mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merging with dev
This commit is contained in:
anuprulez
@@ -12,7 +12,11 @@ var jQuery = require( 'jquery' ),
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GridView = require( 'mvc/grid/grid-view' ),
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PageList = require( 'mvc/page/page-list' ),
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Workflows = require( 'mvc/workflow/workflow' ),
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WorkflowsConfigureMenu = require( 'mvc/workflow/workflow-configure-menu' );
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HistoryList = require( 'mvc/history/history-list' ),
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WorkflowsConfigureMenu = require( 'mvc/workflow/workflow-configure-menu' ),
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ToolFormComposite = require( 'mvc/tool/tool-form-composite' ),
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Utils = require( 'utils/utils' ),
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Ui = require( 'mvc/ui/ui-misc' );
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/** define the 'Analyze Data'/analysis/main/home page for Galaxy
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* * has a masthead
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@@ -82,9 +86,12 @@ window.app = function app( options, bootstrapped ){
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'(/)user(/)' : 'show_user',
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'(/)user(/)(:form_id)' : 'show_user_form',
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'(/)workflow(/)' : 'show_workflows',
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'(/)workflow/run(/)' : 'show_run',
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'(/)pages(/)(:action_id)' : 'show_pages',
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'(/)datasets(/)(:action_id)' : 'show_datasets',
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'(/)histories(/)list(/)' : 'show_histories',
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'(/)datasets(/)list(/)' : 'show_datasets',
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'(/)workflow/configure_menu(/)' : 'show_configure_menu',
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'(/)workflow/import_workflow' : 'show_import_workflow',
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'(/)custom_builds' : 'show_custom_builds'
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},
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@@ -119,6 +126,10 @@ window.app = function app( options, bootstrapped ){
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this.page.display( new UserPreferences.Forms( { form_id: form_id, user_id: Galaxy.params.id } ) );
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},
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show_histories : function() {
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this.page.display( new HistoryList.View() );
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},
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show_datasets : function() {
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this.page.display( new GridView( { url_base: Galaxy.root + 'dataset/list', dict_format: true } ) );
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},
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@@ -135,6 +146,14 @@ window.app = function app( options, bootstrapped ){
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this.page.display( new Workflows.View() );
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},
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show_run : function() {
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this._loadWorkflow();
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},
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show_import_workflow : function() {
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this.page.display( new Workflows.ImportWorkflowView() );
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},
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show_configure_menu : function(){
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this.page.display( new WorkflowsConfigureMenu.View() );
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},
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@@ -163,7 +182,7 @@ window.app = function app( options, bootstrapped ){
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} else {
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// show the workflow run form
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if( params.workflow_id ){
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this._loadCenterIframe( 'workflow/run?id=' + params.workflow_id );
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this._loadWorkflow();
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// load the center iframe with controller.action: galaxy.org/?m_c=history&m_a=list -> history/list
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} else if( params.m_c ){
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this._loadCenterIframe( params.m_c + '/' + params.m_a );
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@@ -188,6 +207,22 @@ window.app = function app( options, bootstrapped ){
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this.page.$( '#galaxy_main' ).prop( 'src', url );
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},
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/** load workflow by its url in run mode */
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_loadWorkflow: function() {
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var self = this;
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Utils.get({
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url: Galaxy.root + 'api/workflows/' + Utils.getQueryString( 'id' ) + '/download',
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data: { 'style': 'run' },
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success: function( response ) {
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self.page.display( new ToolFormComposite.View( response ) );
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},
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error: function( response ) {
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var error_msg = "Error occurred while loading the resource.",
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options = { 'message': error_msg, 'status': 'error', 'persistent': true, 'cls': 'errormessage' };
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self.page.display( new Ui.Message( options ) );
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}
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});
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}
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});
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// render and start the router
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@@ -1,6 +1,7 @@
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var Tools = require( 'mvc/tool/tools' ),
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Upload = require( 'mvc/upload/upload-view' ),
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_l = require( 'utils/localization' );
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_l = require( 'utils/localization' ),
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ToolForm = require( 'mvc/tool/tool-form-composite' );
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var ToolPanel = Backbone.View.extend({
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initialize: function( page, options ) {
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@@ -58,7 +59,7 @@ var ToolPanel = Backbone.View.extend({
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href : 'workflow'
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}));
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_.each( this.stored_workflow_menu_entries, function( menu_entry ){
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self.$( '#internal-workflows' ).append( self._templateTool({
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self.$( '#internal-workflows' ).append( self._templateWorkflowLink({
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title : menu_entry.stored_workflow.name,
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href : 'workflow/run?id=' + menu_entry.encoded_stored_workflow_id
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}));
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@@ -84,6 +85,15 @@ var ToolPanel = Backbone.View.extend({
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].join('');
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},
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/** build links to workflows in toolpanel */
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_templateWorkflowLink: function( wf ) {
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return [
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'<div class="toolTitle">',
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'<a class="'+ wf.cls +' " href="', Galaxy.root, wf.href, '">', wf.title, '</a>',
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'</div>'
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].join('');
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},
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/** override to include inital menu dom and workflow section */
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_template : function() {
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return [
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@@ -278,8 +278,8 @@ var Collection = Backbone.Collection.extend({
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divider : true
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},{
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title : _l('Saved Histories'),
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url : 'history/list',
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target : 'galaxy_main'
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url : 'histories/list',
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target : '_top'
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},{
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title : _l('Saved Datasets'),
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url : 'datasets/list',
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@@ -19,18 +19,19 @@ define( [ 'layout/masthead', 'layout/panel', 'mvc/ui/ui-modal' ], function( Mast
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Galaxy.display = this.display = function( view ) { self.center.display( view ) };
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Galaxy.router = this.router = options.Router && new options.Router( self, options );
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this.masthead = new Masthead.View( this.config );
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this.center = new Panel.CenterPanel();
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// build page template
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this.$el.attr( 'scroll', 'no' );
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this.$el.html( this._template() );
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this.$( '#masthead' ).replaceWith( this.masthead.$el );
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this.$( '#center' ).append( this.center.$el );
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this.$el.append( this.masthead.frame.$el );
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this.$el.append( this.modal.$el );
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this.$messagebox = this.$( '#messagebox' );
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this.$inactivebox = this.$( '#inactivebox' );
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// build panels
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this.center = new Panel.CenterPanel();
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this.panels = {};
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_.each( this._panelids, function( panel_id ) {
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var panel_class_name = panel_id.charAt( 0 ).toUpperCase() + panel_id.slice( 1 );
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@@ -98,14 +99,12 @@ define( [ 'layout/masthead', 'layout/panel', 'mvc/ui/ui-modal' ], function( Mast
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/** Render panels */
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renderPanels : function() {
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var self = this;
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this.center.setElement( '#center' );
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this.center.render();
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_.each( this._panelids, function( panel_id ) {
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var panel = self.panels[ panel_id ];
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if ( panel ) {
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panel.render();
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} else {
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self.center.$el.css( panel_id, 0 );
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self.$( '#center' ).css( panel_id, 0 );
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self.$( '#' + panel_id ).hide();
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}
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});
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@@ -189,29 +189,20 @@ define( [ 'jquery', 'libs/underscore', 'libs/backbone' ], function( $, _, Backbo
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var CenterPanel = Backbone.View.extend({
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initialize : function( options ){
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/** previous view contained in the center panel - cached for removal later */
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this.prev = null;
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this.setElement( $( this.template() ) );
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this.$frame = this.$( '.center-frame' );
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this.$panel = this.$( '.center-panel' );
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this.$frame.on( 'load', _.bind( this._iframeChangeHandler, this ) );
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},
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render : function(){
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this.$el.html( this.template() );
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// ?: doesn't work/listen in events map
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this.$( '#galaxy_main' ).on( 'load', _.bind( this._iframeChangeHandler, this ) );
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},
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/** */
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_iframeChangeHandler : function( ev ){
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/** Display iframe if its target url changes, hide center panel */
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_iframeChangeHandler : function( ev ) {
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var iframe = ev.currentTarget;
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var location = iframe.contentWindow && iframe.contentWindow.location;
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if( location && location.host ){
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// show the iframe and hide MVCview div, remove any views in the MVCview div
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if( location && location.host ) {
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$( iframe ).show();
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if( this.prev ){
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this.prev.remove();
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}
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this.$( '#center-panel' ).hide();
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// TODO: move to Galaxy
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Galaxy.trigger( 'galaxy_main:load', {
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this.$panel.empty().hide();
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Galaxy.trigger( 'center-frame:load', {
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fullpath: location.pathname + location.search + location.hash,
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pathname: location.pathname,
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search : location.search,
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@@ -220,43 +211,26 @@ define( [ 'jquery', 'libs/underscore', 'libs/backbone' ], function( $, _, Backbo
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}
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},
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/** */
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/** Display a view in the center panel, hide iframe */
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display: function( view ) {
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// we need to display an MVC view: hide the iframe and show the other center panel
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// first checking for any onbeforeunload handlers on the iframe
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var contentWindow = this.$( '#galaxy_main' )[ 0 ].contentWindow || {};
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var contentWindow = this.$frame[ 0 ].contentWindow || {};
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var message = contentWindow.onbeforeunload && contentWindow.onbeforeunload();
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if ( !message || confirm( message ) ) {
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contentWindow.onbeforeunload = undefined;
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// remove any previous views
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if( this.prev ){
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this.prev.remove();
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}
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this.prev = view;
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this.$( '#galaxy_main' ).attr( 'src', 'about:blank' ).hide();
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this.$( '#center-panel' ).scrollTop( 0 ).append( view.$el ).show();
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this.$frame.attr( 'src', 'about:blank' ).hide();
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this.$panel.empty().scrollTop( 0 ).append( view.$el ).show();
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Galaxy.trigger( 'center-panel:load', view );
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} else {
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if( view ){
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view.remove();
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}
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}
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},
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template: function(){
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return [
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//TODO: remove inline styling
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'<div style="position: absolute; width: 100%; height: 100%">',
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'<iframe name="galaxy_main" id="galaxy_main" frameborder="0" ',
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'style="position: absolute; width: 100%; height: 100%;"/>',
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'<div id="center-panel" ',
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'style="display: none; position: absolute; width: 100%; height: 100%; padding: 10px; overflow: auto;"/>',
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'</div>'
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].join('');
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template: function() {
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return '<div class="center-container">' +
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'<iframe id="galaxy_main" name="galaxy_main" frameborder="0" class="center-frame" />' +
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'<div class="center-panel" />' +
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'</div>';
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},
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toString : function(){ return 'CenterPanel' }
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toString : function() { return 'CenterPanel' }
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});
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return {
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||||
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@@ -252,53 +252,36 @@ return Backbone.View.extend({
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return;
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}
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//
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// add operation popup menus
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//
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for (var i in options.items)
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{
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// get items
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var item = options.items[i];
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_.each( options.items, function( item, index ) {
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var button = self.$( '#grid-' + index + '-popup' ).off();
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var popup = new PopupMenu( button );
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_.each( options[ 'operations' ], function( operation ) {
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self._add_operation( popup, operation, item );
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});
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||||
});
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},
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// get identifiers
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var button = this.$el.find('#grid-' + i + '-popup');
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button.off();
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var popup = new PopupMenu(button);
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// load details
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for (var j in options['operations'])
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{
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// get operation details
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var operation = options['operations'][j];
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var operation_id = operation['label'];
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var operation_settings = item['operation_config'][operation_id];
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var encode_id = item['encode_id'];
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// check
|
||||
if (operation_settings['allowed'] && operation['allow_popup'])
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{
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// popup configuration
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var popupConfig =
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||||
{
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||||
html : operation['label'],
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||||
href : operation_settings['url_args'],
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||||
target : operation_settings['target'],
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||||
confirmation_text : operation['confirm']
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};
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||||
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||||
// add popup function
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popupConfig.func = function(e)
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||||
{
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e.preventDefault();
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var label = $(e.target).html();
|
||||
var options = this.findItemByHtml(label);
|
||||
self.execute(options);
|
||||
};
|
||||
|
||||
// add item
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popup.addItem(popupConfig);
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/** Add an operation to the items menu */
|
||||
_add_operation: function( popup, operation, item ) {
|
||||
var self = this;
|
||||
var settings = item.operation_config[ operation.label ];
|
||||
if ( settings.allowed && operation.allow_popup ) {
|
||||
popup.addItem({
|
||||
html : operation.label,
|
||||
href : settings.url_args,
|
||||
target : settings.target,
|
||||
confirmation_text : operation.confirm,
|
||||
func : function( e ) {
|
||||
e.preventDefault();
|
||||
var label = $( e.target ).html();
|
||||
if ( operation.onclick ) {
|
||||
operation.onclick( item.encode_id );
|
||||
} else {
|
||||
self.execute( this.findItemByHtml( label ) );
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
}
|
||||
},
|
||||
|
||||
|
||||
@@ -0,0 +1,49 @@
|
||||
/** This class renders the grid list. */
|
||||
define( [ 'utils/utils', 'mvc/grid/grid-view', 'mvc/history/history-model', 'mvc/history/copy-dialog' ], function( Utils, GridView, HistoryModel, historyCopyDialog ) {
|
||||
|
||||
var View = Backbone.View.extend({
|
||||
initialize: function( options ) {
|
||||
var self = this;
|
||||
this.setElement( $( '<div/>' ) );
|
||||
this.model = new Backbone.Model();
|
||||
Utils.get({
|
||||
url : Galaxy.root + 'history/list',
|
||||
success : function( response ) {
|
||||
response[ 'dict_format' ] = true;
|
||||
_.each( response[ 'operations' ], function( operation ) {
|
||||
if ( operation.label == 'Copy' ) {
|
||||
operation.onclick = function( id ) { self._showCopyDialog( id ) };
|
||||
}
|
||||
});
|
||||
self.model.set( response );
|
||||
self.render();
|
||||
}
|
||||
});
|
||||
},
|
||||
|
||||
render: function() {
|
||||
var grid = new GridView( this.model.attributes );
|
||||
this.$el.empty().append( grid.$el );
|
||||
},
|
||||
|
||||
_showCopyDialog: function( id ) {
|
||||
var history = new HistoryModel.History( { id : id } );
|
||||
history.fetch()
|
||||
.fail( function() {
|
||||
alert( 'History could not be fetched. Please contact an administrator' );
|
||||
})
|
||||
.done( function(){
|
||||
historyCopyDialog( history, {} ).done( function() {
|
||||
if( window.parent && window.parent.Galaxy && window.parent.Galaxy.currHistoryPanel ) {
|
||||
window.parent.Galaxy.currHistoryPanel.loadCurrentHistory();
|
||||
}
|
||||
window.location.reload( true );
|
||||
} );
|
||||
});
|
||||
}
|
||||
});
|
||||
|
||||
return {
|
||||
View: View
|
||||
}
|
||||
});
|
||||
@@ -338,7 +338,7 @@ var CurrentHistoryView = _super.extend(/** @lends CurrentHistoryView.prototype *
|
||||
// compare the url to the following list and if there's a match
|
||||
// pull the id from url and indicate in the history view that
|
||||
// the dataset with that id is the 'current'ly active dataset
|
||||
'galaxy_main:load': function( data ){
|
||||
'center-frame:load': function( data ){
|
||||
var pathToMatch = data.fullpath;
|
||||
var hdaId = null;
|
||||
var useToURLRegexMap = {
|
||||
|
||||
@@ -16,7 +16,9 @@ var menu = [
|
||||
},
|
||||
{
|
||||
html : _l( 'Saved Histories' ),
|
||||
href : 'history/list',
|
||||
href : 'histories/list',
|
||||
target : '_top'
|
||||
|
||||
},
|
||||
{
|
||||
html : _l( 'Histories Shared with Me' ),
|
||||
@@ -205,7 +207,7 @@ function buildMenu( isAnon, purgeAllowed, urlRoot ){
|
||||
//TODO:?? hard-coded galaxy_main
|
||||
if( menuOption.href ){
|
||||
menuOption.href = urlRoot + menuOption.href;
|
||||
menuOption.target = 'galaxy_main';
|
||||
menuOption.target = menuOption.target || 'galaxy_main';
|
||||
}
|
||||
|
||||
if( menuOption.confirm ){
|
||||
|
||||
@@ -22,16 +22,16 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view
|
||||
});
|
||||
}
|
||||
// destroy dom elements
|
||||
this.$el.on( 'remove', function() { self.remove() } );
|
||||
this.$el.on( 'remove', function() { self._destroy() } );
|
||||
},
|
||||
|
||||
/** Wait for deferred build processes before removal */
|
||||
remove: function() {
|
||||
_destroy: function() {
|
||||
var self = this;
|
||||
this.$el.hide();
|
||||
this.$el.off().hide();
|
||||
this.deferred.execute( function() {
|
||||
FormBase.prototype.remove.call( self );
|
||||
Galaxy.emit.debug( 'tool-form-base::remove()', 'Destroy view.' );
|
||||
Galaxy.emit.debug( 'tool-form-base::_destroy()', 'Destroy view.' );
|
||||
});
|
||||
},
|
||||
|
||||
|
||||
@@ -15,9 +15,6 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
|
||||
$( 'body' ).append( this.$el );
|
||||
this._configure();
|
||||
this.render();
|
||||
this._refresh();
|
||||
this.$el.on( 'click', function() { self._refresh() } );
|
||||
this.$steps.scroll( function() { self._refresh() } );
|
||||
$( window ).resize( function() { self._refresh() } );
|
||||
},
|
||||
|
||||
@@ -25,7 +22,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
|
||||
_refresh: function( step_index ) {
|
||||
var margin = _.reduce( this.$el.children(), function( memo, child ) {
|
||||
return memo + $( child ).outerHeight();
|
||||
}, 0 ) - this.$steps.height() + 25;
|
||||
}, 0 ) - this.$steps.height() + 90;
|
||||
this.$steps.css( 'height', $( window ).height() - margin );
|
||||
},
|
||||
|
||||
@@ -314,6 +311,7 @@ define([ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view'
|
||||
}
|
||||
self.forms[ step.index ] = form;
|
||||
self._append( self.$steps, form.$el );
|
||||
self._refresh();
|
||||
step.needs_refresh && self._refreshStep( step );
|
||||
form.portlet[ !self.show_progress ? 'enable' : 'disable' ]();
|
||||
self.show_progress && self.execute_btn.model.set( { wait : true,
|
||||
|
||||
@@ -65,6 +65,14 @@ define( [ 'mvc/form/form-view', 'mvc/ui/ui-misc' ], function( Form, Ui ) {
|
||||
window.location.href = Galaxy.root + 'custom_builds';
|
||||
}
|
||||
},
|
||||
'configure_menu': {
|
||||
title : 'Configure workflow menu',
|
||||
description : 'Configure your workflow items which appear in the Tool panel.',
|
||||
icon : 'fa-cog',
|
||||
onclick : function() {
|
||||
window.location.href = Galaxy.root + 'workflow/configure_menu';
|
||||
}
|
||||
},
|
||||
'logout': {
|
||||
title : 'Sign out',
|
||||
description : 'Click here to sign out of all sessions.',
|
||||
@@ -119,6 +127,7 @@ define( [ 'mvc/form/form-view', 'mvc/ui/ui-misc' ], function( Form, Ui ) {
|
||||
if( config.enable_openid && !config.use_remote_user ) {
|
||||
self._addLink( 'openids' );
|
||||
}
|
||||
self._addLink( 'configure_menu' );
|
||||
self._addLink( 'logout' );
|
||||
self.$preferences.append( self._templateFooter( data ) );
|
||||
self.$el.empty().append( self.$preferences );
|
||||
|
||||
@@ -80,7 +80,7 @@ define( [], function() {
|
||||
data: JSON.stringify( { 'workflow_ids': ids } ),
|
||||
contentType : 'application/json'
|
||||
}).done( function( response ) {
|
||||
window.location = Galaxy.root + 'workflow?status='+ response.status +'&message=' + response.message;
|
||||
window.location = Galaxy.root + 'user';
|
||||
});
|
||||
});
|
||||
},
|
||||
@@ -121,8 +121,8 @@ define( [], function() {
|
||||
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 +'workflow" title="Back to workflow">' +
|
||||
'<span>Back to workflow</span>' +
|
||||
'<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;
|
||||
},
|
||||
|
||||
@@ -1,6 +1,21 @@
|
||||
/** Workflow view */
|
||||
define( [], function() {
|
||||
define( [ 'utils/utils' ], function( Utils ) {
|
||||
|
||||
/** 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 {
|
||||
$el_message.html("");
|
||||
}
|
||||
}
|
||||
|
||||
/** View of the main workflow list page */
|
||||
var View = Backbone.View.extend({
|
||||
|
||||
@@ -17,7 +32,7 @@ define( [], function() {
|
||||
// Add workflow header
|
||||
self.$el.empty().append( self._templateHeader() );
|
||||
// Add user actions message if any
|
||||
self.build_messages( self );
|
||||
build_messages( self );
|
||||
$el_workflow = self.$el.find( '.user-workflows' );
|
||||
// Add the actions buttons
|
||||
$el_workflow.append( self._templateActionButtons() );
|
||||
@@ -37,21 +52,6 @@ define( [], function() {
|
||||
});
|
||||
},
|
||||
|
||||
/** 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>' + _.escape(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 ),
|
||||
@@ -86,11 +86,6 @@ define( [], function() {
|
||||
});
|
||||
},
|
||||
|
||||
/** 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 () {
|
||||
@@ -157,7 +152,7 @@ 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 +163,7 @@ 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>';
|
||||
@@ -182,17 +177,72 @@ define( [], function() {
|
||||
'<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>';
|
||||
}
|
||||
});
|
||||
|
||||
var ImportWorkflowView = Backbone.View.extend({
|
||||
|
||||
initialize: function() {
|
||||
this.setElement( '<div/>' );
|
||||
this.render();
|
||||
},
|
||||
|
||||
/** Open page to import workflow */
|
||||
render: function() {
|
||||
var self = this;
|
||||
$.getJSON( Galaxy.root + 'workflow/upload_import_workflow', function( options ) {
|
||||
self.$el.empty().append( self._mainTemplate( self, options ) );
|
||||
});
|
||||
},
|
||||
|
||||
/** Template for the import workflow page */
|
||||
_mainTemplate: function( self, options ) {
|
||||
return "<div class='toolForm'>" +
|
||||
"<div class='toolFormTitle'>Import Galaxy workflow</div>" +
|
||||
"<div class='toolFormBody'>" +
|
||||
"<form name='import_workflow' id='import_workflow' action='"+ Galaxy.root + 'workflow/upload_import_workflow' +"' enctype='multipart/form-data' method='POST'>" +
|
||||
"<div class='form-row'>" +
|
||||
"<label>Galaxy workflow URL:</label>" +
|
||||
"<input type='text' name='url' class='input-url' value='"+ options.url +"' size='40'>" +
|
||||
"<div class='toolParamHelp' style='clear: both;'>" +
|
||||
"If the workflow is accessible via a URL, enter the URL above and click <b>Import</b>." +
|
||||
"</div>" +
|
||||
"<div style='clear: both'></div>" +
|
||||
"</div>" +
|
||||
"<div class='form-row'>" +
|
||||
"<label>Galaxy workflow file:</label>" +
|
||||
"<div class='form-row-input'>" +
|
||||
"<input type='file' name='file_data' class='input-file'/>" +
|
||||
"</div>" +
|
||||
"<div class='toolParamHelp' style='clear: both;'>" +
|
||||
"If the workflow is in a file on your computer, choose it and then click <b>Import</b>." +
|
||||
"</div>" +
|
||||
"<div style='clear: both'></div>" +
|
||||
"</div>" +
|
||||
"<div class='form-row'>" +
|
||||
"<input type='submit' class='primary-button wf-import' name='import_button' value='Import'>" +
|
||||
"</div>" +
|
||||
"</form>" +
|
||||
"<hr/>" +
|
||||
"<div class='form-row'>" +
|
||||
"<label>Import a Galaxy workflow from myExperiment:</label>" +
|
||||
"<div class='form-row-input'>" +
|
||||
"<a href='" + options.myexperiment_target_url + "'> Visit myExperiment</a>" +
|
||||
"</div>" +
|
||||
"<div class='toolParamHelp' style='clear: both;'>" +
|
||||
"Click the link above to visit myExperiment and browse for Galaxy workflows." +
|
||||
"</div>" +
|
||||
"<div style='clear: both'></div>" +
|
||||
"</div>" +
|
||||
"</div>" +
|
||||
"</div>";
|
||||
},
|
||||
|
||||
});
|
||||
|
||||
return {
|
||||
View : View
|
||||
View : View,
|
||||
ImportWorkflowView : ImportWorkflowView
|
||||
};
|
||||
});
|
||||
|
||||
@@ -289,6 +289,11 @@ define( [], function() {
|
||||
}
|
||||
};
|
||||
|
||||
/** Get querystrings from url */
|
||||
function getQueryString( key ) {
|
||||
return decodeURIComponent( window.location.search.replace(new RegExp("^(?:.*[&\\?]" + encodeURIComponent( key ).replace(/[\.\+\*]/g, "\\$&") + "(?:\\=([^&]*))?)?.*$", "i"), "$1") );
|
||||
};
|
||||
|
||||
return {
|
||||
cssLoadFile: cssLoadFile,
|
||||
cssGetAttribute: cssGetAttribute,
|
||||
@@ -306,6 +311,7 @@ define( [], function() {
|
||||
isJSON: isJSON,
|
||||
clone: clone,
|
||||
linkify: linkify,
|
||||
appendScriptStyle: appendScriptStyle
|
||||
appendScriptStyle: appendScriptStyle,
|
||||
getQueryString: getQueryString
|
||||
};
|
||||
});
|
||||
|
||||
@@ -143,6 +143,24 @@ body {
|
||||
right: 250 + @border-default-color_padding;
|
||||
overflow: hidden;
|
||||
z-index: 1;
|
||||
.center-container {
|
||||
position: absolute;
|
||||
width: 100%;
|
||||
height: 100%;
|
||||
.center-panel {
|
||||
display: none;
|
||||
position: absolute;
|
||||
width: 100%;
|
||||
height: 100%;
|
||||
padding: 10px;
|
||||
overflow: auto;
|
||||
}
|
||||
.center-frame {
|
||||
position: absolute;
|
||||
width: 100%;
|
||||
height: 100%;
|
||||
}
|
||||
}
|
||||
}
|
||||
#right-border {
|
||||
right: 250px;
|
||||
|
||||
@@ -108,8 +108,12 @@ 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( '/pages/{action_id}' )
|
||||
webapp.add_client_route( '/datasets/{action_id}' )
|
||||
webapp.add_client_route( '/pages/list' )
|
||||
webapp.add_client_route( '/pages/list_published' )
|
||||
webapp.add_client_route( '/histories/list' )
|
||||
webapp.add_client_route( '/datasets/list' )
|
||||
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' )
|
||||
|
||||
|
||||
@@ -87,7 +87,6 @@ class HistoryListGrid( grids.Grid ):
|
||||
# Grid definition
|
||||
title = "Saved Histories"
|
||||
model_class = model.History
|
||||
template = '/history/grid.mako'
|
||||
default_sort_key = "-update_time"
|
||||
columns = [
|
||||
HistoryListNameColumn( "Name", key="name", attach_popup=True, filterable="advanced" ),
|
||||
@@ -108,10 +107,10 @@ class HistoryListGrid( grids.Grid ):
|
||||
)
|
||||
operations = [
|
||||
grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=True ),
|
||||
grids.GridOperation( "View", allow_multiple=False ),
|
||||
grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
|
||||
grids.GridOperation( "View", allow_multiple=False, url_args=dict( action='view' ) ),
|
||||
grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), url_args=dict( action='sharing' ) ),
|
||||
grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
|
||||
grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False, target="inbound" ),
|
||||
grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), url_args=dict( action='rename' ) ),
|
||||
grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True ),
|
||||
grids.GridOperation( "Delete Permanently", condition=( lambda item: not item.purged ), confirm="History contents will be removed from disk, this cannot be undone. Continue?", async_compatible=True ),
|
||||
grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), async_compatible=True ),
|
||||
@@ -167,7 +166,6 @@ class SharedHistoryListGrid( grids.Grid ):
|
||||
operations = [
|
||||
grids.GridOperation( "View", allow_multiple=False, target="_top" ),
|
||||
grids.GridOperation( "Copy" ),
|
||||
# grids.GridOperation( "Copy", allow_multiple=False ),
|
||||
grids.GridOperation( "Unshare" )
|
||||
]
|
||||
standard_filters = []
|
||||
@@ -249,6 +247,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
|
||||
return trans.fill_template( "history/list_published.mako", embedded_grid=grid )
|
||||
|
||||
@web.expose
|
||||
@web.json
|
||||
@web.require_login( "work with multiple histories" )
|
||||
def list( self, trans, **kwargs ):
|
||||
"""List all available histories"""
|
||||
@@ -256,20 +255,6 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
|
||||
status = message = None
|
||||
if 'operation' in kwargs:
|
||||
operation = kwargs['operation'].lower()
|
||||
if operation == "share or publish":
|
||||
return self.sharing( trans, **kwargs )
|
||||
if operation == "rename" and kwargs.get('id', None): # Don't call rename if no ids
|
||||
if 'name' in kwargs:
|
||||
del kwargs['name'] # Remove ajax name param that rename method uses
|
||||
return self.rename( trans, **kwargs )
|
||||
if operation == "view":
|
||||
decoded_id = self.decode_id( kwargs.get( 'id', None ) )
|
||||
history = self.history_manager.get_owned( decoded_id, trans.user, current_history=trans.history )
|
||||
return trans.response.send_redirect( url_for( controller='history',
|
||||
action='view',
|
||||
id=kwargs['id'],
|
||||
show_deleted=history.deleted,
|
||||
use_panels=False ) )
|
||||
history_ids = galaxy.util.listify( kwargs.get( 'id', [] ) )
|
||||
# Display no message by default
|
||||
status, message = None, None
|
||||
@@ -296,7 +281,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
|
||||
if use_panels:
|
||||
return trans.response.send_redirect( url_for( "/" ) )
|
||||
else:
|
||||
trans.template_context['refresh_frames'] = ['history']
|
||||
kwargs['refresh_frames'] = ['history']
|
||||
elif operation in ( "delete", "delete permanently" ):
|
||||
if operation == "delete permanently":
|
||||
status, message = self._list_delete( trans, histories, purge=True )
|
||||
@@ -305,7 +290,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
|
||||
if current_history in histories:
|
||||
# Deleted the current history, so a new, empty history was
|
||||
# created automatically, and we need to refresh the history frame
|
||||
trans.template_context['refresh_frames'] = ['history']
|
||||
kwargs['refresh_frames'] = ['history']
|
||||
elif operation == "undelete":
|
||||
status, message = self._list_undelete( trans, histories )
|
||||
elif operation == "unshare":
|
||||
@@ -328,6 +313,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
|
||||
|
||||
trans.sa_session.flush()
|
||||
# Render the list view
|
||||
kwargs[ 'dict_format' ] = True
|
||||
return self.stored_list_grid( trans, status=status, message=message, **kwargs )
|
||||
|
||||
def _list_delete( self, trans, histories, purge=False ):
|
||||
@@ -741,8 +727,8 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
|
||||
history_name = escape( history.name )
|
||||
user_email = escape( user.email )
|
||||
message = "History '%s' does not seem to be shared with user '%s'" % ( history_name, user_email )
|
||||
return trans.fill_template( '/sharing_base.mako', item=history,
|
||||
message=message, status='error' )
|
||||
return trans.fill_template( '/sharing_base.mako', controller_list='histories', item=history,
|
||||
message=message, status='error', use_panels=True )
|
||||
|
||||
# Legacy issue: histories made accessible before recent updates may not have a slug. Create slug for any histories that need them.
|
||||
for history in histories:
|
||||
@@ -751,7 +737,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesI
|
||||
|
||||
session.flush()
|
||||
|
||||
return trans.fill_template( "/sharing_base.mako", item=history )
|
||||
return trans.fill_template( "/sharing_base.mako", controller_list='histories', item=history, use_panels=True )
|
||||
|
||||
@web.expose
|
||||
@web.require_login( "share histories with other users" )
|
||||
|
||||
@@ -15,8 +15,7 @@ from tool_shed.util import encoding_util
|
||||
from galaxy import model
|
||||
from galaxy import util
|
||||
from galaxy import web
|
||||
from galaxy import exceptions
|
||||
from galaxy.managers import workflows, histories
|
||||
from galaxy.managers import workflows
|
||||
from galaxy.model.item_attrs import UsesItemRatings
|
||||
from galaxy.model.mapping import desc
|
||||
from galaxy.util import unicodify, FILENAME_VALID_CHARS
|
||||
@@ -740,7 +739,8 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
return stored_dict
|
||||
|
||||
@web.expose
|
||||
def import_workflow( self, trans, cntrller='workflow', **kwd ):
|
||||
@web.json
|
||||
def upload_import_workflow( self, trans, cntrller='workflow', **kwd ):
|
||||
"""
|
||||
Import a workflow by reading an url, uploading a file, opening and reading the contents
|
||||
of a local file, or receiving the textual representation of a workflow via http.
|
||||
@@ -790,7 +790,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
try:
|
||||
workflow_data = urllib2.urlopen( url ).read()
|
||||
except Exception as e:
|
||||
message = "Failed to open URL: <b>%s</b><br>Exception: %s" % ( escape( url ), escape( str( e ) ) )
|
||||
message = "Failed to open URL: %s. Exception: %s" % ( escape( url ), escape( str( e ) ) )
|
||||
status = 'error'
|
||||
elif workflow_text:
|
||||
# This case occurs when the workflow_text was sent via http from the tool shed.
|
||||
@@ -839,7 +839,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
message += "Imported, but this workflow contains cycles. "
|
||||
status = "error"
|
||||
else:
|
||||
message += "Workflow <b>%s</b> imported successfully. " % escape( workflow.name )
|
||||
message += "Workflow %s imported successfully. " % escape( workflow.name )
|
||||
if missing_tool_tups:
|
||||
if trans.user_is_admin():
|
||||
# A required tool is not available in the local Galaxy instance.
|
||||
@@ -853,7 +853,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.<br/>"
|
||||
for missing_tool_tup in missing_tool_tups:
|
||||
missing_tool_id, missing_tool_name, missing_tool_version, step_id = missing_tool_tup
|
||||
message += "<b>Tool name</b> %s, <b>id</b> %s, <b>version</b> %s<br/>" % (
|
||||
message += "Tool name: %s, id: %s, version: %s." % (
|
||||
escape( missing_tool_name ),
|
||||
escape( missing_tool_id ),
|
||||
escape( missing_tool_version ) )
|
||||
@@ -867,7 +867,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
for missing_tool_tup in missing_tool_tups:
|
||||
missing_tool_id = missing_tool_tup[0]
|
||||
url += '%s,' % escape( missing_tool_id )
|
||||
message += '<a href="%s">%s</a><br/>' % ( url, shed_name )
|
||||
message += 'url: %s, shed name: %s.' % ( url, shed_name )
|
||||
status = 'error'
|
||||
if installed_repository_file or tool_shed_url:
|
||||
# Another Galaxy panels Hack: The request did not originate from the Galaxy
|
||||
@@ -886,13 +886,13 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
pass
|
||||
if tool_shed_url:
|
||||
# We've received the textual representation of a workflow from a Galaxy tool shed.
|
||||
message = "Workflow <b>%s</b> imported successfully." % escape( workflow.name )
|
||||
message = "Workflow %s imported successfully." % escape( workflow.name )
|
||||
url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&message=%s' % \
|
||||
( tool_shed_url, repository_metadata_id, encoding_util.tool_shed_encode( workflow_name ), message )
|
||||
return trans.response.send_redirect( url )
|
||||
elif installed_repository_file:
|
||||
# The workflow was read from a file included with an installed tool shed repository.
|
||||
message = "Workflow <b>%s</b> imported successfully." % escape( workflow.name )
|
||||
message = "Workflow %s imported successfully." % escape( workflow.name )
|
||||
if cntrller == 'api':
|
||||
return status, message
|
||||
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
|
||||
@@ -900,15 +900,20 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
id=repository_id,
|
||||
message=message,
|
||||
status=status ) )
|
||||
return self.list( trans )
|
||||
redirect_url = url_for( '/' ) + 'workflow?status=' + status + '&message=%s' % escape( message )
|
||||
return trans.response.send_redirect( redirect_url )
|
||||
if cntrller == 'api':
|
||||
return status, message
|
||||
return trans.fill_template( "workflow/import.mako",
|
||||
url=url,
|
||||
message=message,
|
||||
status=status,
|
||||
use_panels=True,
|
||||
myexperiment_target_url=myexperiment_target_url )
|
||||
if status == 'error':
|
||||
redirect_url = url_for( '/' ) + 'workflow?status=' + status + '&message=%s' % escape( message )
|
||||
return trans.response.send_redirect( redirect_url )
|
||||
else:
|
||||
return {
|
||||
'url': url,
|
||||
'message': message,
|
||||
'status': status,
|
||||
'myexperiment_target_url': myexperiment_target_url
|
||||
}
|
||||
|
||||
@web.expose
|
||||
def build_from_current_history( self, trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None, dataset_names=None, dataset_collection_names=None ):
|
||||
@@ -947,26 +952,6 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
% ( escape( workflow_name ), url_for( controller='workflow', action='editor', id=workflow_id ),
|
||||
url_for( controller='workflow', action='run', id=workflow_id ) ) )
|
||||
|
||||
@web.expose
|
||||
def run( self, trans, id, history_id=None, **kwargs ):
|
||||
history = None
|
||||
try:
|
||||
if history_id is not None:
|
||||
history_manager = histories.HistoryManager( trans.app )
|
||||
history = history_manager.get_owned( trans.security.decode_id( history_id ), trans.user, current_history=trans.history )
|
||||
else:
|
||||
history = trans.get_history()
|
||||
if history is None:
|
||||
raise exceptions.MessageException( 'History unavailable. Please specify a valid history id' )
|
||||
except Exception as e:
|
||||
raise exceptions.MessageException( '[history_id=%s] Failed to retrieve history. %s.' % ( history_id, str( e ) ) )
|
||||
trans.history = history
|
||||
workflow_manager = workflows.WorkflowsManager( trans.app )
|
||||
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 )
|
||||
|
||||
def get_item( self, trans, id ):
|
||||
return self.get_stored_workflow( trans, id )
|
||||
|
||||
|
||||
File diff suppressed because one or more lines are too long
@@ -1 +1 @@
|
||||
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|
||||
@@ -1 +1 @@
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|
||||
define(["layout/masthead","layout/panel","mvc/ui/ui-modal"],function(a,b,c){var d=Backbone.View.extend({el:"body",className:"full-content",_panelids:["left","right"],initialize:function(d){var e=this;this.config=_.defaults(d.config||{},{message_box_visible:!1,message_box_content:"",message_box_class:"info",show_inactivity_warning:!1,inactivity_box_content:""}),Galaxy.modal=this.modal=new c.View,Galaxy.display=this.display=function(a){e.center.display(a)},Galaxy.router=this.router=d.Router&&new d.Router(e,d),this.masthead=new a.View(this.config),this.center=new b.CenterPanel,this.$el.attr("scroll","no"),this.$el.html(this._template()),this.$("#masthead").replaceWith(this.masthead.$el),this.$("#center").append(this.center.$el),this.$el.append(this.masthead.frame.$el),this.$el.append(this.modal.$el),this.$messagebox=this.$("#messagebox"),this.$inactivebox=this.$("#inactivebox"),this.panels={},_.each(this._panelids,function(a){var c=a.charAt(0).toUpperCase()+a.slice(1),f=d[c];if(f){var g=new f(e,d);e[g.toString()]=g,e.panels[a]=new b.SidePanel({id:a,el:e.$("#"+a),view:g})}}),this.render()},render:function(){return $(".select2-hidden-accessible").remove(),this.masthead.render(),this.renderMessageBox(),this.renderInactivityBox(),this.renderPanels(),this._checkCommunicationServerOnline(),this},renderMessageBox:function(){if(this.config.message_box_visible){var a=this.config.message_box_content||"",b=this.config.message_box_class||"info";this.$el.addClass("has-message-box"),this.$messagebox.attr("class","panel-"+b+"-message").html(a).toggle(!!a).show()}else this.$el.removeClass("has-message-box"),this.$messagebox.hide();return this},renderInactivityBox:function(){if(this.config.show_inactivity_warning){var a=this.config.inactivity_box_content||"",b=$("<a/>").attr("href",Galaxy.root+"user/resend_verification").text("Resend verification");this.$el.addClass("has-inactivity-box"),this.$inactivebox.html(a+" ").append(b).toggle(!!a).show()}else this.$el.removeClass("has-inactivity-box"),this.$inactivebox.hide();return this},renderPanels:function(){var a=this;return _.each(this._panelids,function(b){var c=a.panels[b];c?c.render():(a.$("#center").css(b,0),a.$("#"+b).hide())}),this},_template:function(){return['<div id="everything">','<div id="background"/>','<div id="masthead"/>','<div id="messagebox"/>','<div id="inactivebox" class="panel-warning-message" />','<div id="left" />','<div id="center" class="inbound" />','<div id="right" />',"</div>",'<div id="dd-helper" />'].join("")},toString:function(){return"PageLayoutView"},_checkCommunicationServerOnline:function(){var a=window.Galaxy.config.communication_server_host,b=window.Galaxy.config.communication_server_port,c=window.Galaxy.user.attributes.preferences,d=$("#show-chat-online");c&&-1!=["1","true"].indexOf(c.communication_server)?$.ajax({url:a+":"+b}).success(function(){null!==window.Galaxy.user.id&&"hidden"===d.css("visibility")&&d.css("visibility","visible")}).error(function(){d.css("visibility","hidden")}):d.css("visibility","hidden")}});return{View:d}});
|
||||
//# sourceMappingURL=../../maps/layout/page.js.map
|
||||
@@ -1,2 +1,2 @@
|
||||
define(["jquery","libs/underscore","libs/backbone"],function(a,b,c){"use strict";var d=160,e=800,f=c.View.extend({initialize:function(a){this.view=a.view,this.hidden=!1,this.saved_size=null,this.hiddenByTool=!1},$center:function(){return this.$el.siblings("#center")},$toggleButton:function(){return this.$(".unified-panel-footer > .panel-collapse")},render:function(){var a=this,c=this.view,d=this.view.model.attributes||{};this.$el.html(this._templatePanel(this.id)),b.each(d.buttons,function(b){a.$(".panel-header-buttons").append(b.$el)}),this.$el.addClass(d.cls),this.$(".panel-header-text").html(b.escape(d.title)),this.$(".unified-panel-body").append(c.$el),c.render()},_templatePanel:function(){return[this._templateHeader(),this._templateBody(),this._templateFooter()].join("")},_templateHeader:function(){return['<div class="unified-panel-header" unselectable="on">','<div class="unified-panel-header-inner">','<div class="panel-header-buttons" style="float: right"/>','<div class="panel-header-text"/>',"</div>","</div>"].join("")},_templateBody:function(){return'<div class="unified-panel-body"/>'},_templateFooter:function(){return['<div class="unified-panel-footer">','<div class="panel-collapse ',b.escape(this.id),'"/>','<div class="drag"/>',"</div>"].join("")},events:{"mousedown .unified-panel-footer > .drag":"_mousedownDragHandler","click .unified-panel-footer > .panel-collapse":"toggle"},_mousedownDragHandler:function(b){function c(a){var b=a.pageX-h;h=a.pageX;var c=f.$el.width(),i=g?c+b:c-b;i=Math.min(e,Math.max(d,i)),f.resize(i)}var f=this,g="left"===this.id,h=b.pageX;a("#dd-helper").show().on("mousemove",c).one("mouseup",function(){a(this).hide().off("mousemove",c)})},resize:function(a){return this.$el.css("width",a),this.$center().css(this.id,a),this},show:function(){if(this.hidden){var a=this,b={},c=this.id;return b[c]=0,a.$el.css(c,-this.saved_size).show().animate(b,"fast",function(){a.resize(a.saved_size)}),a.hidden=!1,a.$toggleButton().removeClass("hidden"),this}},hide:function(){if(!this.hidden){var a={},b=this.id;return this.saved_size=this.$el.width(),a[b]=-this.saved_size,this.$el.animate(a,"fast"),this.$center().css(b,0),this.hidden=!0,this.$toggleButton().addClass("hidden"),this}},toggle:function(){return this.hidden?this.show():this.hide(),this.hiddenByTool=!1,this},handle_minwidth_hint:function(a){var b=this.$center().width()-(this.hidden?this.saved_size:0);return a>b?this.hidden||(this.toggle(),this.hiddenByTool=!0):this.hiddenByTool&&(this.toggle(),this.hiddenByTool=!1),self},force_panel:function(a){return"show"==a?this.show():"hide"==a?this.hide():self},toString:function(){return"SidePanel("+this.id+")"}}),g=f.extend({id:"left"}),h=f.extend({id:"right"}),i=c.View.extend({initialize:function(){this.prev=null},render:function(){this.$el.html(this.template()),this.$("#galaxy_main").on("load",b.bind(this._iframeChangeHandler,this))},_iframeChangeHandler:function(b){var c=b.currentTarget,d=c.contentWindow&&c.contentWindow.location;d&&d.host&&(a(c).show(),this.prev&&this.prev.remove(),this.$("#center-panel").hide(),Galaxy.trigger("galaxy_main:load",{fullpath:d.pathname+d.search+d.hash,pathname:d.pathname,search:d.search,hash:d.hash}))},display:function(a){var b=this.$("#galaxy_main")[0].contentWindow||{},c=b.onbeforeunload&&b.onbeforeunload();!c||confirm(c)?(b.onbeforeunload=void 0,this.prev&&this.prev.remove(),this.prev=a,this.$("#galaxy_main").attr("src","about:blank").hide(),this.$("#center-panel").scrollTop(0).append(a.$el).show(),Galaxy.trigger("center-panel:load",a)):a&&a.remove()},template:function(){return['<div style="position: absolute; width: 100%; height: 100%">','<iframe name="galaxy_main" id="galaxy_main" frameborder="0" ','style="position: absolute; width: 100%; height: 100%;"/>','<div id="center-panel" ','style="display: none; position: absolute; width: 100%; height: 100%; padding: 10px; overflow: auto;"/>',"</div>"].join("")},toString:function(){return"CenterPanel"}});return{SidePanel:f,LeftPanel:g,RightPanel:h,CenterPanel:i}});
|
||||
define(["jquery","libs/underscore","libs/backbone"],function(a,b,c){"use strict";var d=160,e=800,f=c.View.extend({initialize:function(a){this.view=a.view,this.hidden=!1,this.saved_size=null,this.hiddenByTool=!1},$center:function(){return this.$el.siblings("#center")},$toggleButton:function(){return this.$(".unified-panel-footer > .panel-collapse")},render:function(){var a=this,c=this.view,d=this.view.model.attributes||{};this.$el.html(this._templatePanel(this.id)),b.each(d.buttons,function(b){a.$(".panel-header-buttons").append(b.$el)}),this.$el.addClass(d.cls),this.$(".panel-header-text").html(b.escape(d.title)),this.$(".unified-panel-body").append(c.$el),c.render()},_templatePanel:function(){return[this._templateHeader(),this._templateBody(),this._templateFooter()].join("")},_templateHeader:function(){return['<div class="unified-panel-header" unselectable="on">','<div class="unified-panel-header-inner">','<div class="panel-header-buttons" style="float: right"/>','<div class="panel-header-text"/>',"</div>","</div>"].join("")},_templateBody:function(){return'<div class="unified-panel-body"/>'},_templateFooter:function(){return['<div class="unified-panel-footer">','<div class="panel-collapse ',b.escape(this.id),'"/>','<div class="drag"/>',"</div>"].join("")},events:{"mousedown .unified-panel-footer > .drag":"_mousedownDragHandler","click .unified-panel-footer > .panel-collapse":"toggle"},_mousedownDragHandler:function(b){function c(a){var b=a.pageX-h;h=a.pageX;var c=f.$el.width(),i=g?c+b:c-b;i=Math.min(e,Math.max(d,i)),f.resize(i)}var f=this,g="left"===this.id,h=b.pageX;a("#dd-helper").show().on("mousemove",c).one("mouseup",function(){a(this).hide().off("mousemove",c)})},resize:function(a){return this.$el.css("width",a),this.$center().css(this.id,a),this},show:function(){if(this.hidden){var a=this,b={},c=this.id;return b[c]=0,a.$el.css(c,-this.saved_size).show().animate(b,"fast",function(){a.resize(a.saved_size)}),a.hidden=!1,a.$toggleButton().removeClass("hidden"),this}},hide:function(){if(!this.hidden){var a={},b=this.id;return this.saved_size=this.$el.width(),a[b]=-this.saved_size,this.$el.animate(a,"fast"),this.$center().css(b,0),this.hidden=!0,this.$toggleButton().addClass("hidden"),this}},toggle:function(){return this.hidden?this.show():this.hide(),this.hiddenByTool=!1,this},handle_minwidth_hint:function(a){var b=this.$center().width()-(this.hidden?this.saved_size:0);return a>b?this.hidden||(this.toggle(),this.hiddenByTool=!0):this.hiddenByTool&&(this.toggle(),this.hiddenByTool=!1),self},force_panel:function(a){return"show"==a?this.show():"hide"==a?this.hide():self},toString:function(){return"SidePanel("+this.id+")"}}),g=f.extend({id:"left"}),h=f.extend({id:"right"}),i=c.View.extend({initialize:function(){this.setElement(a(this.template())),this.$frame=this.$(".center-frame"),this.$panel=this.$(".center-panel"),this.$frame.on("load",b.bind(this._iframeChangeHandler,this))},_iframeChangeHandler:function(b){var c=b.currentTarget,d=c.contentWindow&&c.contentWindow.location;d&&d.host&&(a(c).show(),this.$panel.empty().hide(),Galaxy.trigger("center-frame:load",{fullpath:d.pathname+d.search+d.hash,pathname:d.pathname,search:d.search,hash:d.hash}))},display:function(a){var b=this.$frame[0].contentWindow||{},c=b.onbeforeunload&&b.onbeforeunload();(!c||confirm(c))&&(b.onbeforeunload=void 0,this.$frame.attr("src","about:blank").hide(),this.$panel.empty().scrollTop(0).append(a.$el).show(),Galaxy.trigger("center-panel:load",a))},template:function(){return'<div class="center-container"><iframe id="galaxy_main" name="galaxy_main" frameborder="0" class="center-frame" /><div class="center-panel" /></div>'},toString:function(){return"CenterPanel"}});return{SidePanel:f,LeftPanel:g,RightPanel:h,CenterPanel:i}});
|
||||
//# sourceMappingURL=../../maps/layout/panel.js.map
|
||||
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|
||||
define(["utils/utils","mvc/grid/grid-view","mvc/history/history-model","mvc/history/copy-dialog"],function(a,b,c,d){var e=Backbone.View.extend({initialize:function(){var b=this;this.setElement($("<div/>")),this.model=new Backbone.Model,a.get({url:Galaxy.root+"history/list",success:function(a){a.dict_format=!0,_.each(a.operations,function(a){"Copy"==a.label&&(a.onclick=function(a){b._showCopyDialog(a)})}),b.model.set(a),b.render()}})},render:function(){var a=new b(this.model.attributes);this.$el.empty().append(a.$el)},_showCopyDialog:function(a){var b=new c.History({id:a});b.fetch().fail(function(){alert("History could not be fetched. Please contact an administrator")}).done(function(){d(b,{}).done(function(){window.parent&&window.parent.Galaxy&&window.parent.Galaxy.currHistoryPanel&&window.parent.Galaxy.currHistoryPanel.loadCurrentHistory(),window.location.reload(!0)})})}});return{View:e}});
|
||||
//# sourceMappingURL=../../../maps/mvc/history/history-list.js.map
|
||||
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|
||||
define(["mvc/ui/popup-menu","mvc/history/copy-dialog","mvc/base-mvc","utils/localization","mvc/webhooks"],function(a,b,c,d,e){"use strict";function f(a,b,c){return _.clone(g).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target="galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var g=[{html:d("History Lists"),header:!0},{html:d("Saved Histories"),href:"history/list"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("Current History"),header:!0,anon:!0},{html:d("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:d("Copy History"),func:function(){b(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Show Structure"),href:"history/display_structured",anon:!0},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Dataset Actions"),header:!0,anon:!0},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:d("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:d("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really unhide all hidden datasets?"))&&$.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete all hidden datasets?"))&&$.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:d("Downloads"),header:!0},{html:d("Export Tool Citations"),href:"history/citations",anon:!0},{html:d("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:d("Other Actions"),header:!0},{html:d("Import from File"),href:"history/import_archive"}];e.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(a){var b=[];$.each(a.models,function(a,c){var e=c.toJSON();e.activate&&b.push({html:d(e.config.title),anon:!0})}),b.length>0&&(b.unshift({html:d("Webhooks"),header:!0}),$.merge(g,b))}});var h=function(b,c){c=c||{};var d=void 0===c.anonymous?!0:c.anonymous,e=c.purgeAllowed||!1,g=f(d,e,Galaxy.root);return new a(b,g)};return h});
|
||||
define(["mvc/ui/popup-menu","mvc/history/copy-dialog","mvc/base-mvc","utils/localization","mvc/webhooks"],function(a,b,c,d,e){"use strict";function f(a,b,c){return _.clone(g).filter(function(d){return a&&!d.anon?!1:!b&&d.purge?!1:(d.href&&(d.href=c+d.href,d.target=d.target||"galaxy_main"),d.confirm&&(d.func=function(){confirm(d.confirm)&&(galaxy_main.location=d.href)}),!0)})}var g=[{html:d("History Lists"),header:!0},{html:d("Saved Histories"),href:"histories/list",target:"_top"},{html:d("Histories Shared with Me"),href:"history/list_shared"},{html:d("Current History"),header:!0,anon:!0},{html:d("Create New"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.createNewHistory()}},{html:d("Copy History"),func:function(){b(Galaxy.currHistoryPanel.model).done(function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Share or Publish"),href:"history/sharing"},{html:d("Show Structure"),href:"history/display_structured",anon:!0},{html:d("Extract Workflow"),href:"workflow/build_from_current_history"},{html:d("Delete"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history?"))&&(galaxy_main.window.location.href="history/delete?id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Delete Permanently"),purge:!0,anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete the current history permanently? This cannot be undone."))&&(galaxy_main.window.location.href="history/delete?purge=True&id="+Galaxy.currHistoryPanel.model.id)}},{html:d("Dataset Actions"),header:!0,anon:!0},{html:d("Copy Datasets"),href:"dataset/copy_datasets"},{html:d("Dataset Security"),href:"root/history_set_default_permissions"},{html:d("Resume Paused Jobs"),href:"history/resume_paused_jobs?current=True",anon:!0},{html:d("Collapse Expanded Datasets"),func:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.collapseAll()}},{html:d("Unhide Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really unhide all hidden datasets?"))&&$.post(Galaxy.root+"history/adjust_hidden",{user_action:"unhide"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Delete Hidden Datasets"),anon:!0,func:function(){Galaxy&&Galaxy.currHistoryPanel&&confirm(d("Really delete all hidden datasets?"))&&$.post(Galaxy.root+"history/adjust_hidden",{user_action:"delete"},function(){Galaxy.currHistoryPanel.loadCurrentHistory()})}},{html:d("Purge Deleted Datasets"),confirm:d("Really delete all deleted datasets permanently? This cannot be undone."),href:"history/purge_deleted_datasets",purge:!0,anon:!0},{html:d("Downloads"),header:!0},{html:d("Export Tool Citations"),href:"history/citations",anon:!0},{html:d("Export History to File"),href:"history/export_archive?preview=True",anon:!0},{html:d("Other Actions"),header:!0},{html:d("Import from File"),href:"history/import_archive"}];e.add({url:"api/webhooks/history-menu/all",async:!1,callback:function(a){var b=[];$.each(a.models,function(a,c){var e=c.toJSON();e.activate&&b.push({html:d(e.config.title),anon:!0})}),b.length>0&&(b.unshift({html:d("Webhooks"),header:!0}),$.merge(g,b))}});var h=function(b,c){c=c||{};var d=void 0===c.anonymous?!0:c.anonymous,e=c.purgeAllowed||!1,g=f(d,e,Galaxy.root);return new a(b,g)};return h});
|
||||
//# sourceMappingURL=../../../maps/mvc/history/options-menu.js.map
|
||||
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|
||||
define([],function(){var a=Backbone.View.extend({initialize:function(){this.setElement("<div/>"),this.render()},render:function(){var a=this;$.getJSON(Galaxy.root+"api/workflows/menu/",function(b){var c=b.workflows,d=b.ids_in_menu,e=null;a.$el.empty().append(a._templateConfigWorkflowHeader()),e=a.$el.find(".configure-workflows"),e.append(a._templateActionButtons()),c.length>0?(e.append(a._templateConfigureWorkflow(a,c,d)),a.save_workflow_menu(a),a.make_checked(a,d),a.register_check_uncheck_all(a)):e.append(a._templateNoWorkflow())})},register_check_uncheck_all:function(a){var b=a.$el.find(".check-all-wf"),c=a.$el.find(".uncheck-all-wf");b.click(function(){a.check_uncheck_all(a,!0)}),c.click(function(){a.check_uncheck_all(a,!1)})},check_uncheck_all:function(a,b){$.each(a.$el.find(".wf-config-item"),function(){var a=$(this)[0];a.checked=b})},make_checked:function(a,b){$.each(a.$el.find(".wf-config-item"),function(){var a=$(this)[0];_.each(b,function(b){parseInt(a.value)===b&&(a.checked=!0)})})},save_workflow_menu:function(a){var b=a.$el.find(".wf-save-menu");b.click(function(){var b=[];$.each(a.$el.find(".wf-config-item"),function(){var a=$(this)[0];(a.checked||"true"===a.checked)&&b.push(parseInt(a.value))}),$.ajax({type:"PUT",url:Galaxy.root+"api/workflows/menu/",data:JSON.stringify({workflow_ids:b}),contentType:"application/json"}).done(function(a){window.location=Galaxy.root+"workflow?status="+a.status+"&message="+a.message})})},_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>'},_templateConfigureWorkflow:function(a,b,c){var d="",e="";return d+='<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(b,function(b){e=e+'<tr><td class="wf-td">'+_.escape(b.name)+"</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">'+a._templateInputCheckbox(a,b,c)+"</td></tr>"}),d=d+'<tbody class="workflow-config-menu">'+e+"</tbody></table>",d=d+'<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+'workflow" title="Back to workflow"><span>Back to workflow</span></a>'},_templateNoWorkflow:function(){return'<div class="wf-nodata"> You do not have any accessible workflows. </div>'},_templateInputCheckbox:function(a,b){return'<input type="checkbox" class="wf-config-item" name="workflow_ids" value="'+b.id+'" />'},_templateConfigWorkflowHeader:function(){return'<div class="page-container"><div class="configure-workflows wf"><h2>Configure workflow menu</h2></div></div>'}});return{View:a}});
|
||||
define([],function(){var a=Backbone.View.extend({initialize:function(){this.setElement("<div/>"),this.render()},render:function(){var a=this;$.getJSON(Galaxy.root+"api/workflows/menu/",function(b){var c=b.workflows,d=b.ids_in_menu,e=null;a.$el.empty().append(a._templateConfigWorkflowHeader()),e=a.$el.find(".configure-workflows"),e.append(a._templateActionButtons()),c.length>0?(e.append(a._templateConfigureWorkflow(a,c,d)),a.save_workflow_menu(a),a.make_checked(a,d),a.register_check_uncheck_all(a)):e.append(a._templateNoWorkflow())})},register_check_uncheck_all:function(a){var b=a.$el.find(".check-all-wf"),c=a.$el.find(".uncheck-all-wf");b.click(function(){a.check_uncheck_all(a,!0)}),c.click(function(){a.check_uncheck_all(a,!1)})},check_uncheck_all:function(a,b){$.each(a.$el.find(".wf-config-item"),function(){var a=$(this)[0];a.checked=b})},make_checked:function(a,b){$.each(a.$el.find(".wf-config-item"),function(){var a=$(this)[0];_.each(b,function(b){parseInt(a.value)===b&&(a.checked=!0)})})},save_workflow_menu:function(a){var b=a.$el.find(".wf-save-menu");b.click(function(){var b=[];$.each(a.$el.find(".wf-config-item"),function(){var a=$(this)[0];(a.checked||"true"===a.checked)&&b.push(parseInt(a.value))}),$.ajax({type:"PUT",url:Galaxy.root+"api/workflows/menu/",data:JSON.stringify({workflow_ids:b}),contentType:"application/json"}).done(function(){window.location=Galaxy.root+"user"})})},_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>'},_templateConfigureWorkflow:function(a,b,c){var d="",e="";return d+='<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(b,function(b){e=e+'<tr><td class="wf-td">'+_.escape(b.name)+"</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">'+a._templateInputCheckbox(a,b,c)+"</td></tr>"}),d=d+'<tbody class="workflow-config-menu">'+e+"</tbody></table>",d=d+'<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>'},_templateNoWorkflow:function(){return'<div class="wf-nodata"> You do not have any accessible workflows. </div>'},_templateInputCheckbox:function(a,b){return'<input type="checkbox" class="wf-config-item" name="workflow_ids" value="'+b.id+'" />'},_templateConfigWorkflowHeader:function(){return'<div class="page-container"><div class="configure-workflows wf"><h2>Configure workflow menu</h2></div></div>'}});return{View:a}});
|
||||
//# sourceMappingURL=../../../maps/mvc/workflow/workflow-configure-menu.js.map
|
||||
File diff suppressed because one or more lines are too long
@@ -1,2 +1,2 @@
|
||||
define([],function(){function a(a){return'<iframe src="'+a+'" frameborder="0" style="width: 100%; height: 100%;"/>'}function b(a,c){for(var d in a){var e=a[d];if(_.isObject(e)){var f=c(e);f&&(a[d]=f),b(e,c)}}}function c(a){var b,c,d,e;return c=/(\b(https?|ftp):\/\/[-A-Z0-9+&@#\/%?=~_|!:,.;]*[-A-Z0-9+&@#\/%=~_|])/gim,b=a.replace(c,'<a href="$1" target="_blank">$1</a>'),d=/(^|[^\/])(www\.[\S]+(\b|$))/gim,b=b.replace(d,'$1<a href="http://$2" target="_blank">$2</a>'),e=/(([a-zA-Z0-9\-\_\.])+@[a-zA-Z\_]+?(\.[a-zA-Z]{2,6})+)/gim,b=b.replace(e,'<a href="mailto:$1">$1</a>')}function d(a){return JSON.parse(JSON.stringify(a)||null)}function e(a){return/^[\],:{}\s]*$/.test(a.replace(/\\["\\\/bfnrtu]/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))}function f(a){return $("<div/>").text(a).html()}function g(a){if(a instanceof Array||(a=[a]),0===a.length)return!0;for(var b in a)if(["__null__","__undefined__",null,void 0].indexOf(a[b])>-1)return!0;return!1}function h(a){if($.isArray(a)){var a=a.toString().replace(/,/g,", "),b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+2)),a}return""}function i(a){top.__utils__get__=top.__utils__get__||{};var b=JSON.stringify(a);a.cache&&top.__utils__get__[b]?(a.success&&a.success(top.__utils__get__[b]),window.console.debug("utils.js::get() - Fetching from cache ["+a.url+"].")):j({url:a.url,data:a.data,success:function(c){top.__utils__get__[b]=c,a.success&&a.success(c)},error:function(b,c){a.error&&a.error(b,c)}})}function j(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?($.isEmptyObject(b.data)||(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url+=$.param(b.data,!0)),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){console.debug(c)}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b.status)}).always(function(){a.complete&&a.complete()})}function k(a,b){var c=$('<div class="'+a+'"></div>');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function l(a){$('link[href^="'+a+'"]').length||$('<link href="'+Galaxy.root+a+'" rel="stylesheet">').appendTo("head")}function m(a,b){return a?_.defaults(a,b):b}function n(a,b){for(var c=1,d=0;b>d;d++)c*=10;return Math.round(a*c)/c}function o(a,b,c){c=void 0!==c?c:1;var d="";if(a>=v)a/=v,d="TB";else if(a>=u)a/=u,d="GB";else if(a>=t)a/=t,d="MB";else if(a>=s)a/=s,d="KB";else{if(!(a>0))return b?"0 b":"<strong>-</strong>";d="b"}var e="b"==d?a:n(a,c);return b?e+" "+d:"<strong>"+e+"</strong> "+d}function p(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function q(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes();return datetime=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c}function r(a){a.script&&""!==a.script&&$("<script/>",{type:"text/javascript"}).text(a.script).appendTo("head"),a.styles&&""!==a.styles&&$("<style/>",{type:"text/css"}).text(a.styles).appendTo("head")}var s=1024,t=s*s,u=t*s,v=u*s;return{cssLoadFile:l,cssGetAttribute:k,get:i,merge:m,iframe:a,bytesToString:o,uid:p,time:q,request:j,sanitize:f,textify:h,isEmpty:g,deepeach:b,isJSON:e,clone:d,linkify:c,appendScriptStyle:r}});
|
||||
define([],function(){function a(a){return'<iframe src="'+a+'" frameborder="0" style="width: 100%; height: 100%;"/>'}function b(a,c){for(var d in a){var e=a[d];if(_.isObject(e)){var f=c(e);f&&(a[d]=f),b(e,c)}}}function c(a){var b,c,d,e;return c=/(\b(https?|ftp):\/\/[-A-Z0-9+&@#\/%?=~_|!:,.;]*[-A-Z0-9+&@#\/%=~_|])/gim,b=a.replace(c,'<a href="$1" target="_blank">$1</a>'),d=/(^|[^\/])(www\.[\S]+(\b|$))/gim,b=b.replace(d,'$1<a href="http://$2" target="_blank">$2</a>'),e=/(([a-zA-Z0-9\-\_\.])+@[a-zA-Z\_]+?(\.[a-zA-Z]{2,6})+)/gim,b=b.replace(e,'<a href="mailto:$1">$1</a>')}function d(a){return JSON.parse(JSON.stringify(a)||null)}function e(a){return/^[\],:{}\s]*$/.test(a.replace(/\\["\\\/bfnrtu]/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))}function f(a){return $("<div/>").text(a).html()}function g(a){if(a instanceof Array||(a=[a]),0===a.length)return!0;for(var b in a)if(["__null__","__undefined__",null,void 0].indexOf(a[b])>-1)return!0;return!1}function h(a){if($.isArray(a)){var a=a.toString().replace(/,/g,", "),b=a.lastIndexOf(", ");return-1!=b&&(a=a.substr(0,b)+" or "+a.substr(b+2)),a}return""}function i(a){top.__utils__get__=top.__utils__get__||{};var b=JSON.stringify(a);a.cache&&top.__utils__get__[b]?(a.success&&a.success(top.__utils__get__[b]),window.console.debug("utils.js::get() - Fetching from cache ["+a.url+"].")):j({url:a.url,data:a.data,success:function(c){top.__utils__get__[b]=c,a.success&&a.success(c)},error:function(b,c){a.error&&a.error(b,c)}})}function j(a){var b={contentType:"application/json",type:a.type||"GET",data:a.data||{},url:a.url};"GET"==b.type||"DELETE"==b.type?($.isEmptyObject(b.data)||(b.url+=-1==b.url.indexOf("?")?"?":"&",b.url+=$.param(b.data,!0)),b.data=null):(b.dataType="json",b.url=b.url,b.data=JSON.stringify(b.data)),$.ajax(b).done(function(b){if("string"==typeof b)try{b=b.replace("Infinity,",'"Infinity",'),b=jQuery.parseJSON(b)}catch(c){console.debug(c)}a.success&&a.success(b)}).fail(function(b){var c=null;try{c=jQuery.parseJSON(b.responseText)}catch(d){c=b.responseText}a.error&&a.error(c,b.status)}).always(function(){a.complete&&a.complete()})}function k(a,b){var c=$('<div class="'+a+'"></div>');c.appendTo(":eq(0)");var d=c.css(b);return c.remove(),d}function l(a){$('link[href^="'+a+'"]').length||$('<link href="'+Galaxy.root+a+'" rel="stylesheet">').appendTo("head")}function m(a,b){return a?_.defaults(a,b):b}function n(a,b){for(var c=1,d=0;b>d;d++)c*=10;return Math.round(a*c)/c}function o(a,b,c){c=void 0!==c?c:1;var d="";if(a>=w)a/=w,d="TB";else if(a>=v)a/=v,d="GB";else if(a>=u)a/=u,d="MB";else if(a>=t)a/=t,d="KB";else{if(!(a>0))return b?"0 b":"<strong>-</strong>";d="b"}var e="b"==d?a:n(a,c);return b?e+" "+d:"<strong>"+e+"</strong> "+d}function p(){return top.__utils__uid__=top.__utils__uid__||0,"uid-"+top.__utils__uid__++}function q(){var a=new Date,b=(a.getHours()<10?"0":"")+a.getHours(),c=(a.getMinutes()<10?"0":"")+a.getMinutes();return datetime=a.getDate()+"/"+(a.getMonth()+1)+"/"+a.getFullYear()+", "+b+":"+c}function r(a){a.script&&""!==a.script&&$("<script/>",{type:"text/javascript"}).text(a.script).appendTo("head"),a.styles&&""!==a.styles&&$("<style/>",{type:"text/css"}).text(a.styles).appendTo("head")}function s(a){return decodeURIComponent(window.location.search.replace(new RegExp("^(?:.*[&\\?]"+encodeURIComponent(a).replace(/[\.\+\*]/g,"\\$&")+"(?:\\=([^&]*))?)?.*$","i"),"$1"))}var t=1024,u=t*t,v=u*t,w=v*t;return{cssLoadFile:l,cssGetAttribute:k,get:i,merge:m,iframe:a,bytesToString:o,uid:p,time:q,request:j,sanitize:f,textify:h,isEmpty:g,deepeach:b,isJSON:e,clone:d,linkify:c,appendScriptStyle:r,getQueryString:s}});
|
||||
//# sourceMappingURL=../../maps/utils/utils.js.map
|
||||
File diff suppressed because one or more lines are too long
@@ -1,40 +0,0 @@
|
||||
<%inherit file="../grid_base.mako"/>
|
||||
|
||||
<%namespace file="grid_js.mako" import="copy_dialog_hack" />
|
||||
<%def name="load( embedded=False, insert=None )">
|
||||
<!-- saved history grid.mako -->
|
||||
${parent.load( embedded=embedded, insert=insert )}
|
||||
|
||||
## define the module required below
|
||||
${copy_dialog_hack()}
|
||||
<script type="text/javascript">
|
||||
require([ 'copy-dialog-hack' ], function( copyDialogHack ){
|
||||
function findHistoryId( menuButton ){
|
||||
var $link = $( menuButton ).children( '.menubutton-label' );
|
||||
// TODO: ohdearlord. stahp.
|
||||
return ( $link.attr( 'href' ).match( /id=(\w+)/ ) || [] )[1];
|
||||
}
|
||||
|
||||
// wait for page ready and set it all up, do it again when the grid refreshes
|
||||
$(function(){
|
||||
if( !gridView ){
|
||||
console.warn( 'no grid' );
|
||||
return;
|
||||
}
|
||||
|
||||
function replaceCopyFunction(){
|
||||
gridView.$( '.popup.menubutton' ).each( function( i ){
|
||||
copyDialogHack.call( this, i, findHistoryId );
|
||||
});
|
||||
}
|
||||
replaceCopyFunction();
|
||||
|
||||
var originalInitGrid = gridView.init_grid;
|
||||
gridView.init_grid = function __patched_init_grid( json ){
|
||||
originalInitGrid.call( gridView, json );
|
||||
replaceCopyFunction();
|
||||
};
|
||||
});
|
||||
});
|
||||
</script>
|
||||
</%def>
|
||||
@@ -1,65 +0,0 @@
|
||||
<%def name="copy_dialog_hack()">
|
||||
## TODO: remove!!!!! when grids are iterated over again
|
||||
<script type="text/javascript">
|
||||
// define a module that has:
|
||||
// an hack for which to override the url based history copy function in the popupmenus
|
||||
// and replace it with a dialog that uses the API instead
|
||||
define( 'copy-dialog-hack', [
|
||||
'mvc/history/history-model',
|
||||
'mvc/history/copy-dialog'
|
||||
], function( mHistory, historyCopyDialog ){
|
||||
|
||||
// callbacks
|
||||
function tellTheUserItFailed(){
|
||||
// history failed to copy, put the relevant techy crap in the console and alert the user
|
||||
console.error( arguments );
|
||||
alert( "${_('History could not be fetched. Please contact an administrator')}" );
|
||||
}
|
||||
function refreshEverything(){
|
||||
// history was copied
|
||||
// if we're in a frame, check for the parent Galaxy and try to refresh the history
|
||||
if( window.parent && window.parent.Galaxy && window.parent.Galaxy.currHistoryPanel ){
|
||||
window.parent.Galaxy.currHistoryPanel.loadCurrentHistory();
|
||||
}
|
||||
// in any case reload the save history panel
|
||||
window.location.reload( true );
|
||||
}
|
||||
|
||||
// get the id from the dom somehow (the two doms (saved/shared) are different...)
|
||||
function findHistoryId( $menuButton ){
|
||||
var title = '${grid.title}';
|
||||
if( title === 'Saved Histories' ){
|
||||
var $link = $menuButton.children( '.menubutton-label' );
|
||||
// TODO: ohdearlord. stahp.
|
||||
return ( $link.attr( 'href' ).match( /id=(\w+)/ ) || [] )[1];
|
||||
}
|
||||
// Histories shared with you
|
||||
var $label = $menuButton.children( 'label' );
|
||||
return $label.attr( 'id' );
|
||||
}
|
||||
|
||||
// for each popupmenu, (this == a popup activator button), remove the link and add a click function
|
||||
// that fetches the history and shows a copy dialog for it
|
||||
// pass in a fn for extracting the id from the dom and an (optional) object with dialog options
|
||||
function copyDialogHack( i, historyIdFindFn, dialogOptions ){
|
||||
dialogOptions = dialogOptions || {};
|
||||
var $this = $( this ),
|
||||
historyId = historyIdFindFn( this ),
|
||||
menuOptions = $this.data( 'popupmenu' ).options,
|
||||
copyOption = menuOptions.filter( function( o ){ return o.html === 'Copy' })[0];
|
||||
|
||||
copyOption.href = 'javascript:void(0)';
|
||||
copyOption.func = function copyOptionClicked( ev ){
|
||||
ev.preventDefault();
|
||||
var history = new mHistory.History({ id : historyId });
|
||||
history.fetch()
|
||||
.fail( tellTheUserItFailed )
|
||||
.done( function(){
|
||||
historyCopyDialog( history, dialogOptions ).done( refreshEverything );
|
||||
});
|
||||
}
|
||||
}
|
||||
return copyDialogHack;
|
||||
});
|
||||
</script>
|
||||
</%def>
|
||||
@@ -1,69 +0,0 @@
|
||||
<%inherit file="/webapps/galaxy/base_panels.mako"/>
|
||||
<%namespace file="/message.mako" import="render_msg" />
|
||||
|
||||
<%def name="stylesheets()">
|
||||
${parent.stylesheets()}
|
||||
${h.css( "workflow" )}
|
||||
</%def>
|
||||
|
||||
<%def name="javascripts()">
|
||||
${parent.javascripts()}
|
||||
</%def>
|
||||
|
||||
<%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()">Import Galaxy workflow</%def>
|
||||
|
||||
<%def name="center_panel()">
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%endif
|
||||
<div class="toolForm">
|
||||
<div class="toolFormTitle">Import Galaxy workflow</div>
|
||||
<div class="toolFormBody">
|
||||
<form name="import_workflow" id="import_workflow" action="${h.url_for( controller='workflow', action='import_workflow' )}" enctype="multipart/form-data" method="POST">
|
||||
<div class="form-row">
|
||||
<label>Galaxy workflow URL:</label>
|
||||
<input type="text" name="url" value="${url | h}" size="40">
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
If the workflow is accessible via a URL, enter the URL above and click <b>Import</b>.
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<label>Galaxy workflow file:</label>
|
||||
<div class="form-row-input">
|
||||
<input type="file" name="file_data"/>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
If the workflow is in a file on your computer, choose it and then click <b>Import</b>.
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
<div class="form-row">
|
||||
<input type="submit" class="primary-button" name="import_button" value="Import">
|
||||
</div>
|
||||
</form>
|
||||
<hr/>
|
||||
<div class="form-row">
|
||||
<label>Import a Galaxy workflow from myExperiment:</label>
|
||||
<div class="form-row-input">
|
||||
<a href="${h.url_for( myexperiment_target_url )}">
|
||||
Visit myExperiment
|
||||
</a>
|
||||
</div>
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
Click the link above to visit myExperiment and browse for Galaxy workflows.
|
||||
</div>
|
||||
<div style="clear: both"></div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</%def>
|
||||
@@ -1,10 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
${h.js("libs/bibtex", "libs/jquery/jquery-ui")}
|
||||
${h.css('jquery-ui/smoothness/jquery-ui')}
|
||||
<script>
|
||||
require(['mvc/tool/tool-form-composite'], function( ToolForm ) {
|
||||
$(function() {
|
||||
var form = new ToolForm.View(${ h.dumps( workflow_dict ) });
|
||||
});
|
||||
});
|
||||
</script>
|
||||
Reference in New Issue
Block a user