Merge pull request #4047 from bgruening/workflowexport_mako

New Workflow Management Screen UI using JavaScript

client/galaxy/scripts/apps/analysis.js

@@ -8,9 +8,10 @@ var jQuery = require( 'jquery' ),
     HistoryPanel = require( './history-panel' ),
     PAGE = require( 'layout/page' ),
     ToolForm = require( 'mvc/tool/tool-form' ),
-    UserPreferences = require( 'mvc/user/user-preferences' );
-    CustomBuilds = require( 'mvc/user/user-custom-builds' );
-    Tours = require( 'mvc/tours' );
+    UserPreferences = require( 'mvc/user/user-preferences' ),
+    CustomBuilds = require( 'mvc/user/user-custom-builds' ),
+    Tours = require( 'mvc/tours' ),
+    Workflows = require( 'mvc/workflow/workflow' );
 
 /** define the 'Analyze Data'/analysis/main/home page for Galaxy
  *  * has a masthead
@@ -121,6 +122,7 @@ window.app = function app( options, bootstrapped ){
             '(/)tours(/)(:tour_id)' : 'show_tours',
             '(/)user(/)' : 'show_user',
             '(/)user(/)(:form_id)' : 'show_user_form',
+            '(/)workflow(/)' : 'show_workflows',
             '(/)custom_builds' : 'show_custom_builds'
         },
 
@@ -153,6 +155,10 @@ window.app = function app( options, bootstrapped ){
             centerPanel.display( new UserPreferences.Forms( { form_id: form_id, user_id: Galaxy.params.id } ) );
         },
 
+        show_workflows : function(){
+            centerPanel.display( new Workflows.View() );
+        },
+
         show_custom_builds : function() {
             var self = this;
             if ( !Galaxy.currHistoryPanel || !Galaxy.currHistoryPanel.model || !Galaxy.currHistoryPanel.model.id ) {

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

@@ -63,9 +63,9 @@ var ToolPanel = LeftPanel.extend({
     _renderWorkflowMenu : function(){
         var self = this;
         // add internal workflow list
-        self.$( '#internal-workflows' ).append( self._templateTool({
+        self.$( '#internal-workflows' ).append( self._templateAllWorkflow({
             title   : _l( 'All workflows' ),
-            href    : 'workflow/list_for_run'
+            href    : 'workflow'
         }));
         _.each( self.stored_workflow_menu_entries, function( menu_entry ){
             self.$( '#internal-workflows' ).append( self._templateTool({
@@ -85,6 +85,16 @@ var ToolPanel = LeftPanel.extend({
         ].join('');
     },
 
+    /** build a link to 'All Workflows' */
+    _templateAllWorkflow: function( tool ) {
+        return [
+            '<div class="toolTitle">',
+                // global
+                '<a href="', Galaxy.root, tool.href, '">', tool.title, '</a>',
+            '</div>'
+        ].join('');
+    },
+
     /** override to include inital menu dom and workflow section */
     _templateBody : function(){
         return [

client/galaxy/scripts/layout/menu.js

@@ -33,9 +33,13 @@ var Collection = Backbone.Collection.extend({
         this.add({
             id              : 'workflow',
             title           : _l('Workflow'),
-            url             : 'workflow',
             tooltip         : _l('Chain tools into workflows'),
-            disabled        : !Galaxy.user.id
+            disabled        : !Galaxy.user.id,
+            url             : 'workflow',
+            target          : 'galaxy_main',
+            onclick         : function() {
+                                  window.location = Galaxy.root + 'workflow';
+                            }
         });
 
         //

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

@@ -0,0 +1,198 @@
+/** Workflow view */
+define( [], function() {
+
+    /** View of the main workflow list page */
+    var View = Backbone.View.extend({
+
+        initialize: function() {
+            this.setElement( '<div/>' );
+            this.render();
+        },
+
+        render: function() {
+            var self = this,
+                min_query_length = 3;
+            $.getJSON( Galaxy.root + 'api/workflows/', function( workflows ) {
+                var $el_workflow = null;
+                // Add workflow header
+                self.$el.empty().append( self._templateHeader() );
+                // Add user actions message if any
+                self.build_messages( self );
+                $el_workflow = self.$el.find( '.user-workflows' );
+                // Add the actions buttons
+                $el_workflow.append( self._templateActionButtons() );
+                if( workflows.length > 0) {
+                    $el_workflow.append( self._templateWorkflowTable( self, workflows) );
+                    self.adjust_actiondropdown( $el_workflow );
+                    // Register delete and run workflow events
+                    _.each( workflows, function( wf ) {
+                        self.confirm_delete( self, wf );
+                    });
+                    // Register search workflow event
+                    self.search_workflow( self, self.$el.find( '.search-wf' ), self.$el.find( '.workflow-search tr' ), min_query_length );
+                }
+                else {
+                    $el_workflow.append( self._templateNoWorkflow() );
+                }
+            });
+        },
+
+        /** Build messages after user action */
+        build_messages: function( self ) {
+            var $el_message = self.$el.find( '.response-message' ),
+                status = self.get_querystring( 'status' ),
+                message = self.get_querystring( 'message' );
+
+            if( message && message !== null && message !== "" ) {
+                $el_message.addClass( status + 'message' );
+                $el_message.html( '<p>' + message + '</p>' );
+            }
+            else {
+                $el_message.html("");
+            }
+        },
+
+        /** Add confirm box before removing/unsharing workflow */
+        confirm_delete: function( self, workflow ) {
+            var $el_wf_link = self.$el.find( '.link-confirm-' + workflow.id ),
+                $el_shared_wf_link = self.$el.find( '.link-confirm-shared-' + workflow.id );
+            $el_wf_link.click( function() {
+                return confirm( "Are you sure you want to delete workflow '" + workflow.name + "'?" );
+            });
+            $el_shared_wf_link.click( function() {
+                return confirm( "Are you sure you want to remove the shared workflow '" + workflow.name + "'?" );
+            });
+        },
+
+        /** Implement client side workflow search/filtering */
+        search_workflow: function( self, $el_searchinput, $el_tabletr, min_querylen ) {
+            $el_searchinput.on( 'keyup', function () {
+                var query = $( this ).val();
+                // Filter when query is at least 3 characters
+                // otherwise show all rows
+                if( query.length >= min_querylen ) {
+                    // Ignore the query's case using 'i'
+                    var regular_expression = new RegExp( query, 'i' );
+                    $el_tabletr.hide();
+                    $el_tabletr.filter(function () {
+                        // Apply regular expression on each row's text
+                        // and show when there is a match
+                        return regular_expression.test( $( this ).text() );
+                    }).show();
+                }
+                else {
+                    $el_tabletr.show();
+                }
+            });
+        },
+
+        /** Get querystrings from url */
+        get_querystring: function( key ) {
+            return decodeURIComponent( window.location.search.replace(new RegExp("^(?:.*[&\\?]" + encodeURIComponent( key ).replace(/[\.\+\*]/g, "\\$&") + "(?:\\=([^&]*))?)?.*$", "i"), "$1") );
+        },
+
+        /** Ajust the position of dropdown with respect to table */
+        adjust_actiondropdown: function( $el ) {
+            $el.on( 'show.bs.dropdown', function () {
+                $el.css( "overflow", "inherit" );
+            });
+
+            $el.on( 'hide.bs.dropdown', function () {
+                $el.css( "overflow", "auto" );
+            });
+        },
+
+        /** Template for no workflow */
+        _templateNoWorkflow: function() {
+            return '<div class="wf-nodata"> You have no workflows. </div>';
+        },
+
+        /** Template for actions buttons */
+        _templateActionButtons: function() {
+           return '<ul class="manage-table-actions">' +
+                '<li>' +
+                    '<input class="search-wf form-control" type="text" autocomplete="off" placeholder="search for workflow...">' +
+                '</li>' +
+                '<li>' +
+                    '<a class="action-button fa fa-plus wf-action" id="new-workflow" title="Create new workflow" href="'+ Galaxy.root +'workflow/create">' +
+                    '</a>' +
+                '</li>' +
+                '<li>' +
+                    '<a class="action-button fa fa-upload wf-action" id="import-workflow" title="Upload or import workflow" href="'+ Galaxy.root +'workflow/import_workflow">' +
+                    '</a>' +
+                '</li>' +
+            '</ul>';
+        },
+
+        /** Template for workflow table */
+        _templateWorkflowTable: function( self, workflows ) {
+            var tableHtml = "", trHtml = "";
+            tableHtml = tableHtml + '<table class="table colored"><thead>' +
+                    '<tr class="header">' +
+                        '<th class="wf-td">Name</th>' +
+                        '<th class="wf-td">Owner</th>' +
+                        '<th class="wf-td"># of Steps</th>' +
+                        '<th class="wf-td">Published</th>' +
+                    '</tr></thead>';
+            _.each( workflows, function( wf ) {
+                trHtml = trHtml + '<tr>' +
+                             '<td class="wf-td wf-dpd">' +
+                                 '<div class="dropdown">' +
+                                     '<button class="menubutton" type="button" data-toggle="dropdown">' +
+                                         _.escape( wf.name ) + '<span class="caret"></span>' +
+                                     '</button>' +
+                                     self._templateActions( wf ) +
+                                 '</div>' +
+                              '</td>' +
+                              '<td>' + ( wf.owner === Galaxy.user.attributes.username ? "You" : wf.owner ) +'</td>' +
+                              '<td class="wf-td">' + wf.number_of_steps + '</td>' +
+                              '<td class="wf-td">' + ( wf.published ? "Yes" : "No" ) + '</td>' +
+                         '</tr>';
+            });
+            return tableHtml + '<tbody class="workflow-search">' + trHtml + '</tbody></table>';
+        },
+
+        /** Template for user actions for workflows */
+        _templateActions: function( workflow ) {
+            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/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>' +
+                           '<li><a href="'+ Galaxy.root +'workflow/display_by_id?id='+ workflow.id +'">View</a></li>' +
+                           '<li><a class="link-confirm-'+ workflow.id +'" href="'+ Galaxy.root +'workflow/delete?id='+ workflow.id +'">Delete</a></li>' +
+                      '</ul>';
+            }
+            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/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>';
+            }
+        },
+
+        /** Main template */
+        _templateHeader: function() {
+            return '<div class="page-container">' +
+                       '<div class="user-workflows wf">' +
+                           '<div class="response-message"></div>' +
+                           '<h2>Your workflows</h2>' +
+                       '</div>'+
+                       '<div class="other-options wf">' +
+                           '<h2>Other options</h2>' +
+                           '<a class="action-button fa fa-cog wf-action" href="'+ Galaxy.root +'workflow/configure_menu" title="Configure your workflow menu">' +
+                               '<span>Configure your workflow menu</span>' +
+                           '</a>' +
+                       '</div>' +
+                   '</div>';
+        }
+    });
+
+    return {
+        View  : View
+    };
+});

client/galaxy/style/less/base.less

@@ -1766,4 +1766,27 @@ div.toolTitleNoSection
         color:black;
         text-align:left;
     }
-}
+}
+
+
+// workflow
+.wf {
+    overflow: auto;
+}
+
+.wf-action span {
+    padding-left: 3px;
+    font-family: "Lucida Grande", verdana, arial, helvetica, sans-serif;
+}
+
+.wf-td {
+    width: 25%;
+}
+
+.wf-nodata {
+    padding-left: 1%;
+}
+
+.other-options {
+    margin-bottom: 2%;
+}

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -65,6 +65,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             encoded_id = trans.security.encode_id(wf.id)
             item['url'] = url_for('workflow', id=encoded_id)
             item['owner'] = wf.user.username
+            item['number_of_steps'] = len( wf.latest_workflow.steps )
             rval.append(item)
         for wf_sa in trans.sa_session.query( trans.app.model.StoredWorkflowUserShareAssociation ).filter_by(
                 user=trans.user ).join( 'stored_workflow' ).filter(
@@ -74,6 +75,8 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
             item['url'] = url_for( 'workflow', id=encoded_id )
             item['owner'] = wf_sa.stored_workflow.user.username
+            item['number_of_steps'] = len( wf_sa.stored_workflow.latest_workflow.steps )
+            item['slug'] = wf_sa.stored_workflow.slug
             rval.append(item)
         return rval
 

lib/galaxy/webapps/galaxy/buildapp.py

@@ -107,6 +107,7 @@ def paste_app_factory( global_conf, **kwargs ):
     webapp.add_client_route( '/tours/{tour_id}' )
     webapp.add_client_route( '/user' )
     webapp.add_client_route( '/user/{form_id}' )
+    webapp.add_client_route( '/workflow' )
     webapp.add_client_route( '/custom_builds' )
 
     # ==== Done

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

@@ -155,10 +155,6 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
 
     __myexp_url = "www.myexperiment.org:80"
 
-    @web.expose
-    def index( self, trans ):
-        return self.list( trans )
-
     @web.expose
     @web.require_login( "use Galaxy workflows" )
     def list_grid( self, trans, **kwargs ):
@@ -179,52 +175,9 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         """
         Render workflow main page (management of existing workflows)
         """
-        user = trans.get_user()
-        workflows = trans.sa_session.query( model.StoredWorkflow ) \
-            .filter_by( user=user, deleted=False ) \
-            .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
-            .all()
-        shared_by_others = trans.sa_session \
-            .query( model.StoredWorkflowUserShareAssociation ) \
-            .filter_by( user=user ) \
-            .join( 'stored_workflow' ) \
-            .filter( model.StoredWorkflow.deleted == expression.false() ) \
-            .order_by( desc( model.StoredWorkflow.update_time ) ) \
-            .all()
-
-        # Legacy issue: all shared workflows must have slugs.
-        slug_set = False
-        for workflow_assoc in shared_by_others:
-            if self.create_item_slug( trans.sa_session, workflow_assoc.stored_workflow ):
-                slug_set = True
-        if slug_set:
-            trans.sa_session.flush()
-
-        return trans.fill_template( "workflow/list.mako",
-                                    workflows=workflows,
-                                    shared_by_others=shared_by_others )
-
-    @web.expose
-    @web.require_login( "use Galaxy workflows" )
-    def list_for_run( self, trans ):
-        """
-        Render workflow list for analysis view (just allows running workflow
-        or switching to management view)
-        """
-        user = trans.get_user()
-        workflows = trans.sa_session.query( model.StoredWorkflow ) \
-            .filter_by( user=user, deleted=False ) \
-            .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
-            .all()
-        shared_by_others = trans.sa_session \
-            .query( model.StoredWorkflowUserShareAssociation ) \
-            .filter_by( user=user ) \
-            .filter( model.StoredWorkflow.deleted == expression.false() ) \
-            .order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
-            .all()
-        return trans.fill_template( "workflow/list_for_run.mako",
-                                    workflows=workflows,
-                                    shared_by_others=shared_by_others )
+        # Take care of proxy prefix in url as well
+        redirect_url = url_for( '/' ) + 'workflow'
+        return trans.response.send_redirect( redirect_url )
 
     @web.expose
     def list_published( self, trans, **kwargs ):
@@ -425,8 +378,11 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
             stored.name = san_new_name
             stored.latest_workflow.name = san_new_name
             trans.sa_session.flush()
-            trans.set_message( "Workflow renamed to '%s'." % san_new_name )
-            return self.list( trans )
+            message = 'Workflow renamed to: %s' % escape( san_new_name )
+            trans.set_message( message )
+            # Take care of proxy prefix in url as well
+            redirect_url = url_for( '/' ) + 'workflow?status=done&message=%s' % escape( message )
+            return trans.response.send_redirect( redirect_url )
         else:
             return form( url_for(controller='workflow', action='rename', id=trans.security.encode_id(stored.id) ),
                          "Rename workflow",
@@ -543,7 +499,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         if (save_as_name):
             new_stored.name = '%s' % save_as_name
         else:
-            new_stored.name = "Copy of '%s'" % stored.name
+            new_stored.name = "Copy of %s" % stored.name
         new_stored.latest_workflow = stored.latest_workflow
         # Copy annotation.
         annotation_obj = self.get_item_annotation_obj( trans.sa_session, stored.user, stored )
@@ -551,15 +507,17 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
             self.add_item_annotation( trans.sa_session, trans.get_user(), new_stored, annotation_obj.annotation )
         new_stored.copy_tags_from(trans.user, stored)
         if not owner:
-            new_stored.name += " shared by '%s'" % stored.user.email
+            new_stored.name += " shared by %s" % stored.user.email
         new_stored.user = user
         # Persist
         session = trans.sa_session
         session.add( new_stored )
         session.flush()
         # Display the management page
-        trans.set_message( 'Created new workflow with name "%s"' % escape( new_stored.name ) )
-        return self.list( trans )
+        message = 'Created new workflow with name: %s' % escape( new_stored.name )
+        trans.set_message( message )
+        return_url = url_for( '/' ) + 'workflow?status=done&message=%s' % escape( message )
+        trans.response.send_redirect( return_url )
 
     @web.expose
     @web.require_login( "create workflows" )
@@ -652,8 +610,9 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         trans.sa_session.add( stored )
         trans.sa_session.flush()
         # Display the management page
-        trans.set_message( "Workflow '%s' deleted" % escape( stored.name ) )
-        return self.list( trans )
+        message = "Workflow deleted: %s" % escape( stored.name )
+        trans.set_message( message )
+        return trans.response.send_redirect( url_for( '/' ) + 'workflow?status=done&message=%s' % escape( message ) )
 
     @web.expose
     @web.require_login( "edit workflows" )

static/maps/mvc/workflow/workflow.js.map

@@ -0,0 +1 @@
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static/scripts/mvc/workflow/workflow.js

@@ -0,0 +1,2 @@
+define([],function(){var a=Backbone.View.extend({initialize:function(){this.setElement("<div/>"),this.render()},render:function(){var a=this,b=3;$.getJSON(Galaxy.root+"api/workflows/",function(c){var d=null;a.$el.empty().append(a._templateHeader()),a.build_messages(a),d=a.$el.find(".user-workflows"),d.append(a._templateActionButtons()),c.length>0?(d.append(a._templateWorkflowTable(a,c)),a.adjust_actiondropdown(d),_.each(c,function(b){a.confirm_delete(a,b)}),a.search_workflow(a,a.$el.find(".search-wf"),a.$el.find(".workflow-search tr"),b)):d.append(a._templateNoWorkflow())})},build_messages:function(a){var b=a.$el.find(".response-message"),c=a.get_querystring("status"),d=a.get_querystring("message");d&&null!==d&&""!==d?(b.addClass(c+"message"),b.html("<p>"+d+"</p>")):b.html("")},confirm_delete:function(a,b){var c=a.$el.find(".link-confirm-"+b.id),d=a.$el.find(".link-confirm-shared-"+b.id);c.click(function(){return confirm("Are you sure you want to delete workflow '"+b.name+"'?")}),d.click(function(){return confirm("Are you sure you want to remove the shared workflow '"+b.name+"'?")})},search_workflow:function(a,b,c,d){b.on("keyup",function(){var a=$(this).val();if(a.length>=d){var b=new RegExp(a,"i");c.hide(),c.filter(function(){return b.test($(this).text())}).show()}else c.show()})},get_querystring:function(a){return decodeURIComponent(window.location.search.replace(new RegExp("^(?:.*[&\\?]"+encodeURIComponent(a).replace(/[\.\+\*]/g,"\\$&")+"(?:\\=([^&]*))?)?.*$","i"),"$1"))},adjust_actiondropdown:function(a){a.on("show.bs.dropdown",function(){a.css("overflow","inherit")}),a.on("hide.bs.dropdown",function(){a.css("overflow","auto")})},_templateNoWorkflow:function(){return'<div class="wf-nodata"> You have no workflows. </div>'},_templateActionButtons:function(){return'<ul class="manage-table-actions"><li><input class="search-wf form-control" type="text" autocomplete="off" placeholder="search for workflow..."></li><li><a class="action-button fa fa-plus wf-action" id="new-workflow" title="Create new workflow" href="'+Galaxy.root+'workflow/create"></a></li><li><a class="action-button fa fa-upload wf-action" id="import-workflow" title="Upload or import workflow" href="'+Galaxy.root+'workflow/import_workflow"></a></li></ul>'},_templateWorkflowTable:function(a,b){var c="",d="";return c+='<table class="table colored"><thead><tr class="header"><th class="wf-td">Name</th><th class="wf-td">Owner</th><th class="wf-td"># of Steps</th><th class="wf-td">Published</th></tr></thead>',_.each(b,function(b){d=d+'<tr><td class="wf-td wf-dpd"><div class="dropdown"><button class="menubutton" type="button" data-toggle="dropdown">'+_.escape(b.name)+'<span class="caret"></span></button>'+a._templateActions(b)+"</div></td><td>"+(b.owner===Galaxy.user.attributes.username?"You":b.owner)+'</td><td class="wf-td">'+b.number_of_steps+'</td><td class="wf-td">'+(b.published?"Yes":"No")+"</td></tr>"}),c+'<tbody class="workflow-search">'+d+"</tbody></table>"},_templateActions:function(a){return a.owner===Galaxy.user.attributes.username?'<ul class="dropdown-menu action-dpd"><li><a href="'+Galaxy.root+"workflow/editor?id="+a.id+'">Edit</a></li><li><a href="'+Galaxy.root+"workflow/run?id="+a.id+'" target="galaxy_main">Run</a></li><li><a href="'+Galaxy.root+"workflow/sharing?id="+a.id+'">Share or Download</a></li><li><a href="'+Galaxy.root+"workflow/copy?id="+a.id+'">Copy</a></li><li><a href="'+Galaxy.root+"workflow/rename?id="+a.id+'">Rename</a></li><li><a href="'+Galaxy.root+"workflow/display_by_id?id="+a.id+'">View</a></li><li><a class="link-confirm-'+a.id+'" href="'+Galaxy.root+"workflow/delete?id="+a.id+'">Delete</a></li></ul>':'<ul class="dropdown-menu action-dpd"><li><a href="'+Galaxy.root+"workflow/display_by_username_and_slug?username="+a.owner+"&slug="+a.slug+'">View</a></li><li><a href="'+Galaxy.root+"workflow/run?id="+a.id+'" target="galaxy_main">Run</a></li><li><a href="'+Galaxy.root+"workflow/copy?id="+a.id+'">Copy</a></li><li><a class="link-confirm-shared-'+a.id+'" href="'+Galaxy.root+"workflow/sharing?unshare_me=True&id="+a.id+'">Remove</a></li></ul>'},_templateHeader:function(){return'<div class="page-container"><div class="user-workflows wf"><div class="response-message"></div><h2>Your workflows</h2></div><div class="other-options wf"><h2>Other options</h2><a class="action-button fa fa-cog wf-action" href="'+Galaxy.root+'workflow/configure_menu" title="Configure your workflow menu"><span>Configure your workflow menu</span></a></div></div>'}});return{View:a}});
+//# sourceMappingURL=../../../maps/mvc/workflow/workflow.js.map

templates/webapps/galaxy/workflow/list.mako

@@ -1,122 +0,0 @@
-<%inherit file="/webapps/galaxy/base_panels.mako"/>
-
-<%def name="init()">
-<%
-    self.has_left_panel=False
-    self.has_right_panel=False
-    self.active_view="workflow"
-    self.message_box_visible=False
-%>
-</%def>
-
-<%def name="title()">Workflow home</%def>
-
-<%def name="center_panel()">
-    <div style="overflow: auto; height: 100%;">
-        <div class="page-container" style="padding: 10px;">
-            %if message:
-                <%
-                    try:
-                        status
-                    except:
-                        status = "done"
-                %>
-                <p />
-                <div class="${status}message">
-                    ${h.to_unicode( message )}
-                </div>
-            %endif
-
-            <h2>Your workflows</h2>
-
-            <ul class="manage-table-actions">
-                <li>
-                    <a class="action-button" id="new-workflow" href="${h.url_for( controller='workflow', action='create' )}">
-                        <img src="${h.url_for('/static/images/silk/add.png')}" />
-                        <span>Create new workflow</span>
-                    </a>
-                </li>
-                <li>
-                    <a class="action-button" id="import-workflow" href="${h.url_for( controller='workflow', action='import_workflow' )}">
-                        <img src="${h.url_for('/static/images/fugue/arrow-090.png')}" />
-                        <span>Upload or import workflow</span>
-                    </a>
-                </li>
-            </ul>
-
-            %if workflows:
-                <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" style="width:100%;">
-                    <tr class="header">
-                        <th>Name</th>
-                        <th># of Steps</th>
-                        ## <th>Last Updated</th>
-                        <th></th>
-                    </tr>
-                    %for i, workflow in enumerate( workflows ):
-                        <tr>
-                            <td>
-                                <div class="menubutton" style="float: left;" id="wf-${i}-popup">
-                                ${h.to_unicode( workflow.name ) | h}
-                                </div>
-                            </td>
-                            <td>${len(workflow.latest_workflow.steps)}</td>
-                            ## <td>${str(workflow.update_time)[:19]}</td>
-                            <td>
-                                <div popupmenu="wf-${i}-popup">
-                                <a class="action-button" href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id( workflow.id ) )}" target="_parent">Edit</a>
-                                <a class="action-button" href="${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id( workflow.id ) )}" target="_parent">Run</a>
-                                <a class="action-button" href="${h.url_for( controller='workflow', action='sharing', id=trans.security.encode_id( workflow.id ) )}">Share or Download</a>
-                                <a class="action-button" href="${h.url_for( controller='workflow', action='copy', id=trans.security.encode_id( workflow.id ) )}">Copy</a>
-                                <a class="action-button" href="${h.url_for( controller='workflow', action='rename', id=trans.security.encode_id( workflow.id ) )}">Rename</a>
-                                <a class="action-button" href="${h.url_for( controller='workflow', action='display_by_id', id=trans.security.encode_id( workflow.id ) )}" target="_top">View</a>
-                                <a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='delete', id=trans.security.encode_id( workflow.id ) )}">Delete</a>
-                                </div>
-                            </td>
-                        </tr>
-                    %endfor
-                </table>
-            %else:
-                You have no workflows.
-            %endif
-
-            <h2>Workflows shared with you by others</h2>
-
-            %if shared_by_others:
-                <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%">
-                    <tr class="header">
-                        <th>Name</th>
-                        <th>Owner</th>
-                        <th># of Steps</th>
-                        <th></th>
-                    </tr>
-                    %for i, association in enumerate( shared_by_others ):
-                        <% workflow = association.stored_workflow %>
-                        <tr>
-                            <td>
-                                <a class="menubutton" id="shared-${i}-popup" href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${h.to_unicode( workflow.name ) | h}</a>
-                            </td>
-                            <td>${workflow.user.email}</td>
-                            <td>${len(workflow.latest_workflow.steps)}</td>
-                            <td>
-                                <div popupmenu="shared-${i}-popup">
-                                    <a class="action-button" href="${h.url_for( controller='workflow', action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug )}" target="_top">View</a>
-                                    <a class="action-button" href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">Run</a>
-                                    <a class="action-button" href="${h.url_for( controller='workflow', action='copy', id=trans.security.encode_id( workflow.id ) )}">Copy</a>
-                                    <a class="action-button" confirm="Are you sure you want to remove the shared workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='sharing', unshare_me=True, id=trans.security.encode_id( workflow.id ))}">Remove</a>
-                                </div>
-                            </td>
-                        </tr>
-                    %endfor
-                </table>
-            %else:
-                No workflows have been shared with you.
-            %endif
-
-            <h2>Other options</h2>
-
-            <a class="action-button" href="${h.url_for( controller='workflow', action='configure_menu' )}">
-                <span>Configure your workflow menu</span>
-            </a>
-        </div>
-    </div>
-</%def>

templates/webapps/galaxy/workflow/list_for_run.mako

@@ -1,66 +0,0 @@
-<%inherit file="/base.mako"/>
-
-<%def name="title()">Workflow home</%def>
-
-<h2>Your workflows</h2>
-
-<ul class="manage-table-actions">
-    <li>
-        <a class="action-button" href="${h.url_for( controller='workflow', action='index' )}" target="_parent">
-            <span>Switch to workflow management view</span>
-        </a>
-    </li>
-</ul>
-  
-%if workflows:
-    <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
-        <tr class="header">
-            <th>Name</th>
-            <th># of Steps</th>
-            ## <th>Last Updated</th>
-            <th></th>
-        </tr>
-        %for i, workflow in enumerate( workflows ):
-            <tr>
-                <td>
-                    <a href="${h.url_for(controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${h.to_unicode( workflow.name ) | h}</a>
-                    <a id="wf-${i}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
-                </td>
-                <td>${len(workflow.latest_workflow.steps)}</td>
-                ## <td>${str(workflow.update_time)[:19]}</td>
-            </tr>    
-        %endfor
-    </table>
-%else:
-
-    You have no workflows.
-
-%endif
-
-<h2>Workflows shared with you by others</h2>
-
-%if shared_by_others:
-    <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%">
-        <tr class="header">
-            <th>Name</th>
-            <th>Owner</th>
-            <th># of Steps</th>
-            <th></th>
-        </tr>
-        %for i, association in enumerate( shared_by_others ):
-            <% workflow = association.stored_workflow %>
-            <tr>
-                <td>
-                    <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name | h}</a>
-                    <a id="shared-${i}-popup" class="popup-arrow" style="display: none;">&#9660;</a>
-                </td>
-                <td>${workflow.user.email | h}</td>
-                <td>${len(workflow.latest_workflow.steps)}</td>
-            </tr>    
-        %endfor
-    </table>
-%else:
-
-    No workflows have been shared with you.
-
-%endif

test/galaxy_selenium/navigates_galaxy.py

@@ -394,17 +394,16 @@ class NavigatesGalaxy(HasDriver):
         self.click_masthead_workflow()
 
     def workflow_index_table_elements(self):
-        self.wait_for_selector_visible(".manage-table tbody")
-        table_elements = self.driver.find_elements_by_css_selector(".manage-table tbody > tr")
-        # drop header
-        return table_elements[1:]
+        self.wait_for_selector_visible("tbody.workflow-search")
+        table_elements = self.driver.find_elements_by_css_selector("tbody.workflow-search > tr")
+        return table_elements
 
     def workflow_index_click_option(self, option_title, workflow_index=0):
         table_elements = self.workflow_index_table_elements()
         workflow_row = table_elements[workflow_index]
         workflow_button = workflow_row.find_element_by_css_selector(".menubutton")
         workflow_button.click()
-        menu_element = self.wait_for_selector_visible(".popmenu-wrapper .dropdown-menu")
+        menu_element = self.wait_for_selector_visible("ul.action-dpd")
         menu_options = menu_element.find_elements_by_css_selector("li a")
         found_option = False
         for menu_option in menu_options:

test/selenium_tests/test_workflow_management.py

@@ -45,7 +45,8 @@ class WorkflowManagementTestCase(SeleniumTestCase):
         assert 'CoolNewName' in renamed_workflow_button.text, renamed_workflow_button.text
 
     def _workflow_import_from_url(self):
-        self.click_selector(self.test_data["selectors"]["workflows"]["import_button"])
+        element = self.wait_for_selector_clickable(self.test_data["selectors"]["workflows"]["import_button"])
+        element.click()
         url = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test/base/data/test_workflow_1.ga"
         form_element = self.driver.find_element_by_css_selector("#center form")
         url_element = form_element.find_element_by_css_selector("input[type='text']")