Merge remote-tracking branch 'jmchilton/dev' into download_collection

.ci/flake8_lint_include_list.txt

@@ -5,7 +5,6 @@ cron/cleanup_datasets.py
 cron/parse_builds_3_sites.py
 cron/parse_builds.py
 doc/parse_gx_xsd.py
-doc/patch.py
 lib/galaxy/actions/
 lib/galaxy/auth/
 lib/galaxy/config.py

CONTRIBUTORS.md

@@ -104,7 +104,7 @@ The following individuals have contributed code to Galaxy:
 * Michael Li <michael.li@uwaterloo.ca>
 * Pierre Lindenbaum <plindenbaum@yahoo.fr>
 * Mikael Loaec <mikael.loaec@versailles.inra.fr>
-* Thoba Lose @thobalose
+* Thoba Lose <lose.thoba@gmail.com>
 * Philip Mabon <philipmabon@gmail.com>
 * Remi Marenco <remi.marenco@gmail.com> <remimarenco@gmail.com>
 * Zipho Mashologu <zipho@trustpay.biz>

README.rst

@@ -49,7 +49,7 @@ done in the ``config/galaxy.ini`` file. Tools can be either installed
 from the Tool Shed or added manually. For details please see the Galaxy
 wiki:
 
-https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial
+https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/
 
 Not all dependencies are included for the tools provided in the sample
 ``tool_conf.xml``. A full list of external dependencies is available at:

client/galaxy/scripts/apps/analysis.js

@@ -9,7 +9,9 @@ var jQuery = require( 'jquery' ),
     UserPreferences = require( 'mvc/user/user-preferences' ),
     CustomBuilds = require( 'mvc/user/user-custom-builds' ),
     Tours = require( 'mvc/tours' ),
-    Workflows = require( 'mvc/workflow/workflow' );
+    GridView = require( 'mvc/grid/grid-view' )
+    Workflows = require( 'mvc/workflow/workflow' ),
+    WorkflowsConfigureMenu = require( 'mvc/workflow/workflow-configure-menu' );
 
 /** define the 'Analyze Data'/analysis/main/home page for Galaxy
  *  * has a masthead
@@ -79,12 +81,16 @@ window.app = function app( options, bootstrapped ){
             '(/)user(/)' : 'show_user',
             '(/)user(/)(:form_id)' : 'show_user_form',
             '(/)workflow(/)' : 'show_workflows',
+            '(/)pages(/)(:action_id)' : 'show_pages',
+            '(/)workflow/configure_menu(/)' : 'show_configure_menu',
             '(/)custom_builds' : 'show_custom_builds'
         },
 
         require_login: [
             'show_user',
-            'show_user_form'
+            'show_user_form',
+            'show_workflows',
+            'show_configure_menu'
         ],
 
         loginRequired: function() {
@@ -111,10 +117,18 @@ window.app = function app( options, bootstrapped ){
             this.page.display( new UserPreferences.Forms( { form_id: form_id, user_id: Galaxy.params.id } ) );
         },
 
+        show_pages : function( action_id ) {
+            this.page.display( new GridView( { url_base: Galaxy.root + 'page/list_published', dict_format: true } ) );
+        },
+
         show_workflows : function(){
             this.page.display( new Workflows.View() );
         },
 
+        show_configure_menu : function(){
+            this.page.display( new WorkflowsConfigureMenu.View() );
+        },
+
         show_custom_builds : function() {
             var self = this;
             var historyPanel = this.page.historyPanel.historyView;

client/galaxy/scripts/layout/menu.js

@@ -65,7 +65,7 @@ var Collection = Backbone.Collection.extend({
                     url     : 'visualization/list_published'
                 },{
                     title   : _l('Pages'),
-                    url     : 'page/list_published'
+                    url     : 'pages/list_published'
             }]
         });
 

client/galaxy/scripts/mvc/dataset/dataset-li.js

@@ -307,7 +307,7 @@ var DatasetListItemView = _super.extend(
 
     _renderNametags : function(){
         var tpl =  _.template([
-            '<% _.each(tags, function(tag){ %>',
+            '<% _.each(_.sortBy(_.uniq(tags), function(x) { return x }), function(tag){ %>',
                 '<% if (tag.indexOf("name:") == 0){ %>',
                     '<span class="label label-info"><%- tag.slice(5) %></span>',
                 '<% } %>',

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

@@ -11,7 +11,8 @@ define([], function() {
                 text_enable     : this.app_options.text_enable   || 'Enable',
                 text_disable    : this.app_options.text_disable  || 'Disable',
                 cls_enable      : this.app_options.cls_enable    || 'fa fa-caret-square-o-down',
-                cls_disable     : this.app_options.cls_disable   || 'fa fa-caret-square-o-up'
+                cls_disable     : this.app_options.cls_disable   || 'fa fa-caret-square-o-up',
+                always_refresh  : this.app_options.always_refresh
             }).set( options );
 
             // set element and link components
@@ -44,6 +45,11 @@ define([], function() {
                 app.trigger && app.trigger( 'change' );
                 self.render();
             });
+
+            // hide error on value change
+            if ( this.field.model && !this.model.get( 'always_refresh' ) ) {
+                this.listenTo( this.field.model, 'change:value', function() { self.reset() } );
+            }
         },
 
         /** Set backdrop for input element */

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

@@ -215,7 +215,7 @@ return {
         }
         return tmpl;
     },
-    
+
     // template
     footer: function(options) {
 
@@ -304,7 +304,7 @@ return {
                         '<input type="hidden" id="operation" name="operation" value="">' +
                         '<td></td>' +
                         '<td colspan="100">' +
-                            'For <span class="grid-selected-count"></span> selected ' + options.get_class_plural + ': ';
+                            'For <span class="grid-selected-count"></span> selected items: ';
 
             // configure buttons for operations
             for (i in options.operations) {

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

@@ -4,10 +4,11 @@ jQuery.ajaxSettings.traditional = true;
 
 // dependencies
 define([
+    'utils/utils',
     'mvc/grid/grid-model',
     'mvc/grid/grid-template',
     "mvc/ui/popup-menu"
-], function(GridModel, Templates, PopupMenu) {
+], function(Utils, GridModel, Templates, PopupMenu) {
 
 // grid view
 return Backbone.View.extend({
@@ -18,8 +19,36 @@ return Backbone.View.extend({
     // Initialize
     initialize: function(grid_config)
     {
+        this.dict_format = grid_config.dict_format;
+        var self = this;
+        window.add_tag_to_grid_filter = function( tag_name, tag_value ){
+            // Put tag name and value together.
+            var tag = tag_name + ( tag_value !== undefined && tag_value !== "" ? ":" + tag_value : "" );
+            var advanced_search = $( '#advanced-search').is(":visible" );
+            if( !advanced_search ){
+                $('#standard-search').slideToggle('fast');
+                $('#advanced-search').slideToggle('fast');
+            }
+            self.add_filter_condition( "tags", tag );
+        };
+
         // set element
-        this.setElement('#grid-container');
+        if ( this.dict_format ) {
+            this.setElement('<div/>');
+            if ( grid_config.url_base && !grid_config.items ) {
+                Utils.get({
+                    url: grid_config.url_base,
+                    success: function( response ) {
+                        self.init_grid( response );
+                    }
+                });
+            } else {
+                this.init_grid(grid_config);
+            }
+        } else {
+            this.setElement('#grid-container');
+            this.init_grid(grid_config);
+        }
 
         // fix padding
         if (grid_config.use_panels) {
@@ -28,9 +57,6 @@ return Backbone.View.extend({
                 overflow    : 'auto'
             });
         }
-
-        // initialize controls
-        this.init_grid(grid_config);
     },
 
     // refresh frames
@@ -545,7 +571,7 @@ return Backbone.View.extend({
             });
 
             // Do operation. If operation cannot be performed asynchronously, redirect to location.
-            if (this.grid.can_async_op(operation)) {
+            if (this.grid.can_async_op(operation) || this.dict_format) {
                 this.update_grid();
             } else {
                 this.go_to(target, href);
@@ -562,7 +588,7 @@ return Backbone.View.extend({
         }
 
         // refresh grid
-        if (this.grid.get('async')) {
+        if (this.grid.get('async') || this.dict_format) {
             this.update_grid();
         } else {
             this.go_to(target, href);
@@ -630,7 +656,7 @@ return Backbone.View.extend({
                 var insert = self.grid.get('insert');
 
                 // request new configuration
-                var json = $.parseJSON(response_text);
+                var json = self.dict_format ? response_text.embedded_grid || response_text : $.parseJSON(response_text);
 
                 // update
                 json.embedded = embedded;

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

@@ -16,7 +16,7 @@ var _super = DATASET_LI.DatasetListItemView;
 var HDAListItemView = _super.extend(
 /** @lends HDAListItemView.prototype */{
 
-    className   : _super.prototype.className + " history-content",
+    className : _super.prototype.className + " history-content",
 
     initialize : function( attributes, options ){
         _super.prototype.initialize.call( this, attributes, options );
@@ -45,7 +45,7 @@ HDAListItemView.prototype.templates = (function(){
             '</div>',
             '</br>',
             '<span class="nametags">',
-                '<% _.each(dataset.tags, function(tag){ %>',
+                '<% _.each(_.sortBy(_.uniq(dataset.tags), function(x) { return x }), function(tag){ %>',
                     '<% if (tag.indexOf("name:") == 0){ %>',
                         '<span class="label label-info"><%- tag.slice(5) %></span>',
                     '<% } %>',

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

@@ -85,7 +85,7 @@ HDCAListItemView.prototype.templates = (function(){
             '</div>',
             '<div class="subtitle"></div>',
             '<span class="nametags">',
-                '<% _.each(collection.tags, function(tag){ %>',
+                '<% _.each(_.sortBy(_.uniq(collection.tags), function(x) { return x }), function(tag){ %>',
                     '<% if (tag.indexOf("name:") == 0){ %>',
                         '<span class="label label-info"><%- tag.slice(5) %></span>',
                     '<% } %>',

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

@@ -352,7 +352,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
                                     var wp_field = self.wp_form.field_list[ self.wp_form.data.match( match[ 1 ] ) ];
                                     var wp_value = wp_field && wp_field.value();
                                     if ( wp_value ) {
-                                        new_value = new_value.replace( new RegExp( '\\' + match[ 0 ], 'g' ), wp_value );
+                                        new_value = new_value.split( match[ 0 ] ).join( wp_value );
                                     }
                                 }
                             }