Removing run mako from workflows

client/galaxy/scripts/apps/analysis.js

@@ -79,7 +79,8 @@ window.app = function app( options, bootstrapped ){
             '(/)user(/)' : 'show_user',
             '(/)user(/)(:form_id)' : 'show_user_form',
             '(/)workflow(/)' : 'show_workflows',
-            '(/)custom_builds' : 'show_custom_builds'
+            '(/)custom_builds' : 'show_custom_builds',
+            '(/)workflow/run(/)' : 'show_run',
         },
 
         require_login: [
@@ -115,6 +116,10 @@ window.app = function app( options, bootstrapped ){
             this.page.display( new Workflows.View() );
         },
 
+        show_run : function() {
+            this.page.display( new Workflows.Run_Workflow_View() )
+        },
+
         show_custom_builds : function() {
             var self = this;
             var historyPanel = this.page.historyPanel.historyView;
@@ -139,7 +144,7 @@ window.app = function app( options, bootstrapped ){
             } else {
                 // show the workflow run form
                 if( params.workflow_id ){
-                    this._loadCenterIframe( 'workflow/run?id=' + params.workflow_id );
+                    this.page.display( new Workflows.Run_Workflow_View() )
                 // load the center iframe with controller.action: galaxy.org/?m_c=history&m_a=list -> history/list
                 } else if( params.m_c ){
                     this._loadCenterIframe( params.m_c + '/' + params.m_a );

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

@@ -1,6 +1,7 @@
 var Tools = require( 'mvc/tool/tools' ),
     Upload = require( 'mvc/upload/upload-view' ),
-    _l = require( 'utils/localization' );
+    _l = require( 'utils/localization' ),
+    ToolForm = require( 'mvc/tool/tool-form-composite' );
 
 var ToolPanel = Backbone.View.extend({
     initialize: function( page, options ) {
@@ -58,10 +59,26 @@ var ToolPanel = Backbone.View.extend({
             href    : 'workflow'
         }));
         _.each( this.stored_workflow_menu_entries, function( menu_entry ){
-            self.$( '#internal-workflows' ).append( self._templateTool({
+            self.$( '#internal-workflows' ).append( self._templateWorkflowLink({
                 title : menu_entry.stored_workflow.name,
-                href  : 'workflow/run?id=' + menu_entry.encoded_stored_workflow_id
+                href  : 'workflow/run?id=' + menu_entry.encoded_stored_workflow_id,
+                cls   : 'workflow-menu-' + menu_entry.encoded_stored_workflow_id
             }));
+            self._registerWorkflowMenuClick( self, menu_entry.encoded_stored_workflow_id );
+        });
+    },
+
+    /** Open the items in workflow menu in the center panel */
+    _registerWorkflowMenuClick: function( self, workflow_id ) {
+        $( '.workflow-menu-' + workflow_id ).click(function( e ) {
+            var url = Galaxy.root + 'workflow/run_workflow?id=' + workflow_id;
+            $.getJSON(url, function( response ) {
+                var wf_parsed = JSON.parse( JSON.stringify( response ) );
+                var form = new ToolForm.View( wf_parsed[0] );
+                $( '#galaxy_main' ).hide();
+                $( "#center-panel" ).show();
+                $( "#center-panel" ).empty().append( form.$el );
+            });
         });
     },
 
@@ -84,6 +101,15 @@ var ToolPanel = Backbone.View.extend({
         ].join('');
     },
 
+    /** build links to workflows in toolpanel */
+    _templateWorkflowLink: function( wf ) {
+        return [
+            '<div class="toolTitle">',
+                '<a class="'+ wf.cls +' " href="', Galaxy.root, wf.href, '">', wf.title, '</a>',
+            '</div>'
+        ].join('');
+    },
+
     /** override to include inital menu dom and workflow section */
     _template : function() {
         return [

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

@@ -1,5 +1,5 @@
 /** Workflow view */
-define( [], function() {
+define( [ 'mvc/tool/tool-form-composite' ], function( ToolForm ) {
 
     /** View of the main workflow list page */
     var View = Backbone.View.extend({
@@ -157,7 +157,7 @@ define( [], function() {
             if( workflow.owner === Galaxy.user.attributes.username ) {
                 return '<ul class="dropdown-menu action-dpd">' +
                            '<li><a href="'+ Galaxy.root +'workflow/editor?id='+ workflow.id +'">Edit</a></li>' +
-                           '<li><a href="'+ Galaxy.root +'workflow/run?id='+ workflow.id +'" target="galaxy_main">Run</a></li>' +
+                           '<li><a href="'+ Galaxy.root +'workflow/run?id='+ workflow.id +'">Run</a></li>' +
                            '<li><a href="'+ Galaxy.root +'workflow/sharing?id='+ workflow.id +'">Share or Download</a></li>' +
                            '<li><a href="'+ Galaxy.root +'workflow/copy?id='+ workflow.id +'">Copy</a></li>' +
                            '<li><a href="'+ Galaxy.root +'workflow/rename?id='+ workflow.id +'">Rename</a></li>' +
@@ -168,7 +168,7 @@ define( [], function() {
             else {
                 return '<ul class="dropdown-menu action-dpd">' +
                          '<li><a href="'+ Galaxy.root +'workflow/display_by_username_and_slug?username='+ workflow.owner +'&slug='+ workflow.slug +'">View</a></li>' +
-                         '<li><a href="'+ Galaxy.root +'workflow/run?id='+ workflow.id +'" target="galaxy_main">Run</a></li>' +
+                         '<li><a href="'+ Galaxy.root +'workflow/run?id='+ workflow.id +'">Run</a></li>' +
                          '<li><a href="'+ Galaxy.root +'workflow/copy?id='+ workflow.id +'">Copy</a></li>' +
                          '<li><a class="link-confirm-shared-'+ workflow.id +'" href="'+ Galaxy.root +'workflow/sharing?unshare_me=True&id='+ workflow.id +'">Remove</a></li>' +
                       '</ul>';
@@ -192,7 +192,33 @@ define( [], function() {
         }
     });
 
+    var Run_Workflow_View = Backbone.View.extend({
+
+        initialize: function( options ) {
+            this.setElement( '<div/>' );
+            this.run_workflow( options );
+        },
+
+        /** Open workflow to run */
+        run_workflow: function() {
+            var self = this,
+                id = self.get_querystring( 'id' ),
+                url = Galaxy.root + 'workflow/run_workflow?id=' + id;
+            $.getJSON(url, function( response ) {
+                var wf_parsed = JSON.parse( JSON.stringify( response ) );
+                var form = new ToolForm.View( wf_parsed[0] );
+                self.$el.empty().append( form.$el );
+            });
+        },
+
+        /** Get querystrings from url */
+        get_querystring: function( key ) {
+            return decodeURIComponent( window.location.search.replace(new RegExp("^(?:.*[&\\?]" + encodeURIComponent( key ).replace(/[\.\+\*]/g, "\\$&") + "(?:\\=([^&]*))?)?.*$", "i"), "$1") );
+        },
+    });
+
     return {
-        View  : View
+        View  : View,
+        Run_Workflow_View : Run_Workflow_View
     };
 });

lib/galaxy/webapps/galaxy/buildapp.py

@@ -108,6 +108,7 @@ def paste_app_factory( global_conf, **kwargs ):
     webapp.add_client_route( '/user' )
     webapp.add_client_route( '/user/{form_id}' )
     webapp.add_client_route( '/workflow' )
+    webapp.add_client_route( '/workflow/run' )
     webapp.add_client_route( '/custom_builds' )
 
     # ==== Done

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -948,7 +948,7 @@ def build_from_current_history( self, trans, job_ids=None, dataset_ids=None, dat
                                            url_for( controller='workflow', action='run', id=workflow_id ) ) )
 
     @web.expose
-    def run( self, trans, id, history_id=None, **kwargs ):
+    def run_workflow( self, trans, id, history_id=None, **kwargs ):
         history = None
         try:
             if history_id is not None:
@@ -965,7 +965,9 @@ def run( self, trans, id, history_id=None, **kwargs ):
         workflow_contents_manager = workflows.WorkflowContentsManager( trans.app )
         stored = workflow_manager.get_stored_accessible_workflow( trans, id )
         workflow_dict = workflow_contents_manager.workflow_to_dict( trans, stored, style='run' )
-        return trans.fill_template( 'workflow/run.mako', workflow_dict=workflow_dict )
+        wf_dict = list()
+        wf_dict.append( workflow_dict )
+        return json.dumps( wf_dict )
 
     def get_item( self, trans, id ):
         return self.get_stored_workflow( trans, id )