Merge pull request #3 from galaxyproject/dev

Merge from upstream

.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

.gitignore

@@ -93,7 +93,7 @@ tool-data/genome/*
 tool-data/*.sample
 tool-data/testtoolshed.g2.bx.psu.edu/
 tool-data/toolshed.g2.bx.psu.edu/
-tool-data/**/*.fa 
+tool-data/**/*.fa
 
 # Test output
 test-data-cache
@@ -135,4 +135,3 @@ doc/source/dev/schema.rst
 .DS_Store
 *.rej
 *~
-.idea/

client/galaxy/scripts/apps/analysis.js

@@ -9,6 +9,8 @@ var jQuery = require( 'jquery' ),
     UserPreferences = require( 'mvc/user/user-preferences' ),
     CustomBuilds = require( 'mvc/user/user-custom-builds' ),
     Tours = require( 'mvc/tours' ),
+    GridView = require( 'mvc/grid/grid-view' ),
+    PageList = require( 'mvc/page/page-list' ),
     Workflows = require( 'mvc/workflow/workflow' ),
     WorkflowsConfigureMenu = require( 'mvc/workflow/workflow-configure-menu' );
 
@@ -80,6 +82,8 @@ window.app = function app( options, bootstrapped ){
             '(/)user(/)' : 'show_user',
             '(/)user(/)(:form_id)' : 'show_user_form',
             '(/)workflow(/)' : 'show_workflows',
+            '(/)pages(/)(:action_id)' : 'show_pages',
+            '(/)datasets(/)(:action_id)' : 'show_datasets',
             '(/)workflow/configure_menu(/)' : 'show_configure_menu',
             '(/)custom_builds' : 'show_custom_builds'
         },
@@ -115,6 +119,18 @@ window.app = function app( options, bootstrapped ){
             this.page.display( new UserPreferences.Forms( { form_id: form_id, user_id: Galaxy.params.id } ) );
         },
 
+        show_datasets : function() {
+            this.page.display( new GridView( { url_base: Galaxy.root + 'dataset/list', dict_format: true } ) );
+        },
+
+        show_pages : function( action_id ) {
+            if ( action_id == 'list' ) {
+                this.page.display( new PageList.View() );
+            } else {
+                this.page.display( new GridView( { url_base: Galaxy.root + 'page/list_published', dict_format: true } ) );
+            }
+        },
+
         show_workflows : function(){
             this.page.display( new Workflows.View() );
         },

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'
             }]
         });
 
@@ -122,13 +122,21 @@ var Collection = Backbone.Collection.extend({
                     $.each(webhooks.models, function(index, model) {
                         var webhook = model.toJSON();
                         if (webhook.activate) {
-                            self.add({
+                            var obj = {
                                 id      : webhook.name,
                                 icon    : webhook.config.icon,
                                 url     : webhook.config.url,
                                 tooltip : webhook.config.tooltip,
                                 onclick : webhook.config.function && new Function(webhook.config.function),
-                            });
+                            };
+
+                            // Galaxy.page is undefined for data libraries, workflows pages
+                            if( Galaxy.page ) {
+                                Galaxy.page.masthead.collection.add(obj);
+                            }
+                            else if( Galaxy.masthead ) {
+                                Galaxy.masthead.collection.add(obj);
+                            }
                         }
                     });
                 });
@@ -271,11 +279,11 @@ var Collection = Backbone.Collection.extend({
                         target  : 'galaxy_main'
                     },{
                         title   : _l('Saved Datasets'),
-                        url     : 'dataset/list',
-                        target  : 'galaxy_main'
+                        url     : 'datasets/list',
+                        target  : '_top'
                     },{
                         title   : _l('Saved Pages'),
-                        url     : 'page/list',
+                        url     : 'pages/list',
                         target  : '_top'
                     }]
             };

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

@@ -45,6 +45,7 @@ var CollectionView = _super.extend(
         this.parentName = attributes.parentName;
         /** foldout or drilldown */
         this.foldoutStyle = attributes.foldoutStyle || 'foldout';
+        this.downloadUrl = this.model.attributes.url + '/download';
     },
 
     _queueNewRender : function( $newRender, speed ) {
@@ -171,7 +172,14 @@ CollectionView.prototype.templates = (function(){
             '</div>',
 
             '<div class="tags-display"></div>',
-        '</div>'
+
+            '<div class="actions">',
+                '<a class="download-btn icon-btn" ',
+                    'href="<%- view.downloadUrl %>', '" title="" download="" data-original-title="Download Collection">',
+                    '<span class="fa fa-floppy-o"></span>',
+                '</a>',
+            '</div>',
+        '</div>',
     ], 'collection' );
 
     return _.extend( _.clone( _super.prototype.templates ), {

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

@@ -307,7 +307,7 @@ var DatasetListItemView = _super.extend(
 
     _renderNametags : function(){
         var tpl =  _.template([
-            '<% _.each(_.uniq(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 : $.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(_.uniq(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/page/page-list.js

@@ -0,0 +1,56 @@
+/** This class renders the page list. */
+define( [ 'utils/utils', 'mvc/grid/grid-view' ], function( Utils, GridView ) {
+    var View = Backbone.View.extend({
+        initialize: function( options ) {
+            var self = this;
+            this.setElement( $( '<div/>' ) );
+            this.model = new Backbone.Model();
+            Utils.get({
+                url     : Galaxy.root + 'page/list',
+                success : function( response ) {
+                    response[ 'dict_format' ] = true;
+                    self.model.set( response );
+                    self.render();
+                }
+            });
+        },
+
+        render: function() {
+            var grid = new GridView( this.model.attributes );
+            this.$el.empty().append( grid.$el );
+            this.$el.append( this._templateShared() );
+        },
+
+        _templateShared: function() {
+            var $tmpl = $(  '<div>' +
+                                '<h2>Pages shared with you by others</h2>' +
+                            '</div>' );
+            var options = this.model.attributes;
+            if ( options.shared_by_others && options.shared_by_others.length > 0 ) {
+                var $table = $( '<table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%">' +
+                                    '<tr class="header">' +
+                                        '<th>Title</th>' +
+                                        '<th>Owner</th>' +
+                                    '</tr>' +
+                                '</table>' );
+                _.each( options.shared_by_others, function( page, index ) {
+                    var display_url = Galaxy.root + 'page/display_by_username_and_slug?username=' + page.username + '&slug=' + page.slug;
+                    $table.append(  '<tr>' +
+                                        '<td>' +
+                                            '<a href="' + display_url + '">' + _.escape( page.title ) + '</a>' +
+                                        '</td>' +
+                                        '<td>' + _.escape( page.username ) + '</td>' +
+                                    '</tr>' );
+                });
+                $tmpl.append( $table );
+            } else {
+                $tmpl.append( 'No pages have been shared with you.' );
+            }
+            return $tmpl;
+        }
+    });
+
+    return {
+        View: View
+    }
+});

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

@@ -243,6 +243,22 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view
                 });
             }
 
+            // add tool menu webhooks
+            $.getJSON('/api/webhooks/tool-menu/all', function(webhooks) {
+                _.each(webhooks, function(webhook) {
+                    if (webhook.activate && webhook.config.function) {
+                        menu_button.addMenu({
+                            icon    : webhook.config.icon,
+                            title   : webhook.config.title,
+                            onclick : function() {
+                                var func = new Function('options', webhook.config.function);
+                                func(options);
+                            }
+                        });
+                    }
+                });
+            });
+
             return {
                 menu        : menu_button,
                 versions    : versions_button

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

@@ -457,7 +457,9 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
                         if ($.isArray( response ) && response.length > 0) {
                             self.$el.append( $( '<div/>', { id: 'webhook-view' } ) );
                             var WebhookApp = new Webhooks.WebhookView({
-                                urlRoot: Galaxy.root + 'api/webhooks/workflow'
+                                urlRoot: Galaxy.root + 'api/webhooks/workflow',
+                                toolId: job_def.tool_id,
+                                toolVersion: job_def.tool_version,
                             });
                         }
 

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

@@ -110,7 +110,8 @@ define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-modal', 'mvc/tool/tool-form
                     if ( response.jobs && response.jobs.length > 0 ) {
                         self.$el.append( $( '<div/>', { id: 'webhook-view' } ) );
                         var WebhookApp = new Webhooks.WebhookView({
-                            urlRoot: Galaxy.root + 'api/webhooks/tool'
+                            urlRoot: Galaxy.root + 'api/webhooks/tool',
+                            toolId: job_def.tool_id
                         });
                     }
                     parent.Galaxy && parent.Galaxy.currHistoryPanel && parent.Galaxy.currHistoryPanel.refreshContents();