Merge pull request #4353 from bgruening/workflow_configure_menu

Merging configure menu with main workflow view
2026-09-24 16:30:27 +08:00 · 2017-08-02 15:51:04 -04:00
parent f41d2ba8ec 324ec35c86
commit 14360d6737
16 changed files with 101 additions and 236 deletions
@@ -13,7 +13,6 @@ var jQuery = require( 'jquery' ),
    GridShared = require( 'mvc/grid/grid-shared' ),
    Workflows = require( 'mvc/workflow/workflow' ),
    HistoryList = require( 'mvc/history/history-list' ),
-    WorkflowsConfigureMenu = require( 'mvc/workflow/workflow-configure-menu' ),
    ToolFormComposite = require( 'mvc/tool/tool-form-composite' ),
    Utils = require( 'utils/utils' ),
    Ui = require( 'mvc/ui/ui-misc' ),
@@ -93,7 +92,6 @@ window.app = function app( options, bootstrapped ){
            '(/)workflows/list_published(/)' : 'show_workflows_published',
            '(/)histories(/)(:action_id)' : 'show_histories',
            '(/)datasets(/)list(/)' : 'show_datasets',
-            '(/)workflow/configure_menu(/)' : 'show_configure_menu',
            '(/)workflow/import_workflow' : 'show_import_workflow',
            '(/)custom_builds' : 'show_custom_builds',
            '(/)datasets/edit': 'show_dataset_edit_attributes'
@@ -102,8 +100,7 @@ window.app = function app( options, bootstrapped ){
        require_login: [
            'show_user',
            'show_user_form',
-            'show_workflows',
-            'show_configure_menu'
+            'show_workflows'
        ],

        loginRequired: function() {
@@ -162,10 +159,6 @@ window.app = function app( options, bootstrapped ){
            this.page.display( new Workflows.ImportWorkflowView() );
        },

-        show_configure_menu : function(){
-            this.page.display( new WorkflowsConfigureMenu.View() );
-        },
-
        show_custom_builds : function() {
            var self = this;
            var historyPanel = this.page.historyPanel.historyView;
@@ -65,14 +65,6 @@ define( [ 'mvc/form/form-view', 'mvc/ui/ui-misc' ], function( Form, Ui ) {
                        window.location.href = Galaxy.root + 'custom_builds';
                    }
                },
-                'configure_menu': {
-                    title           : 'Configure workflow menu',
-                    description     : 'Configure your workflow items which appear in the Tool panel.',
-                    icon            : 'fa-cog',
-                    onclick         : function() {
-                        window.location.href = Galaxy.root + 'workflow/configure_menu';
-                    }
-                },
                'logout': {
                    title           : 'Sign out',
                    description     : 'Click here to sign out of all sessions.',
@@ -127,7 +119,6 @@ define( [ 'mvc/form/form-view', 'mvc/ui/ui-misc' ], function( Form, Ui ) {
                if( config.enable_openid && !config.use_remote_user ) {
                    self._addLink( 'openids' );
                }
-                self._addLink( 'configure_menu' );
                self._addLink( 'logout' );
                self.$preferences.append( self._templateFooter( data ) );
                self.$el.empty().append( self.$preferences );
@@ -1,153 +0,0 @@
-/** Configure Workflow Menu View */
-define( [], function() {
-    var View = Backbone.View.extend({
-
-        initialize: function( options ) {
-            this.setElement( '<div/>' );
-            this.render();
-        },
-
-        render: function() {
-            var self = this;
-            $.getJSON( Galaxy.root + 'api/workflows/menu/', function( response ) {
-                var workflows = response.workflows,
-                    ids_in_menu = response.ids_in_menu,
-                    $el_config_worflow = null;
-
-                // Add configure workflow header
-                self.$el.empty().append( self._templateConfigWorkflowHeader() );
-                $el_config_worflow = self.$el.find( '.configure-workflows' );
-                $el_config_worflow.append( self._templateActionButtons() );
-                if( workflows.length > 0 ) {
-                    $el_config_worflow.append( self._templateConfigureWorkflow( self, workflows, ids_in_menu ) );
-                    self.save_workflow_menu( self );
-                    self.make_checked( self, ids_in_menu );
-                    self.register_check_uncheck_all( self );
-                }
-                else {
-                    $el_config_worflow.append( self._templateNoWorkflow() );
-                }
-            });
-        },
-
-        /** Register check and uncheck all callbacks*/
-        register_check_uncheck_all: function( self ) {
-            var $el_check_all = self.$el.find( '.check-all-wf' ),
-                $el_uncheck_all = self.$el.find( '.uncheck-all-wf' );
-            
-            $el_check_all.click(function( e ) {
-                self.check_uncheck_all( self, true );
-            });
-            $el_uncheck_all.click(function( e ) {
-                self.check_uncheck_all( self, false );
-            });
-        },
-
-        /** Check or uncheck all workflows */
-        check_uncheck_all: function( self, checked ) {
-            $.each(self.$el.find( '.wf-config-item' ), function() {
-                var wf_checkbox = $( this )[0];
-                wf_checkbox.checked = checked;
-            });
-        },
-
-        /** Make the worflows as checked if present in the menu */
-        make_checked: function( self, ids_in_menu ) {
-            $.each(self.$el.find( '.wf-config-item' ), function() {
-                var wf_checkbox = $( this )[0];
-                _.each( ids_in_menu, function( id ) {
-                    if ( parseInt( wf_checkbox.value ) === id ) {
-                        wf_checkbox.checked = true;
-                    }
-                });
-            });
-        },
-
-        /** Save the changes for workflow menu */
-        save_workflow_menu: function( self ) {
-            var $el_save_workflow_menu = self.$el.find( '.wf-save-menu' );
-            $el_save_workflow_menu.click( function( e ) {
-                var ids = [];
-                $.each(self.$el.find( '.wf-config-item' ), function() {
-                    var wf_checkbox = $( this )[0];
-                    if( wf_checkbox.checked || wf_checkbox.checked === 'true' ) {
-                        ids.push( parseInt( wf_checkbox.value ) );
-                    }
-                });
-                $.ajax({
-                    type: 'PUT',
-                    url: Galaxy.root + 'api/workflows/menu/',
-                    data: JSON.stringify( { 'workflow_ids': ids } ),
-                    contentType : 'application/json'
-                }).done( function( response ) {
-                    window.location = Galaxy.root + 'user';
-                });
-            });
-        },
-
-        /** Template for actions buttons */
-        _templateActionButtons: function() {
-           return '<ul class="manage-table-actions">' +
-                '<li>' +
-                    '<a class="fa fa-check-square-o wf-action check-all-wf" title="Select all workflows" href="#">' +
-                    '</a>' +
-                '</li>' +
-                '<li>' +
-                    '<a class="fa fa-square-o wf-action uncheck-all-wf" title="Unselect all workflows" href="#">' +
-                    '</a>' +
-                '</li>' +
-            '</ul>';
-        },
-
-        /** Template for configure workflow table */
-        _templateConfigureWorkflow: function( self, workflows, ids_in_menu ) {
-            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">Show in menu</th>' +
-                    '</tr></thead>';
-            _.each( workflows, function( wf ) {
-                trHtml = trHtml + '<tr>' +
-                    '<td class="wf-td">' + _.escape( wf.name ) +'</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">' + self._templateInputCheckbox( self, wf, ids_in_menu ) + '</td>' +
-                '</tr>';
-            });
-            tableHtml = tableHtml + '<tbody class="workflow-config-menu">' + trHtml + '</tbody></table>';
-            tableHtml = tableHtml + '<a class="action-button wf-save-menu wf-action fa fa-floppy-o" href="#" title="Save">' +
-                                        '<span>Save</span>' +
-                                    '</a>' +
-                                    '<a class="action-button wf-back wf-action fa fa-arrow-left" href="'+ Galaxy.root +'user" title="Back to User Preferences">' +
-                                        '<span>Back to User Preferences</span>' +
-                                    '</a>';
-            return tableHtml;
-        },
-
-       /** Template for no workflow */
-        _templateNoWorkflow: function() {
-            return '<div class="wf-nodata"> You do not have any accessible workflows. </div>';
-        },
-
-        /** Template for checkboxes */
-        _templateInputCheckbox: function( self, wf ) {
-            return '<input type="checkbox" class="wf-config-item" name="workflow_ids" value="'+ wf.id +'" />';
-        },
-
-        /** Template for main config workflow menu */
-        _templateConfigWorkflowHeader: function() {
-            return '<div class="page-container">' +
-                       '<div class="configure-workflows wf">' +
-                           '<h2>Configure workflow menu</h2>' +
-                       '</div>'+
-                   '</div>';
-        }
-    });
-    
-    return {
-        View : View
-    };
-});
@@ -1,19 +1,17 @@
 /** Workflow view */
-define( [ 'utils/utils' ], function( Utils ) {
+define( [ 'utils/utils', 'mvc/ui/ui-misc' ], function( Utils, Ui ) {

    /** Build messages after user action */
-    function build_messages( self ) {
-        var $el_message = self.$el.find( '.response-message' ),
-            status = Utils.getQueryString( 'status' ),
-            message = Utils.getQueryString( 'message' );
-
-        if( message && message !== null && message !== "" ) {
-            $el_message.addClass( status + 'message' );
-            $el_message.html( '<p>' + _.escape( message ) + '</p>' );
-        }
-        else {
-            $el_message.html("");
-        }
+    function build_messages() {
+        var $el_message = this.$( '.response-message' ),
+            response = {};
+        response = {
+            'status': Utils.getQueryString( 'status' ),
+            'message': _.escape( Utils.getQueryString( 'message' ) ),
+            'persistent': true,
+            'cls': Utils.getQueryString( 'status' ) + 'message'
+        };
+        $el_message.empty().html( new Ui.Message( response ).$el );
    }
 
    /** View of the main workflow list page */
@@ -32,8 +30,8 @@ define( [ 'utils/utils' ], function( Utils ) {
                // Add workflow header
                self.$el.empty().append( self._templateHeader() );
                // Add user actions message if any
-                build_messages( self );
-                $el_workflow = self.$el.find( '.user-workflows' );
+                build_messages();
+                $el_workflow = self.$( '.user-workflows' );
                // Add the actions buttons
                $el_workflow.append( self._templateActionButtons() );
                if( workflows.length > 0) {
@@ -41,10 +39,11 @@ define( [ 'utils/utils' ], function( Utils ) {
                    self.adjust_actiondropdown( $el_workflow );
                    // Register delete and run workflow events
                    _.each( workflows, function( wf ) {
-                        self.confirm_delete( self, wf );
+                        self.confirm_delete( wf );
                    });
+                    self.register_show_tool_menu();
                    // Register search workflow event
-                    self.search_workflow( self, self.$el.find( '.search-wf' ), self.$el.find( '.workflow-search tr' ), min_query_length );
+                    self.search_workflow( self.$( '.search-wf' ), self.$( '.workflow-search tr' ), min_query_length );
                }
                else {
                    $el_workflow.append( self._templateNoWorkflow() );
@@ -52,10 +51,34 @@ define( [ 'utils/utils' ], function( Utils ) {
            });
        },

+        // Save the workflow as an item in Tool panel
+        register_show_tool_menu: function() {
+            var $el_checkboxes = this.$( '.show-in-tool-panel' );
+            $el_checkboxes.on( 'click', function( e ) {
+                var ids = [];
+                // Look for all the checked checkboxes
+                for( var item = 0; item < $el_checkboxes.length; item++ ) {
+                    var checkbox = $el_checkboxes[ item ];
+                    if( checkbox.checked ) {
+                        ids.push( checkbox.value );
+                    }
+                }
+                // Save all the checked workflows
+                $.ajax({
+                    type: 'PUT',
+                    url: Galaxy.root + 'api/workflows/menu/',
+                    data: JSON.stringify( { 'workflow_ids': ids } ),
+                    contentType : 'application/json'
+                }).done( function( response ) {
+                    window.location = Galaxy.root + 'workflow';
+                });
+            });
+        },
+
        /** 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 );
+        confirm_delete: function( workflow ) {
+            var $el_wf_link = this.$( '.link-confirm-' + workflow.id ),
+                $el_shared_wf_link = this.$( '.link-confirm-shared-' + workflow.id );
            $el_wf_link.click( function() {
                return confirm( "Are you sure you want to delete workflow '" + workflow.name + "'?" );
            });
@@ -65,7 +88,7 @@ define( [ 'utils/utils' ], function( Utils ) {
        },

        /** Implement client side workflow search/filtering */
-        search_workflow: function( self, $el_searchinput, $el_tabletr, min_querylen ) {
+        search_workflow: function( $el_searchinput, $el_tabletr, min_querylen ) {
            $el_searchinput.on( 'keyup', function () {
                var query = $( this ).val();
                // Filter when query is at least 3 characters
@@ -128,8 +151,10 @@ define( [ 'utils/utils' ], function( Utils ) {
                        '<th>Owner</th>' +
                        '<th># of Steps</th>' +
                        '<th>Published</th>' +
+                        '<th>Show in tools panel</th>' +
                    '</tr></thead>';
            _.each( workflows, function( wf ) {
+                var checkbox_html = '<input type="checkbox" class="show-in-tool-panel" '+ ( wf.show_in_tool_panel ? 'checked="' + wf.show_in_tool_panel + '"' : "" ) +' value="' + wf.id + '">';
                trHtml = trHtml + '<tr>' +
                             '<td>' +
                                 '<div class="dropdown">' +
@@ -142,6 +167,7 @@ define( [ 'utils/utils' ], function( Utils ) {
                              '<td>' + ( wf.owner === Galaxy.user.attributes.username ? "You" : wf.owner ) +'</td>' +
                              '<td>' + wf.number_of_steps + '</td>' +
                              '<td>' + ( wf.published ? "Yes" : "No" ) + '</td>' +
+                              '<td>'+ checkbox_html +'</td>' +
                         '</tr>';
            });
            return tableHtml + '<tbody class="workflow-search">' + trHtml + '</tbody></table>';
@@ -192,12 +218,12 @@ define( [ 'utils/utils' ], function( Utils ) {
        render: function() {
            var self = this;
            $.getJSON( Galaxy.root + 'workflow/upload_import_workflow', function( options ) {
-                self.$el.empty().append( self._mainTemplate( self, options ) );
+                self.$el.empty().append( self._mainTemplate( options ) );
            });
        },

        /** Template for the import workflow page */
-        _mainTemplate: function( self, options ) {
+        _mainTemplate: function( options ) {
            return "<div class='toolForm'>" +
                       "<div class='toolFormTitle'>Import Galaxy workflow</div>" +
                        "<div class='toolFormBody'>" +
@@ -1812,6 +1812,6 @@ div.toolTitleNoSection
    margin-left: 0.5%;
 }

-.other-options, .configure-workflows {
+.other-options {
    margin-bottom: 2%;
 }
@@ -54,7 +54,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
        """
        GET /api/workflows
        """
-        return self.get_workflows_list( trans, False, kwd )
+        return self.get_workflows_list( trans, kwd )

    @expose_api
    def get_workflow_menu( self, trans, **kwd ):
@@ -66,7 +66,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
        ids_in_menu = [ x.stored_workflow_id for x in user.stored_workflow_menu_entries ]
        return {
            'ids_in_menu': ids_in_menu,
-            'workflows': self.get_workflows_list( trans, True, kwd )
+            'workflows': self.get_workflows_list( trans, kwd )
        }

    @expose_api
@@ -82,6 +82,10 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
            workflow_ids = []
        elif type( workflow_ids ) != list:
            workflow_ids = [ workflow_ids ]
+        workflow_ids_decoded = []
+        # Decode the encoded workflow ids
+        for ids in workflow_ids:
+            workflow_ids_decoded.append( trans.security.decode_id( ids ) )
        sess = trans.sa_session
        # This explicit remove seems like a hack, need to figure out
        # how to make the association do it automatically.
@@ -91,20 +95,20 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
        q = sess.query( model.StoredWorkflow )
        # To ensure id list is unique
        seen_workflow_ids = set()
-        for id in workflow_ids:
-            if id in seen_workflow_ids:
+        for wf_id in workflow_ids_decoded:
+            if wf_id in seen_workflow_ids:
                continue
            else:
-                seen_workflow_ids.add( id )
+                seen_workflow_ids.add( wf_id )
            m = model.StoredWorkflowMenuEntry()
-            m.stored_workflow = q.get( id )
+            m.stored_workflow = q.get( wf_id )
            user.stored_workflow_menu_entries.append( m )
        sess.flush()
        message = "Menu updated."
        trans.set_message( message )
        return { 'message': message, 'status': 'done' }

-    def get_workflows_list( self, trans, for_menu, kwd ):
+    def get_workflows_list( self, trans, kwd ):
        """
        Displays a collection of workflows.

@@ -117,33 +121,39 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
        missing_tools = util.string_as_bool( kwd.get( 'missing_tools', 'False' ) )
        rval = []
        filter1 = ( trans.app.model.StoredWorkflow.user == trans.user )
+        user = trans.get_user()
        if show_published:
            filter1 = or_( filter1, ( trans.app.model.StoredWorkflow.published == true() ) )
        for wf in trans.sa_session.query( trans.app.model.StoredWorkflow ).filter(
                filter1, trans.app.model.StoredWorkflow.table.c.deleted == false() ).order_by(
                desc( trans.app.model.StoredWorkflow.table.c.update_time ) ).all():
-            if for_menu:
-                item = wf.to_dict()
-            else:
-                item = wf.to_dict( value_mapper={ 'id': trans.security.encode_id } )
-                encoded_id = trans.security.encode_id(wf.id)
-                item['url'] = url_for('workflow', id=encoded_id)
+
+            item = wf.to_dict( value_mapper={ 'id': trans.security.encode_id } )
+            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 )
+            item['show_in_tool_panel'] = False
+            for x in user.stored_workflow_menu_entries:
+                if x.stored_workflow_id == wf.id:
+                    item['show_in_tool_panel'] = True
+                    break
            rval.append(item)
        for wf_sa in trans.sa_session.query( trans.app.model.StoredWorkflowUserShareAssociation ).filter_by(
                user=trans.user ).join( 'stored_workflow' ).filter(
                trans.app.model.StoredWorkflow.deleted == false() ).order_by(
                desc( trans.app.model.StoredWorkflow.update_time ) ).all():
-            if for_menu:
-                item = wf_sa.stored_workflow.to_dict()
-            else:
-                item = wf_sa.stored_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } )
-                encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
-                item['url'] = url_for( 'workflow', id=encoded_id )
-                item['slug'] = wf_sa.stored_workflow.slug
+            item = wf_sa.stored_workflow.to_dict( value_mapper={ 'id': trans.security.encode_id } )
+            encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
+            item['url'] = url_for( 'workflow', id=encoded_id )
+            item['slug'] = wf_sa.stored_workflow.slug
            item['owner'] = wf_sa.stored_workflow.user.username
            item['number_of_steps'] = len( wf_sa.stored_workflow.latest_workflow.steps )
+            item['show_in_tool_panel'] = False
+            for x in user.stored_workflow_menu_entries:
+                if x.stored_workflow_id == wf_sa.id:
+                    item['show_in_tool_panel'] = True
+                    break
            rval.append(item)
        if missing_tools:
            workflows_missing_tools = []
@@ -120,7 +120,6 @@ def paste_app_factory( global_conf, **kwargs ):
    webapp.add_client_route( '/datasets/edit' )
    webapp.add_client_route( '/workflow/run' )
    webapp.add_client_route( '/workflow/import_workflow' )
-    webapp.add_client_route( '/workflow/configure_menu' )
    webapp.add_client_route( '/custom_builds' )

    # ==== Done
@@ -1 +1 @@
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