Merge remote-tracking branch 'upstream/dev' into remove_gridhelper_001

client/galaxy/scripts/apps/admin.js

@@ -10,7 +10,7 @@ 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 Vue from "vue";
 import UserAPIKeys from "components/UserAPIKeys.vue";
 
 window.app = function app(options, bootstrapped) {

client/galaxy/scripts/apps/analysis.js

@@ -22,7 +22,7 @@ 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";
+import Vue from "vue";
 
 /** define the 'Analyze Data'/analysis/main/home page for Galaxy
  *  * has a masthead

client/galaxy/scripts/galaxy.interactive_environments.js

@@ -6,9 +6,7 @@
 export function append_notebook(url) {
     clear_main_area();
     $("#main").append(
-        `<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:hidden;" scrolling="no" src="${
-            url
-        }"></iframe>`
+        `<iframe frameBorder="0" seamless="seamless" style="width: 100%; height: 100%; overflow:hidden;" scrolling="no" src="${url}"></iframe>`
     );
 }
 
@@ -21,9 +19,7 @@ export function clear_main_area() {
 
 export function display_spinner() {
     $("#main").append(
-        `<img id="spinner" src="${
-            galaxy_root
-        }static/style/largespinner.gif" style="position:absolute;margin:auto;top:0;left:0;right:0;bottom:0;">`
+        `<img id="spinner" src="${galaxy_root}static/style/largespinner.gif" style="position:absolute;margin:auto;top:0;left:0;right:0;bottom:0;">`
     );
 }
 

client/galaxy/scripts/galaxy.pages.js

@@ -154,11 +154,7 @@ WYMeditor.editor.prototype.dialog = function(dialogType, dialogFeatures, bodyHtm
         }
         show_modal(
             "Create Link",
-            `<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='${
-                curURL
-            }' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='${
-                curTitle
-            }' size='40' /></div><div>`,
+            `<div><div><label id='link_attribute_label'>URL <span style='float: right; font-size: 90%'><a href='#' id='set_link_id'>Create in-page anchor</a></span></label><br><input type='text' class='wym_href' value='${curURL}' size='40' /></div><div><label>Title</label><br><input type='text' class='wym_title' value='${curTitle}' size='40' /></div><div>`,
             {
                 "Make link": function() {
                     // Get URL, name/title.

client/galaxy/scripts/layout/modal.js

@@ -154,9 +154,9 @@ function show_in_overlay(options) {
         closeButton: true,
         title: " ",
         body: $(
-            `<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='${options.url}' width='${
-                width
-            }' height='${height}' scrolling='${scroll}' frameborder='0'></iframe></div>`
+            `<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='${
+                options.url
+            }' width='${width}' height='${height}' scrolling='${scroll}' frameborder='0'></iframe></div>`
         )
     });
     modal.show({ backdrop: true });

client/galaxy/scripts/mvc/grid/grid-template.js

@@ -180,9 +180,7 @@ export default {
                         if (options.operations.length !== 0) {
                             tmpl += `<div id="${id}" class="${cls}" style="float: left;">`;
                         }
-                        tmpl += `<a class="menubutton-label use-target" target="${target}" href="${
-                            link
-                        }" onclick="return false;">${value}</a>`;
+                        tmpl += `<a class="menubutton-label use-target" target="${target}" href="${link}" onclick="return false;">${value}</a>`;
                         if (options.operations.length !== 0) {
                             tmpl += "</div>";
                         }
@@ -262,21 +260,13 @@ export default {
                 if (page_index == options.cur_page_num) {
                     tmpl += `<span class="page-link inactive-link" id="page-link-${page_index}">${page_index}</span>`;
                 } else {
-                    tmpl += `<span class="page-link" id="page-link-${
-                        page_index
-                    }"><a href="javascript:void(0);" onclick="return false;" page_num="${page_index}">${
-                        page_index
-                    }</a></span>`;
+                    tmpl += `<span class="page-link" id="page-link-${page_index}"><a href="javascript:void(0);" onclick="return false;" page_num="${page_index}">${page_index}</a></span>`;
                 }
             }
 
             // show last page
             if (max_page < num_pages) {
-                tmpl += `...<span class="page-link" id="page-link-${
-                    num_pages
-                }"><a href="javascript:void(0);" onclick="return false;" page_num="${num_pages}">${
-                    num_pages
-                }</a></span>`;
+                tmpl += `...<span class="page-link" id="page-link-${num_pages}"><a href="javascript:void(0);" onclick="return false;" page_num="${num_pages}">${num_pages}</a></span>`;
             }
             tmpl += "</span>";
 
@@ -386,9 +376,7 @@ export default {
         //
         // standard search
         //
-        var tmpl = `<div id="standard-search" style="display: ${
-            standard_search_display
-        };"><table><tr><td style="padding: 0;"><table>`;
+        var tmpl = `<div id="standard-search" style="display: ${standard_search_display};"><table><tr><td style="padding: 0;"><table>`;
 
         // add standard filters
         for (let column of options.columns) {
@@ -411,9 +399,7 @@ export default {
         //
         // advanced search
         //
-        tmpl += `<div id="advanced-search" style="display: ${
-            advanced_search_display
-        }; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>`;
+        tmpl += `<div id="advanced-search" style="display: ${advanced_search_display}; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>`;
 
         // add advanced filters
         for (let column of options.columns) {
@@ -456,9 +442,9 @@ export default {
                         if (column.is_text) {
                             filter_value = JSON.stringify(filter_value);
                         }
-                        tmpl += `<input type="hidden" id="${column.key}" name="f-${column.key}" value="${
-                            filter_value
-                        }"/>`;
+                        tmpl += `<input type="hidden" id="${column.key}" name="f-${
+                            column.key
+                        }" value="${filter_value}"/>`;
                     }
                 }
             }
@@ -510,9 +496,7 @@ export default {
             // print input field for column
             tmpl += `
                 <span class="search-box">
-                    <input class="search-box-input" id="input-${column_key}-filter" name="f-${
-                column_key
-            }" type="text" placeholder="${value}" size="${size}"/>
+                    <input class="search-box-input" id="input-${column_key}-filter" name="f-${column_key}" type="text" placeholder="${value}" size="${size}"/>
                     <button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;">
                         <i class="fa fa-search"></i>
                     </button>
@@ -547,11 +531,7 @@ export default {
                 if (filter && cf[column_key] && filter == cf_arg) {
                     tmpl += `<span class="categorical-filter ${column_key}-filter current-filter">${cf_label}</span>`;
                 } else {
-                    tmpl += `<span class="categorical-filter ${
-                        column_key
-                    }-filter"><a href="javascript:void(0);" filter_key="${cf_key}" filter_val="${cf_arg}">${
-                        cf_label
-                    }</a></span>`;
+                    tmpl += `<span class="categorical-filter ${column_key}-filter"><a href="javascript:void(0);" filter_key="${cf_key}" filter_val="${cf_arg}">${cf_label}</a></span>`;
                 }
             }
             tmpl += "</span>";
@@ -565,10 +545,6 @@ export default {
     // template for filter items
     filter_element: function(filter_key, filter_value) {
         filter_value = Utils.sanitize(filter_value);
-        return `<span class="text-filter-val">${filter_value}<a href="javascript:void(0);" filter_key="${
-            filter_key
-        }" filter_val="${
-            filter_value
-        }"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>`;
+        return `<span class="text-filter-val">${filter_value}<a href="javascript:void(0);" filter_key="${filter_key}" filter_val="${filter_value}"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>`;
     }
 };

client/galaxy/scripts/mvc/history/hdca-li.js

@@ -75,9 +75,7 @@ var HDCAListItemView = _super.extend(
             } else if (!jobStatesSummary || !jobStatesSummary.hasDetails()) {
                 return `
                     <div class="progress state-progress">
-                        <span class="note">Loading job data for ${
-                            collectionTypeDescription
-                        }.<span class="blinking">..</span></span>
+                        <span class="note">Loading job data for ${collectionTypeDescription}.<span class="blinking">..</span></span>
                         <div class="progress-bar info" style="width:100%">
                     </div>`;
             } else {

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

@@ -910,9 +910,9 @@ var FolderToolbarView = Backbone.View.extend({
         }
         var promise = $.when(
             $.post(
-                `${Galaxy.root}api/libraries/datasets?encoded_folder_id=${that.id}&source=${options.source}&path=${
-                    popped_item
-                }&file_type=${options.file_type}&link_data=${options.link_data}&space_to_tab=${
+                `${Galaxy.root}api/libraries/datasets?encoded_folder_id=${that.id}&source=${
+                    options.source
+                }&path=${popped_item}&file_type=${options.file_type}&link_data=${options.link_data}&space_to_tab=${
                     options.space_to_tab
                 }&to_posix_lines=${options.to_posix_lines}&dbkey=${options.dbkey}&tag_using_filenames=${
                     options.tag_using_filenames
@@ -959,13 +959,13 @@ var FolderToolbarView = Backbone.View.extend({
         }
         var promise = $.when(
             $.post(
-                `${Galaxy.root}api/libraries/datasets?encoded_folder_id=${that.id}&source=${options.source}&path=${
-                    popped_item
-                }&preserve_dirs=${options.preserve_dirs}&link_data=${options.link_data}&to_posix_lines=${
-                    options.to_posix_lines
-                }&space_to_tab=${options.space_to_tab}&file_type=${options.file_type}&dbkey=${
-                    options.dbkey
-                }&tag_using_filenames=${options.tag_using_filenames}`
+                `${Galaxy.root}api/libraries/datasets?encoded_folder_id=${that.id}&source=${
+                    options.source
+                }&path=${popped_item}&preserve_dirs=${options.preserve_dirs}&link_data=${
+                    options.link_data
+                }&to_posix_lines=${options.to_posix_lines}&space_to_tab=${options.space_to_tab}&file_type=${
+                    options.file_type
+                }&dbkey=${options.dbkey}&tag_using_filenames=${options.tag_using_filenames}`
             )
         );
         promise

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

@@ -124,9 +124,9 @@ var LibraryView = Backbone.View.extend({
             placeholder: "Click to select a role",
             container: self.$el.find(`#${id}`),
             ajax: {
-                url: `${Galaxy.root}api/libraries/${self.id}/permissions?scope=available&is_library_access=${
-                    is_library_access
-                }`,
+                url: `${Galaxy.root}api/libraries/${
+                    self.id
+                }/permissions?scope=available&is_library_access=${is_library_access}`,
                 dataType: "json",
                 quietMillis: 100,
                 data: function(term, page) {

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

@@ -7,7 +7,7 @@ import Deferred from "utils/deferred";
 import Ui from "mvc/ui/ui-misc";
 import FormBase from "mvc/form/form-view";
 import Citations from "components/Citations.vue";
-import Vue from "libs/vue";
+import Vue from "vue";
 export default FormBase.extend({
     initialize: function(options) {
         var self = this;

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

@@ -269,9 +269,7 @@ var View = Backbone.View.extend({
                 } else if (batch_n !== n) {
                     this.form.highlight(
                         input_id,
-                        `Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>${
-                            n
-                        }</b> selection(s) while a previous field contains <b>${batch_n}</b>.`
+                        `Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>${n}</b> selection(s) while a previous field contains <b>${batch_n}</b>.`
                     );
                     return false;
                 }

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

@@ -35,9 +35,7 @@ $.extend(Workflow.prototype, {
         }
         if (!this.canLabelOutputWith(toLabel)) {
             Toastr.warning(
-                `Workflow contains duplicate workflow output labels ${
-                    toLabel
-                }. This must be fixed before it can be saved.`
+                `Workflow contains duplicate workflow output labels ${toLabel}. This must be fixed before it can be saved.`
             );
         }
         if (toLabel) {

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

@@ -277,9 +277,7 @@ export default Backbone.View.extend({
                 if (upgrade_message) {
                     window.show_modal(
                         "Issues loading this workflow",
-                        `Please review the following issues, possibly resulting from tool upgrades or changes.<p><ul>${
-                            upgrade_message
-                        }</ul></p>`,
+                        `Please review the following issues, possibly resulting from tool upgrades or changes.<p><ul>${upgrade_message}</ul></p>`,
                         { Continue: hide_modal }
                     );
                 } else {
@@ -560,9 +558,7 @@ export default Backbone.View.extend({
                 if (upgrade_message) {
                     window.show_modal(
                         "Subworkflow embedded with changes",
-                        `Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>${
-                            upgrade_message
-                        }</ul>`,
+                        `Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save.<ul>${upgrade_message}</ul>`,
                         { Continue: hide_modal }
                     );
                 } else {

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

@@ -103,9 +103,7 @@ var WorkflowItemView = Backbone.View.extend({
         } value="${wfId}">`;
         var trHtml = `<td><div class="dropdown"><button class="menubutton" type="button" data-toggle="dropdown">${_.escape(
             this.model.get("name")
-        )}<span class="caret"></span></button>${this._templateActions()}</div></td><td><span><div class="${
-            wfId
-        } tags-display"></div></td><td>${
+        )}<span class="caret"></span></button>${this._templateActions()}</div></td><td><span><div class="${wfId} tags-display"></div></td><td>${
             this.model.get("owner") === Galaxy.user.attributes.username ? "You" : this.model.get("owner")
         }</span></td><td>${this.model.get("number_of_steps")}</td><td>${
             this.model.get("published") ? "Yes" : "No"
@@ -323,9 +321,7 @@ var WorkflowListView = Backbone.View.extend({
             "<th>Published</th>" +
             "<th>Show in tools panel</th>" +
             "</tr></thead>";
-        return `${
-            tableHtml
-        }<tbody class="workflow-search "><div class="hidden_description_layer"><p>Drop workflow files here to import</p></tbody></table></div>`;
+        return `${tableHtml}<tbody class="workflow-search "><div class="hidden_description_layer"><p>Drop workflow files here to import</p></tbody></table></div>`;
     },
 
     /** Main template */

client/gulpfile.js

@@ -34,8 +34,7 @@ var paths = {
         'jquery-mousewheel': [ 'jquery.mousewheel.js', 'jquery/jquery.mousewheel.js' ],
         'raven-js': ['dist/raven.js', 'raven.js'],
         'requirejs': [ 'require.js', 'require.js' ],
-        'underscore': [ 'underscore.js', 'underscore.js' ],
-        'vue': [ 'dist/vue.js', 'vue.js' ]
+        'underscore': [ 'underscore.js', 'underscore.js' ]
     },
     libs: ['galaxy/scripts/libs/**/*.js']
 };