnSetAction",
+                        pja_arg: "chromCol",
+                        label: "Chrom column",
+                        type: "integer",
+                        value: "",
+                        ignore: ""
+                    },
+                    {
+                        action: "ColumnSetAction",
+                        pja_arg: "startCol",
+                        label: "Start column",
+                        type: "integer",
+                        value: "",
+                        ignore: ""
+                    },
+                    {
+                        action: "ColumnSetAction",
+                        pja_arg: "endCol",
+                        label: "End column",
+                        type: "integer",
+                        value: "",
+                        ignore: ""
+                    },
+                    {
+                        action: "ColumnSetAction",
+                        pja_arg: "strandCol",
+                        label: "Strand column",
+                        type: "integer",
+                        value: "",
+                        ignore: ""
+                    },
+                    {
+                        action: "ColumnSetAction",
+                        pja_arg: "nameCol",
+                        label: "Name column",
+                        type: "integer",
+                        value: "",
+                        ignore: ""
+                    }
+                ],
+                help: "This action will set column assignments in the output dataset. Blank fields are ignored."
+            }
+        ]
+    };
+    _visit(input_config, [], output_id, options);
+    return input_config;
+}
+
 /** Builds all sub sections */
 function _addSections(form) {
     var options = form.model.attributes;
     var inputs = options.inputs;
-    var datatypes = options.datatypes;
     var node = options.node;
-    var workflow = options.workflow;
     var post_job_actions = node.post_job_actions;
     var output_id = node.output_terminals && Object.keys(node.output_terminals)[0];
 
-    /** Visit input nodes and enrich by name/value pairs from server data */
-    function visit(head, head_list) {
-        head_list = head_list || [];
-        head_list.push(head);
-        for (var i in head.inputs) {
-            var input = head.inputs[i];
-            var action = input.action;
-            if (action) {
-                input.name = `pja__${output_id}__${input.action}`;
-                if (input.pja_arg) {
-                    input.name += `__${input.pja_arg}`;
-                }
-                if (input.payload) {
-                    for (var p_id in input.payload) {
-                        input.payload[`${input.name}__${p_id}`] = input.payload[p_id];
-                        delete input.payload[p_id];
-                    }
-                }
-                var d = post_job_actions[input.action + output_id];
-                if (d) {
-                    for (var j in head_list) {
-                        head_list[j].expanded = true;
-                    }
-                    if (input.pja_arg) {
-                        input.value = (d.action_arguments && d.action_arguments[input.pja_arg]) || input.value;
-                    } else {
-                        input.value = "true";
-                    }
-                }
-            }
-            input.inputs && visit(input, head_list.slice(0));
-        }
-    }
-
-    /** Builds sub section with step actions/annotation */
-    function _makeSection(output_id, datatypes) {
-        var extensions = [];
-        var input_terminal_names = [];
-        for (var key in datatypes) {
-            extensions.push({ 0: datatypes[key], 1: datatypes[key] });
-        }
-        for (key in node.input_terminals) {
-            input_terminal_names.push(node.input_terminals[key].name);
-        }
-        extensions.sort((a, b) => (a.label > b.label ? 1 : a.label < b.label ? -1 : 0));
-        extensions.unshift({
-            0: "Sequences",
-            1: "Sequences"
-        });
-        extensions.unshift({
-            0: "Roadmaps",
-            1: "Roadmaps"
-        });
-        extensions.unshift({
-            0: "Leave unchanged",
-            1: "__empty__"
-        });
-        var output;
-        var input_config = {
-            title: `Configure Output: '${output_id}'`,
-            type: "section",
-            flat: true,
-            inputs: [
-                {
-                    label: "Label",
-                    type: "text",
-                    value: ((output = node.getWorkflowOutput(output_id)) && output.label) || "",
-                    help:
-                        "This will provide a short name to describe the output - this must be unique across workflows.",
-                    onchange: function(new_value) {
-                        workflow.attemptUpdateOutputLabel(node, output_id, new_value);
-                    }
-                },
-                {
-                    action: "RenameDatasetAction",
-                    pja_arg: "newname",
-                    label: "Rename dataset",
-                    type: "text",
-                    value: "",
-                    ignore: "",
-                    help: `This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables/">here</a> for more information. Valid inputs are: <strong>${input_terminal_names.join(
-                        ", "
-                    )}</strong>.`
-                },
-                {
-                    action: "ChangeDatatypeAction",
-                    pja_arg: "newtype",
-                    label: "Change datatype",
-                    type: "select",
-                    ignore: "__empty__",
-                    value: "__empty__",
-                    options: extensions,
-                    help: "This action will change the datatype of the output to the indicated value."
-                },
-                {
-                    action: "TagDatasetAction",
-                    pja_arg: "tags",
-                    label: "Add Tags",
-                    type: "text",
-                    value: "",
-                    ignore: "",
-                    help: "This action will set tags for the dataset."
-                },
-                {
-                    action: "RemoveTagDatasetAction",
-                    pja_arg: "tags",
-                    label: "Remove Tags",
-                    type: "text",
-                    value: "",
-                    ignore: "",
-                    help: "This action will remove tags for the dataset."
-                },
-                {
-                    title: "Assign columns",
-                    type: "section",
-                    flat: true,
-                    inputs: [
-                        {
-                            action: "ColumnSetAction",
-                            pja_arg: "chromCol",
-                            label: "Chrom column",
-                            type: "integer",
-                            value: "",
-                            ignore: ""
-                        },
-                        {
-                            action: "ColumnSetAction",
-                            pja_arg: "startCol",
-                            label: "Start column",
-                            type: "integer",
-                            value: "",
-                            ignore: ""
-                        },
-                        {
-                            action: "ColumnSetAction",
-                            pja_arg: "endCol",
-                            label: "End column",
-                            type: "integer",
-                            value: "",
-                            ignore: ""
-                        },
-                        {
-                            action: "ColumnSetAction",
-                            pja_arg: "strandCol",
-                            label: "Strand column",
-                            type: "integer",
-                            value: "",
-                            ignore: ""
-                        },
-                        {
-                            action: "ColumnSetAction",
-                            pja_arg: "nameCol",
-                            label: "Name column",
-                            type: "integer",
-                            value: "",
-                            ignore: ""
-                        }
-                    ],
-                    help: "This action will set column assignments in the output dataset. Blank fields are ignored."
-                }
-            ]
-        };
-        visit(input_config);
-        return input_config;
-    }
-
     if (output_id) {
         inputs.push({
             name: `pja__${output_id}__EmailAction`,
@@ -349,7 +355,7 @@ function _addSections(form) {
                 "Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."
         });
         for (var i in node.output_terminals) {
-            inputs.push(_makeSection(i, datatypes));
+            inputs.push(_makeSection(i, options));
         }
     }
 }

client/galaxy/scripts/mvc/workflow/workflow-node.js

@@ -14,7 +14,7 @@ var Node = Backbone.Model.extend({
         });
     },
     isWorkflowOutput: function(outputName) {
-        return this.getWorkflowOutput(outputName) != undefined;
+        return this.getWorkflowOutput(outputName) !== undefined;
     },
     removeWorkflowOutput: function(outputName) {
         while (this.isWorkflowOutput(outputName)) {
@@ -25,7 +25,7 @@ var Node = Backbone.Model.extend({
         if (!this.isWorkflowOutput(outputName)) {
             var output = { output_name: outputName };
             if (label) {
-                output["label"] = label;
+                output.label = label;
             }
             this.workflow_outputs.push(output);
             return true;
@@ -37,8 +37,8 @@ var Node = Backbone.Model.extend({
         var oldLabel = null;
         if (this.isWorkflowOutput(outputName)) {
             var workflowOutput = this.getWorkflowOutput(outputName);
-            oldLabel = workflowOutput["label"];
-            workflowOutput["label"] = label;
+            oldLabel = workflowOutput.label;
+            workflowOutput.label = label;
             changed = oldLabel != label;
         } else {
             changed = this.addWorkflowOutput(outputName, label);
@@ -239,7 +239,7 @@ var Node = Backbone.Model.extend({
         this.config_form = data.config_form;
         this.tool_version = this.config_form && this.config_form.version;
         this.errors = data.errors;
-        this.annotation = data["annotation"];
+        this.annotation = data.annotation;
         this.label = data.label;
         if ("post_job_actions" in data) {
             // Won't be present in response for data inputs
@@ -271,7 +271,7 @@ var Node = Backbone.Model.extend({
         old_body.replaceWith(new_body);
         if ("workflow_outputs" in data) {
             // Won't be present in response for data inputs
-            this.workflow_outputs = workflow_outputs ? workflow_outputs : [];
+            this.workflow_outputs = data.workflow_outputs ? data.workflow_outputs : [];
         }
         // If active, reactivate with new config_form
         this.markChanged();

client/galaxy/scripts/qunit/assets/base.css

@@ -0,0 +1 @@
+../../../../../static/style/blue/base.css

client/galaxy/scripts/qunit/test-app.js

@@ -0,0 +1,54 @@
+/** Creates a generic/global Galaxy environment, loads shared libraries and a fake server */
+define(
+    [
+        "jquery",
+        "sinon",
+        "libs/bootstrap",
+        "qunit/test-data/bootstrapped",
+        "qunit/test-data/fakeserver",
+        "galaxy",
+        "libs/jquery/select2",
+        "libs/jquery/jstorage",
+        "libs/jquery/jquery-ui"
+    ],
+    function($, sinon, bootstrap, bootstrapped, serverdata, appBase) {
+        var Galaxy = {
+            root: "/"
+        };
+
+        window.Galaxy = Galaxy;
+
+        $("head").append(
+            $('<link rel="stylesheet" type="text/css"  />').attr("href", "/base/galaxy/scripts/qunit/assets/base.css")
+        );
+
+        appBase = appBase.default;
+        return {
+            create: function() {
+                window.Galaxy = new appBase.GalaxyApp(bootstrapped);
+                window.Galaxy.currHistoryPanel = { model: new Backbone.Model() };
+                window.Galaxy.emit = {
+                    debug: function() {},
+                    error: function(v) {
+                        window.console.error(v);
+                    }
+                };
+                window.WAIT_FADE = 300;
+                window.fakeserver = sinon.fakeServer.create();
+                for (var route in serverdata) {
+                    window.fakeserver.respondWith("GET", window.Galaxy.root + route, [
+                        200,
+                        { "Content-Type": "application/json" },
+                        serverdata[route].data
+                    ]);
+                }
+            },
+            destroy: function() {
+                if (window.fakeserver) {
+                    window.fakeserver.restore();
+                    delete window.fakeserver;
+                }
+            }
+        };
+    }
+);

client/galaxy/scripts/qunit/test-data/bootstrapped.js

@@ -0,0 +1,29 @@
+define([], function() {
+    return {
+        config: {
+            allow_user_deletion: false,
+            allow_user_creation: true,
+            wiki_url: "https://galaxyproject.org/",
+            ftp_upload_site: null,
+            support_url: "https://galaxyproject.org/support/",
+            allow_user_dataset_purge: false,
+            allow_library_path_paste: false,
+            user_library_import_dir: null,
+            terms_url: null,
+            ftp_upload_dir: null,
+            library_import_dir: null,
+            logo_url: null,
+            enable_unique_workflow_defaults: false
+        },
+        user: {
+            username: "test",
+            quota_percent: null,
+            total_disk_usage: 61815527,
+            nice_total_disk_usage: "59.0 MB",
+            email: "test@test.test",
+            tags_used: ["test"],
+            model_class: "User",
+            id: "f2db41e1fa331b3e"
+        }
+    };
+});

client/galaxy/scripts/qunit/test-data/fakeserver.js

@@ -0,0 +1,15 @@
+define([], function() {
+    return {
+        "api/datatypes/mapping": {
+            data:
+                '{"ext_to_class_name" : {"txt" : "Text", "data":"Data","tabular":"Tabular", "binary": "Binary", "bam": "Bam" }, "class_to_classes": { "Data": { "Data": true }, "Text": { "Text": true, "Data": true }, "Tabular": { "Tabular": true, "Text": true, "Data": true }, "Binary": { "Data": true, "Binary": true }, "Bam": { "Data": true, "Binary": true, "Bam": true }}}'
+        },
+        "api/datatypes": {
+            data: '["RData", "ab1", "affybatch", "txt"]'
+        },
+        "api/tools/test/build": {
+            data:
+                '{ "id": "test", "name": "_name", "version": "_version", "description": "_description", "display": "true", "requirements": [ { "name": "req_name_a", "version": "req_version_a" }, { "name": "req_name_b", "version": "req_version_b" } ], "inputs": [ { "name": "a", "type": "text" }, { "name": "b",  "type": "conditional", "test_param": { "name": "c",  "type": "select", "value": "h", "options": [ [ "d", "d", false ], [ "h", "h", false ] ] }, "cases": [ { "name": "d", "value": "d", "inputs": [ { "name": "f", "type": "text", "value": "f" }, { "name": "g",  "type": "text", "value": "g" } ] }, { "name": "h", "value": "h", "inputs": [ { "name": "i",  "type": "text", "value": "i" }, { "name": "j",  "type": "text", "value": "j" } ] } ] }, { "name": "k",  "min": 1, "max": 2, "type": "repeat", "cache": [[ { "name": "l", "type": "text", "value": "l"}, { "name": "m",  "type": "conditional", "test_param": { "name": "n",  "type": "select", "value": "r", "options": [ [ "o", "o", false ], [ "r", "r", false ] ] }, "cases": [ { "name": "o", "value": "o", "inputs": [ { "name": "p",  "type": "text", "value": "p" }, { "name": "q",  "type": "text", "value": "q" } ] }, { "name": "r", "value": "r", "inputs": [ { "name": "s",  "type": "text", "value": "s" }, { "name": "t",  "type": "text", "value": "t"  } ] } ] } ] ], "inputs" : [ { "name": "l",  "type": "text", "value": "l" }, { "name": "m",  "type": "conditional", "test_param": { "name": "n",  "type": "select", "value": "o", "options": [ [ "o", "o", false ], [ "r", "r", false ] ] }, "cases": [ { "name": "o", "value": "o", "inputs": [ { "name": "p",  "type": "text", "value": "p" }, { "name": "q",  "type": "text", "value": "q" } ] }, { "name": "r", "value": "r", "inputs": [ { "name": "s",  "type": "text", "value": "s" }, { "name": "t",  "type": "text", "value": "t" } ] } ] } ] } ] }'
+        }
+    };
+});

client/galaxy/scripts/qunit/test-data/job-dag-1.js

@@ -0,0 +1,531 @@
+define([], function() {
+    // ============================================================================
+    var tools = {
+        upload1: {},
+        "Show beginning1": {},
+        "Show tail1": {},
+        random_lines1: {},
+        __SET_METADATA__: {},
+        cat1: {}
+    };
+
+    // ============================================================================
+    // plain 3 step job chain
+    var jobs1 = [
+        {
+            tool_id: "upload1",
+            update_time: "2014-10-03T15:12:25.904033",
+            inputs: {},
+            outputs: {
+                output0: {
+                    src: "hda",
+                    id: "8c959c9304a2bc4b"
+                }
+            },
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-03T15:12:22.589152",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "8a81cf6f989c4467",
+            tool: null
+        },
+        {
+            tool_id: "Show beginning1",
+            update_time: "2014-10-03T15:14:04.328484",
+            inputs: {
+                input: {
+                    src: "hda",
+                    id: "8c959c9304a2bc4b"
+                }
+            },
+            outputs: {
+                out_file1: {
+                    src: "hda",
+                    id: "132016f833b57406"
+                }
+            },
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-03T15:14:01.060662",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "6505e875ddb66fd2",
+            tool: null
+        },
+        {
+            tool_id: "Show tail1",
+            update_time: "2014-10-03T15:14:21.596871",
+            inputs: {
+                input: {
+                    src: "hda",
+                    id: "132016f833b57406"
+                }
+            },
+            outputs: {
+                out_file1: {
+                    src: "hda",
+                    id: "846fb0a2a64137c0"
+                }
+            },
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-03T15:14:18.425681",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "77f74776fd03cbc5",
+            tool: null
+        }
+    ];
+
+    var historyContents1 = [
+        {
+            deleted: false,
+            extension: "interval",
+            hid: 1,
+            history_content_type: "dataset",
+            history_id: "911dde3ddb677bcd",
+            id: "8c959c9304a2bc4b",
+            name: "1.interval",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/911dde3ddb677bcd/contents/datasets/8c959c9304a2bc4b",
+            visible: true
+        },
+        {
+            deleted: false,
+            extension: "interval",
+            hid: 2,
+            history_content_type: "dataset",
+            history_id: "911dde3ddb677bcd",
+            id: "132016f833b57406",
+            name: "Select first on data 1",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/911dde3ddb677bcd/contents/datasets/132016f833b57406",
+            visible: true
+        },
+        {
+            deleted: false,
+            extension: "interval",
+            hid: 3,
+            history_content_type: "dataset",
+            history_id: "911dde3ddb677bcd",
+            id: "846fb0a2a64137c0",
+            name: "Select last on data 2",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/911dde3ddb677bcd/contents/datasets/846fb0a2a64137c0",
+            visible: true
+        }
+    ];
+
+    // ============================================================================
+    // single job chain with a __SET_METADATA__ job
+    var jobs2 = [
+        {
+            tool_id: "upload1",
+            update_time: "2014-10-03T16:09:49.590769",
+            inputs: {},
+            outputs: {
+                output0: {
+                    src: "hda",
+                    id: "eca0af6fb47bf90c"
+                }
+            },
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-03T16:09:45.190023",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "bf60fd5f5f7f44bf",
+            tool: null
+        },
+        {
+            tool_id: "random_lines1",
+            update_time: "2014-10-03T16:10:44.743610",
+            inputs: {
+                input: {
+                    src: "hda",
+                    id: "eca0af6fb47bf90c"
+                }
+            },
+            outputs: {
+                out_file1: {
+                    src: "hda",
+                    id: "6fc9fbb81c497f69"
+                }
+            },
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-03T16:10:41.446413",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "90240358ebde1489",
+            tool: null
+        },
+        {
+            tool_id: "__SET_METADATA__",
+            update_time: "2014-10-03T16:14:44.196697",
+            inputs: {
+                input1: {
+                    src: "hda",
+                    id: "eca0af6fb47bf90c"
+                }
+            },
+            outputs: {},
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-03T16:14:37.901222",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "86cf1d3beeec9f1c",
+            tool: null
+        }
+    ];
+
+    var historyContents2 = [
+        {
+            deleted: false,
+            extension: "interval",
+            hid: 1,
+            history_content_type: "dataset",
+            history_id: "ff5476bcf6c921fa",
+            id: "eca0af6fb47bf90c",
+            name: "1.interval",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/ff5476bcf6c921fa/contents/datasets/eca0af6fb47bf90c",
+            visible: true
+        },
+        {
+            deleted: false,
+            extension: "interval",
+            hid: 2,
+            history_content_type: "dataset",
+            history_id: "ff5476bcf6c921fa",
+            id: "6fc9fbb81c497f69",
+            name: "Select random lines on data 1",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/ff5476bcf6c921fa/contents/datasets/6fc9fbb81c497f69",
+            visible: true
+        }
+    ];
+
+    var jobs3 = [
+        {
+            tool_id: "upload1",
+            update_time: "2014-10-13T20:28:58.549844",
+            inputs: {},
+            outputs: {
+                output0: {
+                    src: "hda",
+                    id: "6fb17d0cc6e8fae5"
+                }
+            },
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-13T20:28:43.162803",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "8c959c9304a2bc4b",
+            tool: null
+        },
+        {
+            tool_id: "upload1",
+            update_time: "2014-10-13T20:28:58.932152",
+            inputs: {},
+            outputs: {
+                output0: {
+                    src: "hda",
+                    id: "5114a2a207b7caff"
+                }
+            },
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-13T20:28:47.421452",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "132016f833b57406",
+            tool: null
+        },
+        {
+            tool_id: "Show beginning1",
+            update_time: "2014-10-13T20:29:31.424058",
+            inputs: {
+                input: {
+                    src: "hda",
+                    id: "6fb17d0cc6e8fae5"
+                }
+            },
+            outputs: {
+                out_file1: {
+                    src: "hda",
+                    id: "06ec17aefa2d49dd"
+                }
+            },
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-13T20:29:28.769495",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "846fb0a2a64137c0",
+            tool: null
+        },
+        {
+            tool_id: "Show beginning1",
+            update_time: "2014-10-13T20:29:55.851096",
+            inputs: {
+                input: {
+                    src: "hda",
+                    id: "5114a2a207b7caff"
+                }
+            },
+            outputs: {
+                out_file1: {
+                    src: "hda",
+                    id: "b8a0d6158b9961df"
+                }
+            },
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-13T20:29:53.291703",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "eca0af6fb47bf90c",
+            tool: null
+        },
+        {
+            tool_id: "Show tail1",
+            update_time: "2014-10-13T20:30:16.225937",
+            inputs: {
+                input: {
+                    src: "hda",
+                    id: "b8a0d6158b9961df"
+                }
+            },
+            outputs: {
+                out_file1: {
+                    src: "hda",
+                    id: "24d84bcf64116fe7"
+                }
+            },
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-13T20:30:13.789842",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "6fc9fbb81c497f69",
+            tool: null
+        }
+    ];
+
+    var historyContents3 = [
+        {
+            deleted: false,
+            extension: "bed",
+            hid: 1,
+            history_content_type: "dataset",
+            history_id: "5564089c81cf7fe8",
+            id: "6fb17d0cc6e8fae5",
+            name: "1.bed",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/5564089c81cf7fe8/contents/datasets/6fb17d0cc6e8fae5",
+            visible: true
+        },
+        {
+            deleted: false,
+            extension: "interval",
+            hid: 2,
+            history_content_type: "dataset",
+            history_id: "5564089c81cf7fe8",
+            id: "5114a2a207b7caff",
+            name: "1.interval",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/5564089c81cf7fe8/contents/datasets/5114a2a207b7caff",
+            visible: true
+        },
+        {
+            deleted: false,
+            extension: "bed",
+            hid: 3,
+            history_content_type: "dataset",
+            history_id: "5564089c81cf7fe8",
+            id: "06ec17aefa2d49dd",
+            name: "Select first on data 1",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/5564089c81cf7fe8/contents/datasets/06ec17aefa2d49dd",
+            visible: true
+        },
+        {
+            deleted: false,
+            extension: "interval",
+            hid: 4,
+            history_content_type: "dataset",
+            history_id: "5564089c81cf7fe8",
+            id: "b8a0d6158b9961df",
+            name: "Select first on data 2",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/5564089c81cf7fe8/contents/datasets/b8a0d6158b9961df",
+            visible: true
+        },
+        {
+            deleted: false,
+            extension: "interval",
+            hid: 5,
+            history_content_type: "dataset",
+            history_id: "5564089c81cf7fe8",
+            id: "24d84bcf64116fe7",
+            name: "Select last on data 4",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/5564089c81cf7fe8/contents/datasets/24d84bcf64116fe7",
+            visible: true
+        }
+    ];
+
+    var jobs4 = [
+        {
+            tool_id: "cat1",
+            update_time: "2014-10-21T17:33:36.960857",
+            inputs: {
+                input1: {
+                    src: "hda",
+                    id: "422eef6b1b545329",
+                    name: "input1"
+                },
+                "queries_0|input2": {
+                    src: "hda",
+                    id: "c86c1b73aa7102dd",
+                    name: "queries_0|input2"
+                }
+            },
+            outputs: {
+                out_file1: {
+                    src: "hda",
+                    id: "52d6bdfafedbb5e5",
+                    name: "out_file1"
+                }
+            },
+            exit_code: 0,
+            state: "ok",
+            create_time: "2014-10-21T17:33:34.302245",
+            params: {
+                // ...
+            },
+            model_class: "Job",
+            id: "92b83968e0b52980"
+        }
+    ];
+
+    var historyContents4 = [
+        {
+            dataset_id: 29,
+            deleted: false,
+            extension: "vcf",
+            hid: 1,
+            history_content_type: "dataset",
+            history_id: "c24141d7e4e77705",
+            id: "422eef6b1b545329",
+            name: "1.vcf",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/c24141d7e4e77705/contents/datasets/422eef6b1b545329",
+            visible: true
+        },
+        {
+            dataset_id: 56,
+            deleted: false,
+            extension: "maf",
+            hid: 2,
+            history_content_type: "dataset",
+            history_id: "c24141d7e4e77705",
+            id: "c86c1b73aa7102dd",
+            name: "3.maf",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/c24141d7e4e77705/contents/datasets/c86c1b73aa7102dd",
+            visible: true
+        },
+        {
+            dataset_id: 131,
+            deleted: false,
+            extension: "maf",
+            hid: 3,
+            history_content_type: "dataset",
+            history_id: "c24141d7e4e77705",
+            id: "52d6bdfafedbb5e5",
+            name: "Concatenate datasets on data 1 and data 2",
+            purged: false,
+            resubmitted: false,
+            state: "ok",
+            type: "file",
+            url: "/api/histories/c24141d7e4e77705/contents/datasets/52d6bdfafedbb5e5",
+            visible: true
+        }
+    ];
+
+    // ============================================================================
+    return {
+        tools: tools,
+        jobs1: jobs1,
+        historyContents1: historyContents1,
+        jobs2: jobs2,
+        historyContents2: historyContents2,
+        jobs3: jobs3,
+        historyContents3: historyContents3,
+        jobs4: jobs4,
+        historyContents4: historyContents4
+    };
+});

client/galaxy/scripts/qunit/test-data/paired-collection-creator.data.js

@@ -0,0 +1,154 @@
+define([], function() {
+    // ============================================================================
+    // plain 3 step job chain
+    var datasets1 = [
+        { name: "SET1-01_1.fastq" },
+        { name: "SET1-01_2.fastq" },
+        { name: "SET1-02_1.fastq" },
+        { name: "SET1-02_2.fastq" },
+        { name: "SET1-03_1.fastq" },
+        { name: "SET1-03_2.fastq" },
+        { name: "SET1-04_1.fastq" },
+        { name: "SET1-04_2.fastq" },
+        { name: "SET1-05_1.fastq" },
+        { name: "SET1-05_2.fastq" },
+        { name: "SET1-06_1.fastq" },
+        { name: "SET1-06_2.fastq" },
+        { name: "SET1-07_1.fastq" },
+        { name: "SET1-07_2.fastq" }
+    ];
+
+    var datasets1CreateRequestJSON = {
+        type: "dataset_collection",
+        collection_type: "list:paired",
+        name: "Heres a collection",
+        hide_source_items: false,
+        element_identifiers: [
+            {
+                collection_type: "paired",
+                src: "new_collection",
+                name: "SET1-07",
+                element_identifiers: [
+                    {
+                        name: "forward",
+                        id: "2",
+                        src: "hda"
+                    },
+                    {
+                        name: "reverse",
+                        id: "3",
+                        src: "hda"
+                    }
+                ]
+            },
+            {
+                collection_type: "paired",
+                src: "new_collection",
+                name: "SET1-06",
+                element_identifiers: [
+                    {
+                        name: "forward",
+                        id: "4",
+                        src: "hda"
+                    },
+                    {
+                        name: "reverse",
+                        id: "5",
+                        src: "hda"
+                    }
+                ]
+            },
+            {
+                collection_type: "paired",
+                src: "new_collection",
+                name: "SET1-05",
+                element_identifiers: [
+                    {
+                        name: "forward",
+                        id: "6",
+                        src: "hda"
+                    },
+                    {
+                        name: "reverse",
+                        id: "7",
+                        src: "hda"
+                    }
+                ]
+            },
+            {
+                collection_type: "paired",
+                src: "new_collection",
+                name: "SET1-04",
+                element_identifiers: [
+                    {
+                        name: "forward",
+                        id: "8",
+                        src: "hda"
+                    },
+                    {
+                        name: "reverse",
+                        id: "9",
+                        src: "hda"
+                    }
+                ]
+            },
+            {
+                collection_type: "paired",
+                src: "new_collection",
+                name: "SET1-03",
+                element_identifiers: [
+                    {
+                        name: "forward",
+                        id: "10",
+                        src: "hda"
+                    },
+                    {
+                        name: "reverse",
+                        id: "11",
+                        src: "hda"
+                    }
+                ]
+            },
+            {
+                collection_type: "paired",
+                src: "new_collection",
+                name: "SET1-02",
+                element_identifiers: [
+                    {
+                        name: "forward",
+                        id: "12",
+                        src: "hda"
+                    },
+                    {
+                        name: "reverse",
+                        id: "13",
+                        src: "hda"
+                    }
+                ]
+            },
+            {
+                collection_type: "paired",
+                src: "new_collection",
+                name: "SET1-01",
+                element_identifiers: [
+                    {
+                        name: "forward",
+                        id: "14",
+                        src: "hda"
+                    },
+                    {
+                        name: "reverse",
+                        id: "15",
+                        src: "hda"
+                    }
+                ]
+            }
+        ]
+    };
+
+    // ============================================================================
+    return {
+        _1: datasets1,
+        _1requestJSON: datasets1CreateRequestJSON
+    };
+});

client/galaxy/scripts/qunit/tests/form_tests.js

@@ -0,0 +1,182 @@
+/* global define */
+define(
+    [
+        "qunit/test-app",
+        "sinon",
+        "mvc/form/form-input",
+        "mvc/ui/ui-misc",
+        "mvc/form/form-data",
+        "mvc/tool/tool-form",
+        "utils/utils"
+    ],
+    function(testApp, sinon, InputElement, Ui, FormData, ToolForm, Utils) {
+        "use strict";
+        InputElement = InputElement.default;
+        Ui = Ui.default;
+        FormData = FormData.default;
+        ToolForm = ToolForm.default;
+        Utils = Utils.default;
+        QUnit.module("Form test", {
+            beforeEach: function() {
+                testApp.create();
+                this.clock = sinon.useFakeTimers();
+            },
+            afterEach: function() {
+                testApp.destroy();
+                this.clock.restore();
+            }
+        });
+
+        QUnit.test("tool-form", function(assert) {
+            var toolform = new ToolForm.View({ id: "test" });
+            var form = toolform.form;
+            $("body").prepend(toolform.$el);
+            window.fakeserver.respond();
+            var output = "";
+            for (var property in assert) {
+                output += property + ": ; ";
+            }
+            assert.ok(true, "MooCow");
+            assert.ok(
+                form.$(".portlet-title-text").html() == "<b>_name</b> _description (Galaxy Version _version)",
+                "Title correct"
+            );
+            var tour_ids = [];
+            $("[tour_id]").each(function() {
+                tour_ids.push($(this).attr("tour_id"));
+            });
+            assert.ok(
+                JSON.stringify(tour_ids) == '["a","b|c","b|i","b|j","k_0|l","k_0|m|n","k_0|m|s","k_0|m|t"]',
+                "Tour ids correct"
+            );
+            assert.ok(
+                JSON.stringify(form.data.create()) ==
+                    '{"a":"","b|c":"h","b|i":"i","b|j":"j","k_0|l":"l","k_0|m|n":"r","k_0|m|s":"s","k_0|m|t":"t"}',
+                "Created data correct"
+            );
+            var mapped_ids = [];
+            form.data.matchModel(form.model.attributes, function(input, id) {
+                mapped_ids.push($("#" + id).attr("tour_id"));
+            });
+            assert.ok(
+                JSON.stringify(mapped_ids) == '["a","b|c","b|i","b|j","k_0|l","k_0|m|n","k_0|m|s","k_0|m|t"]',
+                "Remapped tour ids correct"
+            );
+            this.clock.tick(window.WAIT_FADE);
+            var dropdown = form.$("#menu > .dropdown-menu");
+            assert.ok(dropdown.children().length == 2, "Found two menu items");
+            dropdown
+                .find(".fa-info-circle")
+                .parent()
+                .click();
+            this.clock.tick(window.WAIT_FADE);
+            assert.ok(
+                form.$(".ui-message").html() ===
+                    '<span>This tool requires req_name_a (Version req_version_a) and req_name_b (Version req_version_b). Click <a target="_blank" href="https://galaxyproject.org/tools/requirements/">here</a> for more information.</span>',
+                "Check requirements message"
+            );
+            assert.ok(form.$(".form-repeat-delete").css("display") == "none", "Delete button disabled");
+            var $add = form.$(".form-repeat-add");
+            assert.ok(!$add.attr("disabled"), "Adding new repeat possible");
+            $add.click();
+            this.clock.tick(window.WAIT_FADE);
+            assert.ok($add.attr("disabled"), "Adding new repeat has been disabled");
+            form.$(".form-repeat-delete").each(function(i, d) {
+                assert.ok($(d).css("display") == "block", "Delete buttons " + i + " enabled");
+            });
+            assert.ok(
+                JSON.stringify(form.data.create()) ==
+                    '{"a":"","b|c":"h","b|i":"i","b|j":"j","k_0|l":"l","k_0|m|n":"r","k_0|m|s":"s","k_0|m|t":"t","k_1|l":"l","k_1|m|n":"o","k_1|m|p":"p","k_1|m|q":"q"}',
+                "Created data correct, after adding repeat"
+            );
+            form.$(".form-repeat-delete:first").click();
+            assert.ok(form.$(".form-repeat-delete").css("display") == "none", "Delete button disabled");
+            this.clock.tick(window.WAIT_FADE);
+            assert.ok(
+                JSON.stringify(form.data.create()) ==
+                    '{"a":"","b|c":"h","b|i":"i","b|j":"j","k_0|l":"l","k_0|m|n":"o","k_0|m|p":"p","k_0|m|q":"q"}',
+                "Created data correct, after removing first repeat"
+            );
+        });
+
+        QUnit.test("data", function(assert) {
+            var visits = [];
+            Utils.get({
+                url: Galaxy.root + "api/tools/test/build",
+                success: function(response) {
+                    FormData.visitInputs(response.inputs, function(node, name, context) {
+                        visits.push({ name: name, node: node });
+                    });
+                }
+            });
+            window.fakeserver.respond();
+            assert.ok(
+                JSON.stringify(visits) ==
+                    '[{"name":"a","node":{"name":"a","type":"text"}},{"name":"b|c","node":{"name":"c","type":"select","value":"h","options":[["d","d",false],["h","h",false]]}},{"name":"b|i","node":{"name":"i","type":"text","value":"i"}},{"name":"b|j","node":{"name":"j","type":"text","value":"j"}},{"name":"k_0|l","node":{"name":"l","type":"text","value":"l"}},{"name":"k_0|m|n","node":{"name":"n","type":"select","value":"r","options":[["o","o",false],["r","r",false]]}},{"name":"k_0|m|s","node":{"name":"s","type":"text","value":"s"}},{"name":"k_0|m|t","node":{"name":"t","type":"text","value":"t"}}]',
+                "Testing value visitor"
+            );
+        });
+
+        QUnit.test("input", function(assert) {
+            var input = new InputElement(
+                {},
+                {
+                    field: new Ui.Input({})
+                }
+            );
+            $("body").prepend(input.$el);
+            assert.ok(input.$field.css("display") == "block", "Input field shown");
+            assert.ok(input.$preview.css("display") == "none", "Preview hidden");
+            assert.ok(input.$collapsible.css("display") == "none", "Collapsible hidden");
+            assert.ok(input.$title_text.css("display") == "inline", "Title visible");
+            assert.ok(input.$title_text.html() == "", "Title content unavailable");
+            input.model.set("label", "_label");
+            assert.ok(input.$title_text.html() == "_label", "Title content available");
+            assert.ok(input.$error.css("display") == "none", "Error hidden");
+            input.model.set("error_text", "_error_text");
+            assert.ok(input.$error.css("display") == "block", "Error visible");
+            assert.ok(input.$error_text.html() == "_error_text", "Error text correct");
+            input.model.set("error_text", null);
+            assert.ok(input.$error.css("display") == "none", "Error hidden, again");
+            assert.ok(input.$backdrop.css("display") == "none", "Backdrop hidden");
+            input.model.set("backdrop", true);
+            assert.ok(input.$backdrop.css("display") == "block", "Backdrop shown");
+            assert.ok(input.$backdrop.css("opacity") == 0, "Backdrop transparent");
+            assert.ok(input.$backdrop.css("cursor") == "default", "Backdrop regular cursor");
+            input.model.set("backdrop", false);
+            assert.ok(input.$backdrop.css("display") == "none", "Backdrop hidden, again");
+            input.model.set("disabled", true);
+            assert.ok(input.$field.css("display") == "none", "Input field hidden");
+            input.model.set("disabled", false);
+            this.clock.tick(window.WAIT_FADE);
+            assert.ok(input.$field.css("display") == "block", "Input field shown, again");
+            this.clock.tick(window.WAIT_FADE);
+            input.model.set("color", "red");
+            assert.ok(
+                input.$field
+                    .children()
+                    .first()
+                    .css("color") == "rgb(255, 0, 0)",
+                "Shows correct new color"
+            );
+            input.model.set("color", null);
+            assert.ok(
+                input.$field
+                    .children()
+                    .first()
+                    .css("color") == "rgb(85, 85, 85)",
+                "Shows correct old color"
+            );
+            input.model.set("collapsible_value", "_collapsible_value");
+            assert.ok(input.$collapsible.css("display") == "block", "Collapsible field");
+            assert.ok(input.$collapsible_text.html() == "_label", "Title content available");
+            assert.ok(input.$title_text.css("display") == "none", "Regular title not visible");
+            input.model.set("help", "_help");
+            assert.ok(input.$info.html() == "_help", "Correct help text");
+            input.model.set("argument", "_argument");
+            assert.ok(input.$info.html() == "_help (_argument)", "Correct help text with argument");
+            input.model.set("help", "_help (_argument)");
+            assert.ok(input.$info.html() == "_help (_argument)", "Correct help text with argument from help");
+        });
+    }
+);

client/galaxy/scripts/qunit/tests/galaxy-app-base.js

@@ -0,0 +1,96 @@
+/* global define */
+define(["qunit/test-app", "galaxy", "jquery"], function(testApp, appBase, $) {
+    "use strict";
+    appBase = appBase.default;
+    QUnit.module("Galaxy client app tests");
+
+    var options = {
+        config: {
+            allow_user_deletion: false,
+            allow_user_creation: true,
+            wiki_url: "https://galaxyproject.org/",
+            ftp_upload_site: null,
+            support_url: "https://galaxyproject.org/support/",
+            allow_user_dataset_purge: false,
+            allow_library_path_paste: false,
+            user_library_import_dir: null,
+            terms_url: null,
+            ftp_upload_dir: null,
+            library_import_dir: null,
+            logo_url: null,
+            enable_unique_workflow_defaults: false
+        },
+        user: {
+            username: "test",
+            quota_percent: null,
+            total_disk_usage: 61815527,
+            nice_total_disk_usage: "59.0 MB",
+            email: "test@test.test",
+            tags_used: ["test"],
+            model_class: "User",
+            id: "f2db41e1fa331b3e"
+        }
+    };
+
+    QUnit.test("App base construction/initializiation defaults", function(assert) {
+        var app = new appBase.GalaxyApp({});
+        assert.ok(app.hasOwnProperty("options") && typeof app.options === "object");
+        assert.ok(app.hasOwnProperty("logger") && typeof app.logger === "object");
+        assert.ok(app.hasOwnProperty("localize") && typeof app.localize === "function");
+        assert.ok(app.hasOwnProperty("config") && typeof app.config === "object");
+        assert.ok(app.hasOwnProperty("user") && typeof app.config === "object");
+        assert.equal(app.localize, window._l);
+    });
+
+    QUnit.test("App base default options", function(assert) {
+        var app = new appBase.GalaxyApp({});
+        assert.ok(app.hasOwnProperty("options") && typeof app.options === "object");
+        assert.equal(app.options.root, "/");
+        assert.equal(app.options.patchExisting, true);
+    });
+
+    QUnit.test("App base extends from Backbone.Events", function(assert) {
+        var app = new appBase.GalaxyApp({});
+        ["on", "off", "trigger", "listenTo", "stopListening"].forEach(function(fn) {
+            assert.ok(app.hasOwnProperty(fn) && typeof app[fn] === "function");
+        });
+    });
+
+    QUnit.test("App base has logging methods from utils/add-logging.js", function(assert) {
+        var app = new appBase.GalaxyApp({});
+        ["debug", "info", "warn", "error", "metric"].forEach(function(fn) {
+            assert.ok(typeof app[fn] === "function");
+        });
+        assert.ok(app._logNamespace === "GalaxyApp");
+    });
+
+    QUnit.test("App base will patch in attributes from existing Galaxy objects", function(assert) {
+        window.Galaxy = {
+            attribute: {
+                subattr: 1
+            }
+        };
+        var app = new appBase.GalaxyApp({});
+        assert.ok(typeof app.attribute === "object" && app.attribute.subattr === 1);
+    });
+
+    QUnit.test("App base logger", function(assert) {
+        var app = new appBase.GalaxyApp({});
+        assert.ok(app.hasOwnProperty("logger") && typeof app.config === "object");
+    });
+
+    QUnit.test("App base config", function(assert) {
+        var app = new appBase.GalaxyApp(options);
+        assert.ok(app.hasOwnProperty("config") && typeof app.config === "object");
+        assert.equal(app.config.allow_user_deletion, false);
+        assert.equal(app.config.allow_user_creation, true);
+        assert.equal(app.config.wiki_url, "https://galaxyproject.org/");
+        assert.equal(app.config.ftp_upload_site, null);
+    });
+
+    QUnit.test("App base user", function(assert) {
+        var app = new appBase.GalaxyApp({});
+        assert.ok(app.hasOwnProperty("user") && typeof app.user === "object");
+        assert.ok(app.user.isAdmin() === false);
+    });
+});

client/galaxy/scripts/qunit/tests/graph.js

@@ -0,0 +1,515 @@
+/* global define */
+define(["qunit/test-app", "utils/graph", "jquery"], function(testApp, GRAPH, $) {
+    "use strict";
+    GRAPH = GRAPH.default;
+    QUnit.module("utils/graph.js library tests");
+    ///*
+    function testEmptyObject(assert, o) {
+        assert.ok(typeof o === "object");
+        assert.ok(Object.keys(o).length === 0);
+    }
+
+    // ------------------------------------------------------------------------ vertices
+    QUnit.test("Empty vertex construction", function(assert) {
+        var vert = new GRAPH.Vertex();
+        assert.ok(vert instanceof GRAPH.Vertex);
+        assert.ok(vert.name === "(unnamed)");
+        assert.ok(vert.data === null);
+        testEmptyObject(assert, vert.edges);
+        assert.ok(vert.degree === 0);
+        assert.ok(vert + "" === "Vertex((unnamed))");
+        assert.deepEqual(vert.toJSON(), { name: "(unnamed)", data: null });
+    });
+
+    QUnit.test("Vertex construction", function(assert) {
+        var vert = new GRAPH.Vertex("blah", { blorp: 1, bleep: 2 });
+        assert.ok(vert instanceof GRAPH.Vertex);
+        assert.ok(vert.name === "blah");
+        assert.deepEqual(vert.data, { blorp: 1, bleep: 2 });
+        testEmptyObject(assert, vert.edges);
+        assert.ok(vert.degree === 0);
+        assert.ok(vert + "" === "Vertex(blah)");
+        assert.deepEqual(vert.toJSON(), { name: "blah", data: { blorp: 1, bleep: 2 } });
+    });
+
+    // ------------------------------------------------------------------------ edges
+    QUnit.test("Empty edge construction", function(assert) {
+        var edge = new GRAPH.Edge();
+        assert.ok(edge instanceof GRAPH.Edge);
+        assert.ok(edge.source === null);
+        assert.ok(edge.target === null);
+        assert.ok(edge.data === null);
+        assert.ok(edge + "" === "null->null");
+        assert.deepEqual(edge.toJSON(), { source: null, target: null });
+    });
+
+    QUnit.test("Edge construction", function(assert) {
+        var edge = new GRAPH.Edge("A", "B", { one: 1, two: 2 });
+        assert.ok(edge instanceof GRAPH.Edge);
+        assert.ok(edge.source === "A");
+        assert.ok(edge.target === "B");
+        assert.deepEqual(edge.data, { one: 1, two: 2 });
+        assert.ok(edge + "" === "A->B");
+        assert.deepEqual(edge.toJSON(), { source: "A", target: "B", data: { one: 1, two: 2 } });
+    });
+
+    // ------------------------------------------------------------------------ graphs
+    function testEmptyGraph(assert, graph) {
+        assert.ok(graph instanceof GRAPH.Graph);
+        testEmptyObject(assert, graph.vertices);
+        assert.ok(graph.numEdges === 0);
+    }
+
+    QUnit.test("Empty graph construction", function(assert) {
+        var graph = new GRAPH.Graph();
+
+        assert.ok(graph.directed === false);
+        assert.ok(graph.allowReflexiveEdges === false);
+
+        testEmptyGraph(assert, graph);
+    });
+
+    QUnit.test("Bad data graph construction", function(assert) {
+        var graph = new GRAPH.Graph(false, {});
+        testEmptyGraph(assert, graph);
+
+        graph = new GRAPH.Graph(false, null);
+        testEmptyGraph(assert, graph);
+    });
+
+    QUnit.test("Test directed and options", function(assert) {
+        var graph = new GRAPH.Graph(true, {}, { allowReflexiveEdges: true });
+
+        assert.ok(graph.directed);
+        assert.ok(graph.allowReflexiveEdges);
+
+        testEmptyGraph(assert, graph);
+    });
+
+    function testSampleDirectedGraph(assert, graph) {
+        assert.ok(!graph.directed);
+
+        assert.ok(Object.keys(graph.vertices).length === 3);
+        assert.ok(graph.vertices.A instanceof GRAPH.Vertex);
+        assert.ok(graph.vertices.B instanceof GRAPH.Vertex);
+        assert.ok(graph.vertices.C instanceof GRAPH.Vertex);
+
+        assert.deepEqual(Object.keys(graph.vertices.A.edges), ["B", "C"]);
+        assert.deepEqual(Object.keys(graph.vertices.B.edges), ["A", "C"]);
+        assert.deepEqual(Object.keys(graph.vertices.C.edges), ["A", "B"]);
+
+        assert.ok(graph.vertices.A.degree === 2);
+        assert.ok(graph.vertices.B.degree === 2);
+        assert.ok(graph.vertices.C.degree === 2);
+
+        assert.deepEqual(graph.vertices.A.edges.B.toJSON(), { source: "A", target: "B" });
+        assert.deepEqual(graph.vertices.A.edges.C.toJSON(), { source: "A", target: "C" });
+        assert.deepEqual(graph.vertices.B.edges.A.toJSON(), { source: "B", target: "A" });
+        assert.deepEqual(graph.vertices.B.edges.C.toJSON(), { source: "B", target: "C" });
+        assert.deepEqual(graph.vertices.C.edges.A.toJSON(), { source: "C", target: "A" });
+        assert.deepEqual(graph.vertices.C.edges.B.toJSON(), { source: "C", target: "B" });
+
+        assert.ok(graph.numEdges === 6);
+    }
+
+    function testSampleNonDirectedGraph(assert, graph) {
+        assert.ok(graph.directed);
+
+        assert.ok(Object.keys(graph.vertices).length === 3);
+        assert.ok(graph.vertices.A instanceof GRAPH.Vertex);
+        assert.ok(graph.vertices.B instanceof GRAPH.Vertex);
+        assert.ok(graph.vertices.C instanceof GRAPH.Vertex);
+
+        assert.deepEqual(Object.keys(graph.vertices.A.edges), ["B", "C"]);
+        assert.deepEqual(Object.keys(graph.vertices.B.edges), ["C"]);
+        assert.deepEqual(Object.keys(graph.vertices.C.edges), []);
+
+        assert.ok(graph.vertices.A.degree === 2);
+        assert.ok(graph.vertices.B.degree === 1);
+        assert.ok(graph.vertices.C.degree === 0);
+
+        assert.deepEqual(graph.vertices.A.edges.B.toJSON(), { source: "A", target: "B" });
+        assert.deepEqual(graph.vertices.A.edges.C.toJSON(), { source: "A", target: "C" });
+        assert.deepEqual(graph.vertices.B.edges.C.toJSON(), { source: "B", target: "C" });
+
+        assert.ok(graph.numEdges === 3);
+    }
+
+    var nodeLinkData = {
+        nodes: [{ name: "A", data: 100 }, { name: "B", data: 200 }, { name: "C", data: 300 }],
+        links: [{ source: 0, target: 1 }, { source: 0, target: 2 }, { source: 1, target: 2 }]
+    };
+
+    QUnit.test("Test nodes and links data input on *non-directed* graph", function(assert) {
+        var graph = new GRAPH.Graph(false, nodeLinkData);
+        testSampleDirectedGraph(assert, graph);
+    });
+
+    QUnit.test("Test nodes and links data input on *directed* graph", function(assert) {
+        var graph = new GRAPH.Graph(true, nodeLinkData);
+        testSampleNonDirectedGraph(assert, graph);
+    });
+
+    var vertexEdgeData = {
+        vertices: [{ name: "A", data: 100 }, { name: "B", data: 200 }, { name: "C", data: 300 }],
+        edges: [{ source: "A", target: "B" }, { source: "A", target: "C" }, { source: "B", target: "C" }]
+    };
+
+    QUnit.test("Test vertex and edge data input on *non-directed* graph", function(assert) {
+        var graph = new GRAPH.Graph(false, vertexEdgeData);
+        testSampleDirectedGraph(assert, graph);
+    });
+
+    QUnit.test("Test vertex and edge data input on *directed* graph", function(assert) {
+        var graph = new GRAPH.Graph(true, vertexEdgeData);
+        testSampleNonDirectedGraph(assert, graph);
+    });
+
+    QUnit.test("Test vertex eachEdge", function(assert) {
+        var graph = new GRAPH.Graph(false, nodeLinkData);
+        assert.ok(typeof graph.vertices.A.eachEdge === "function");
+        assert.deepEqual(
+            graph.vertices.A.eachEdge(function(e) {
+                return e.target;
+            }),
+            ["B", "C"]
+        );
+        assert.ok(graph.vertices.A.eachEdge({ target: "B" }).length === 1);
+    });
+
+    QUnit.test("Test graph eachVertex", function(assert) {
+        var graph = new GRAPH.Graph(true, nodeLinkData);
+        assert.ok(typeof graph.eachVertex === "function");
+        assert.deepEqual(
+            graph.eachVertex(function(v) {
+                return { n: v.name, d: v.degree };
+            }),
+            [{ n: "A", d: 2 }, { n: "B", d: 1 }, { n: "C", d: 0 }]
+        );
+        assert.ok(graph.eachVertex({ degree: 2 })[0] === graph.vertices.A);
+    });
+
+    QUnit.test("Test createVertex", function(assert) {
+        var graph = new GRAPH.Graph();
+        var vert1 = graph.createVertex("A", { blah: 1 });
+        assert.ok(vert1 instanceof GRAPH.Vertex);
+        assert.ok(vert1 === graph.vertices.A);
+        assert.ok(graph.createVertex("A", { blah: 1 }) === vert1);
+    });
+
+    QUnit.test("Test createEdge", function(assert) {
+        var graph, A, B, edge;
+
+        graph = new GRAPH.Graph();
+        A = graph.createVertex("A");
+        B = graph.createVertex("B");
+        edge = graph.createEdge("A", "B");
+        assert.ok(edge instanceof GRAPH.Edge);
+        assert.ok(A.degree === 1);
+        assert.ok(B.degree === 1);
+        assert.ok(A.edges.B);
+        assert.ok(B.edges.A);
+        assert.ok(graph.numEdges === 2);
+
+        // bad target
+        graph = new GRAPH.Graph();
+        A = graph.createVertex("A");
+        B = graph.createVertex("B");
+        edge = graph.createEdge("A", "C");
+        assert.ok(edge === null);
+        assert.ok(A.degree === 0);
+        assert.ok(B.degree === 0);
+        assert.ok(!A.edges.B);
+        assert.ok(!B.edges.A);
+        assert.ok(graph.numEdges === 0);
+
+        // bad source
+        graph = new GRAPH.Graph();
+        A = graph.createVertex("A");
+        B = graph.createVertex("B");
+        edge = graph.createEdge("C", "A");
+        assert.ok(graph.numEdges === 0);
+
+        // reflexive
+        graph = new GRAPH.Graph();
+        A = graph.createVertex("A");
+        B = graph.createVertex("B");
+        edge = graph.createEdge("A", "A");
+        assert.ok(graph.numEdges === 0);
+
+        // reflexive (allowed)
+        graph = new GRAPH.Graph(false, {}, { allowReflexiveEdges: true });
+        A = graph.createVertex("A");
+        edge = graph.createEdge("A", "A");
+        // reflexive edges shouldn't mirror
+        assert.ok(graph.numEdges === 1);
+        assert.ok(A.edges.A);
+    });
+
+    QUnit.test("Test graph.edges", function(assert) {
+        var graph = new GRAPH.Graph(false, nodeLinkData);
+        assert.ok(graph.edges().length === 6);
+        assert.deepEqual(
+            graph.edges(function(e) {
+                return e.source;
+            }),
+            ["A", "A", "B", "B", "C", "C"]
+        );
+        assert.deepEqual(graph.edges({ source: "A" }), [graph.vertices.A.edges.B, graph.vertices.A.edges.C]);
+
+        graph = new GRAPH.Graph(true, nodeLinkData);
+        assert.ok(graph.edges().length === 3);
+        assert.deepEqual(
+            graph.edges(function(e) {
+                return e.source;
+            }),
+            ["A", "A", "B"]
+        );
+        assert.deepEqual(graph.edges({ source: "A" }), [graph.vertices.A.edges.B, graph.vertices.A.edges.C]);
+    });
+
+    QUnit.test("Test graph.adjacent", function(assert) {
+        var graph = new GRAPH.Graph(true, nodeLinkData);
+        assert.deepEqual(graph.adjacent(graph.vertices.A), [graph.vertices.B, graph.vertices.C]);
+        assert.deepEqual(graph.adjacent(graph.vertices.B), [graph.vertices.C]);
+        assert.deepEqual(graph.adjacent(graph.vertices.C), []);
+    });
+
+    QUnit.test("Test graph.eachAdjacent", function(assert) {
+        var graph = new GRAPH.Graph(true, nodeLinkData);
+        assert.deepEqual(
+            graph.eachAdjacent(graph.vertices.A, function(v, e) {
+                return v;
+            }),
+            [graph.vertices.B, graph.vertices.C]
+        );
+    });
+
+    // ------------------------------------------------------------------------ breadth first search
+    QUnit.test("Empty BreadthFirstSearch", function(assert) {
+        var search = new GRAPH.BreadthFirstSearch();
+        assert.ok(search instanceof GRAPH.BreadthFirstSearch);
+        assert.ok(search.graph === undefined);
+        assert.ok(typeof search.processFns === "object");
+        assert.ok(typeof search.processFns.vertexEarly === "function");
+        assert.ok(typeof search.processFns.edge === "function");
+        assert.ok(typeof search.processFns.vertexLate === "function");
+        assert.ok(typeof search._cache === "object");
+    });
+
+    QUnit.test("BreadthFirstSearch on undirected graph", function(assert) {
+        var graph = new GRAPH.Graph(false, nodeLinkData),
+            bfs = new GRAPH.BreadthFirstSearch(graph);
+        assert.ok(bfs instanceof GRAPH.BreadthFirstSearch);
+        assert.ok(bfs.graph === graph);
+
+        var search = bfs.search("A"),
+            tree = bfs.searchTree("A");
+        assert.deepEqual(search, {
+            discovered: { A: true, B: true, C: true },
+            edges: [{ source: "A", target: "B" }, { source: "A", target: "C" }]
+        });
+        assert.ok(tree instanceof GRAPH.Graph);
+        assert.deepEqual(tree.vertices.A.toJSON(), graph.vertices.A.toJSON());
+        assert.deepEqual(
+            tree.eachVertex(function(v) {
+                return v.degree;
+            }),
+            [2, 0, 0]
+        );
+
+        assert.deepEqual(bfs.search("B").edges, [{ source: "B", target: "A" }, { source: "B", target: "C" }]);
+        assert.deepEqual(bfs.search("C").edges, [{ source: "C", target: "A" }, { source: "C", target: "B" }]);
+        assert.ok(typeof bfs._cache.A === "object");
+        assert.deepEqual(Object.keys(bfs._cache), ["A", "B", "C"]);
+    });
+
+    QUnit.test("BreadthFirstSearch on directed graph", function(assert) {
+        var graph = new GRAPH.Graph(true, nodeLinkData),
+            bfs = new GRAPH.BreadthFirstSearch(graph);
+        assert.ok(bfs instanceof GRAPH.BreadthFirstSearch);
+        assert.ok(bfs.graph === graph);
+
+        var search = bfs.search("A"),
+            tree = bfs.searchTree("A");
+        assert.deepEqual(search, {
+            discovered: { A: true, B: true, C: true },
+            edges: [{ source: "A", target: "B" }, { source: "A", target: "C" }]
+        });
+        assert.ok(tree instanceof GRAPH.Graph);
+        assert.deepEqual(tree.vertices.A.toJSON(), graph.vertices.A.toJSON());
+        assert.deepEqual(
+            tree.eachVertex(function(v) {
+                return v.degree;
+            }),
+            [2, 0, 0]
+        );
+
+        assert.deepEqual(bfs.search("B").edges, [{ source: "B", target: "C" }]);
+        assert.deepEqual(bfs.search("C").edges, []);
+        assert.ok(typeof bfs._cache.A === "object");
+        assert.deepEqual(Object.keys(bfs._cache), ["A", "B", "C"]);
+    });
+
+    // ------------------------------------------------------------------------ depth first search
+    var DFSData = {
+        vertices: [{ name: "A" }, { name: "B" }, { name: "C" }, { name: "D" }, { name: "E" }, { name: "F" }],
+        edges: [
+            { source: "A", target: "B" },
+            { source: "B", target: "C" },
+            // confound it
+            { source: "A", target: "C" },
+            { source: "C", target: "D" },
+            { source: "A", target: "E" },
+            { source: "E", target: "F" },
+            // confound it
+            { source: "F", target: "A" }
+        ]
+    };
+
+    QUnit.test("Empty DepthFirstSearch", function(assert) {
+        var search = new GRAPH.DepthFirstSearch();
+        assert.ok(search instanceof GRAPH.DepthFirstSearch);
+        assert.ok(search.graph === undefined);
+        assert.ok(typeof search.processFns === "object");
+        assert.ok(typeof search.processFns.vertexEarly === "function");
+        assert.ok(typeof search.processFns.edge === "function");
+        assert.ok(typeof search.processFns.vertexLate === "function");
+        assert.ok(typeof search._cache === "object");
+    });
+
+    QUnit.test("DepthFirstSearch on undirected graph", function(assert) {
+        var graph = new GRAPH.Graph(false, DFSData),
+            dfs = new GRAPH.DepthFirstSearch(graph);
+        assert.ok(dfs instanceof GRAPH.DepthFirstSearch);
+        assert.ok(dfs.graph === graph);
+
+        var search = dfs.search("A"),
+            tree = dfs.searchTree("A");
+        assert.deepEqual(search, {
+            discovered: { A: true, B: true, C: true, D: true, E: true, F: true },
+            edges: [
+                { source: "A", target: "B" },
+                { source: "B", target: "C" },
+                { source: "C", target: "D" },
+                { source: "A", target: "E" },
+                { source: "E", target: "F" }
+            ],
+            entryTimes: { A: 0, B: 1, C: 2, D: 3, E: 7, F: 8 },
+            exitTimes: { A: 11, B: 6, C: 5, D: 4, E: 10, F: 9 }
+        });
+        assert.ok(tree instanceof GRAPH.Graph);
+        assert.deepEqual(tree.vertices.A.toJSON(), graph.vertices.A.toJSON());
+        assert.deepEqual(
+            tree.eachVertex(function(v) {
+                return v.degree;
+            }),
+            [2, 1, 1, 0, 1, 0]
+        );
+
+        assert.deepEqual(dfs.search("B").edges, [
+            { source: "B", target: "A" },
+            { source: "A", target: "C" },
+            { source: "C", target: "D" },
+            { source: "A", target: "E" },
+            { source: "E", target: "F" }
+        ]);
+
+        assert.ok(typeof dfs._cache.A === "object");
+        assert.deepEqual(Object.keys(dfs._cache), ["A", "B"]);
+    });
+
+    QUnit.test("DepthFirstSearch on directed graph", function(assert) {
+        var graph = new GRAPH.Graph(true, DFSData),
+            dfs = new GRAPH.DepthFirstSearch(graph);
+        assert.ok(dfs instanceof GRAPH.DepthFirstSearch);
+        assert.ok(dfs.graph === graph);
+
+        var search = dfs.search("A"),
+            tree = dfs.searchTree("A");
+        assert.deepEqual(search, {
+            discovered: { A: true, B: true, C: true, D: true, E: true, F: true },
+            edges: [
+                { source: "A", target: "B" },
+                { source: "B", target: "C" },
+                { source: "C", target: "D" },
+                { source: "A", target: "E" },
+                { source: "E", target: "F" }
+            ],
+            entryTimes: { A: 0, B: 1, C: 2, D: 3, E: 7, F: 8 },
+            exitTimes: { A: 11, B: 6, C: 5, D: 4, E: 10, F: 9 }
+        });
+        assert.ok(tree instanceof GRAPH.Graph);
+        assert.deepEqual(tree.vertices.A.toJSON(), graph.vertices.A.toJSON());
+        assert.deepEqual(
+            tree.eachVertex(function(v) {
+                return v.degree;
+            }),
+            [2, 1, 1, 0, 1, 0]
+        );
+
+        assert.deepEqual(dfs.search("B").edges, [{ source: "B", target: "C" }, { source: "C", target: "D" }]);
+
+        assert.ok(typeof dfs._cache.A === "object");
+        assert.deepEqual(Object.keys(dfs._cache), ["A", "B"]);
+    });
+
+    // ------------------------------------------------------------------------ components
+    //*/
+    QUnit.test("weakComponents on undirected graph", function(assert) {
+        var graph = new GRAPH.Graph(false, {
+            vertices: [{ name: "A" }, { name: "B" }, { name: "C" }, { name: "D" }, { name: "E" }],
+            edges: [{ source: "A", target: "B" }, { source: "C", target: "D" }]
+        });
+        assert.equal(graph.numEdges, 4);
+        var components = graph.weakComponents();
+        assert.equal(components.length, 3);
+    });
+
+    QUnit.test("weakComponents on directed graph", function(assert) {
+        var graph, components;
+        graph = new GRAPH.Graph(true, {
+            vertices: [{ name: "A" }, { name: "B" }, { name: "C" }, { name: "D" }, { name: "E" }],
+            edges: [{ source: "A", target: "B" }, { source: "D", target: "C" }]
+        });
+        assert.equal(graph.numEdges, 2);
+
+        components = graph.weakComponents();
+        assert.equal(components.length, 3);
+
+        graph = new GRAPH.Graph(true, {
+            vertices: [
+                { name: "A", data: 100 },
+                { name: "B", data: 200 },
+                { name: "C", data: 30 },
+                { name: "D", data: 40 },
+                { name: "E", data: 500 },
+                { name: "F", data: 600 },
+                { name: "G", data: 7 }
+            ],
+            edges: [
+                { source: "A", target: "B" },
+                { source: "D", target: "C" },
+                { source: "E", target: "A" },
+                { source: "F", target: "E" }
+            ]
+        });
+        components = graph.weakComponents();
+        assert.equal(components.length, 3);
+        // data retained
+        assert.equal(components[0].vertices[0].data, 100);
+
+        assert.equal(components[0].vertices.length, 4);
+        assert.deepEqual(components[0].edges, [
+            { source: "A", target: "B" },
+            { source: "E", target: "A" },
+            { source: "F", target: "E" }
+        ]);
+
+        assert.equal(components[1].vertices.length, 2);
+        assert.deepEqual(components[1].edges, [{ source: "D", target: "C" }]);
+
+        assert.deepEqual(components[2].vertices, [{ name: "G", data: 7 }]);
+        assert.deepEqual(components[2].edges.length, 0);
+    });
+});

client/galaxy/scripts/qunit/tests/hda-base.js

@@ -0,0 +1,30 @@
+// This file isn't really testing anything useful yet, it is just testing
+// (or demonstrating) qunit+backbone interactions.
+/* global define */
+define(["qunit/test-app", "mvc/history/hda-model", "mvc/history/hda-li", "jquery"], function(
+    testApp,
+    HDA_MODEL,
+    HDA_BASE,
+    $
+) {
+    "use strict";
+    HDA_MODEL = HDA_MODEL.default;
+    HDA_BASE = HDA_BASE.default;
+    QUnit.module("HDA base backbone view tests");
+
+    QUnit.test("Base HDA view default construction, initialize", function(assert) {
+        var hda = new HDA_MODEL.HistoryDatasetAssociation({
+                id: "123"
+            }),
+            view = new HDA_BASE.HDAListItemView({ model: hda });
+
+        assert.strictEqual(view.model, hda);
+
+        assert.equal(view.linkTarget, "_blank");
+        assert.equal(view.selectable, false);
+        assert.equal(view.selected, false);
+        assert.equal(view.expanded, false);
+        assert.equal(view.draggable, false);
+        assert.equal(view.id(), "dataset-123");
+    });
+});

client/galaxy/scripts/qunit/tests/history_contents_model_tests.js

@@ -0,0 +1,38 @@
+/* global define */
+define(["qunit/test-app", "mvc/history/hda-model", "jquery", "sinon"], function(testApp, HDA_MODEL, $, sinon) {
+    HDA_MODEL = HDA_MODEL.default;
+    QUnit.module("History Contents Model QUnit.Tests");
+
+    QUnit.test("HDA Constructions with Default Attributes", function(assert) {
+        var hda = new HDA_MODEL.HistoryDatasetAssociation({});
+        assert.equal(hda.get("name"), "(unnamed dataset)");
+        assert.equal(hda.get("state"), "new");
+    });
+
+    QUnit.test("HDA Construction with Supplied Attributes", function(assert) {
+        var hda = new HDA_MODEL.HistoryDatasetAssociation({
+            history_content_type: "dataset",
+            name: "my dataset",
+            state: "ok"
+        });
+        assert.equal(hda.get("name"), "my dataset");
+        assert.equal(hda.get("state"), "ok");
+    });
+
+    QUnit.test("HDA Deletion", function(assert) {
+        var hda = new HDA_MODEL.HistoryDatasetAssociation({
+            history_content_type: "dataset",
+            id: "hda1",
+            history_id: "h1",
+            deleted: false
+        });
+        assert.equal(hda.get("deleted"), false);
+
+        sinon.stub($, "ajax").yieldsTo("success", { deleted: true });
+        hda["delete"]();
+        // to get the url sinon used:
+        //console.debug( $.ajax.lastCall.args[0].url )
+        assert.ok($.ajax.calledWithMatch({ url: "/api/histories/h1/contents/datasets/hda1" }));
+        assert.equal(hda.get("deleted"), true);
+    });
+});

client/galaxy/scripts/qunit/tests/job-dag.js

@@ -0,0 +1,294 @@
+/* global define */
+define(["qunit/test-app", "mvc/history/job-dag", "jquery", "qunit/test-data/job-dag-1"], function(
+    testApp,
+    JobDAG,
+    $,
+    testData
+) {
+    "use strict";
+    JobDAG = JobDAG.default;
+    QUnit.module("mvc/history/job-dag.js tests");
+
+    // ------------------------------------------------------------------------
+    QUnit.test("Empty JobDAG construction", function(assert) {
+        var dag = new JobDAG();
+        assert.ok(dag instanceof JobDAG);
+
+        // default options
+        assert.deepEqual(dag.filters, []);
+        assert.deepEqual(dag.options, {
+            excludeSetMetadata: false
+        });
+
+        // test (empty) instance vars
+        assert.deepEqual(dag._jobsData, []);
+        assert.deepEqual(dag._historyContentsMap, {});
+        assert.deepEqual(dag._toolMap, {});
+        assert.equal(dag.noInputJobs.length, 0);
+        assert.equal(dag.noOutputJobs.length, 0);
+
+        // logging
+        assert.equal(typeof dag.debug, "function");
+        assert.equal(typeof dag.info, "function");
+        assert.equal(typeof dag.warn, "function");
+        assert.equal(typeof dag.error, "function");
+    });
+
+    QUnit.test("Empty JobDAG construction - changing options", function(assert) {
+        var dag;
+        dag = new JobDAG({
+            excludeSetMetadata: true
+        });
+
+        // excludeSetMetadata
+        assert.deepEqual(dag.options, {
+            excludeSetMetadata: true
+        });
+        assert.equal(dag.filters.length, 1);
+        assert.equal(typeof dag.filters[0], "function");
+
+        // filters
+        function testFilter(job, index, jobData) {
+            return true;
+        }
+        dag = new JobDAG({
+            filters: [testFilter]
+        });
+        assert.equal(dag.filters[0], testFilter);
+    });
+
+    QUnit.test("JobDAG construction with history and jobs", function(assert) {
+        assert.equal(testData.jobs1.length, 3);
+        assert.equal(testData.historyContents1.length, 3);
+
+        var history = testData.historyContents1,
+            jobs = testData.jobs1,
+            dag;
+        dag = new JobDAG({
+            historyContents: history,
+            tools: testData.tools,
+            jobs: jobs
+        });
+
+        assert.deepEqual(dag._outputIdToJobMap, {
+            "8c959c9304a2bc4b": "8a81cf6f989c4467",
+            "132016f833b57406": "6505e875ddb66fd2",
+            "846fb0a2a64137c0": "77f74776fd03cbc5"
+        });
+        assert.deepEqual(dag._jobsData, [
+            {
+                job: _.findWhere(jobs, { id: "8a81cf6f989c4467" }),
+                inputs: {},
+                outputs: {
+                    "8c959c9304a2bc4b": {
+                        src: "hda",
+                        id: "8c959c9304a2bc4b",
+                        name: "output0",
+                        content: _.findWhere(history, { id: "8c959c9304a2bc4b" })
+                    }
+                },
+                tool: {}
+            },
+            {
+                job: _.findWhere(jobs, { id: "6505e875ddb66fd2" }),
+                inputs: {
+                    "8c959c9304a2bc4b": {
+                        src: "hda",
+                        id: "8c959c9304a2bc4b",
+                        name: "input",
+                        content: _.findWhere(history, { id: "8c959c9304a2bc4b" })
+                    }
+                },
+                outputs: {
+                    "132016f833b57406": {
+                        src: "hda",
+                        id: "132016f833b57406",
+                        name: "out_file1",
+                        content: _.findWhere(history, { id: "132016f833b57406" })
+                    }
+                },
+                tool: {}
+            },
+            {
+                job: _.findWhere(jobs, { id: "77f74776fd03cbc5" }),
+                inputs: {
+                    "132016f833b57406": {
+                        src: "hda",
+                        id: "132016f833b57406",
+                        name: "input",
+                        content: _.findWhere(history, { id: "132016f833b57406" })
+                    }
+                },
+                outputs: {
+                    "846fb0a2a64137c0": {
+                        src: "hda",
+                        id: "846fb0a2a64137c0",
+                        name: "out_file1",
+                        content: _.findWhere(history, { id: "846fb0a2a64137c0" })
+                    }
+                },
+                tool: {}
+            }
+        ]);
+
+        var jobsDataMap = dag._jobsDataMap();
+        assert.deepEqual(dag.toNodesAndLinks(), {
+            nodes: [
+                { name: "8a81cf6f989c4467", data: jobsDataMap["8a81cf6f989c4467"] },
+                { name: "6505e875ddb66fd2", data: jobsDataMap["6505e875ddb66fd2"] },
+                { name: "77f74776fd03cbc5", data: jobsDataMap["77f74776fd03cbc5"] }
+            ],
+            links: [
+                { source: 0, target: 1, data: { dataset: "8c959c9304a2bc4b" } },
+                { source: 1, target: 2, data: { dataset: "132016f833b57406" } }
+            ]
+        });
+
+        assert.deepEqual(dag.toVerticesAndEdges(), {
+            vertices: [
+                { name: "8a81cf6f989c4467", data: jobsDataMap["8a81cf6f989c4467"] },
+                { name: "6505e875ddb66fd2", data: jobsDataMap["6505e875ddb66fd2"] },
+                { name: "77f74776fd03cbc5", data: jobsDataMap["77f74776fd03cbc5"] }
+            ],
+            edges: [
+                {
+                    source: "8a81cf6f989c4467",
+                    target: "6505e875ddb66fd2",
+                    data: { dataset: "8c959c9304a2bc4b" }
+                },
+                {
+                    source: "6505e875ddb66fd2",
+                    target: "77f74776fd03cbc5",
+                    data: { dataset: "132016f833b57406" }
+                }
+            ]
+        });
+
+        // test cloning
+    });
+
+    QUnit.test("JobDAG removal of __SET_METADATA__ jobs", function(assert) {
+        assert.equal(testData.jobs2.length, 3);
+        assert.equal(testData.historyContents2.length, 2);
+
+        var history = testData.historyContents2,
+            jobs = testData.jobs2,
+            dag;
+        dag = new JobDAG({
+            historyContents: history,
+            tools: testData.tools,
+            jobs: jobs,
+            excludeSetMetadata: true
+        });
+
+        var jobsDataMap = dag._jobsDataMap();
+        assert.deepEqual(dag.toNodesAndLinks(), {
+            nodes: [
+                { name: "bf60fd5f5f7f44bf", data: jobsDataMap["bf60fd5f5f7f44bf"] },
+                { name: "90240358ebde1489", data: jobsDataMap["90240358ebde1489"] }
+            ],
+            links: [{ source: 0, target: 1, data: { dataset: "eca0af6fb47bf90c" } }]
+        });
+    });
+
+    //TODO: test filtering out errored jobs
+    QUnit.test("JobDAG construction with history and jobs", function(assert) {
+        assert.equal(testData.jobs3.length, 5);
+        assert.equal(testData.historyContents3.length, 5);
+
+        var history = testData.historyContents3,
+            jobs = testData.jobs3,
+            dag;
+        dag = new JobDAG({
+            historyContents: history,
+            tools: testData.tools,
+            jobs: jobs
+        });
+
+        var jobsDataMap = dag._jobsDataMap();
+        assert.deepEqual(dag.toVerticesAndEdges(), {
+            vertices: [
+                { name: "8c959c9304a2bc4b", data: jobsDataMap["8c959c9304a2bc4b"] },
+                { name: "132016f833b57406", data: jobsDataMap["132016f833b57406"] },
+                { name: "846fb0a2a64137c0", data: jobsDataMap["846fb0a2a64137c0"] },
+                { name: "eca0af6fb47bf90c", data: jobsDataMap["eca0af6fb47bf90c"] },
+                { name: "6fc9fbb81c497f69", data: jobsDataMap["6fc9fbb81c497f69"] }
+            ],
+            edges: [
+                {
+                    source: "8c959c9304a2bc4b",
+                    target: "846fb0a2a64137c0",
+                    data: { dataset: "6fb17d0cc6e8fae5" }
+                },
+                {
+                    source: "132016f833b57406",
+                    target: "eca0af6fb47bf90c",
+                    data: { dataset: "5114a2a207b7caff" }
+                },
+                {
+                    source: "eca0af6fb47bf90c",
+                    target: "6fc9fbb81c497f69",
+                    data: { dataset: "b8a0d6158b9961df" }
+                }
+            ]
+        });
+
+        var components = dag.weakComponents();
+        assert.deepEqual(components, [
+            {
+                vertices: [
+                    { name: "8c959c9304a2bc4b", data: jobsDataMap["8c959c9304a2bc4b"] },
+                    { name: "846fb0a2a64137c0", data: jobsDataMap["846fb0a2a64137c0"] }
+                ],
+                edges: [{ source: "8c959c9304a2bc4b", target: "846fb0a2a64137c0" }]
+            },
+            {
+                vertices: [
+                    { name: "132016f833b57406", data: jobsDataMap["132016f833b57406"] },
+                    { name: "eca0af6fb47bf90c", data: jobsDataMap["eca0af6fb47bf90c"] },
+                    { name: "6fc9fbb81c497f69", data: jobsDataMap["6fc9fbb81c497f69"] }
+                ],
+                edges: [
+                    { source: "132016f833b57406", target: "eca0af6fb47bf90c" },
+                    { source: "eca0af6fb47bf90c", target: "6fc9fbb81c497f69" }
+                ]
+            }
+        ]);
+    });
+
+    //TODO: test filtering out errored jobs
+    QUnit.test("JobDAG construction with copied history contents", function(assert) {
+        assert.equal(testData.jobs4.length, 1);
+        assert.equal(testData.historyContents4.length, 3);
+
+        var history = testData.historyContents4,
+            jobs = testData.jobs4,
+            dag;
+        dag = new JobDAG({
+            historyContents: history,
+            tools: testData.tools,
+            jobs: jobs
+        });
+
+        var jobsDataMap = dag._jobsDataMap();
+        assert.deepEqual(dag.toVerticesAndEdges(), {
+            vertices: [
+                { name: "92b83968e0b52980", data: jobsDataMap["92b83968e0b52980"] },
+                { name: "copy-422eef6b1b545329", data: _.findWhere(history, { id: "422eef6b1b545329" }) },
+                { name: "copy-c86c1b73aa7102dd", data: _.findWhere(history, { id: "c86c1b73aa7102dd" }) }
+            ],
+            edges: [
+                {
+                    source: "copy-422eef6b1b545329",
+                    target: "92b83968e0b52980",
+                    data: { dataset: "422eef6b1b545329" }
+                },
+                {
+                    source: "copy-c86c1b73aa7102dd",
+                    target: "92b83968e0b52980",
+                    data: { dataset: "c86c1b73aa7102dd" }
+                }
+            ]
+        });
+    });
+});

client/galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js

@@ -0,0 +1,107 @@
+/* global define */
+define(
+    [
+        "qunit/test-app",
+        "mvc/collection/list-of-pairs-collection-creator",
+        "qunit/test-data/paired-collection-creator.data",
+        "jquery",
+        "sinon"
+    ],
+    function(testApp, PAIRED_COLLECTION_CREATOR, DATA, $, sinon) {
+        "use strict";
+        PAIRED_COLLECTION_CREATOR = PAIRED_COLLECTION_CREATOR.default;
+        var PCC = PAIRED_COLLECTION_CREATOR.PairedCollectionCreator;
+
+        QUnit.module("Galaxy client app tests");
+
+        QUnit.test("Collection creation", function(assert) {
+            var pcc = new PCC({
+                    datasets: DATA._1,
+                    historyId: "fakeHistoryId"
+                }),
+                server = sinon.fakeServer.create();
+
+            var requestJSON;
+            server.respondWith("POST", "/api/histories/fakeHistoryId/contents/dataset_collections", function(request) {
+                requestJSON = JSON.parse(request.requestBody);
+                request.respond(
+                    200,
+                    { "Content-Type": "application/json" },
+                    JSON.stringify({
+                        fakeResponse: "yes"
+                    })
+                );
+            });
+
+            //console.debug( 'requestBody:', JSON.stringify( requestJSON, null, '  ' ) );
+            pcc.createList("Heres a collection");
+            server.respond();
+            assert.deepEqual(requestJSON, DATA._1requestJSON);
+        });
+
+        QUnit.test("Creator base/empty construction/initializiation defaults", function(assert) {
+            var pcc = new PCC([]);
+            assert.ok(pcc instanceof PCC);
+            assert.deepEqual(pcc.filters, pcc.commonFilters[pcc.DEFAULT_FILTERS]);
+            assert.ok(pcc.automaticallyPair);
+            assert.equal(pcc.matchPercentage, 0.9);
+            assert.equal(pcc.strategy, "autopairLCS");
+        });
+
+        QUnit.test("Creator construction/initializiation with datasets", function(assert) {
+            var pcc = new PCC({
+                datasets: DATA._1
+            });
+            //pcc.initialList.forEach( function( dataset, i ){
+            //    console.log( i + ':\n' + JSON.stringify( dataset ) );
+            //});
+            // pcc maintains the original list - which, in this case, is already sorted
+            assert.deepEqual(pcc.initialList, DATA._1);
+            // datasets 1 has no ids, so the pcc will create them
+            assert.ok(
+                _.every(pcc.initialList, function(dataset) {
+                    return dataset.id;
+                })
+            );
+            // datasets 1 is very easy to auto pair
+            assert.equal(pcc.unpaired.length, 0);
+            assert.equal(pcc.paired.length, pcc.initialList.length / 2);
+        });
+
+        QUnit.test("Try easy autopairing with simple exact matching", function(assert) {
+            var pcc = new PCC({
+                datasets: DATA._1,
+                strategy: "simple",
+                twoPassAutopairing: false
+            });
+            assert.equal(pcc.unpaired.length, 0);
+            assert.equal(pcc.paired.length, pcc.initialList.length / 2);
+        });
+
+        QUnit.test("Try easy autopairing with LCS", function(assert) {
+            var pcc = new PCC({
+                datasets: DATA._1,
+                strategy: "lcs",
+                twoPassAutopairing: false
+            });
+            assert.equal(pcc.unpaired.length, 0);
+            assert.equal(pcc.paired.length, pcc.initialList.length / 2);
+        });
+
+        QUnit.test("Try easy autopairing with Levenshtein", function(assert) {
+            var pcc = new PCC({
+                datasets: DATA._1,
+                strategy: "levenshtein",
+                twoPassAutopairing: false
+            });
+            assert.equal(pcc.unpaired.length, 0);
+            assert.equal(pcc.paired.length, pcc.initialList.length / 2);
+        });
+
+        //TODO:
+        //  filters: clearing, setting via popover, regex
+        //  partition: maximize paired, maximize unpaired, split evenly
+        //  pairing: manually pairing and unpairing
+        //  misc: renaming pairs, removing file extensions
+    }
+);

client/galaxy/scripts/qunit/tests/masthead_tests.js

@@ -0,0 +1,124 @@
+/* global define */
+define(["qunit/test-app", "layout/masthead", "galaxy"], function(testApp, Masthead, Galaxy) {
+    "use strict";
+    Masthead = Masthead.default;
+    QUnit.module("Masthead test", {
+        beforeEach: function() {
+            testApp.create();
+            var self = this;
+            this.masthead = new Masthead.View({
+                brand: "brand",
+                use_remote_user: "use_remote_user",
+                remote_user_logout_href: "remote_user_logout_href",
+                lims_doc_url: "lims_doc_url",
+                biostar_url: "biostar_url",
+                biostar_url_redirect: "biostar_url_redirect",
+                support_url: "support_url",
+                search_url: "search_url",
+                mailing_lists: "mailing_lists",
+                screencasts_url: "screencasts_url",
+                wiki_url: "wiki_url",
+                citation_url: "citation_url",
+                terms_url: "terms_url",
+                logo_url: "logo_url",
+                logo_src: "../../../static/images/galaxyIcon_noText.png",
+                is_admin_user: "is_admin_user",
+                active_view: "analysis",
+                ftp_upload_dir: "ftp_upload_dir",
+                ftp_upload_site: "ftp_upload_site",
+                datatypes_disable_auto: true,
+                allow_user_creation: true,
+                enable_cloud_launch: true,
+                user_requests: true
+            });
+            $("body").append(this.masthead.render().$el);
+        },
+        afterEach: function() {
+            testApp.destroy();
+        }
+    });
+
+    QUnit.test("tabs", function(assert) {
+        var tab = this.masthead.collection.findWhere({ id: "analysis" });
+        var $tab = $("#analysis").find(".dropdown");
+        var $toggle = $tab.find(".dropdown-toggle");
+        var $note = $tab.find(".dropdown-note");
+        var $menu = $tab.find("ul");
+        assert.ok(tab && $tab.length == 1, "Found analysis tab");
+        tab.set("title", "Analyze");
+        assert.ok($toggle.html() == "Analyze", "Correct title");
+        assert.ok(tab.get("target") == "_parent", "Correct initial target");
+        tab.set("target", "_target");
+        assert.ok($toggle.attr("target") == "_target", "Correct test target");
+        assert.ok($tab.css("visibility") == "visible", "Tab visible");
+        tab.set("visible", false);
+        assert.ok($tab.css("visibility") == "hidden", "Tab hidden");
+        tab.set("visible", true);
+        assert.ok($tab.css("visibility") == "visible", "Tab visible, again");
+        assert.ok($toggle.attr("href") == Galaxy.root, "Correct initial url");
+        tab.set("url", "_url");
+        assert.ok($toggle.attr("href") == "/_url", "Correct test url");
+        tab.set("url", "http://_url");
+        assert.ok($toggle.attr("href") == "http://_url", "Correct http url");
+        tab.set("tooltip", "_tooltip");
+        $toggle.trigger("mouseover");
+        assert.ok($(".tooltip-inner").html() == "_tooltip", "Correct tooltip");
+        tab.set("tooltip", null);
+        $toggle.trigger("mouseover");
+        assert.ok($(".tooltip-inner").length == 0, "Tooltip removed");
+        tab.set("tooltip", "_tooltip_new");
+        $toggle.trigger("mouseover");
+        assert.ok($(".tooltip-inner").html() == "_tooltip_new", "Correct new tooltip");
+        tab.set("cls", "_cls");
+        assert.ok($toggle.hasClass("_cls"), "Correct extra class");
+        tab.set("cls", "_cls_new");
+        assert.ok($toggle.hasClass("_cls_new") && !$toggle.hasClass("_cls"), "Correct new extra class");
+        assert.ok($note.html() == "", "Correct empty note");
+        tab.set({ note: "_note", show_note: true });
+        assert.ok($note.html() == "_note", "Correct new note");
+        tab.set("toggle", true);
+        assert.ok($toggle.hasClass("toggle"), "Toggled");
+        tab.set("toggle", false);
+        assert.ok(!$toggle.hasClass("toggle"), "Untoggled");
+        tab.set("disabled", true);
+        assert.ok($tab.hasClass("disabled"), "Correctly disabled");
+        tab.set("disabled", false);
+        assert.ok(!$tab.hasClass("disabled"), "Correctly enabled");
+        assert.ok($tab.hasClass("active"), "Highlighted");
+        tab.set("active", false);
+        assert.ok(!$tab.hasClass("active"), "Not highlighted");
+        tab.set("active", true);
+        assert.ok($tab.hasClass("active"), "Highlighted, again");
+        tab.set("menu", [{ title: "_menu_title", url: "_menu_url", target: "_menu_target" }]);
+        assert.ok($menu.hasClass("dropdown-menu"), "Menu has correct class");
+        assert.ok($menu.css("display") == "none", "Menu hidden");
+        $toggle.trigger("click");
+        assert.ok($menu.css("display") == "block", "Menu shown");
+        var $item = $menu.find("a");
+        assert.ok($item.length == 1, "Added one menu item");
+        assert.ok($item.html() == "_menu_title", "Menu item has correct title");
+        assert.ok($item.attr("href") == "/_menu_url", "Menu item has correct url");
+        assert.ok($item.attr("target") == "_menu_target", "Menu item has correct target");
+        tab.set("menu", null);
+        $item = $menu.find("a");
+        assert.ok($item.length == 0, "All menu items removed");
+        tab.set("menu", [
+            { title: "_menu_title_0", url: "_menu_url_0", target: "_menu_target_0" },
+            { title: "_menu_title_1", url: "_menu_url_1", target: "_menu_target_1" }
+        ]);
+        $item = $menu.find("a");
+        assert.ok($item.length == 2, "Two menu items added");
+        tab.set("show_menu", false);
+        assert.ok($menu.css("display", "none"), "Menu manually hidden");
+        tab.set("show_menu", true);
+        assert.ok($menu.css("display", "block"), "Menu manually shown, again");
+        var tab = this.masthead.collection.findWhere({ id: "enable-scratchbook" });
+        var $tab = $("#enable-scratchbook").find(".dropdown");
+        assert.ok(tab && $tab.length == 1, "Found tab to enable scratchbook");
+        var $toggle = $tab.find(".dropdown-toggle");
+        assert.ok(!$toggle.hasClass("toggle"), "Untoggled before click");
+        $toggle.trigger("click");
+        assert.ok($toggle.hasClass("toggle"), "Toggled after click");
+        assert.ok(Galaxy.frame.active, "Scratchbook is active");
+    });
+});

client/galaxy/scripts/qunit/tests/metrics-logger.js

@@ -0,0 +1,370 @@
+// This file isn't really testing anything useful yet, it is just testing
+// (or demonstrating) qunit+backbone interactions.
+/* global define */
+define(["qunit/test-app", "utils/metrics-logger", "jquery", "sinon"], function(testApp, metrics, $, sinon) {
+    "use strict";
+    metrics = metrics.default;
+
+    var MockConsole = function() {
+        var self = this;
+        self.lastMessage = null;
+        ["log", "debug", "info", "warn", "error"].forEach(function(fnName) {
+            self[fnName] = function() {
+                var args = Array.prototype.slice.call(arguments, 0);
+                self.lastMessage = { level: fnName, args: args };
+            };
+        });
+        return self;
+    };
+
+    (window.bootstrapped = {}).user = {
+        id: "test"
+    };
+
+    QUnit.module("Metrics logger tests");
+    // ======================================================================== MetricsLogger
+    QUnit.test("logger construction/initializiation defaults", function(assert) {
+        var logger = new metrics.MetricsLogger({});
+        assert.equal(logger.consoleLogger, null);
+        assert.equal(logger.options.logLevel, metrics.MetricsLogger.NONE);
+        assert.equal(logger.options.consoleLevel, metrics.MetricsLogger.NONE);
+        assert.equal(logger.options.defaultNamespace, "Galaxy");
+        assert.equal(logger.options.clientPrefix, "client.");
+        assert.equal(logger.options.postSize, 1000);
+        assert.equal(logger.options.maxCacheSize, 3000);
+        assert.equal(logger.options.addTime, true);
+        assert.equal(logger.options.postUrl, "/api/metrics");
+        assert.equal(logger.options.getPingData, undefined);
+        assert.equal(logger.options.onServerResponse, undefined);
+
+        assert.equal(logger._postSize, 1000);
+        assert.equal(logger.cache.constructor, metrics.LoggingCache);
+    });
+
+    QUnit.test("_parseLevel", function(assert) {
+        var logger = new metrics.MetricsLogger({});
+        assert.equal(logger._parseLevel("all"), metrics.MetricsLogger.ALL);
+        assert.equal(logger._parseLevel("debug"), metrics.MetricsLogger.DEBUG);
+        assert.equal(logger._parseLevel("info"), metrics.MetricsLogger.INFO);
+        assert.equal(logger._parseLevel("warn"), metrics.MetricsLogger.WARN);
+        assert.equal(logger._parseLevel("error"), metrics.MetricsLogger.ERROR);
+        assert.equal(logger._parseLevel("metric"), metrics.MetricsLogger.METRIC);
+        assert.equal(logger._parseLevel("none"), metrics.MetricsLogger.NONE);
+        assert.equal(logger._parseLevel(15), 15);
+
+        assert.throws(
+            function() {
+                logger._parseLevel(undefined);
+            },
+            /Unknown log level/,
+            "Unknown log level throws error"
+        );
+        assert.throws(
+            function() {
+                logger._parseLevel("nope");
+            },
+            /Unknown log level/,
+            "Unknown log level throws error"
+        );
+    });
+
+    // ------------------------------------------------------------------------ Emit to cache
+    QUnit.test("emit to cache at level", function(assert) {
+        var logger = new metrics.MetricsLogger({
+            logLevel: "metric"
+        });
+        logger.cache.empty();
+
+        assert.equal(logger.options.logLevel, metrics.MetricsLogger.METRIC);
+        logger.emit("metric", "test", [1, 2, { three: 3 }]);
+        assert.equal(logger.cache.length(), 1);
+
+        var cached = logger.cache.get(1)[0];
+        //console.debug( 'cached:', JSON.stringify( cached ) );
+        assert.equal(cached.level, metrics.MetricsLogger.METRIC);
+        assert.equal(cached.namespace, "client.test");
+        assert.equal(cached.args.length, 3);
+        assert.equal(cached.args[2].three, 3);
+        assert.ok(typeof cached.time === "string");
+        assert.ok(cached.time === new Date(cached.time).toISOString());
+    });
+
+    QUnit.test("emit to cache below does not cache", function(assert) {
+        var logger = new metrics.MetricsLogger({
+            logLevel: "metric"
+        });
+        logger.cache.empty();
+
+        logger.emit("error", "test", [1, 2, { three: 3 }]);
+        assert.equal(logger.cache.length(), 0);
+    });
+
+    QUnit.test("emit to cache (silently) drops non-parsable", function(assert) {
+        var logger = new metrics.MetricsLogger({
+            logLevel: "metric"
+        });
+        logger.cache.empty();
+
+        logger.emit("metric", "test", [{ window: window }]);
+        assert.equal(logger.cache.length(), 0);
+    });
+
+    function metricsFromRequestBody(request) {
+        // assumes 'metrics' is only entry in requestBody
+        return JSON.parse(decodeURIComponent(request.requestBody.replace("metrics=", "")));
+    }
+
+    QUnit.test("_postCache success", function(assert) {
+        var callback = sinon.spy(),
+            logger = new metrics.MetricsLogger({
+                logLevel: "metric",
+                onServerResponse: function(response) {
+                    callback();
+                }
+            });
+        logger.cache.empty();
+
+        var server = sinon.fakeServer.create(),
+            metricsOnServer;
+        server.respondWith("POST", "/api/metrics", function(request) {
+            metricsOnServer = metricsFromRequestBody(request);
+            //console.debug( 'requestBody:', request.requestBody );
+            //console.debug( 'metricsOnServer:', JSON.stringify( metricsOnServer, null, '  ' ) );
+            request.respond(
+                200,
+                { "Content-Type": "application/json" },
+                JSON.stringify({
+                    fakeResponse: "yes"
+                })
+            );
+        });
+
+        logger.emit("metric", "test", [1, 2, { three: 3 }]);
+        logger._postCache();
+        server.respond();
+
+        assert.ok(callback.calledOnce, "onServerResponse was called");
+        assert.equal(logger.cache.length(), 0, "should have emptied cache (on success)");
+        assert.equal(logger._postSize, 1000, "_postSize still at default");
+
+        // metrics were in proper form on server
+        assert.equal(metricsOnServer.length, 1);
+        var metric = metricsOnServer[0];
+        assert.equal(metric.level, metrics.MetricsLogger.METRIC);
+        assert.equal(metric.namespace, "client.test");
+        assert.equal(metric.args.length, 3);
+        assert.equal(metric.args[2].three, 3);
+        assert.ok(typeof metric.time === "string");
+        assert.ok(metric.time === new Date(metric.time).toISOString());
+
+        server.restore();
+    });
+
+    QUnit.test("_postCache failure", function(assert) {
+        var callback = sinon.spy(),
+            logger = new metrics.MetricsLogger({
+                logLevel: "metric",
+                onServerResponse: function(response) {
+                    callback();
+                }
+            });
+        logger.cache.empty();
+
+        var server = sinon.fakeServer.create();
+        server.respondWith("POST", "/api/metrics", function(request) {
+            request.respond(
+                500,
+                { "Content-Type": "application/json" },
+                JSON.stringify({
+                    err_msg: "NoooOPE!"
+                })
+            );
+        });
+
+        logger.emit("metric", "test", [1, 2, { three: 3 }]);
+        logger._postCache();
+        server.respond();
+        //TODO: is the following what we want?
+        assert.ok(!callback.calledOnce, "onServerResponse was NOT called");
+        assert.equal(logger.cache.length(), 1, "should NOT have emptied cache");
+        assert.equal(logger._postSize, logger.options.maxCacheSize, "_postSize changed to max");
+
+        server.restore();
+    });
+
+    // ------------------------------------------------------------------------ Emit to console
+    QUnit.test("emit to console at level", function(assert) {
+        var mockConsole = new MockConsole(),
+            logger = new metrics.MetricsLogger({
+                consoleLevel: "debug",
+                consoleLogger: mockConsole
+            });
+        assert.equal(logger.options.consoleLevel, metrics.MetricsLogger.DEBUG);
+        assert.equal(logger.consoleLogger.constructor, MockConsole);
+
+        logger.emit("debug", "test", [1, 2, { three: 3 }]);
+        assert.equal(logger.cache.length(), 1);
+        //console.debug( JSON.stringify( mockConsole.lastMessage ) );
+        assert.equal(mockConsole.lastMessage.level, "debug");
+        assert.equal(mockConsole.lastMessage.args.length, 4);
+        assert.equal(mockConsole.lastMessage.args[0], "test");
+        assert.equal(mockConsole.lastMessage.args[3].three, 3);
+    });
+
+    QUnit.test("emit to console below does not output", function(assert) {
+        var mockConsole = new MockConsole(),
+            logger = new metrics.MetricsLogger({
+                consoleLevel: "error",
+                consoleLogger: mockConsole
+            });
+        logger.emit("debug", "test", [1, 2, { three: 3 }]);
+        assert.equal(mockConsole.lastMessage, null);
+    });
+
+    // ------------------------------------------------------------------------ Shortcuts
+    QUnit.test("logger shortcuts emit to default namespace properly", function(assert) {
+        var logger = new metrics.MetricsLogger({
+            logLevel: "all"
+        });
+        logger.cache.empty();
+
+        assert.equal(logger.options.logLevel, metrics.MetricsLogger.ALL);
+        logger.log(0);
+        logger.debug(1);
+        logger.info(2);
+        logger.warn(3);
+        logger.error(4);
+        logger.metric(5);
+
+        assert.equal(logger.cache.length(), 6);
+        var cached = logger.cache.remove(6),
+            entry;
+
+        cached.forEach(function(entry) {
+            assert.ok(entry.namespace === logger.options.clientPrefix + logger.options.defaultNamespace);
+            assert.ok(jQuery.type(entry.args) === "array");
+            assert.ok(typeof entry.time === "string");
+        });
+
+        // log is different
+        entry = cached[0];
+        assert.ok(entry.level === 1);
+        assert.ok(entry.args[0] === 0);
+
+        ["debug", "info", "warn", "error", "metric"].forEach(function(level, i) {
+            entry = cached[i + 1];
+            assert.ok(entry.level === logger._parseLevel(level));
+            assert.ok(entry.args[0] === i + 1);
+        });
+    });
+
+    // ======================================================================== LoggingCache
+    QUnit.test("cache construction/initializiation defaults", function(assert) {
+        // use empty to prevent tests stepping on one another due to persistence
+        var cache = new metrics.LoggingCache({ key: "logs-test" }).empty();
+        assert.equal(cache.maxSize, 5000);
+        assert.equal(window.localStorage.getItem("logs-test"), "[]");
+    });
+
+    QUnit.test("cache construction/initializiation failure", function(assert) {
+        ////TODO: doesn't work - readonly
+        //window.localStorage = null;
+        //console.debug( 'localStorage:', window.localStorage );
+        var oldFn = metrics.LoggingCache.prototype._hasStorage;
+        metrics.LoggingCache.prototype._hasStorage = function() {
+            return false;
+        };
+        assert.throws(
+            function() {
+                return new metrics.LoggingCache({ key: "logs-test" });
+            },
+            /LoggingCache needs localStorage/,
+            "lack of localStorage throws error"
+        );
+        metrics.LoggingCache.prototype._hasStorage = oldFn;
+
+        assert.throws(
+            function() {
+                return new metrics.LoggingCache();
+            },
+            /LoggingCache needs key for localStorage/,
+            "lack of key throws error"
+        );
+    });
+
+    QUnit.test("cache construction/initializiation setting max cache size", function(assert) {
+        var cache = new metrics.LoggingCache({
+            key: "logs-test",
+            maxSize: 5
+        }).empty();
+        assert.equal(cache.maxSize, 5);
+    });
+
+    QUnit.test("cache plays well with no data", function(assert) {
+        var cache = new metrics.LoggingCache({ key: "logs-test" }).empty();
+
+        assert.equal(cache.length(), 0);
+        var get = cache.get(10);
+        assert.ok(jQuery.type(get) === "array" && get.length === 0);
+        var remove = cache.remove(10);
+        assert.ok(jQuery.type(remove) === "array" && remove.length === 0);
+        assert.equal(cache.length(), 0);
+    });
+
+    QUnit.test("cache add properly adds and removes data", function(assert) {
+        var cache = new metrics.LoggingCache({
+            key: "logs-test",
+            maxSize: 5
+        }).empty();
+
+        var entry1 = [{ one: 1 }, "two"];
+        cache.add(entry1);
+
+        assert.equal(cache.length(), 1);
+        assert.equal(JSON.stringify(cache.get(1)[0]), JSON.stringify(entry1));
+
+        var entry2 = { blah: { one: 1 }, bler: ["three", { two: 2 }] };
+        cache.add(entry2);
+        assert.equal(cache.length(), 2);
+        assert.equal(cache.stringify(2), "[" + JSON.stringify(entry1) + "," + JSON.stringify(entry2) + "]");
+
+        // FIFO
+        var returned = cache.remove(1);
+        assert.equal(cache.length(), 1);
+        assert.ok(jQuery.type(returned) === "array" && returned.length === 1);
+        var returned0 = returned[0];
+        assert.ok(jQuery.type(returned0) === "array" && JSON.stringify(returned0) === JSON.stringify(entry1));
+    });
+
+    QUnit.test("cache past max loses oldest", function(assert) {
+        var cache = new metrics.LoggingCache({
+            key: "logs-test",
+            maxSize: 5
+        }).empty();
+
+        for (var i = 0; i < 10; i += 1) {
+            cache.add({ index: i });
+        }
+        assert.equal(cache.length(), 5);
+        var get = cache.get(5);
+        assert.ok(get[0].index === 5);
+        assert.ok(get[1].index === 6);
+        assert.ok(get[2].index === 7);
+        assert.ok(get[3].index === 8);
+        assert.ok(get[4].index === 9);
+    });
+
+    QUnit.test("cache is properly persistent", function(assert) {
+        var cache1 = new metrics.LoggingCache({ key: "logs-test" }).empty(),
+            entry = [{ one: 1 }, "two"];
+        cache1.add(entry);
+        assert.equal(cache1.length(), 1);
+
+        var cache2 = new metrics.LoggingCache({ key: "logs-test" });
+        assert.equal(cache2.length(), 1, "old key gets previously stored");
+        assert.equal(JSON.stringify(cache2.get(1)[0]), JSON.stringify(entry));
+
+        var cache3 = new metrics.LoggingCache({ key: "logs-bler" });
+        assert.equal(cache3.length(), 0, "new key causes new storage");
+    });
+});

client/galaxy/scripts/qunit/tests/modal_tests.js

@@ -0,0 +1,92 @@
+/* global define */
+
+define(["qunit/test-app", "mvc/ui/ui-modal", "sinon"], function(testApp, GalaxyModal, sinon) {
+    "use strict";
+    GalaxyModal = GalaxyModal.default;
+    QUnit.module("Modal dialog test", {
+        beforeEach: function() {
+            testApp.create();
+            this.clock = sinon.useFakeTimers();
+            var self = this;
+            this.app = new GalaxyModal.View({
+                title: "Test title",
+                body: "Test body",
+                buttons: {
+                    Ok: function() {},
+                    Cancel: function() {
+                        self.app.hide();
+                    }
+                }
+            });
+        },
+        afterEach: function() {
+            testApp.destroy();
+            this.clock.restore();
+        }
+    });
+
+    QUnit.test("test dialog attributes", function(assert) {
+        assert.ok(this.app.$header.find(".title").html() == "Test title", "Modal header has correct title.");
+        assert.ok(this.app.$body.html() == "Test body", "Modal header has correct body.");
+    });
+
+    QUnit.test("test dialog visibility", function(assert) {
+        assert.ok(this.app.$el.css("display") == "block", "Modal is initially visible");
+        this.app.hide();
+        this.clock.tick(WAIT_FADE);
+        assert.ok(this.app.$el.css("display") == "none", "Modal hidden manually");
+        this.app.show();
+        this.clock.tick(WAIT_FADE);
+        assert.ok(this.app.$el.css("display") == "block", "Modal shown manually");
+        this.app.getButton("Ok").trigger("click");
+        this.clock.tick(WAIT_FADE);
+        assert.ok(this.app.$el.css("display") == "block", "Modal still visible after clicking Ok");
+        this.app.getButton("Cancel").trigger("click");
+        this.clock.tick(WAIT_FADE);
+        assert.ok(this.app.$el.css("display") == "none", "Modal hidden after clicking Cancel");
+        this.app.show();
+        this.clock.tick(WAIT_FADE);
+        assert.ok(this.app.$el.css("display") == "block", "Modal manually shown again");
+        assert.ok(!this.app.$header.hasClass("no-separator"), "Title separator tagged as visible.");
+        this.app.show({ title_separator: false });
+        assert.ok(this.app.$header.hasClass("no-separator"), "Title separator tagged as hidden.");
+        assert.ok(this.app.$backdrop.hasClass("in"), "Backdrop tagged as shown.");
+        this.app.show({ backdrop: false });
+        assert.ok(!this.app.$backdrop.hasClass("in"), "Backdrop tagged as hidden.");
+    });
+
+    QUnit.test("test dialog closing events", function(assert) {
+        this.app.$backdrop.trigger("click");
+        this.clock.tick(WAIT_FADE);
+        assert.ok(this.app.$el.css("display") == "block", "Modal shown after backdrop click");
+        this.app.show({ closing_events: true });
+        assert.ok(this.app.$el.css("display") == "block", "Modal shown with closing events");
+        this.app.$backdrop.trigger("click");
+        this.clock.tick(WAIT_FADE);
+        assert.ok(this.app.$el.css("display") == "none", "Modal hidden after backdrop click");
+    });
+
+    QUnit.test("test dialog rendering", function(assert) {
+        var before = this.app.$el.html();
+        this.app.render();
+        assert.ok(before == this.app.$el.html(), "Re-rendering successful");
+        this.app.options.title = "New Title";
+        this.app.render();
+        assert.ok(this.app.$header.find(".title").html() == "New Title", "Modal header has correct new title.");
+    });
+
+    QUnit.test("test button states", function(assert) {
+        assert.ok(this.app.getButton("Ok").html() === "Ok", "Ok has correct label");
+        assert.ok(!this.app.getButton("Ok").prop("disabled"), "Ok is active");
+        assert.ok(!this.app.getButton("Cancel").prop("disabled"), "Cancel is active");
+        this.app.disableButton("Ok");
+        assert.ok(this.app.getButton("Ok").prop("disabled"), "Ok is disabled");
+        assert.ok(!this.app.getButton("Cancel").prop("disabled"), "Cancel is still active");
+        this.app.disableButton("Cancel");
+        assert.ok(this.app.getButton("Cancel").prop("disabled"), "Cancel is also disabled");
+        assert.ok(this.app.getButton("Ok").prop("disabled"), "Ok is still disabled");
+        this.app.enableButton("Ok");
+        assert.ok(this.app.getButton("Cancel").prop("disabled"), "Cancel is still disabled");
+        assert.ok(!this.app.getButton("Ok").prop("disabled"), "Ok is active again");
+    });
+});

client/galaxy/scripts/qunit/tests/page_tests.js

@@ -0,0 +1,56 @@
+/* global define */
+
+define(["qunit/test-app", "layout/page", "layout/panel"], function(testApp, Page, Panel) {
+    "use strict";
+    Page = Page.default;
+    Panel = Panel.default;
+    QUnit.module("Page test", {
+        beforeEach: function() {
+            testApp.create();
+            $("body").append((this.$container = $("<div/>").css("display", "none")));
+        },
+        afterEach: function() {
+            testApp.destroy();
+        }
+    });
+
+    function _check(assert, page, sidePanels) {
+        assert.ok(page.$("#center").length == 1, "Center panel found.");
+        _.each(sidePanels, function(panelVisible, panelId) {
+            assert.ok(
+                page.$("#" + panelId).css("display") == panelVisible,
+                (panelVisible ? "" : "No") + " " + panelId + " panel found."
+            );
+        });
+    }
+
+    QUnit.test("test center/right", function(assert) {
+        this.$container.empty();
+        var page = new Page.View({
+            Right: Backbone.View.extend({
+                initialize: function() {
+                    this.setElement($("<div/>"));
+                    this.model = new Backbone.Model({});
+                }
+            })
+        }).render();
+        _check(assert, page, { left: "none", right: "block" });
+    });
+    QUnit.test("test center", function(assert) {
+        this.$container.empty();
+        var page = new Page.View({}).render();
+        _check(assert, page, { left: "none", right: "none" });
+    });
+    QUnit.test("test left/center", function(assert) {
+        this.$container.empty();
+        var page = new Page.View({
+            Left: Backbone.View.extend({
+                initialize: function() {
+                    this.setElement($("<div/>"));
+                    this.model = new Backbone.Model({});
+                }
+            })
+        }).render();
+        _check(assert, page, { left: "block", right: "none" });
+    });
+});

client/galaxy/scripts/qunit/tests/popover_tests.js

@@ -0,0 +1,41 @@
+/* global define */
+define(["qunit/test-app", "mvc/ui/ui-misc", "mvc/ui/ui-popover"], function(testApp, Ui, Popover) {
+    "use strict";
+    Ui = Ui.default;
+    Popover = Popover.default;
+    QUnit.module("Popover test", {
+        beforeEach: function() {
+            testApp.create();
+            var self = this;
+            this.button = new Ui.Button({
+                title: "Test button",
+                onclick: function() {
+                    self.popover.show();
+                }
+            });
+            this.$parent = $("<div/>").append(this.button.$el);
+            this.popover = new Popover.View({
+                title: "Test Title",
+                body: "Test Body",
+                placement: "bottom",
+                container: this.button.$el
+            });
+            $("body").append(this.$parent);
+        },
+        afterEach: function() {
+            testApp.destroy();
+        }
+    });
+
+    QUnit.test("test popover visibility", function(assert) {
+        assert.ok(this.popover.$el.css("display") == "none", "Popover is hidden.");
+        this.button.$el.trigger("click");
+        assert.ok(this.popover.$el.css("display") == "block", "Popover is shown.");
+        assert.ok(this.popover.$el.hasClass("bottom"), "Popover at bottom.");
+        this.popover.hide();
+        assert.ok(this.popover.$el.css("display") == "none", "Popover is hidden manually.");
+        assert.ok(this.popover.$title.html() == "Test Title", "Initial title correct.");
+        this.popover.title("New Title");
+        assert.ok(this.popover.$title.html() == "New Title", "New title correct.");
+    });
+});

client/galaxy/scripts/qunit/tests/upload_dialog_tests.js

@@ -0,0 +1,87 @@
+/* global define */
+define(["qunit/test-app", "mvc/upload/upload-view"], function(testApp, GalaxyUpload) {
+    "use strict";
+    GalaxyUpload = GalaxyUpload.default;
+    QUnit.module("Upload dialog test", {
+        beforeEach: function() {
+            testApp.create();
+            this.app = new GalaxyUpload();
+        },
+        afterEach: function() {
+            testApp.destroy();
+        }
+    });
+
+    QUnit.test("test initial dialog state", function(assert) {
+        $(this.app.ui_button.$el).trigger("click");
+        assert.ok(this.app.default_view.collection.length == 0, "Invalid initial upload item collection.");
+        assert.ok($("#btn-start").hasClass("disabled"), "Start button should be disabled.");
+        assert.ok($("#btn-stop").hasClass("disabled"), "Stop button should be disabled.");
+        assert.ok($("#btn-reset").hasClass("disabled"), "Reset button should be disabled.");
+    });
+
+    QUnit.test("test adding/removing paste/fetch upload item", function(assert) {
+        $(this.app.ui_button.$el).trigger("click");
+        $("#btn-new").trigger("click");
+        assert.ok(!$("#btn-start").hasClass("disabled"), "Start button should be enabled.");
+        assert.ok($("#btn-stop").hasClass("disabled"), "Stop button should (still) be disabled.");
+        assert.ok(!$("#btn-reset").hasClass("disabled"), "Reset button should be enabled.");
+        assert.ok(
+            this.app.default_view.collection.length == 1,
+            "Invalid upload item collection length after adding item."
+        );
+        assert.ok(
+            $("#btn-new")
+                .find("i")
+                .hasClass("fa-edit"),
+            "Paste/fetch icon changed"
+        );
+        assert.ok($("#btn-start").hasClass("btn-primary"), "Start button should be enabled/highlighted.");
+        assert.ok(
+            $("#upload-row-0")
+                .find(".upload-symbol")
+                .hasClass("fa-trash-o"),
+            "Should show regular trash icon."
+        );
+        $("#upload-row-0")
+            .find(".upload-settings")
+            .trigger("click");
+        assert.ok(
+            $("#upload-row-0")
+                .find(".upload-settings-cover")
+                .css("display") == "none",
+            "Settings should be enabled."
+        );
+        $("#upload-row-0")
+            .find(".popover-close")
+            .trigger("click");
+        $("#btn-start").trigger("click");
+        assert.ok(
+            $("#upload-row-0")
+                .find(".upload-symbol")
+                .hasClass("fa-exclamation-triangle"),
+            "Upload attempt should have failed."
+        );
+        assert.ok(
+            $("#upload-row-0")
+                .find(".upload-settings")
+                .trigger("click")
+        );
+        assert.ok(
+            $("#upload-row-0")
+                .find(".upload-settings-cover")
+                .css("display") == "block",
+            "Settings should be disabled."
+        );
+        $("#upload-row-0")
+            .find(".upload-symbol")
+            .trigger("click");
+        assert.ok(this.app.default_view.collection.length == 0, "Removing item from collection failed.");
+    });
+
+    QUnit.test("test ftp popup", function(assert) {
+        $(this.app.ui_button.$el).trigger("click");
+        $("#btn-ftp").trigger("click");
+        assert.ok($(".upload-ftp").length == 1, "Should show ftp popover.");
+    });
+});

client/galaxy/scripts/qunit/tests/utils_test.js

@@ -0,0 +1,20 @@
+/* global define */
+define(["qunit/test-app", "utils/utils"], function(testApp, Utils) {
+    "use strict";
+    Utils = Utils.default;
+    QUnit.module("Utils test", {});
+
+    QUnit.test("isEmpty", function(assert) {
+        assert.ok(Utils.isEmpty([]), "Empty array");
+        assert.ok(Utils.isEmpty(["data", undefined]), "Array contains `undefined`");
+        assert.ok(Utils.isEmpty(["data", null]), "Array contains `null`");
+        assert.ok(Utils.isEmpty(["data", "__null__"]), "Array contains `__null__`");
+        assert.ok(Utils.isEmpty(["data", "__undefined__"]), "Array contains `__undefined__`");
+        assert.ok(Utils.isEmpty(null), "Array is null");
+        assert.ok(Utils.isEmpty("__null__"), "Array is __null__");
+        assert.ok(Utils.isEmpty("__undefined__"), "Array is __undefined__");
+        assert.ok(!Utils.isEmpty(["data"]), "Array contains `data`");
+        assert.ok(!Utils.isEmpty(1), "Value is int");
+        assert.ok(!Utils.isEmpty(0), "Value is zero");
+    });
+});

client/galaxy/style/less/base.less

@@ -1855,3 +1855,8 @@ div.toolTitleNoSection
   visibility: visible;
   opacity: 1;
 }
+
+/* For Vue */
+[v-cloak] {
+    display:none;
+}

client/gulpfile.js

@@ -16,8 +16,9 @@ var paths = {
     node_modules: './node_modules',
     scripts: [
         'galaxy/scripts/**/*.js',
-        '!galaxy/scripts/apps/**/*.js',
-        '!galaxy/scripts/libs/**/*.js'
+        '!galaxy/scripts/qunit/**/*',
+        '!galaxy/scripts/apps/**/*',
+        '!galaxy/scripts/libs/**/*'
     ],
     lib_locs: {
         // This is a stepping stone towards having all this staged
@@ -25,7 +26,7 @@ var paths = {
         // not be necessary.
         'backbone': [ 'backbone.js', 'backbone.js' ],
         'd3': [ 'd3.js', 'd3.js' ],
-        'bib2json': [ 'Parser.js', 'bibtex.js' ],
+        'bibtex-parse-js': [ 'bibtexParse.js', 'bibtexParse.js' ],
         'jquery': ['dist/jquery.js', 'jquery/jquery.js'],
         'jquery.complexify':     [ 'jquery.complexify.js', 'jquery/jquery.complexify.js' ],
         'jquery.cookie': [ 'jquery.cookie.js', 'jquery/jquery.cookie.js' ],
@@ -34,6 +35,7 @@ var paths = {
         'raven-js': ['dist/raven.js', 'raven.js'],
         'requirejs': [ 'require.js', 'require.js' ],
         'underscore': [ 'underscore.js', 'underscore.js' ],
+        'vue': [ 'dist/vue.js', 'vue.js' ]
     },
     libs: ['galaxy/scripts/libs/**/*.js']
 };

client/karma.config.js

@@ -0,0 +1,70 @@
+var webpackConfig = require('./webpack.config');
+
+// CommonsChunkPlugin not compatible with karma.
+// https://github.com/webpack-contrib/karma-webpack/issues/24
+webpackConfig.plugins.splice(0, 1);
+
+// karma.conf.js
+module.exports = function(config) {
+  config.set({
+    basepath: '.',
+    files: [
+      // Broken into uncommented working tests and commented out broken tests,
+      // this can be replaced with a glob when they all just work.
+
+      // Working tests:
+      'galaxy/scripts/qunit/tests/list-of-pairs-collection-creator.js',
+      'galaxy/scripts/qunit/tests/galaxy-app-base.js',
+      'galaxy/scripts/qunit/tests/graph.js',
+      'galaxy/scripts/qunit/tests/hda-base.js',
+      'galaxy/scripts/qunit/tests/history_contents_model_tests.js',
+      'galaxy/scripts/qunit/tests/job-dag.js',
+      'galaxy/scripts/qunit/tests/metrics-logger.js',
+      'galaxy/scripts/qunit/tests/popover_tests.js',
+      'galaxy/scripts/qunit/tests/utils_test.js',
+      'galaxy/scripts/qunit/tests/page_tests.js',
+      'galaxy/scripts/qunit/tests/workflow_editor_tests.js',
+
+      // The following tests don't work for state reasons:
+
+      // Error: Following test works on its own or with rest but not with 
+      //     list-of-pairs-collection-creator in the same suite. Not as much isolation
+      //     as seperate page setup of previous runner.
+      // 'galaxy/scripts/qunit/tests/ui_tests.js',
+      // Error: things displayed wrong I guess cause assertions fail on CSS stuff
+      // 'galaxy/scripts/qunit/tests/modal_tests.js',
+      // 'galaxy/scripts/qunit/tests/upload_dialog_tests.js',
+      // Error: Cannot find module "libs/bibtexParse"
+      // 'galaxy/scripts/qunit/tests/form_tests.js',
+      // 'galaxy/scripts/qunit/tests/masthead_tests.js',
+
+      // Non-test assets that will be served by web server.
+      // CSS needed by tests.
+      'galaxy/scripts/qunit/assets/*.css',
+    ],
+
+    plugins: [
+      'karma-webpack',
+      'karma-qunit',
+      'karma-polyfill',
+      'karma-phantomjs-launcher',
+    ],
+    polyfill: [ 'Object.assign' ],
+    browsers: [ 'PhantomJS' ],
+    // logLevel: config.LOG_DEBUG,
+
+    // Tried to do some awesome babel, ES6 stuff in here but I was encountering
+    // problems so I simplified - might be worth adding it back in though now
+    // that we have a working setup.
+    preprocessors: {
+      // add webpack as preprocessor
+      'galaxy/scripts/qunit/tests/*.js': ['webpack'],
+    },
+
+    frameworks: ['polyfill', 'qunit'],
+
+    webpack: webpackConfig,
+    webpackMiddleware: { noInfo: false }
+
+  });
+};

client/package.json

@@ -12,17 +12,21 @@
   "license": "AFL-3.0",
   "dependencies": {
     "amdi18n-loader": "^0.6.1",
+    "axios": "^0.17.0",
     "backbone": "1.3",
-    "bib2json": "^0.0.1",
+    "bibtex-parse-js": "^0.0.24",
     "d3": "3",
     "jquery": "2",
     "jquery-migrate": "~1.4",
     "jquery-mousewheel": "^3.1.13",
     "jquery.complexify": "^0.5.2",
     "jquery.cookie": "^1.4.1",
+    "latex-parser": "^0.6.2",
+    "latex-to-unicode-converter": "^0.5.0",
     "raven-js": "^3.17.0",
     "requirejs": "2",
-    "underscore": "^1.8.3"
+    "underscore": "^1.8.3",
+    "vue": "^2.5.3"
   },
   "scripts": {
     "watch": "gulp stage-libs && concurrently \"yarn run webpack-watch\" \"yarn run gulp watch\" \"yarn run style-watch\"",
@@ -33,6 +37,7 @@
     "webpack-dev-watch": "webpack -d --watch",
     "style": "grunt style",
     "style-watch": "grunt watch-style",
+    "test": "karma start --verbose --single-run --no-auto-watch karma.config.js",
     "gulp": "gulp",
     "build-toolshed": "grunt --app=toolshed",
     "jshint": "jshint --exclude='galaxy/scripts/libs/**' galaxy/scripts/**/*.js",
@@ -44,6 +49,7 @@
     "babel-loader": "^7.1.1",
     "babel-preset-env": "^1.3.2",
     "concurrently": "^3.4.0",
+    "css-loader": "^0.28.7",
     "del": "^3.0.0",
     "expose-loader": "^0.7.3",
     "grunt": "^0.4.5",
@@ -66,7 +72,18 @@
     "gulp-uglify": "^3.0.0",
     "gulp-watch": "^4.3.11",
     "jshint": "^2.9.4",
+    "karma": "^1.7.1",
+    "karma-phantomjs-launcher": "^1.0.4",
+    "karma-polyfill": "^1.0.0",
+    "karma-qunit": "^1.2.1",
+    "karma-webpack": "^2.0.6",
+    "phantomjs-polyfill": "0.0.2",
+    "phantomjs-prebuilt": "^2.1.7",
     "prettier": "^1.7.4",
+    "qunitjs": "^2.4.1",
+    "sinon": "^4.1.2",
+    "vue-loader": "^13.5.0",
+    "vue-template-compiler": "^2.5.3",
     "webpack": "^3.6.0"
   }
 }

client/webpack.config.js

@@ -25,6 +25,7 @@ var commonLibs = [
     "libs/farbtastic",
     "libs/bootstrap",
     "libs/bootstrap-tour",
+    "libs/vue",
     // mvc
     "libs/underscore",
     "libs/backbone",
@@ -42,14 +43,19 @@ module.exports = {
         libs: commonLibs,
         login: "./galaxy/scripts/apps/login.js",
         analysis: "./galaxy/scripts/apps/analysis.js",
-        admin: "./galaxy/scripts/apps/admin.js"
+        admin: "./galaxy/scripts/apps/admin.js",
+        workflow: "./galaxy/scripts/apps/workflow.js",
+        masthead: "./galaxy/scripts/apps/masthead.js",
+        viz: "./galaxy/scripts/apps/viz.js",
+        library: "./galaxy/scripts/apps/library.js",
+        adminToolshed: "./galaxy/scripts/apps/admin-toolshed.js"
     },
     output: {
         path: path.join(__dirname, "../", "static/scripts/bundled"),
         filename: "[name].bundled.js"
     },
     resolve: {
-        modules: [scriptsBase],
+        modules: [scriptsBase, "node_modules"],
         alias: {
             //TODO: correct our imports and remove these rules
             // Backbone looks for these in the same root directory
@@ -76,9 +82,16 @@ module.exports = {
                         options: "$"
                     }
                 ]
-            }
+            },
+              {
+                test: /\.vue$/,
+                loader: 'vue-loader',
+              }
         ]
     },
+    node: {
+        setImmediate: false
+    },
     resolveLoader: {
         alias: {
             // since we support both requirejs i18n and non-requirejs and both use a similar syntax,

config/datatypes_conf.xml.sample

@@ -146,6 +146,7 @@
     <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="true" />
     <datatype extension="h5" type="galaxy.datatypes.binary:H5" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="mz5" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="cool" type="galaxy.datatypes.binary:Cool" subclass="true" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/>
     <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order)." >
       <converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
@@ -677,6 +678,7 @@
     <sniffer type="galaxy.datatypes.binary:MzSQlite"/>
     <sniffer type="galaxy.datatypes.binary:IdpDB"/>
     <sniffer type="galaxy.datatypes.binary:SQlite"/>
+    <sniffer type="galaxy.datatypes.binary:Cool"/>
     <sniffer type="galaxy.datatypes.binary:Biom2"/>
     <sniffer type="galaxy.datatypes.binary:H5"/>
     <sniffer type="galaxy.datatypes.binary:Bam"/>

lib/galaxy/datatypes/binary.py

@@ -25,7 +25,6 @@ from galaxy.util import FILENAME_VALID_CHARS, nice_size, sqlite, which
 from galaxy.util.checkers import is_bz2, is_gzip
 from . import data, dataproviders
 
-
 log = logging.getLogger(__name__)
 
 # Currently these supported binary data types must be manually set on upload
@@ -890,6 +889,60 @@ class Biom2(H5):
             return "Biom2 (HDF5) file (%s)" % (nice_size(dataset.get_size()))
 
 
+class Cool(H5):
+    """
+    Class describing the cool format (https://github.com/mirnylab/cooler)
+    """
+
+    file_ext = "cool"
+
+    def sniff(self, filename):
+        """
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname( 'matrix.cool' )
+        >>> Cool().sniff( fname )
+        True
+        >>> fname = get_test_fname( 'test.mz5' )
+        >>> Cool().sniff( fname )
+        False
+        >>> fname = get_test_fname( 'wiggle.wig' )
+        >>> Cool().sniff( fname )
+        False
+        >>> fname = get_test_fname( 'biom2_sparse_otu_table_hdf5.biom' )
+        >>> Cool().sniff( fname )
+        False
+        """
+
+        MAGIC = "HDF5::Cooler"
+        URL = "https://github.com/mirnylab/cooler"
+
+        if super(Cool, self).sniff(filename):
+            keys = ['chroms', 'bins', 'pixels', 'indexes']
+            with h5py.File(filename, 'r') as handle:
+                fmt = handle.attrs.get('format', None)
+                url = handle.attrs.get('format-url', None)
+                if fmt == MAGIC or url == URL:
+                    if not all(name in handle.keys() for name in keys):
+                        return False
+                    return True
+        return False
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = "Cool (HDF5) file for storing genomic interaction data."
+            dataset.blurb = nice_size(dataset.get_size())
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek(self, dataset):
+        try:
+            return dataset.peek
+        except Exception:
+            return "Cool (HDF5) file (%s)." % (nice_size(dataset.get_size()))
+
+
+Binary.register_sniffable_binary_format("cool", "cool", Cool)
 Binary.register_sniffable_binary_format("biom2", "biom2", Biom2)
 Binary.register_sniffable_binary_format("h5", "h5", H5)
 

lib/galaxy/jobs/actions/post.py

@@ -228,7 +228,7 @@ class ColumnSetAction(DefaultJobAction):
         for dataset_assoc in job.output_datasets:
             if action.output_name == '' or dataset_assoc.name == action.output_name:
                 for k, v in action.action_arguments.items():
-                    if v != '':
+                    if v:
                         # Try to use both pure integer and 'cX' format.
                         if v[0] == 'c':
                             v = v[1:]

lib/galaxy/jobs/metrics/instrumenters/core.py

@@ -8,6 +8,7 @@ from ...metrics import formatting
 log = logging.getLogger(__name__)
 
 GALAXY_SLOTS_KEY = "galaxy_slots"
+GALAXY_MEMORY_MB_KEY = "galaxy_memory_mb"
 START_EPOCH_KEY = "start_epoch"
 END_EPOCH_KEY = "end_epoch"
 RUNTIME_SECONDS_KEY = "runtime_seconds"
@@ -19,6 +20,8 @@ class CorePluginFormatter(formatting.JobMetricFormatter):
         value = int(value)
         if key == GALAXY_SLOTS_KEY:
             return ("Cores Allocated", "%d" % value)
+        elif key == GALAXY_MEMORY_MB_KEY:
+            return ("Memory Allocated (MB)", "%d" % value)
         elif key == RUNTIME_SECONDS_KEY:
             return ("Job Runtime (Wall Clock)", formatting.seconds_to_str(value))
         else:
@@ -40,6 +43,7 @@ class CorePlugin(InstrumentPlugin):
     def pre_execute_instrument(self, job_directory):
         commands = []
         commands.append(self.__record_galaxy_slots_command(job_directory))
+        commands.append(self.__record_galaxy_memory_mb_command(job_directory))
         commands.append(self.__record_seconds_since_epoch_to_file(job_directory, "start"))
         return commands
 
@@ -50,9 +54,11 @@ class CorePlugin(InstrumentPlugin):
 
     def job_properties(self, job_id, job_directory):
         galaxy_slots_file = self.__galaxy_slots_file(job_directory)
+        galaxy_memory_mb_file = self.__galaxy_memory_mb_file(job_directory)
 
         properties = {}
         properties[GALAXY_SLOTS_KEY] = self.__read_integer(galaxy_slots_file)
+        properties[GALAXY_MEMORY_MB_KEY] = self.__read_integer(galaxy_memory_mb_file)
         start = self.__read_seconds_since_epoch(job_directory, "start")
         end = self.__read_seconds_since_epoch(job_directory, "end")
         if start is not None and end is not None:
@@ -65,6 +71,10 @@ class CorePlugin(InstrumentPlugin):
         galaxy_slots_file = self.__galaxy_slots_file(job_directory)
         return '''echo "$GALAXY_SLOTS" > '%s' ''' % galaxy_slots_file
 
+    def __record_galaxy_memory_mb_command(self, job_directory):
+        galaxy_memory_mb_file = self.__galaxy_memory_mb_file(job_directory)
+        return '''echo "$GALAXY_MEMORY_MB" > '%s' ''' % galaxy_memory_mb_file
+
     def __record_seconds_since_epoch_to_file(self, job_directory, name):
         path = self._instrument_file_path(job_directory, "epoch_%s" % name)
         return 'date +"%s" > ' + path
@@ -76,6 +86,9 @@ class CorePlugin(InstrumentPlugin):
     def __galaxy_slots_file(self, job_directory):
         return self._instrument_file_path(job_directory, "galaxy_slots")
 
+    def __galaxy_memory_mb_file(self, job_directory):
+        return self._instrument_file_path(job_directory, "galaxy_memory_mb")
+
     def __read_integer(self, path):
         value = None
         try:

lib/galaxy/managers/collections.py

@@ -187,14 +187,17 @@ class DatasetCollectionManager(object):
         changed = self._set_from_dict(trans, dataset_collection_instance, payload)
         return changed
 
-    def copy(self, trans, parent, source, encoded_source_id):
+    def copy(self, trans, parent, source, encoded_source_id, copy_elements=False):
         """
         PRECONDITION: security checks on ability to add to parent occurred
         during load.
         """
         assert source == "hdca"  # for now
         source_hdca = self.__get_history_collection_instance(trans, encoded_source_id)
-        new_hdca = source_hdca.copy()
+        copy_kwds = {}
+        if copy_elements:
+            copy_kwds["element_destination"] = parent
+        new_hdca = source_hdca.copy(**copy_kwds)
         tags_str = self.tag_manager.get_tags_str(source_hdca.tags)
         self.tag_manager.apply_item_tags(trans.get_user(), new_hdca, tags_str)
         parent.add_dataset_collection(new_hdca)

lib/galaxy/webapps/galaxy/api/configuration.py

@@ -90,6 +90,18 @@ class ConfigurationController(BaseAPIController):
         confs = self.app.toolbox.dynamic_confs(include_migrated_tool_conf=True)
         return map(_tool_conf_to_dict, confs)
 
+    @expose_api
+    @require_admin
+    def decode_id(self, trans, encoded_id, **kwds):
+        """Decode a given id."""
+        decoded_id = None
+        # Handle the special case for library folders
+        if ((len(encoded_id) % 16 == 1) and encoded_id.startswith('F')):
+            decoded_id = trans.security.decode_id(encoded_id[1:])
+        else:
+            decoded_id = trans.security.decode_id(encoded_id)
+        return {"decoded_id": decoded_id}
+
     @expose_api
     @require_admin
     def tool_lineages(self, trans):

lib/galaxy/webapps/galaxy/api/history_contents.py

@@ -252,6 +252,9 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
             copy from history dataset collection (for type 'dataset_collection')
             'source'    = 'hdca'
             'content'   = [the encoded id from the HDCA]
+            'copy_elements' = Copy child HDAs into the target history as well,
+                              defaults to False but this is less than ideal and may
+                              be changed in future releases.
 
             create new history dataset collection (for type 'dataset_collection')
             'source'              = 'new_collection' (default 'source' if type is
@@ -434,11 +437,13 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
             content = payload.get('content', None)
             if content is None:
                 raise exceptions.RequestParameterMissingException("'content' id of target to copy is missing")
+            copy_elements = payload.get('copy_elements', False)
             dataset_collection_instance = service.copy(
                 trans=trans,
                 parent=history,
                 source="hdca",
                 encoded_source_id=content,
+                copy_elements=copy_elements,
             )
         else:
             message = "Invalid 'source' parameter in request %s" % source

lib/galaxy/webapps/galaxy/buildapp.py

@@ -105,7 +105,8 @@ def paste_app_factory(global_conf, **kwargs):
     webapp.add_client_route('/admin/repositories', 'admin')
     webapp.add_client_route('/admin/tool_versions', 'admin')
     webapp.add_client_route('/admin/quotas', 'admin')
-    webapp.add_client_route('/admin/form/{form_id}', 'admin')
+    webapp.add_client_route('/admin/forms/{form_id}', 'admin')
+    webapp.add_client_route('/admin/api_keys', 'admin')
     webapp.add_client_route('/tours')
     webapp.add_client_route('/tours/{tour_id}')
     webapp.add_client_route('/user')
@@ -117,6 +118,7 @@ def paste_app_factory(global_conf, **kwargs):
     webapp.add_client_route('/pages/list_published')
     webapp.add_client_route('/pages/create')
     webapp.add_client_route('/pages/edit')
+    webapp.add_client_route('/histories/citations')
     webapp.add_client_route('/histories/list')
     webapp.add_client_route('/histories/list_published')
     webapp.add_client_route('/histories/list_shared')
@@ -340,6 +342,10 @@ def populate_api_routes(webapp, app):
                           "/api/whoami", controller='configuration',
                           action='whoami',
                           conditions=dict(method=["GET"]))
+    webapp.mapper.connect("api_decode",
+                          "/api/configuration/decode/{encoded_id}", controller='configuration',
+                          action='decode_id',
+                          conditions=dict(method=["GET"]))
     webapp.mapper.resource('datatype',
                            'datatypes',
                            path_prefix='/api',

lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py

@@ -173,12 +173,13 @@ class AdminToolshed(AdminGalaxy):
     @web.require_admin
     def browse_toolsheds(self, trans, **kwd):
         app = {
-            'jscript': "admin.toolshed"
+            'jscript': "adminToolshedApp"
         }
         return trans.fill_template('galaxy.panels.mako',
                                    config={
                                        'title': 'Galaxy Tool Sheds',
-                                       'app': app})
+                                       'app': app,
+                                       'bundle': 'adminToolshed'})
 
     @web.expose
     @web.require_admin

lib/galaxy/webapps/galaxy/controllers/history.py

@@ -457,14 +457,6 @@ class HistoryController(BaseUIController, SharableMixin, UsesAnnotations, UsesIt
         kwargs['dict_format'] = True
         return self.shared_list_grid(trans, status=status, message=message, **kwargs)
 
-    # ......................................................................... html
-    @web.expose
-    def citations(self, trans):
-        # Get history
-        history = trans.history
-        history_id = trans.security.encode_id(history.id)
-        return trans.fill_template("history/citations.mako", history=history, history_id=history_id)
-
     @web.expose
     def as_xml(self, trans, id=None, show_deleted=None, show_hidden=None):
         """

lib/galaxy/webapps/galaxy/controllers/library.py

@@ -13,9 +13,10 @@ class Library(BaseUIController):
     def list(self, trans, **kwd):
         # define app configuration for generic mako template
         app = {
-            'jscript'       : "galaxy.library"
+            'jscript'       : "libraryApp"
         }
         return trans.fill_template('galaxy.panels.mako',
                                    config={
                                        'title': 'Data Libraries',
-                                       'app': app})
+                                       'app': app,
+                                       'bundle': 'library'})

lib/galaxy/webapps/galaxy/controllers/userskeys.py

@@ -2,9 +2,6 @@
 Contains the user interface in the Universe class
 """
 
-import logging
-
-from markupsafe import escape
 from sqlalchemy import false
 
 from galaxy import (
@@ -13,55 +10,35 @@ from galaxy import (
 )
 from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin
 
-log = logging.getLogger(__name__)
-
-require_login_template = """
-<p>
-    This %s has been configured such that only users who are logged in may use it.%s
-</p>
-"""
-
-# FIXME: This controller is using unencoded IDs, but I am not going to address
-# this now since it is admin-side and should be reimplemented in the API
-# anyway.
-
 
 class User(BaseUIController, UsesFormDefinitionsMixin):
     @web.expose
     @web.require_login()
     @web.require_admin
     def index(self, trans, cntrller, **kwd):
-        return trans.fill_template('webapps/galaxy/user/list_users.mako', action='all_users', cntrller=cntrller)
+        return self.get_all_users(trans)
 
     @web.expose
     @web.require_login()
     @web.require_admin
-    def admin_api_keys(self, trans, cntrller, uid, **kwd):
+    def admin_api_keys(self, trans, uid, **kwd):
         params = util.Params(kwd)
-        message = escape(util.restore_text(params.get('message', '')))
-        status = params.get('status', 'done')
         uid = params.get('uid', uid)
-        if params.get('new_api_key_button', False):
-            new_key = trans.app.model.APIKeys()
-            new_key.user_id = uid
-            new_key.key = trans.app.security.get_new_guid()
-            trans.sa_session.add(new_key)
-            trans.sa_session.flush()
-            message = "A new web API key has been generated for (%s)" % escape(new_key.user.email)
-            status = "done"
-        return trans.response.send_redirect(web.url_for(controller='userskeys',
-                                                        action='all_users',
-                                                        cntrller=cntrller,
-                                                        message=message,
-                                                        status=status))
+        new_key = trans.app.model.APIKeys()
+        new_key.user_id = trans.security.decode_id(uid)
+        new_key.key = trans.app.security.get_new_guid()
+        trans.sa_session.add(new_key)
+        trans.sa_session.flush()
+        return self.get_all_users(trans)
 
     @web.expose
     @web.require_login()
     @web.require_admin
-    def all_users(self, trans, cntrller="userskeys", **kwd):
-        params = util.Params(kwd)
-        message = escape(util.restore_text(params.get('message', '')))
-        status = params.get('status', 'done')
+    def all_users(self, trans, **kwd):
+        return self.get_all_users(trans)
+
+    @web.json
+    def get_all_users(self, trans):
         users = []
         for user in trans.sa_session.query(trans.app.model.User) \
                                     .filter(trans.app.model.User.table.c.deleted == false()) \
@@ -71,9 +48,5 @@ class User(BaseUIController, UsesFormDefinitionsMixin):
             for api_user in trans.sa_session.query(trans.app.model.APIKeys) \
                     .filter(trans.app.model.APIKeys.user_id == uid):
                 userkey = api_user.key
-            users.append({'uid': uid, 'email': user.email, 'key': userkey})
-        return trans.fill_template('webapps/galaxy/user/list_users.mako',
-                                   cntrller=cntrller,
-                                   users=users,
-                                   message=message,
-                                   status=status)
+            users.append({'uid': trans.security.encode_id(uid), 'email': user.email, 'key': userkey})
+        return users

lib/galaxy/webapps/galaxy/controllers/visualization.py

@@ -736,7 +736,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
         """
 
         # define app configuration
-        app = {'jscript' : "viz/trackster"}
+        app = {"jscript" : "tracksterApp"}
 
         # get dataset to add
         id = kwargs.get("id", None)
@@ -780,7 +780,7 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
             }
 
         # fill template
-        return trans.fill_template('galaxy.panels.mako', config={'right_panel': True, 'app': app})
+        return trans.fill_template('galaxy.panels.mako', config={'right_panel': True, 'app': app, 'bundle': 'viz'})
 
     @web.expose
     def circster(self, trans, id=None, hda_ldda=None, dataset_id=None, dbkey=None):
@@ -836,13 +836,13 @@ class VisualizationController(BaseUIController, SharableMixin, UsesVisualization
 
         # define app configuration for generic mako template
         app = {
-            'jscript'       : "viz/circster",
+            'jscript'       : "circsterApp",
             'viz_config'    : viz_config,
             'genome'        : genome
         }
 
         # fill template
-        return trans.fill_template('galaxy.panels.mako', config={'app' : app})
+        return trans.fill_template('galaxy.panels.mako', config={'app' : app, 'bundle': 'viz'})
 
     @web.expose
     def sweepster(self, trans, id=None, hda_ldda=None, dataset_id=None, regions=None):

lib/galaxy/workflow/scheduling_manager.py

@@ -204,10 +204,10 @@ class WorkflowRequestMonitor(Monitors, object):
         sa_session = self.app.model.context
         workflow_invocation = sa_session.query(model.WorkflowInvocation).get(invocation_id)
 
-        if not workflow_invocation or not workflow_invocation.active:
-            return False
-
         try:
+            if not workflow_invocation or not workflow_invocation.active:
+                return False
+
             # This ensures we're only ever working on the 'first' active
             # workflow invocation in a given history, to force sequential
             # activation.
@@ -220,6 +220,8 @@ class WorkflowRequestMonitor(Monitors, object):
             # TODO: eventually fail this - or fail it right away?
             log.exception("Exception raised while attempting to schedule workflow request.")
             return False
+        finally:
+            sa_session.expunge_all()
 
         # A workflow was obtained and scheduled...
         return True

run_tests.sh

@@ -19,13 +19,11 @@ cat <<EOF
 '${0##*/} -data_managers -id data_manager_id'    for testing one Data Manager with id 'data_manager_id'
 '${0##*/} -unit'                    for running all unit tests (doctests and tests in test/unit)
 '${0##*/} -unit (test_path)'        for running unit tests on specified test path
-'${0##*/} -qunit'                   for running qunit JavaScript tests
-'${0##*/} -qunit testname'          for running single JavaScript test with given name
 '${0##*/} -selenium'                for running all selenium web tests (in test/selenium_tests)
 '${0##*/} -selenium (test_path)'    for running specified selenium web tests (use nosetest path)
 
 This wrapper script largely serves as a point documentation and convenience -
-most tests shipped with Galaxy can be run with nosetests or qunit directly.
+most tests shipped with Galaxy can be run with nosetests directly.
 
 The main test types are as follows:
 
@@ -42,7 +40,7 @@ The main test types are as follows:
 - Unit: These are Python unit tests either defined as doctests or inside of
    test/unit. These should generally not require a Galaxy instance and should
    quickly test just a component or a few components of Galaxy's backend code.
-- QUnit: These are JavaScript unit tests defined in test/qunit.
+- QUnit: These are JavaScript unit tests defined in client/galaxy/scripts/qunit.
 - Selenium: These are full stack tests meant to test the Galaxy UI with real
    browsers and are located in test/selenium_tests.
 - ToolShed: These are web tests that use the older Python web testing
@@ -78,6 +76,13 @@ Run all selenium tests (Under Linux using Docker):
 Run a specific selenium test (under Linux or Mac OS X after installing geckodriver or chromedriver):
     ./run_tests.sh -selenium test/selenium_tests/test_registration.py:RegistrationTestCase.test_reregister_username_fails
 
+Run a selenium test against a running server while watching client (fastest iterating on client tests):
+    ./run.sh & # run Galaxy on 8080
+    make client-watch & # watch for client changes
+    export GALAXY_TEST_EXTERNAL=http://localhost:8080/  # Target tests at server.
+    . .venv/bin/activate # source the virtualenv so can skip run_tests.sh.
+    nosetests test/selenium_tests/test_workflow_editor.py:WorkflowEditorTestCase.test_data_input   
+
 Note About Selenium Tests:
 
 If using a local selenium driver such as a Chrome or Firefox based one
@@ -253,20 +258,6 @@ exists() {
     type "$1" >/dev/null 2>/dev/null
 }
 
-ensure_grunt_for_qunit() {
-    if ! exists "grunt";
-    then
-        PATH="$PATH:./test/qunit/node_modules/grunt/bin"
-        export PATH
-        if ! exists "grunt";
-        then
-            echo "Grunt not on path, cannot run these tests."
-            exit 1
-        fi
-    fi
-}
-
-
 DOCKER_DEFAULT_IMAGE='galaxy/testing-base:18.01.4'
 
 test_script="./scripts/functional_tests.py"
@@ -275,8 +266,6 @@ xunit_report_file=""
 structured_data_report_file=""
 with_framework_test_tools_arg=""
 
-driver="python"
-
 if [ "$1" = "--dockerize" ];
 then
     shift
@@ -502,18 +491,6 @@ do
               shift 1
           fi
           ;;
-      -q|-qunit|--qunit)
-          # Requires grunt installed and dependencies configured see
-          # test/qunit/README.txt for more information.
-          driver="grunt"
-          gruntfile="./test/qunit/Gruntfile.js"
-          if [ $# -gt 1 ]; then
-              qunit_name=$2
-              shift 2
-          else
-              shift 1
-          fi
-          ;;
       --no_cleanup)
           GALAXY_TEST_NO_CLEANUP=1
           export GALAXY_TEST_NO_CLEANUP
@@ -624,39 +601,22 @@ else
     extra_args='--exclude="^get" functional'
 fi
 
-if [ "$driver" = "python" ]; then
-    if [ -n "$xunit_report_file" ]; then
-        xunit_args="--with-xunit --xunit-file $xunit_report_file"
-    else
-        xunit_args=""
-    fi
-    if [ -n "$structured_data_report_file" ]; then
-        structured_data_args="--with-structureddata --structured-data-file $structured_data_report_file"
-    else
-        structured_data_args=""
-    fi
-    if [ -n "$with_framework_test_tools_arg" ]; then
-        GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
-        export GALAXY_TEST_TOOL_CONF
-    fi
-    python $test_script $coverage_arg -v --with-nosehtml --html-report-file $report_file $xunit_args $structured_data_args $extra_args
-    exit_status=$?
-    echo "Testing complete. HTML report is in \"$report_file\"." 1>&2
-    exit ${exit_status}
+if [ -n "$xunit_report_file" ]; then
+    xunit_args="--with-xunit --xunit-file $xunit_report_file"
 else
-    ensure_grunt_for_qunit
-    if [ -n "$watch" ]; then
-        grunt_task="watch"
-    else
-        grunt_task=""
-    fi
-    if [ -n "$qunit_name" ]; then
-        grunt_args="--test=$qunit_name"
-    else
-        grunt_args=""
-    fi
-    # TODO: Exapnd javascript helpers to include setting up
-    # grunt deps in npm, "watch"ing directory, and running casper
-    # functional tests.
-    grunt --gruntfile=$gruntfile $grunt_task $grunt_args
+    xunit_args=""
 fi
+if [ -n "$structured_data_report_file" ]; then
+    structured_data_args="--with-structureddata --structured-data-file $structured_data_report_file"
+else
+    structured_data_args=""
+fi
+if [ -n "$with_framework_test_tools_arg" ]; then
+    GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
+    export GALAXY_TEST_TOOL_CONF
+fi
+python $test_script $coverage_arg -v --with-nosehtml --html-report-file $report_file $xunit_args $structured_data_args $extra_args
+exit_status=$?
+echo "Testing complete. HTML report is in \"$report_file\"." 1>&2
+exit ${exit_status}
+

static/maps/mvc/citation/citation-model.js.map

@@ -1 +1 @@
-{"version":3,"sources":["mvc/citation/citation-model.js"],"names":["parseBibtex","_","extend","ENTRY_TYPES_","online","data","Citation","Backbone","Model","_baseMvc2","default","LoggableMixin","_logNamespace","defaults","content","initialize","parsed","this","attributes","err","errors","length","reduce","all","current","log","entry","first","entries","logNamespace","Fields","key","rawFields","value","lowerKey","toLowerCase","_fields","entryType","EntryType","undefined","fields","BaseCitationCollection","Collection","urlRoot","Galaxy","root","partial","model","HistoryCitationCollection","url","history_id","ToolCitationCollection"],"mappings":"0OAAYA,yKAMZC,EAAEC,OAAOF,EAAYG,cACjBC,OAPQJ,IAQRK,KAAM,MAGV,IAMIC,EAAWC,SAASC,MAAMN,OAAOO,EAAAC,QAAQC,eAAeT,QACxDU,cAPe,WASfC,UACIC,QAAS,IAGbC,WAAY,WACR,IAAIC,EACJ,IAEIA,EAAShB,EAAYiB,KAAKC,WAAWJ,SACvC,MAAOK,GACL,OAGJ,GAAIH,EAAOI,OAAOC,OAAQ,CAEtB,IAAID,EAASJ,EAAOI,OAAOE,OAAO,SAACC,EAAKC,GAAN,OAAqBD,EAArB,KAA6BC,IAE/DP,KAAKQ,IAAL,yBAAkCL,GAKtC,GAlCJf,KAAAA,WAFJY,KAAAS,MAAAzB,EAAA0B,MAAAX,EAAAY,SAoCYX,KAAKS,MAAO,CA/BpBG,IAAAA,EAAeZ,KAAnBS,MAAAI,OACA,IAAA,IAAAC,KAAAC,EAAA,CACA,IAAAC,EAAAD,EAAAD,GAiCoBG,EAAWH,EAAII,cACnBlB,KAAKmB,QAAQF,GAAYD,KAIrCI,UAAW,WA/BXxB,OAAAA,KAAUa,MAAAT,KAAAS,MAAAY,eAAAC,GAAAC,OAHqD,WAsC3D,OAAOvB,KAAKmB,WAzBRK,EAAAlC,SAAAmC,WAAAxC,OAAAO,EAAAC,QAAAC,eAAAT,QACHU,cApBU,WAuBP+B,QAAAC,OAAAC,KAAA,MACAC,SAAA,EAAkCC,MAAAzC,IAElC0C,EAAAP,EAAkCrB,QAoC1C6B,IAAK,WAjCD,OAAKb,KAAAA,QAAL,cAAAnB,KAAAiC,WAAA,gBAIIC,EAAAV,EAA2BvC,QAEvB+C,IAAA,WACA,OAAAhC,KAAA0B,QAAA,UAAaT,KAAYD,QAAzB,cAEPa,SAAA,eAMDxC,SAAAA,EACH0C,0BAAAA,EAvC8DG,uBAAnEA","file":"../../../scripts/mvc/citation/citation-model.js","sourcesContent":["import * as parseBibtex from \"libs/bibtex\";\nimport baseMVC from \"mvc/base-mvc\";\nimport _l from \"utils/localization\";\n\n/* global Backbone */\n\n_.extend(parseBibtex.ENTRY_TYPES_, {\n    online: 998, // Galaxy MOD: Handle @online entries for preprints.\n    data: 999 // Galaxy MOD: Handle @data citations coming from figshare.\n});\n\nvar logNamespace = \"citation\";\n//==============================================================================\n/** @class model for tool citations.\n *  @name Citation\n *  @augments Backbone.Model\n */\nvar Citation = Backbone.Model.extend(baseMVC.LoggableMixin).extend({\n    _logNamespace: logNamespace,\n\n    defaults: {\n        content: \"\"\n    },\n\n    initialize: function() {\n        var parsed;\n        try {\n            // TODO: to model.parse/.validate\n            parsed = parseBibtex(this.attributes.content);\n        } catch (err) {\n            return;\n        }\n        // bibtex returns successfully parsed in .entries and any parsing errors in .errors\n        if (parsed.errors.length) {\n            // the gen. form of these errors seems to be [ line, col, char, error message ]\n            var errors = parsed.errors.reduce((all, current) => `${all}; ${current}`);\n            // throw new Error( 'Error parsing bibtex: ' + errors );\n            this.log(`Error parsing bibtex: ${errors}`);\n        }\n\n        this._fields = {};\n        this.entry = _.first(parsed.entries);\n        if (this.entry) {\n            var rawFields = this.entry.Fields;\n            for (var key in rawFields) {\n                var value = rawFields[key];\n                var lowerKey = key.toLowerCase();\n                this._fields[lowerKey] = value;\n            }\n        }\n    },\n    entryType: function() {\n        return this.entry ? this.entry.EntryType : undefined;\n    },\n    fields: function() {\n        return this._fields;\n    }\n});\n\n//==============================================================================\n/** @class Backbone collection of citations.\n */\nvar BaseCitationCollection = Backbone.Collection.extend(baseMVC.LoggableMixin).extend({\n    _logNamespace: logNamespace,\n\n    /** root api url */\n    urlRoot: `${Galaxy.root}api`,\n    partial: true, // Assume some tools in history/workflow may not be properly annotated yet.\n    model: Citation\n});\n\nvar HistoryCitationCollection = BaseCitationCollection.extend({\n    /** complete api url */\n    url: function() {\n        return `${this.urlRoot}/histories/${this.history_id}/citations`;\n    }\n});\n\nvar ToolCitationCollection = BaseCitationCollection.extend({\n    /** complete api url */\n    url: function() {\n        return `${this.urlRoot}/tools/${this.tool_id}/citations`;\n    },\n    partial: false // If a tool has citations, assume they are complete.\n});\n\n//==============================================================================\n\nexport default {\n    Citation: Citation,\n    HistoryCitationCollection: HistoryCitationCollection,\n    ToolCitationCollection: ToolCitationCollection\n};\n"]}
+{"version":3,"sources":["mvc/citation/citation-model.js"],"names":["bibtexParse","Citation","Backbone","Model","extend","_baseMvc2","default","LoggableMixin","_logNamespace","defaults","content","initialize","parsed","toJSON","this","attributes","err","log","_fields","entry","_","first","rawFields","entryTags","key","value","lowerKey","toLowerCase","entryType","undefined","fields","Collection","partial","model","HistoryCitationCollection","BaseCitationCollection","url","ToolCitationCollection","urlRoot","tool_id"],"mappings":"qKAAYA,oNAWRC,EAAWC,SAASC,MAAMC,OAAOC,EAAAC,QAAQC,eAAeH,QACxDI,cAPe,WASfC,UACIC,QAAS,IAGbC,WAAY,WACR,IAAIC,EACJ,IAEIA,EAASZ,EAAYa,OAAOC,KAAKC,WAAWL,SAC9C,MAAOM,GACLF,KAAKG,IAAI,yBAA2BD,GAKxC,GAFAF,KAAKI,WACLJ,KAAKK,MAAQC,EAAEC,MAAMT,GACjBE,KAAKK,MAAO,CACZ,IAAIG,EAAYR,KAAKK,MAAMI,UAC3B,IAAK,IAAIC,KAAOF,EAAW,CACvB,IAAIG,EAAQH,EAAUE,GAClBE,EAAWF,EAAIG,cA9BnCb,KAAAI,QAAAQ,GAAAD,KAIAG,UAAA,WAgCQ,OAAOd,KAAKK,MAAQL,KAAKK,MAAMS,eAAYC,GAE/CC,OAAQ,WA9BR7B,OAAAA,KAAWC,WAOXS,EAAYT,SAAA6B,WAAW3B,OAAAC,EAAAC,QAAAC,eAAAH,QACnBI,cAdW,WAiBPI,QAAAA,OAAAA,KAAAA,MACHoB,SAHD,EAIIC,MAAAhC,IAGJiC,EAAAC,EAAA/B,QAEAgC,IAAA,WACI,OAAAtB,KAAIQ,QAAJ,cAA2BC,KAAAA,WAA3B,gBAIIc,EAAKnB,EAALd,QAEPgC,IAAA,WACJ,OA1B8DtB,KAAAwB,QA0B9D,UA1B8DxB,KAAAyB,QA0B9D,cAEGP,SAAA,eAqCJ/B,SAAUA,EA9BdiC,0BAAAA,EACAG,uBAAAA","file":"../../../scripts/mvc/citation/citation-model.js","sourcesContent":["import * as bibtexParse from \"libs/bibtexParse\";\nimport baseMVC from \"mvc/base-mvc\";\n\n/* global Backbone */\n\nvar logNamespace = \"citation\";\n//==============================================================================\n/** @class model for tool citations.\n *  @name Citation\n *  @augments Backbone.Model\n */\nvar Citation = Backbone.Model.extend(baseMVC.LoggableMixin).extend({\n    _logNamespace: logNamespace,\n\n    defaults: {\n        content: \"\"\n    },\n\n    initialize: function() {\n        var parsed;\n        try {\n            // TODO: to model.parse/.validate\n            parsed = bibtexParse.toJSON(this.attributes.content);\n        } catch (err) {\n            this.log(\"Error parsing bibtex: \" + err);\n        }\n\n        this._fields = {};\n        this.entry = _.first(parsed);\n        if (this.entry) {\n            var rawFields = this.entry.entryTags;\n            for (var key in rawFields) {\n                var value = rawFields[key];\n                var lowerKey = key.toLowerCase();\n                this._fields[lowerKey] = value;\n            }\n        }\n    },\n    entryType: function() {\n        return this.entry ? this.entry.entryType : undefined;\n    },\n    fields: function() {\n        return this._fields;\n    }\n});\n\n//==============================================================================\n/** @class Backbone collection of citations.\n */\nvar BaseCitationCollection = Backbone.Collection.extend(baseMVC.LoggableMixin).extend({\n    _logNamespace: logNamespace,\n\n    /** root api url */\n    urlRoot: `${Galaxy.root}api`,\n    partial: true, // Assume some tools in history/workflow may not be properly annotated yet.\n    model: Citation\n});\n\nvar HistoryCitationCollection = BaseCitationCollection.extend({\n    /** complete api url */\n    url: function() {\n        return `${this.urlRoot}/histories/${this.history_id}/citations`;\n    }\n});\n\nvar ToolCitationCollection = BaseCitationCollection.extend({\n    /** complete api url */\n    url: function() {\n        return `${this.urlRoot}/tools/${this.tool_id}/citations`;\n    },\n    partial: false // If a tool has citations, assume they are complete.\n});\n\n//==============================================================================\n\nexport default {\n    Citation: Citation,\n    HistoryCitationCollection: HistoryCitationCollection,\n    ToolCitationCollection: ToolCitationCollection\n};\n"]}

static/maps/mvc/user/user_api_keys.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["mvc/user/user_api_keys.js"],"names":["mod_toastr","UserAPIKeysView","Backbone","View","extend","initialize","options","timeOut","this","setElement","render","self","url","Galaxy","root","$el","empty","append","_template","fetchUsers","$","getJSON","users","setTimeout","applyVue","_vue2","default","el","methods","generateKey","id","success","_data","error"],"mappings":"8MACYA,6JAERC,EAAkBC,SAASC,KAAKC,QAChCC,WAAY,WACRL,EAAWM,QAAQC,QAAU,IAC7BC,KAAKC,WAAW,UAChBD,KAAKE,UAGTA,OAAQ,WACJ,IAAIC,EAAOH,KACPI,EAAMC,OAAOC,KAAO,sBACxBH,EAAKI,IAAIC,QAAQC,OAAON,EAAKO,aAC7BP,EAAKQ,WAAWP,IAIpBO,WAAY,SAASP,GACjB,IAAID,EAAOH,KACXY,EAAEC,QAAQT,EAAK,SAASU,GAIpBC,WAAW,WACPZ,EAAKa,SAASF,QAM1BE,SAAU,SAASF,GACA,IAAAG,EAAAC,SACXC,GAAI,iBA9BZ1B,MACAI,MAAYiB,GAERM,SAHmCC,YAAA,SAAAC,GAqCvB,IAAInB,EAAOH,KA7BnBG,EAAAA,MACME,IAAOC,OAAOA,KAAA,2BACfE,MAAQC,IAAON,GACnBQ,QAAL,SAAAG,GAXmCtB,EAAA+B,QAAA,qCAcvCpB,EAAAqB,MAAAV,MAAAA,GAEeW,MAAX,WACejC,EAASsB,QAAO,4CAQlCJ,UAzBsC,WAyDnC,MA9BJ,0jBA2DCjB","file":"../../../scripts/mvc/user/user_api_keys.js","sourcesContent":["import Vue from \"libs/vue\";\nimport * as mod_toastr from \"libs/toastr\";\n\nvar UserAPIKeysView = Backbone.View.extend({\n    initialize: function() {\n        mod_toastr.options.timeOut = 1000;\n        this.setElement(\"<div/>\");\n        this.render();\n    },\n\n    render: function() {\n        var self = this,\n            url = Galaxy.root + \"userskeys/all_users\";\n        self.$el.empty().append(self._template());\n        self.fetchUsers(url);\n    },\n\n    /** Load users and their keys */\n    fetchUsers: function(url) {\n        var self = this;\n        $.getJSON(url, function(users) {\n            // apply vue model on the dom\n            // timeout is used to ensure dom is created first and then\n            // vue model is applied with the required data\n            setTimeout(function() {\n                self.applyVue(users);\n            });\n        });\n    },\n\n    /** Create model for the view using vue */\n    applyVue: function(users) {\n        var form_vue = new Vue({\n            el: \"#form-userkeys\",\n            data: {\n                users: users // data model\n            },\n            methods: {\n                // bind event from view\n                generateKey: function(id) {\n                    var self = this;\n                    // fetch fresh model\n                    $.ajax({\n                        url: Galaxy.root + \"userskeys/admin_api_keys\",\n                        data: { uid: id },\n                        success: function(users) {\n                            mod_toastr.success(\"Successfully generated a user key\");\n                            // refresh the model\n                            self._data.users = users;\n                        },\n                        error: function() {\n                            mod_toastr.success(\"Error occured while loading data\");\n                        }\n                    });\n                }\n            }\n        });\n    },\n\n    _template: function() {\n        return (\n            '<div id=\"form-userkeys\" class=\"toolForm\" v-cloak>' +\n            '<div class=\"toolFormTitle\">User Information</div>' +\n            '<div v-if=\"users && users.length > 0\">' +\n            '<table class=\"grid\">' +\n            \"<thead><th>Encoded UID</th><th>Email</th><th>API Key</th><th>Actions</th></thead>\" +\n            \"<tbody>\" +\n            '<tr v-for=\"user in users\">' +\n            \"<td>\" +\n            \"{{ user.uid }}\" +\n            \"</td>\" +\n            \"<td>\" +\n            \"{{ user.email }}\" +\n            \"</td>\" +\n            \"<td>\" +\n            \"{{ user.key }}\" +\n            \"</td>\" +\n            \"<td>\" +\n            '<input type=\"button\" value=\"Generate a new key now\" v-on:click=\"generateKey( user.uid )\" />' +\n            \"</td>\" +\n            \"</tbody>\" +\n            \"</table>\" +\n            \"</div>\" +\n            \"<div v-else>\" +\n            \"<div>No informations available</div>\" +\n            \"</div>\" +\n            '<div style=\"clear: both\"></div>' +\n            \"</div>\"\n        );\n    }\n});\n\nexport default UserAPIKeysView;\n"]}

static/scripts/layout/panel.js

@@ -1,2 +1,2 @@
-define("layout/panel",["exports","jquery","libs/underscore","libs/backbone"],function(e,t,i,n){"use strict";function a(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}Object.defineProperty(e,"__esModule",{value:!0});var s=function(e){return e&&e.__esModule?e:{default:e}}(t),d=a(i),l=a(n),o=160,r=800,h=l.View.extend({initialize:function(e){this.view=e.view,this.hidden=!1,this.saved_size=null,this.hiddenByTool=!1},$center:function(){return this.$el.siblings("#center")},$toggleButton:function(){return this.$(".unified-panel-footer > .panel-collapse")},render:function(){var e=this,t=this.view,i=this.view.model.attributes||{};this.$el.html(this._templatePanel(this.id)),d.each(i.buttons,function(t){e.$(".panel-header-buttons").append(t.$el)}),this.$el.addClass(i.cls),this.$(".panel-header-text").html(d.escape(i.title)),this.$(".unified-panel-body").append(t.$el),t.render()},_templatePanel:function(){return[this._templateHeader(),this._templateBody(),this._templateFooter()].join("")},_templateHeader:function(e){return['<div class="unified-panel-header" unselectable="on">','<div class="unified-panel-header-inner">','<div class="panel-header-buttons" style="float: right"/>','<div class="panel-header-text"/>',"</div>","</div>"].join("")},_templateBody:function(e){return'<div class="unified-panel-body"/>'},_templateFooter:function(e){return['<div class="unified-panel-footer">','<div class="panel-collapse ',d.escape(this.id),'"/>','<div class="drag"/>',"</div>"].join("")},events:{"mousedown .unified-panel-footer > .drag":"_mousedownDragHandler","click .unified-panel-footer > .panel-collapse":"toggle"},_mousedownDragHandler:function(e){function t(e){var t=e.pageX-a;a=e.pageX;var s=i.$el.width(),d=n?s+t:s-t;d=Math.min(r,Math.max(o,d)),i.resize(d)}var i=this,n="left"===this.id,a=e.pageX;(0,s.default)("#dd-helper").show().on("mousemove",t).one("mouseup",function(e){(0,s.default)(this).hide().off("mousemove",t)})},resize:function(e){return this.$el.css("width",e),this.$center().css(this.id,e),this},show:function(){if(this.hidden){var e=this,t={},i=this.id;return t[i]=0,e.$el.css(i,-this.saved_size).show().animate(t,"fast",function(){e.resize(e.saved_size)}),e.hidden=!1,e.$toggleButton().removeClass("hidden"),this}},hide:function(){if(!this.hidden){var e={},t=this.id;return this.saved_size=this.$el.width(),e[t]=-this.saved_size,this.$el.animate(e,"fast"),this.$center().css(t,0),this.hidden=!0,this.$toggleButton().addClass("hidden"),this}},toggle:function(e){return this.hidden?this.show():this.hide(),this.hiddenByTool=!1,this},handle_minwidth_hint:function(e){return this.$center().width()-(this.hidden?this.saved_size:0)<e?this.hidden||(this.toggle(),this.hiddenByTool=!0):this.hiddenByTool&&(this.toggle(),this.hiddenByTool=!1),self},force_panel:function(e){return"show"==e?this.show():"hide"==e?this.hide():self},toString:function(){return"SidePanel("+this.id+")"}}),u=h.extend({id:"left"}),c=h.extend({id:"right"}),f=l.View.extend({initialize:function(e){this.setElement((0,s.default)(this.template())),this.$frame=this.$(".center-frame"),this.$panel=this.$(".center-panel"),this.$frame.on("load",d.bind(this._iframeChangeHandler,this))},_iframeChangeHandler:function(e){var t=e.currentTarget,i=t.contentWindow&&t.contentWindow.location;i&&i.host&&((0,s.default)(t).show(),this.$panel.empty().hide(),Galaxy.trigger("center-frame:load",{fullpath:i.pathname+i.search+i.hash,pathname:i.pathname,search:i.search,hash:i.hash}))},display:function(e){var t=this.$frame[0].contentWindow||{},i=t.onbeforeunload&&t.onbeforeunload();i&&!confirm(i)||(t.onbeforeunload=void 0,this.$frame.attr("src","about:blank").hide(),this.$panel.empty().scrollTop(0).append(e.$el).show(),Galaxy.trigger("center-panel:load",e))},template:function(){return'<div class="center-container"><iframe id="galaxy_main" name="galaxy_main" frameborder="0" class="center-frame" /><div class="center-panel" /></div>'},toString:function(){return"CenterPanel"}});e.default={SidePanel:h,LeftPanel:u,RightPanel:c,CenterPanel:f}});
+define("layout/panel",["exports","jquery","libs/underscore","libs/backbone"],function(e,t,i,n){"use strict";function a(e){if(e&&e.__esModule)return e;var t={};if(null!=e)for(var i in e)Object.prototype.hasOwnProperty.call(e,i)&&(t[i]=e[i]);return t.default=e,t}Object.defineProperty(e,"__esModule",{value:!0});var s=function(e){return e&&e.__esModule?e:{default:e}}(t),d=a(i),l=a(n),o=160,r=800,h=l.View.extend({initialize:function(e){this.view=e.view,this.hidden=!1,this.saved_size=null,this.hiddenByTool=!1},$center:function(){return this.$el.siblings("#center")},$toggleButton:function(){return this.$(".unified-panel-footer > .panel-collapse")},render:function(){var e=this,t=this.view,i=this.view.model.attributes||{};this.$el.html(this._templatePanel(this.id)),d.each(i.buttons,function(t){e.$(".panel-header-buttons").append(t.$el)}),this.$el.addClass(i.cls),this.$(".panel-header-text").html(d.escape(i.title)),this.$(".unified-panel-body").append(t.$el),t.render()},_templatePanel:function(){return[this._templateHeader(),this._templateBody(),this._templateFooter()].join("")},_templateHeader:function(e){return['<div class="unified-panel-header" unselectable="on">','<div class="unified-panel-header-inner">','<div class="panel-header-buttons" style="float: right"/>','<div class="panel-header-text"/>',"</div>","</div>"].join("")},_templateBody:function(e){return'<div class="unified-panel-body"/>'},_templateFooter:function(e){return['<div class="unified-panel-footer">','<div class="panel-collapse ',d.escape(this.id),'"/>','<div class="drag"/>',"</div>"].join("")},events:{"mousedown .unified-panel-footer > .drag":"_mousedownDragHandler","click .unified-panel-footer > .panel-collapse":"toggle"},_mousedownDragHandler:function(e){function t(e){var t=e.pageX-a;a=e.pageX;var s=i.$el.width(),d=n?s+t:s-t;d=Math.min(r,Math.max(o,d)),i.resize(d)}var i=this,n="left"===this.id,a=e.pageX;(0,s.default)("#dd-helper").show().on("mousemove",t).one("mouseup",function(e){(0,s.default)(this).hide().off("mousemove",t)})},resize:function(e){return this.$el.css("width",e),this.$center().css(this.id,e),this},show:function(){if(this.hidden){var e=this,t={},i=this.id;return t[i]=0,e.$el.css(i,-this.saved_size).show().animate(t,"fast",function(){e.resize(e.saved_size)}),e.hidden=!1,e.$toggleButton().removeClass("hidden"),this}},hide:function(){if(!this.hidden){var e={},t=this.id;return this.saved_size=this.$el.width(),e[t]=-this.saved_size,this.$el.animate(e,"fast"),this.$center().css(t,0),this.hidden=!0,this.$toggleButton().addClass("hidden"),this}},toggle:function(e){return this.hidden?this.show():this.hide(),this.hiddenByTool=!1,this},handle_minwidth_hint:function(e){return this.$center().width()-(this.hidden?this.saved_size:0)<e?this.hidden||(this.toggle(),this.hiddenByTool=!0):this.hiddenByTool&&(this.toggle(),this.hiddenByTool=!1),self},force_panel:function(e){return"show"==e?this.show():"hide"==e?this.hide():self},toString:function(){return"SidePanel("+this.id+")"}}),u=h.extend({id:"left"}),c=h.extend({id:"right"}),f=l.View.extend({initialize:function(e){this.setElement((0,s.default)(this.template())),this.$frame=this.$(".center-frame"),this.$panel=this.$(".center-panel"),this.$frame.on("load",d.bind(this._iframeChangeHandler,this))},_iframeChangeHandler:function(e){var t=e.currentTarget,i=t.contentWindow&&t.contentWindow.location;i&&i.host&&((0,s.default)(t).show(),this.$panel.empty().hide(),Galaxy.trigger("center-frame:load",{fullpath:i.pathname+i.search+i.hash,pathname:i.pathname,search:i.search,hash:i.hash}))},display:function(e){var t=this.$frame[0].contentWindow||{},i=t.onbeforeunload&&t.onbeforeunload();i&&!confirm(i)||(t.onbeforeunload=void 0,this.$frame.attr("src","about:blank").hide(),this.$panel.empty().scrollTop(0).append(e.$el||e).show(),Galaxy.trigger("center-panel:load",e))},template:function(){return'<div class="center-container"><iframe id="galaxy_main" name="galaxy_main" frameborder="0" class="center-frame" /><div class="center-panel" /></div>'},toString:function(){return"CenterPanel"}});e.default={SidePanel:h,LeftPanel:u,RightPanel:c,CenterPanel:f}});
 //# sourceMappingURL=../../maps/layout/panel.js.map