mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 00:12:08 +08:00
Merge branch 'dev' into refactor_panels_000
This commit is contained in:
guerler
@@ -6,9 +6,10 @@ var jQuery = require( 'jquery' ),
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HistoryPanel = require( './history-panel' ),
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Page = require( 'layout/page' ),
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ToolForm = require( 'mvc/tool/tool-form' ),
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UserPreferences = require( 'mvc/user/user-preferences' );
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CustomBuilds = require( 'mvc/user/user-custom-builds' );
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Tours = require( 'mvc/tours' );
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UserPreferences = require( 'mvc/user/user-preferences' ),
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CustomBuilds = require( 'mvc/user/user-custom-builds' ),
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Tours = require( 'mvc/tours' ),
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Workflows = require( 'mvc/workflow/workflow' );
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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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@@ -77,6 +78,7 @@ window.app = function app( options, bootstrapped ){
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'(/)tours(/)(:tour_id)' : 'show_tours',
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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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'(/)custom_builds' : 'show_custom_builds'
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},
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@@ -109,6 +111,10 @@ 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_workflows : function(){
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centerPanel.display( new Workflows.View() );
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},
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show_custom_builds : function() {
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var self = this;
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var historyPanel = this.page.historyPanel.historyView;
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@@ -52,9 +52,10 @@ var ToolPanel = Backbone.View.extend({
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this.tool_panel_view.render();
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}
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// build the dom for the workflow portion of the tool menu
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this.$( '#internal-workflows' ).append( self._templateTool({
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// add internal workflow list
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self.$( '#internal-workflows' ).append( self._templateAllWorkflow({
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title : _l( 'All workflows' ),
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href : 'workflow/list_for_run'
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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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@@ -73,6 +74,16 @@ var ToolPanel = Backbone.View.extend({
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].join('');
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},
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/** build a link to 'All Workflows' */
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_templateAllWorkflow: function( tool ) {
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return [
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'<div class="toolTitle">',
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// global
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'<a href="', Galaxy.root, tool.href, '">', tool.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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@@ -25,7 +25,7 @@ var Collection = Backbone.Collection.extend({
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id : 'analysis',
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title : _l('Analyze Data'),
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url : '',
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tooltip : 'Analysis home view'
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tooltip : _l('Analysis home view')
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});
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//
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@@ -34,9 +34,13 @@ var Collection = Backbone.Collection.extend({
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this.add({
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id : 'workflow',
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title : _l('Workflow'),
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tooltip : _l('Chain tools into workflows'),
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disabled : !Galaxy.user.id,
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url : 'workflow',
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tooltip : 'Chain tools into workflows',
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disabled : !Galaxy.user.id
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target : 'galaxy_main',
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onclick : function() {
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window.location = Galaxy.root + 'workflow';
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}
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});
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//
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@@ -46,7 +50,7 @@ var Collection = Backbone.Collection.extend({
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id : 'shared',
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title : _l('Shared Data'),
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url : 'library/index',
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tooltip : 'Access published resources',
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tooltip : _l('Access published resources'),
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menu : [{
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title : _l('Data Libraries'),
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url : 'library/list'
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@@ -90,7 +94,7 @@ var Collection = Backbone.Collection.extend({
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id : 'visualization',
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title : _l('Visualization'),
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url : 'visualization/list',
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tooltip : 'Visualize datasets',
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tooltip : _l('Visualize datasets'),
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disabled : !Galaxy.user.id,
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menu : [{
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title : _l('New Track Browser'),
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@@ -138,7 +142,7 @@ var Collection = Backbone.Collection.extend({
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id : 'admin',
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title : _l('Admin'),
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url : 'admin',
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tooltip : 'Administer this Galaxy',
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tooltip : _l('Administer this Galaxy'),
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cls : 'admin-only'
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});
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@@ -148,7 +152,7 @@ var Collection = Backbone.Collection.extend({
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var helpTab = {
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id : 'help',
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title : _l('Help'),
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tooltip : 'Support, contact, and community',
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tooltip : _l('Support, contact, and community'),
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menu : [{
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title : _l('Support'),
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url : options.support_url,
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@@ -211,7 +215,7 @@ var Collection = Backbone.Collection.extend({
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id : 'user',
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title : _l('Login or Register'),
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cls : 'loggedout-only',
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tooltip : 'Account registration or login',
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tooltip : _l('Account registration or login'),
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menu : [{
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title : _l('Login'),
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url : 'user/login',
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@@ -231,7 +235,7 @@ var Collection = Backbone.Collection.extend({
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id : 'user',
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title : _l('User'),
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cls : 'loggedin-only',
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tooltip : 'Account and saved data',
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tooltip : _l('Account and saved data'),
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menu : [{
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title : _l('Logged in as') + ' ' + Galaxy.user.get( 'email' )
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},{
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@@ -308,7 +312,7 @@ var Tab = Backbone.View.extend({
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this.$note.html( this.model.get( 'note' ) || '' )
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.removeClass().addClass( 'dropdown-note' )
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.addClass( this.model.get( 'note_cls' ) )
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.css( { 'display' : this.model.get( 'show_note' ) && 'block' || 'none' } )
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.css( { 'display' : this.model.get( 'show_note' ) && 'block' || 'none' } );
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this.$toggle.html( this.model.get( 'title' ) || '' )
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.removeClass().addClass( 'dropdown-toggle' )
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.addClass( this.model.get( 'cls' ) )
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@@ -387,7 +391,7 @@ var Tab = Backbone.View.extend({
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}
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} else {
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function buildLink( label, url ) {
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return $( '<div/>' ).append( $( '<a/>' ).attr( 'href', Galaxy.root + url ).html( label ) ).html()
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return $( '<div/>' ).append( $( '<a/>' ).attr( 'href', Galaxy.root + url ).html( label ) ).html();
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}
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this.$toggle.popover && this.$toggle.popover( 'destroy' );
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this.$toggle.popover({
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@@ -0,0 +1,198 @@
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/** Workflow view */
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define( [], function() {
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/** View of the main workflow list page */
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var View = Backbone.View.extend({
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initialize: function() {
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this.setElement( '<div/>' );
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this.render();
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},
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render: function() {
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var self = this,
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min_query_length = 3;
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$.getJSON( Galaxy.root + 'api/workflows/', function( workflows ) {
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var $el_workflow = null;
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// Add workflow header
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self.$el.empty().append( self._templateHeader() );
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// Add user actions message if any
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self.build_messages( self );
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$el_workflow = self.$el.find( '.user-workflows' );
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// Add the actions buttons
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$el_workflow.append( self._templateActionButtons() );
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if( workflows.length > 0) {
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$el_workflow.append( self._templateWorkflowTable( self, workflows) );
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self.adjust_actiondropdown( $el_workflow );
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// Register delete and run workflow events
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_.each( workflows, function( wf ) {
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self.confirm_delete( self, wf );
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});
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// Register search workflow event
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self.search_workflow( self, self.$el.find( '.search-wf' ), self.$el.find( '.workflow-search tr' ), min_query_length );
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}
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else {
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$el_workflow.append( self._templateNoWorkflow() );
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}
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});
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},
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/** Build messages after user action */
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build_messages: function( self ) {
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var $el_message = self.$el.find( '.response-message' ),
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status = self.get_querystring( 'status' ),
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message = self.get_querystring( 'message' );
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if( message && message !== null && message !== "" ) {
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$el_message.addClass( status + 'message' );
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$el_message.html( '<p>' + message + '</p>' );
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}
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else {
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$el_message.html("");
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}
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},
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/** Add confirm box before removing/unsharing workflow */
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confirm_delete: function( self, workflow ) {
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var $el_wf_link = self.$el.find( '.link-confirm-' + workflow.id ),
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$el_shared_wf_link = self.$el.find( '.link-confirm-shared-' + workflow.id );
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$el_wf_link.click( function() {
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return confirm( "Are you sure you want to delete workflow '" + workflow.name + "'?" );
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});
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$el_shared_wf_link.click( function() {
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return confirm( "Are you sure you want to remove the shared workflow '" + workflow.name + "'?" );
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||||
});
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},
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/** Implement client side workflow search/filtering */
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search_workflow: function( self, $el_searchinput, $el_tabletr, min_querylen ) {
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$el_searchinput.on( 'keyup', function () {
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var query = $( this ).val();
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// Filter when query is at least 3 characters
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// otherwise show all rows
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if( query.length >= min_querylen ) {
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// Ignore the query's case using 'i'
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var regular_expression = new RegExp( query, 'i' );
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$el_tabletr.hide();
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$el_tabletr.filter(function () {
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// Apply regular expression on each row's text
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// and show when there is a match
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return regular_expression.test( $( this ).text() );
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}).show();
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||||
}
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else {
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$el_tabletr.show();
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||||
}
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});
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||||
},
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||||
|
||||
/** Get querystrings from url */
|
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get_querystring: function( key ) {
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return decodeURIComponent( window.location.search.replace(new RegExp("^(?:.*[&\\?]" + encodeURIComponent( key ).replace(/[\.\+\*]/g, "\\$&") + "(?:\\=([^&]*))?)?.*$", "i"), "$1") );
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},
|
||||
|
||||
/** Ajust the position of dropdown with respect to table */
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adjust_actiondropdown: function( $el ) {
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$el.on( 'show.bs.dropdown', function () {
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$el.css( "overflow", "inherit" );
|
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});
|
||||
|
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$el.on( 'hide.bs.dropdown', function () {
|
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$el.css( "overflow", "auto" );
|
||||
});
|
||||
},
|
||||
|
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/** Template for no workflow */
|
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_templateNoWorkflow: function() {
|
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return '<div class="wf-nodata"> You have no workflows. </div>';
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},
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|
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/** Template for actions buttons */
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_templateActionButtons: function() {
|
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return '<ul class="manage-table-actions">' +
|
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'<li>' +
|
||||
'<input class="search-wf form-control" type="text" autocomplete="off" placeholder="search for workflow...">' +
|
||||
'</li>' +
|
||||
'<li>' +
|
||||
'<a class="action-button fa fa-plus wf-action" id="new-workflow" title="Create new workflow" href="'+ Galaxy.root +'workflow/create">' +
|
||||
'</a>' +
|
||||
'</li>' +
|
||||
'<li>' +
|
||||
'<a class="action-button fa fa-upload wf-action" id="import-workflow" title="Upload or import workflow" href="'+ Galaxy.root +'workflow/import_workflow">' +
|
||||
'</a>' +
|
||||
'</li>' +
|
||||
'</ul>';
|
||||
},
|
||||
|
||||
/** Template for workflow table */
|
||||
_templateWorkflowTable: function( self, workflows ) {
|
||||
var tableHtml = "", trHtml = "";
|
||||
tableHtml = tableHtml + '<table class="table colored"><thead>' +
|
||||
'<tr class="header">' +
|
||||
'<th class="wf-td">Name</th>' +
|
||||
'<th class="wf-td">Owner</th>' +
|
||||
'<th class="wf-td"># of Steps</th>' +
|
||||
'<th class="wf-td">Published</th>' +
|
||||
'</tr></thead>';
|
||||
_.each( workflows, function( wf ) {
|
||||
trHtml = trHtml + '<tr>' +
|
||||
'<td class="wf-td wf-dpd">' +
|
||||
'<div class="dropdown">' +
|
||||
'<button class="menubutton" type="button" data-toggle="dropdown">' +
|
||||
_.escape( wf.name ) + '<span class="caret"></span>' +
|
||||
'</button>' +
|
||||
self._templateActions( wf ) +
|
||||
'</div>' +
|
||||
'</td>' +
|
||||
'<td>' + ( wf.owner === Galaxy.user.attributes.username ? "You" : wf.owner ) +'</td>' +
|
||||
'<td class="wf-td">' + wf.number_of_steps + '</td>' +
|
||||
'<td class="wf-td">' + ( wf.published ? "Yes" : "No" ) + '</td>' +
|
||||
'</tr>';
|
||||
});
|
||||
return tableHtml + '<tbody class="workflow-search">' + trHtml + '</tbody></table>';
|
||||
},
|
||||
|
||||
/** Template for user actions for workflows */
|
||||
_templateActions: function( workflow ) {
|
||||
if( workflow.owner === Galaxy.user.attributes.username ) {
|
||||
return '<ul class="dropdown-menu action-dpd">' +
|
||||
'<li><a href="'+ Galaxy.root +'workflow/editor?id='+ workflow.id +'">Edit</a></li>' +
|
||||
'<li><a href="'+ Galaxy.root +'workflow/run?id='+ workflow.id +'" target="galaxy_main">Run</a></li>' +
|
||||
'<li><a href="'+ Galaxy.root +'workflow/sharing?id='+ workflow.id +'">Share or Download</a></li>' +
|
||||
'<li><a href="'+ Galaxy.root +'workflow/copy?id='+ workflow.id +'">Copy</a></li>' +
|
||||
'<li><a href="'+ Galaxy.root +'workflow/rename?id='+ workflow.id +'">Rename</a></li>' +
|
||||
'<li><a href="'+ Galaxy.root +'workflow/display_by_id?id='+ workflow.id +'">View</a></li>' +
|
||||
'<li><a class="link-confirm-'+ workflow.id +'" href="'+ Galaxy.root +'workflow/delete?id='+ workflow.id +'">Delete</a></li>' +
|
||||
'</ul>';
|
||||
}
|
||||
else {
|
||||
return '<ul class="dropdown-menu action-dpd">' +
|
||||
'<li><a href="'+ Galaxy.root +'workflow/display_by_username_and_slug?username='+ workflow.owner +'&slug='+ workflow.slug +'">View</a></li>' +
|
||||
'<li><a href="'+ Galaxy.root +'workflow/run?id='+ workflow.id +'" target="galaxy_main">Run</a></li>' +
|
||||
'<li><a href="'+ Galaxy.root +'workflow/copy?id='+ workflow.id +'">Copy</a></li>' +
|
||||
'<li><a class="link-confirm-shared-'+ workflow.id +'" href="'+ Galaxy.root +'workflow/sharing?unshare_me=True&id='+ workflow.id +'">Remove</a></li>' +
|
||||
'</ul>';
|
||||
}
|
||||
},
|
||||
|
||||
/** Main template */
|
||||
_templateHeader: function() {
|
||||
return '<div class="page-container">' +
|
||||
'<div class="user-workflows wf">' +
|
||||
'<div class="response-message"></div>' +
|
||||
'<h2>Your workflows</h2>' +
|
||||
'</div>'+
|
||||
'<div class="other-options wf">' +
|
||||
'<h2>Other options</h2>' +
|
||||
'<a class="action-button fa fa-cog wf-action" href="'+ Galaxy.root +'workflow/configure_menu" title="Configure your workflow menu">' +
|
||||
'<span>Configure your workflow menu</span>' +
|
||||
'</a>' +
|
||||
'</div>' +
|
||||
'</div>';
|
||||
}
|
||||
});
|
||||
|
||||
return {
|
||||
View : View
|
||||
};
|
||||
});
|
||||
@@ -0,0 +1,327 @@
|
||||
/** en/main localization hash - for use with requirejs' i18n plugin */
|
||||
define({
|
||||
// ----------------------------------------------------------------------------- masthead
|
||||
"Analyze Data":
|
||||
"Daten analysieren",
|
||||
"Workflow":
|
||||
"Arbeitsablauf",
|
||||
"Shared Data":
|
||||
"Gemeinsame Daten",
|
||||
"Data Libraries":
|
||||
"Datenbibliotheken",
|
||||
"Histories":
|
||||
"Geschichten",
|
||||
"Workflows":
|
||||
"Workflows",
|
||||
"Visualizations":
|
||||
"Visualisierungen",
|
||||
"Pages":
|
||||
"Seiten",
|
||||
"Visualization":
|
||||
"Visualisierung",
|
||||
"New Track Browser":
|
||||
"Neuer Track Browser",
|
||||
"Saved Visualizations":
|
||||
"Gespeicherte Visualisierungen",
|
||||
"Interactive Environments":
|
||||
"Interaktive Umgebungen",
|
||||
"Admin":
|
||||
"Administrator",
|
||||
"Help":
|
||||
"Hilfe",
|
||||
"Support":
|
||||
"Unterstützung",
|
||||
"Search":
|
||||
"Suche",
|
||||
"Mailing Lists":
|
||||
"Mailinglisten",
|
||||
"Videos":
|
||||
"Videos",
|
||||
"Wiki":
|
||||
"Wiki",
|
||||
"How to Cite Galaxy":
|
||||
"Wie man Galaxie zitiert",
|
||||
"Interactive Tours":
|
||||
"Interactive Tours",
|
||||
"User":
|
||||
"Benutzer",
|
||||
"Login":
|
||||
"Anmeldung",
|
||||
"Register":
|
||||
"Neu registrieren",
|
||||
"Login or Register":
|
||||
"Einloggen oder Registrieren",
|
||||
"Logged in as":
|
||||
"Angemeldet als",
|
||||
"Preferences":
|
||||
"Präferenzen",
|
||||
"Custom Builds":
|
||||
"Custom Builds",
|
||||
"Logout":
|
||||
"Ausloggen",
|
||||
"Saved Histories":
|
||||
"Gespeicherte Geschichten",
|
||||
"Saved Datasets":
|
||||
"Gespeicherte Datasets",
|
||||
"Saved Pages":
|
||||
"Gespeicherte Seiten",
|
||||
//Tooltip
|
||||
"Account and saved data":
|
||||
"Konto und gespeicherte Daten",
|
||||
"Account registration or login":
|
||||
"Konto Registrierung oder Login",
|
||||
"Support, contact, and community":
|
||||
"Unterstützung, Kontakt und Community",
|
||||
"Administer this Galaxy":
|
||||
"Verwalte diese Galaxie",
|
||||
"Visualize datasets":
|
||||
"Visualisieren von Datensätzen",
|
||||
"Access published resources":
|
||||
"Zugriff auf veröffentlichte Ressourcen",
|
||||
"Chain tools into workflows":
|
||||
"Kettenwerkzeuge in Workflows",
|
||||
"Analysis home view":
|
||||
"Analyse home view",
|
||||
// ---------------------------------------------------------------------------- histories
|
||||
// ---- history/options-menu
|
||||
"History Lists":
|
||||
"History Lists",
|
||||
// Saved histories is defined above.
|
||||
// "Saved Histories":
|
||||
// false,
|
||||
"Histories Shared with Me":
|
||||
"Geschichten mit mir geteilt",
|
||||
"Current History":
|
||||
"Aktuelle Geschichte",
|
||||
"Create New":
|
||||
"Erstelle neu",
|
||||
"Copy History":
|
||||
"Geschichte kopieren",
|
||||
"Share or Publish":
|
||||
"Teilen oder veröffentlichen",
|
||||
"Show Structure":
|
||||
"Struktur anzeigen",
|
||||
"Extract Workflow":
|
||||
"Workflow extrahieren",
|
||||
// Delete is defined elsewhere, but is also in this menu.
|
||||
// "Delete":
|
||||
// false,
|
||||
"Delete Permanently":
|
||||
"Dauerhaft löschen",
|
||||
"Dataset Actions":
|
||||
"Datensatzaktionen",
|
||||
"Copy Datasets":
|
||||
"Datensätze kopieren",
|
||||
"Dataset Security":
|
||||
"Datensatz Sicherheit",
|
||||
"Resume Paused Jobs":
|
||||
"Fortsetzen pausierte Jobs",
|
||||
"Collapse Expanded Datasets":
|
||||
"Collapse Expanded Datasets",
|
||||
"Unhide Hidden Datasets":
|
||||
"Hidden Datasets verstecken",
|
||||
"Delete Hidden Datasets":
|
||||
"Hidden Datasets löschen",
|
||||
"Purge Deleted Datasets":
|
||||
"Gelöschte Datasets löschen",
|
||||
"Downloads":
|
||||
"Downloads",
|
||||
"Export Tool Citations":
|
||||
"Export Tool Zitate",
|
||||
"Export History to File":
|
||||
"Export History to File",
|
||||
"Other Actions":
|
||||
"Andere Aktionen",
|
||||
"Import from File":
|
||||
"Import aus Datei",
|
||||
"Webhooks":
|
||||
"Webhooks",
|
||||
// ---- history-model
|
||||
// ---- history-view
|
||||
"This history is empty":
|
||||
"Diese Geschichte ist leer",
|
||||
"No matching datasets found":
|
||||
"Keine passenden Datensätze gefunden",
|
||||
"An error occurred while getting updates from the server":
|
||||
"Ein Fehler ist aufgetreten beim Aktualisieren vom Server",
|
||||
"Please contact a Galaxy administrator if the problem persists":
|
||||
"Bitte wenden Sie sich an einen Galaxy-Administrator, wenn das Problem weiterhin besteht",
|
||||
//TODO:
|
||||
//"An error was encountered while <% where %>" :
|
||||
//false,
|
||||
"search datasets":
|
||||
"Suchdatensätze",
|
||||
"You are currently viewing a deleted history!":
|
||||
"Du siehst derzeit einen gelöschten Verlauf!",
|
||||
"You are over your disk quota":
|
||||
"Du bist über dein Festplatten-Kontingent",
|
||||
"Tool execution is on hold until your disk usage drops below your allocated quota":
|
||||
"Tool-Ausführung ist in der Warteschleife, bis Ihre Datenträgerverwendung unter Ihrem zugeteilten Kontingent fällt",
|
||||
"All":
|
||||
"Alle",
|
||||
"None":
|
||||
"Keiner",
|
||||
"For all selected":
|
||||
"Für alle ausgewählt",
|
||||
// ---- history-view-edit
|
||||
"Edit history tags":
|
||||
"Geschichte bearbeiten",
|
||||
"Edit history Annotation":
|
||||
"Historie bearbeiten",
|
||||
"Click to rename history":
|
||||
"Klicken Sie hier, um den Verlauf umzubenennen",
|
||||
// multi operations
|
||||
"Operations on multiple datasets":
|
||||
"Operationen auf mehreren Datensätzen",
|
||||
"Hide datasets":
|
||||
"Datensätze ausblenden",
|
||||
"Unhide datasets":
|
||||
"Datasets einblenden",
|
||||
"Delete datasets":
|
||||
"Datensätze löschen",
|
||||
"Undelete datasets":
|
||||
"Undelete-Datasets",
|
||||
"Permanently delete datasets":
|
||||
"Datensätze dauerhaft löschen",
|
||||
"This will permanently remove the data in your datasets. Are you sure?":
|
||||
"Das wird endgültig die Daten in deinen Datasets entfernen. Bist du sicher?",
|
||||
// ---- history-view-annotated
|
||||
"Dataset":
|
||||
"Dataset",
|
||||
"Annotation":
|
||||
"Annotation",
|
||||
// ---- history-view-edit-current
|
||||
"This history is empty. Click 'Get Data' on the left tool menu to start":
|
||||
"Diese Geschichte ist leer. Klicken Sie auf 'Get Data' im linken Tool-Menü, um",
|
||||
"You must be logged in to create histories":
|
||||
"Du musst eingeloggt sein, um Geschichten zu schaffen",
|
||||
//TODO:
|
||||
//"You can <% loadYourOwn %> or <% externalSource %>" :
|
||||
//false,
|
||||
//"load your own data" :
|
||||
//false,
|
||||
//"get data from an external source" :
|
||||
//false,
|
||||
|
||||
// these aren't in zh/ginga.po and the template doesn't localize
|
||||
//"Include Deleted Datasets" :
|
||||
//false,
|
||||
//"Include Hidden Datasets" :
|
||||
//false,
|
||||
|
||||
|
||||
// ---------------------------------------------------------------------------- datasets
|
||||
// ---- hda-model
|
||||
"Unable to purge dataset":
|
||||
"Dataset kann nicht gelöscht werden",
|
||||
// ---- hda-base
|
||||
// display button
|
||||
"Cannot display datasets removed from disk":
|
||||
"Datasets können nicht von der Festplatte entfernt werden",
|
||||
"This dataset must finish uploading before it can be viewed":
|
||||
"Dieser Datensatz muss das Hochladen beenden, bevor es angezeigt werden kann",
|
||||
"This dataset is not yet viewable":
|
||||
"Dieser Datensatz ist noch nicht sichtbar",
|
||||
"View data":
|
||||
"Daten anzeigen",
|
||||
// download button
|
||||
"Download":
|
||||
"Herunterladen",
|
||||
"Download dataset":
|
||||
"Dataset herunterladen",
|
||||
"Additional files":
|
||||
"Zusätzliche Dateien",
|
||||
// info/show_params
|
||||
"View details":
|
||||
"Details anzeigen",
|
||||
// dataset states
|
||||
// state: new
|
||||
"This is a new dataset and not all of its data are available yet":
|
||||
"Dies ist ein neuer Datensatz und nicht alle seine Daten sind noch verfügbar",
|
||||
// state: noPermission
|
||||
"You do not have permission to view this dataset":
|
||||
"Sie haben keine Berechtigung, diesen Datensatz anzuzeigen",
|
||||
// state: discarded
|
||||
"The job creating this dataset was cancelled before completion":
|
||||
"Der Job, der diesen Datensatz erstellt hat, wurde vor der Fertigstellung abgebrochen",
|
||||
// state: queued
|
||||
"This job is waiting to run":
|
||||
"Dieser Job wartet darauf, zu rennen",
|
||||
// state: upload
|
||||
"This dataset is currently uploading":
|
||||
"Dieser Datensatz lädt derzeit",
|
||||
// state: setting_metadata
|
||||
"Metadata is being auto-detected":
|
||||
"Metadaten werden automatisch erkannt",
|
||||
// state: running
|
||||
"This job is currently running":
|
||||
"Dieser Job läuft derzeit",
|
||||
// state: paused
|
||||
"This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume":
|
||||
"Dieser Job wird pausiert. Verwenden Sie die \"Resume Paused Jobs \" im Verlaufsmenü, um",
|
||||
// state: error
|
||||
"An error occurred with this dataset":
|
||||
"Ein Fehler ist mit diesem Datensatz aufgetreten",
|
||||
// state: empty
|
||||
"No data":
|
||||
"Keine Daten",
|
||||
// state: failed_metadata
|
||||
"An error occurred setting the metadata for this dataset":
|
||||
"Ein Fehler ist aufgetreten Einstellung der Metadaten für diese Datenmenge",
|
||||
// ajax error prefix
|
||||
"There was an error getting the data for this dataset":
|
||||
"Es gab einen Fehler, der die Daten für diesen Datensatz bekam",
|
||||
// purged'd/del'd msg
|
||||
"This dataset has been deleted and removed from disk":
|
||||
"Dieser Datensatz wurde gelöscht und von der Festplatte entfernt",
|
||||
"This dataset has been deleted":
|
||||
"Dieser Datensatz wurde gelöscht",
|
||||
"This dataset has been hidden":
|
||||
"Dieser Datensatz wurde ausgeblendet",
|
||||
"format":
|
||||
"Format",
|
||||
"database":
|
||||
"Datenbank",
|
||||
// ---- hda-edit
|
||||
"Edit attributes":
|
||||
"Attribute bearbeiten",
|
||||
"Cannot edit attributes of datasets removed from disk":
|
||||
"Kann keine Attribute von Datasets aus dem Datenträger entfernen",
|
||||
"Undelete dataset to edit attributes":
|
||||
"Undelete-Dataset zum Bearbeiten von Attributen",
|
||||
"This dataset must finish uploading before it can be edited":
|
||||
"Dieser Datensatz muss das Hochladen beenden, bevor es bearbeitet werden kann",
|
||||
"This dataset is not yet editable":
|
||||
"Dieser Datensatz ist noch nicht bearbeitbar",
|
||||
"Delete":
|
||||
"Löschen",
|
||||
"Dataset is already deleted":
|
||||
"Dataset ist bereits gelöscht",
|
||||
"View or report this error":
|
||||
"Diesen Fehler anzeigen oder melden",
|
||||
"Run this job again":
|
||||
"Führen Sie diesen Job wieder",
|
||||
"Visualize":
|
||||
"Visualisieren",
|
||||
"Visualize in":
|
||||
"Visualize in",
|
||||
"Undelete it":
|
||||
"Untelete it",
|
||||
"Permanently remove it from disk":
|
||||
"Permanent aus der Scheibe entfernen",
|
||||
"Unhide it":
|
||||
"Ausblenden",
|
||||
"You may be able to":
|
||||
"Sie können in der Lage sein",
|
||||
"set it manually or retry auto-detection":
|
||||
"Manuell einstellen oder Auto-Erkennung wiederholen",
|
||||
"Edit dataset tags":
|
||||
"Dataset-Tags bearbeiten",
|
||||
"Edit dataset annotation":
|
||||
"Datensatz-Annotation bearbeiten",
|
||||
// ---------------------------------------------------------------------------- misc. MVC
|
||||
"Tags":
|
||||
"Variablen",
|
||||
"Edit annotation":
|
||||
"Anmerkung bearbeiten",
|
||||
});
|
||||
@@ -0,0 +1,327 @@
|
||||
/** en/main localization hash - for use with requirejs' i18n plugin */
|
||||
define({
|
||||
// ----------------------------------------------------------------------------- masthead
|
||||
"Analyze Data":
|
||||
"Analizar datos",
|
||||
"Workflow":
|
||||
"Flujo de trabajo",
|
||||
"Shared Data":
|
||||
"Datos compartidos",
|
||||
"Data Libraries":
|
||||
"Bibliotecas de datos",
|
||||
"Histories":
|
||||
"Historias",
|
||||
"Workflows":
|
||||
"Flujos de trabajo",
|
||||
"Visualizations":
|
||||
"Visualizaciones",
|
||||
"Pages":
|
||||
"Páginas",
|
||||
"Visualization":
|
||||
"Visualización",
|
||||
"New Track Browser":
|
||||
"Nuevo navegador de pistas",
|
||||
"Saved Visualizations":
|
||||
"Visualizaciones Guardadas",
|
||||
"Interactive Environments":
|
||||
"Entornos Interactivos",
|
||||
"Admin":
|
||||
"Administración",
|
||||
"Help":
|
||||
"Ayuda",
|
||||
"Support":
|
||||
"Apoyo",
|
||||
"Search":
|
||||
"Buscar",
|
||||
"Mailing Lists":
|
||||
"Listas de correo",
|
||||
"Videos":
|
||||
"Videos",
|
||||
"Wiki":
|
||||
"Wiki",
|
||||
"How to Cite Galaxy":
|
||||
"Cómo citar a Galaxy",
|
||||
"Interactive Tours":
|
||||
"recorridos interactivos",
|
||||
"User":
|
||||
"Usuario",
|
||||
"Login":
|
||||
"Iniciar sesión",
|
||||
"Register":
|
||||
"Registro",
|
||||
"Login or Register":
|
||||
"Iniciar sesión o Registrarse",
|
||||
"Logged in as":
|
||||
"Conectado como",
|
||||
"Preferences":
|
||||
"Preferencias",
|
||||
"Custom Builds":
|
||||
"Construcciones personalizadas",
|
||||
"Logout":
|
||||
"Cerrar sesión",
|
||||
"Saved Histories":
|
||||
"Historias Guardadas",
|
||||
"Saved Datasets":
|
||||
"Conjuntos de datos guardados",
|
||||
"Saved Pages":
|
||||
"Páginas guardadas",
|
||||
//Tooltip
|
||||
"Account and saved data":
|
||||
"Cuenta y datos guardados",
|
||||
"Account registration or login":
|
||||
"Registro de cuenta o inicio de sesión",
|
||||
"Support, contact, and community":
|
||||
"Apoyo, contacto y comunidad",
|
||||
"Administer this Galaxy":
|
||||
"Administrar esta galaxia",
|
||||
"Visualize datasets":
|
||||
"Visualizar conjuntos de datos",
|
||||
"Access published resources":
|
||||
"Acceso a los recursos publicados",
|
||||
"Chain tools into workflows":
|
||||
"Herramientas de cadena en flujos de trabajo",
|
||||
"Analysis home view":
|
||||
"Vista de inicio del análisis",
|
||||
// ---------------------------------------------------------------------------- histories
|
||||
// ---- history/options-menu
|
||||
"History Lists":
|
||||
"Listas de historia",
|
||||
// Saved histories is defined above.
|
||||
// "Saved Histories":
|
||||
// false,
|
||||
"Histories Shared with Me":
|
||||
"Historias compartidas conmigo",
|
||||
"Current History":
|
||||
"Historia actual",
|
||||
"Create New":
|
||||
"Crear nuevo",
|
||||
"Copy History":
|
||||
"Historial de Copias",
|
||||
"Share or Publish":
|
||||
"Compartir o publicar",
|
||||
"Show Structure":
|
||||
"Mostrar Estructura",
|
||||
"Extract Workflow":
|
||||
"Extraer flujo de trabajo",
|
||||
// Delete is defined elsewhere, but is also in this menu.
|
||||
// "Delete":
|
||||
// false,
|
||||
"Delete Permanently":
|
||||
"Borrar permanentemente",
|
||||
"Dataset Actions":
|
||||
"Acciones de conjuntos de datos",
|
||||
"Copy Datasets":
|
||||
"Conjuntos de datos de copia",
|
||||
"Dataset Security":
|
||||
"Seguridad del conjunto de datos",
|
||||
"Resume Paused Jobs":
|
||||
"Reanudar trabajos en pausa",
|
||||
"Collapse Expanded Datasets":
|
||||
"Contraer conjuntos de datos expandidos",
|
||||
"Unhide Hidden Datasets":
|
||||
"Mostrar conjuntos de datos ocultos",
|
||||
"Delete Hidden Datasets":
|
||||
"Eliminar conjuntos de datos ocultos",
|
||||
"Purge Deleted Datasets":
|
||||
"Eliminar los conjuntos de datos eliminados",
|
||||
"Downloads":
|
||||
"Descargas",
|
||||
"Export Tool Citations":
|
||||
"Citas de herramientas de exportación",
|
||||
"Export History to File":
|
||||
"Exportar historial a archivo",
|
||||
"Other Actions":
|
||||
"Otras acciones",
|
||||
"Import from File":
|
||||
"Importar desde archivo",
|
||||
"Webhooks":
|
||||
"WebHooks",
|
||||
// ---- history-model
|
||||
// ---- history-view
|
||||
"This history is empty":
|
||||
"Esta historia está vacía",
|
||||
"No matching datasets found":
|
||||
"No se encontraron conjuntos de datos coincidentes",
|
||||
"An error occurred while getting updates from the server":
|
||||
"Se ha producido un error al obtener actualizaciones desde el servidor",
|
||||
"Please contact a Galaxy administrator if the problem persists":
|
||||
"Póngase en contacto con un administrador de Galaxy si el problema persiste",
|
||||
//TODO:
|
||||
//"An error was encountered while <% where %>" :
|
||||
//false,
|
||||
"search datasets":
|
||||
"Conjuntos de datos de búsqueda",
|
||||
"You are currently viewing a deleted history!":
|
||||
"¡Actualmente estás viendo un historial eliminado!",
|
||||
"You are over your disk quota":
|
||||
"Has sobrepasado tu cuota de disco",
|
||||
"Tool execution is on hold until your disk usage drops below your allocated quota":
|
||||
"La ejecución de la herramienta está en espera hasta que el uso del disco caiga por debajo de la cuota asignada",
|
||||
"All":
|
||||
"Todas",
|
||||
"None":
|
||||
"Ninguna",
|
||||
"For all selected":
|
||||
"Para todos los seleccionados",
|
||||
// ---- history-view-edit
|
||||
"Edit history tags":
|
||||
"Editar etiquetas de historial",
|
||||
"Edit history Annotation":
|
||||
"Editar anotación de la historia",
|
||||
"Click to rename history":
|
||||
"Haga clic para cambiar el nombre del historial",
|
||||
// multi operations
|
||||
"Operations on multiple datasets":
|
||||
"Operaciones en conjuntos de datos múltiples",
|
||||
"Hide datasets":
|
||||
"Ocultar conjuntos de datos",
|
||||
"Unhide datasets":
|
||||
"Mostrar conjuntos de datos",
|
||||
"Delete datasets":
|
||||
"Borrar conjuntos de datos",
|
||||
"Undelete datasets":
|
||||
"Undelete datasets",
|
||||
"Permanently delete datasets":
|
||||
"Eliminar permanentemente conjuntos de datos",
|
||||
"This will permanently remove the data in your datasets. Are you sure?":
|
||||
"Esto eliminará permanentemente los datos de sus datasets. ¿Está seguro?",
|
||||
// ---- history-view-annotated
|
||||
"Dataset":
|
||||
"Conjunto de datos",
|
||||
"Annotation":
|
||||
"Anotación",
|
||||
// ---- history-view-edit-current
|
||||
"This history is empty. Click 'Get Data' on the left tool menu to start":
|
||||
"Este historial está vacío. Haga clic en 'Obtener datos' en el menú de herramientas de la izquierda para iniciar",
|
||||
"You must be logged in to create histories":
|
||||
"Debe haber iniciado sesión para crear historiales",
|
||||
//TODO:
|
||||
//"You can <% loadYourOwn %> or <% externalSource %>" :
|
||||
//false,
|
||||
//"load your own data" :
|
||||
//false,
|
||||
//"get data from an external source" :
|
||||
//false,
|
||||
|
||||
// these aren't in zh/ginga.po and the template doesn't localize
|
||||
//"Include Deleted Datasets" :
|
||||
//false,
|
||||
//"Include Hidden Datasets" :
|
||||
//false,
|
||||
|
||||
|
||||
// ---------------------------------------------------------------------------- datasets
|
||||
// ---- hda-model
|
||||
"Unable to purge dataset":
|
||||
"No se puede purgar el dataset",
|
||||
// ---- hda-base
|
||||
// display button
|
||||
"Cannot display datasets removed from disk":
|
||||
"No se pueden mostrar conjuntos de datos eliminados del disco",
|
||||
"This dataset must finish uploading before it can be viewed":
|
||||
"Este conjunto de datos debe terminar de cargar antes de que se pueda ver",
|
||||
"This dataset is not yet viewable":
|
||||
"Este conjunto de datos aún no se puede ver",
|
||||
"View data":
|
||||
"Ver datos",
|
||||
// download button
|
||||
"Download":
|
||||
"Descargar",
|
||||
"Download dataset":
|
||||
"Descargar dataset",
|
||||
"Additional files":
|
||||
"Archivos adicionales",
|
||||
// info/show_params
|
||||
"View details":
|
||||
"Ver detalles",
|
||||
// dataset states
|
||||
// state: new
|
||||
"This is a new dataset and not all of its data are available yet":
|
||||
"Este es un nuevo conjunto de datos y no todos sus datos están disponibles todavía",
|
||||
// state: noPermission
|
||||
"You do not have permission to view this dataset":
|
||||
"No tiene permiso para ver este conjunto de datos",
|
||||
// state: discarded
|
||||
"The job creating this dataset was cancelled before completion":
|
||||
"El trabajo que creó este conjunto de datos se canceló antes de completarse",
|
||||
// state: queued
|
||||
"This job is waiting to run":
|
||||
"Este trabajo está a la espera de ejecutar",
|
||||
// state: upload
|
||||
"This dataset is currently uploading":
|
||||
"Este conjunto de datos se está subiendo actualmente",
|
||||
// state: setting_metadata
|
||||
"Metadata is being auto-detected":
|
||||
"Los metadatos se detectan automáticamente",
|
||||
// state: running
|
||||
"This job is currently running":
|
||||
"Este trabajo se está ejecutando actualmente",
|
||||
// state: paused
|
||||
"This job is paused. Use the \"Resume Paused Jobs\" in the history menu to resume":
|
||||
"Este trabajo está en pausa Utilice la opción \" Reanudar pausado Jobs \" en el menú de historial para reanudar",
|
||||
// state: error
|
||||
"An error occurred with this dataset":
|
||||
"Se ha producido un error con este conjunto de datos",
|
||||
// state: empty
|
||||
"No data":
|
||||
"Sin datos",
|
||||
// state: failed_metadata
|
||||
"An error occurred setting the metadata for this dataset":
|
||||
"Se ha producido un error al establecer los metadatos de este conjunto de datos",
|
||||
// ajax error prefix
|
||||
"There was an error getting the data for this dataset":
|
||||
"Hubo un error al obtener los datos de este conjunto de datos",
|
||||
// purged'd/del'd msg
|
||||
"This dataset has been deleted and removed from disk":
|
||||
"Este conjunto de datos ha sido eliminado y eliminado del disco",
|
||||
"This dataset has been deleted":
|
||||
"Este conjunto de datos ha sido eliminado",
|
||||
"This dataset has been hidden":
|
||||
"Este conjunto de datos se ha ocultado",
|
||||
"format":
|
||||
"Formato",
|
||||
"database":
|
||||
"base de datos",
|
||||
// ---- hda-edit
|
||||
"Edit attributes":
|
||||
"Editar atributos",
|
||||
"Cannot edit attributes of datasets removed from disk":
|
||||
"No se pueden editar los atributos de conjuntos de datos eliminados del disco",
|
||||
"Undelete dataset to edit attributes":
|
||||
"Undelete el conjunto de datos para editar atributos",
|
||||
"This dataset must finish uploading before it can be edited":
|
||||
"Este conjunto de datos debe terminar de cargar antes de que pueda ser editado",
|
||||
"This dataset is not yet editable":
|
||||
"Este conjunto de datos aún no es editable",
|
||||
"Delete":
|
||||
"Borrar",
|
||||
"Dataset is already deleted":
|
||||
"El conjunto de datos ya se ha eliminado",
|
||||
"View or report this error":
|
||||
"Ver o informar de este error",
|
||||
"Run this job again":
|
||||
"Ejecutar este trabajo de nuevo",
|
||||
"Visualize":
|
||||
"Visualizar",
|
||||
"Visualize in":
|
||||
"Visualizar en",
|
||||
"Undelete it":
|
||||
"Undelete it",
|
||||
"Permanently remove it from disk":
|
||||
"Eliminar permanentemente del disco",
|
||||
"Unhide it":
|
||||
"Mostrarlo",
|
||||
"You may be able to":
|
||||
"Usted puede ser capaz de",
|
||||
"set it manually or retry auto-detection":
|
||||
"Configurar manualmente o volver a intentar la detección automática",
|
||||
"Edit dataset tags":
|
||||
"Editar etiquetas de dataset",
|
||||
"Edit dataset annotation":
|
||||
"Editar anotación del conjunto de datos",
|
||||
// ---------------------------------------------------------------------------- misc. MVC
|
||||
"Tags":
|
||||
"Tags",
|
||||
"Edit annotation":
|
||||
"Editar anotación",
|
||||
});
|
||||
@@ -58,13 +58,30 @@ define({
|
||||
"Custom Builds":
|
||||
"Mes génomes Builds de référence",
|
||||
"Logout":
|
||||
"Déconnection",
|
||||
"Déconnexion",
|
||||
"Saved Histories":
|
||||
"Historiques sauvegardés",
|
||||
"Saved Datasets":
|
||||
"Jeux de données sauvegardés",
|
||||
"Saved Pages":
|
||||
"Pages sauvegardées",
|
||||
//Tooltip
|
||||
"Account and saved data":
|
||||
"Compte et données sauvegardées",
|
||||
"Account registration or login":
|
||||
"Enregistrement ou authentification",
|
||||
"Support, contact, and community":
|
||||
"Support,contact et communauté",
|
||||
"Administer this Galaxy":
|
||||
"Outils Admin",
|
||||
"Visualize datasets":
|
||||
"Visualiser les jeux de données",
|
||||
"Access published resources":
|
||||
"Accéder aux données partagées",
|
||||
"Chain tools into workflows":
|
||||
"Relier outils dans un workflow",
|
||||
"Analysis home view":
|
||||
"Accueil analyse de donnée",
|
||||
// ---------------------------------------------------------------------------- histories
|
||||
// ---- history/options-menu
|
||||
"History Lists":
|
||||
@@ -106,7 +123,7 @@ define({
|
||||
"Delete Hidden Datasets":
|
||||
"Supprimer les données cachés",
|
||||
"Purge Deleted Datasets":
|
||||
"Purger les données supprimer",
|
||||
"Purger les données supprimées",
|
||||
"Downloads":
|
||||
"Télécharger",
|
||||
"Export Tool Citations":
|
||||
|
||||
@@ -66,6 +66,25 @@ define({
|
||||
false,
|
||||
"Saved Pages":
|
||||
false,
|
||||
|
||||
//Tooltip
|
||||
"Account and saved data" :
|
||||
false,
|
||||
"Account registration or login" :
|
||||
false,
|
||||
"Support, contact, and community" :
|
||||
false,
|
||||
"Administer this Galaxy" :
|
||||
false,
|
||||
"Visualize datasets" :
|
||||
false,
|
||||
"Access published resources" :
|
||||
false,
|
||||
"Chain tools into workflows" :
|
||||
false,
|
||||
"Analysis home view" :
|
||||
false,
|
||||
|
||||
// ---------------------------------------------------------------------------- histories
|
||||
// ---- history/options-menu
|
||||
"History Lists":
|
||||
@@ -322,6 +341,8 @@ false,
|
||||
false,
|
||||
|
||||
|
||||
|
||||
|
||||
// ---------------------------------------------------------------------------- misc. MVC
|
||||
"Tags" :
|
||||
false,
|
||||
|
||||
@@ -1766,4 +1766,27 @@ div.toolTitleNoSection
|
||||
color:black;
|
||||
text-align:left;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// workflow
|
||||
.wf {
|
||||
overflow: auto;
|
||||
}
|
||||
|
||||
.wf-action span {
|
||||
padding-left: 3px;
|
||||
font-family: "Lucida Grande", verdana, arial, helvetica, sans-serif;
|
||||
}
|
||||
|
||||
.wf-td {
|
||||
width: 25%;
|
||||
}
|
||||
|
||||
.wf-nodata {
|
||||
padding-left: 1%;
|
||||
}
|
||||
|
||||
.other-options {
|
||||
margin-bottom: 2%;
|
||||
}
|
||||
|
||||
@@ -65,6 +65,7 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
|
||||
encoded_id = trans.security.encode_id(wf.id)
|
||||
item['url'] = url_for('workflow', id=encoded_id)
|
||||
item['owner'] = wf.user.username
|
||||
item['number_of_steps'] = len( wf.latest_workflow.steps )
|
||||
rval.append(item)
|
||||
for wf_sa in trans.sa_session.query( trans.app.model.StoredWorkflowUserShareAssociation ).filter_by(
|
||||
user=trans.user ).join( 'stored_workflow' ).filter(
|
||||
@@ -74,6 +75,8 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
|
||||
encoded_id = trans.security.encode_id(wf_sa.stored_workflow.id)
|
||||
item['url'] = url_for( 'workflow', id=encoded_id )
|
||||
item['owner'] = wf_sa.stored_workflow.user.username
|
||||
item['number_of_steps'] = len( wf_sa.stored_workflow.latest_workflow.steps )
|
||||
item['slug'] = wf_sa.stored_workflow.slug
|
||||
rval.append(item)
|
||||
return rval
|
||||
|
||||
|
||||
@@ -107,6 +107,7 @@ def paste_app_factory( global_conf, **kwargs ):
|
||||
webapp.add_client_route( '/tours/{tour_id}' )
|
||||
webapp.add_client_route( '/user' )
|
||||
webapp.add_client_route( '/user/{form_id}' )
|
||||
webapp.add_client_route( '/workflow' )
|
||||
webapp.add_client_route( '/custom_builds' )
|
||||
|
||||
# ==== Done
|
||||
|
||||
@@ -155,10 +155,6 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
|
||||
__myexp_url = "www.myexperiment.org:80"
|
||||
|
||||
@web.expose
|
||||
def index( self, trans ):
|
||||
return self.list( trans )
|
||||
|
||||
@web.expose
|
||||
@web.require_login( "use Galaxy workflows" )
|
||||
def list_grid( self, trans, **kwargs ):
|
||||
@@ -179,52 +175,9 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
"""
|
||||
Render workflow main page (management of existing workflows)
|
||||
"""
|
||||
user = trans.get_user()
|
||||
workflows = trans.sa_session.query( model.StoredWorkflow ) \
|
||||
.filter_by( user=user, deleted=False ) \
|
||||
.order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
|
||||
.all()
|
||||
shared_by_others = trans.sa_session \
|
||||
.query( model.StoredWorkflowUserShareAssociation ) \
|
||||
.filter_by( user=user ) \
|
||||
.join( 'stored_workflow' ) \
|
||||
.filter( model.StoredWorkflow.deleted == expression.false() ) \
|
||||
.order_by( desc( model.StoredWorkflow.update_time ) ) \
|
||||
.all()
|
||||
|
||||
# Legacy issue: all shared workflows must have slugs.
|
||||
slug_set = False
|
||||
for workflow_assoc in shared_by_others:
|
||||
if self.create_item_slug( trans.sa_session, workflow_assoc.stored_workflow ):
|
||||
slug_set = True
|
||||
if slug_set:
|
||||
trans.sa_session.flush()
|
||||
|
||||
return trans.fill_template( "workflow/list.mako",
|
||||
workflows=workflows,
|
||||
shared_by_others=shared_by_others )
|
||||
|
||||
@web.expose
|
||||
@web.require_login( "use Galaxy workflows" )
|
||||
def list_for_run( self, trans ):
|
||||
"""
|
||||
Render workflow list for analysis view (just allows running workflow
|
||||
or switching to management view)
|
||||
"""
|
||||
user = trans.get_user()
|
||||
workflows = trans.sa_session.query( model.StoredWorkflow ) \
|
||||
.filter_by( user=user, deleted=False ) \
|
||||
.order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
|
||||
.all()
|
||||
shared_by_others = trans.sa_session \
|
||||
.query( model.StoredWorkflowUserShareAssociation ) \
|
||||
.filter_by( user=user ) \
|
||||
.filter( model.StoredWorkflow.deleted == expression.false() ) \
|
||||
.order_by( desc( model.StoredWorkflow.table.c.update_time ) ) \
|
||||
.all()
|
||||
return trans.fill_template( "workflow/list_for_run.mako",
|
||||
workflows=workflows,
|
||||
shared_by_others=shared_by_others )
|
||||
# Take care of proxy prefix in url as well
|
||||
redirect_url = url_for( '/' ) + 'workflow'
|
||||
return trans.response.send_redirect( redirect_url )
|
||||
|
||||
@web.expose
|
||||
def list_published( self, trans, **kwargs ):
|
||||
@@ -425,8 +378,11 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
stored.name = san_new_name
|
||||
stored.latest_workflow.name = san_new_name
|
||||
trans.sa_session.flush()
|
||||
trans.set_message( "Workflow renamed to '%s'." % san_new_name )
|
||||
return self.list( trans )
|
||||
message = 'Workflow renamed to: %s' % escape( san_new_name )
|
||||
trans.set_message( message )
|
||||
# Take care of proxy prefix in url as well
|
||||
redirect_url = url_for( '/' ) + 'workflow?status=done&message=%s' % escape( message )
|
||||
return trans.response.send_redirect( redirect_url )
|
||||
else:
|
||||
return form( url_for(controller='workflow', action='rename', id=trans.security.encode_id(stored.id) ),
|
||||
"Rename workflow",
|
||||
@@ -543,7 +499,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
if (save_as_name):
|
||||
new_stored.name = '%s' % save_as_name
|
||||
else:
|
||||
new_stored.name = "Copy of '%s'" % stored.name
|
||||
new_stored.name = "Copy of %s" % stored.name
|
||||
new_stored.latest_workflow = stored.latest_workflow
|
||||
# Copy annotation.
|
||||
annotation_obj = self.get_item_annotation_obj( trans.sa_session, stored.user, stored )
|
||||
@@ -551,15 +507,17 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
self.add_item_annotation( trans.sa_session, trans.get_user(), new_stored, annotation_obj.annotation )
|
||||
new_stored.copy_tags_from(trans.user, stored)
|
||||
if not owner:
|
||||
new_stored.name += " shared by '%s'" % stored.user.email
|
||||
new_stored.name += " shared by %s" % stored.user.email
|
||||
new_stored.user = user
|
||||
# Persist
|
||||
session = trans.sa_session
|
||||
session.add( new_stored )
|
||||
session.flush()
|
||||
# Display the management page
|
||||
trans.set_message( 'Created new workflow with name "%s"' % escape( new_stored.name ) )
|
||||
return self.list( trans )
|
||||
message = 'Created new workflow with name: %s' % escape( new_stored.name )
|
||||
trans.set_message( message )
|
||||
return_url = url_for( '/' ) + 'workflow?status=done&message=%s' % escape( message )
|
||||
trans.response.send_redirect( return_url )
|
||||
|
||||
@web.expose
|
||||
@web.require_login( "create workflows" )
|
||||
@@ -652,8 +610,9 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
|
||||
trans.sa_session.add( stored )
|
||||
trans.sa_session.flush()
|
||||
# Display the management page
|
||||
trans.set_message( "Workflow '%s' deleted" % escape( stored.name ) )
|
||||
return self.list( trans )
|
||||
message = "Workflow deleted: %s" % escape( stored.name )
|
||||
trans.set_message( message )
|
||||
return trans.response.send_redirect( url_for( '/' ) + 'workflow?status=done&message=%s' % escape( message ) )
|
||||
|
||||
@web.expose
|
||||
@web.require_login( "edit workflows" )
|
||||
|
||||
File diff suppressed because one or more lines are too long
@@ -0,0 +1 @@
|
||||
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|
||||
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|
||||
define([],function(){var a=Backbone.View.extend({initialize:function(){this.setElement("<div/>"),this.render()},render:function(){var a=this,b=3;$.getJSON(Galaxy.root+"api/workflows/",function(c){var d=null;a.$el.empty().append(a._templateHeader()),a.build_messages(a),d=a.$el.find(".user-workflows"),d.append(a._templateActionButtons()),c.length>0?(d.append(a._templateWorkflowTable(a,c)),a.adjust_actiondropdown(d),_.each(c,function(b){a.confirm_delete(a,b)}),a.search_workflow(a,a.$el.find(".search-wf"),a.$el.find(".workflow-search tr"),b)):d.append(a._templateNoWorkflow())})},build_messages:function(a){var b=a.$el.find(".response-message"),c=a.get_querystring("status"),d=a.get_querystring("message");d&&null!==d&&""!==d?(b.addClass(c+"message"),b.html("<p>"+d+"</p>")):b.html("")},confirm_delete:function(a,b){var c=a.$el.find(".link-confirm-"+b.id),d=a.$el.find(".link-confirm-shared-"+b.id);c.click(function(){return confirm("Are you sure you want to delete workflow '"+b.name+"'?")}),d.click(function(){return confirm("Are you sure you want to remove the shared workflow '"+b.name+"'?")})},search_workflow:function(a,b,c,d){b.on("keyup",function(){var a=$(this).val();if(a.length>=d){var b=new RegExp(a,"i");c.hide(),c.filter(function(){return b.test($(this).text())}).show()}else c.show()})},get_querystring:function(a){return decodeURIComponent(window.location.search.replace(new RegExp("^(?:.*[&\\?]"+encodeURIComponent(a).replace(/[\.\+\*]/g,"\\$&")+"(?:\\=([^&]*))?)?.*$","i"),"$1"))},adjust_actiondropdown:function(a){a.on("show.bs.dropdown",function(){a.css("overflow","inherit")}),a.on("hide.bs.dropdown",function(){a.css("overflow","auto")})},_templateNoWorkflow:function(){return'<div class="wf-nodata"> You have no workflows. </div>'},_templateActionButtons:function(){return'<ul class="manage-table-actions"><li><input class="search-wf form-control" type="text" autocomplete="off" placeholder="search for workflow..."></li><li><a class="action-button fa fa-plus wf-action" id="new-workflow" title="Create new workflow" href="'+Galaxy.root+'workflow/create"></a></li><li><a class="action-button fa fa-upload wf-action" id="import-workflow" title="Upload or import workflow" href="'+Galaxy.root+'workflow/import_workflow"></a></li></ul>'},_templateWorkflowTable:function(a,b){var c="",d="";return c+='<table class="table colored"><thead><tr class="header"><th class="wf-td">Name</th><th class="wf-td">Owner</th><th class="wf-td"># of Steps</th><th class="wf-td">Published</th></tr></thead>',_.each(b,function(b){d=d+'<tr><td class="wf-td wf-dpd"><div class="dropdown"><button class="menubutton" type="button" data-toggle="dropdown">'+_.escape(b.name)+'<span class="caret"></span></button>'+a._templateActions(b)+"</div></td><td>"+(b.owner===Galaxy.user.attributes.username?"You":b.owner)+'</td><td class="wf-td">'+b.number_of_steps+'</td><td class="wf-td">'+(b.published?"Yes":"No")+"</td></tr>"}),c+'<tbody class="workflow-search">'+d+"</tbody></table>"},_templateActions:function(a){return a.owner===Galaxy.user.attributes.username?'<ul class="dropdown-menu action-dpd"><li><a href="'+Galaxy.root+"workflow/editor?id="+a.id+'">Edit</a></li><li><a href="'+Galaxy.root+"workflow/run?id="+a.id+'" target="galaxy_main">Run</a></li><li><a href="'+Galaxy.root+"workflow/sharing?id="+a.id+'">Share or Download</a></li><li><a href="'+Galaxy.root+"workflow/copy?id="+a.id+'">Copy</a></li><li><a href="'+Galaxy.root+"workflow/rename?id="+a.id+'">Rename</a></li><li><a href="'+Galaxy.root+"workflow/display_by_id?id="+a.id+'">View</a></li><li><a class="link-confirm-'+a.id+'" href="'+Galaxy.root+"workflow/delete?id="+a.id+'">Delete</a></li></ul>':'<ul class="dropdown-menu action-dpd"><li><a href="'+Galaxy.root+"workflow/display_by_username_and_slug?username="+a.owner+"&slug="+a.slug+'">View</a></li><li><a href="'+Galaxy.root+"workflow/run?id="+a.id+'" target="galaxy_main">Run</a></li><li><a href="'+Galaxy.root+"workflow/copy?id="+a.id+'">Copy</a></li><li><a class="link-confirm-shared-'+a.id+'" href="'+Galaxy.root+"workflow/sharing?unshare_me=True&id="+a.id+'">Remove</a></li></ul>'},_templateHeader:function(){return'<div class="page-container"><div class="user-workflows wf"><div class="response-message"></div><h2>Your workflows</h2></div><div class="other-options wf"><h2>Other options</h2><a class="action-button fa fa-cog wf-action" href="'+Galaxy.root+'workflow/configure_menu" title="Configure your workflow menu"><span>Configure your workflow menu</span></a></div></div>'}});return{View:a}});
|
||||
//# sourceMappingURL=../../../maps/mvc/workflow/workflow.js.map
|
||||
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|
||||
define({root:{"Analyze Data":!1,Workflow:!1,"Shared Data":!1,"Data Libraries":!1,Histories:!1,Workflows:!1,Visualizations:!1,Pages:!1,Visualization:!1,"New Track Browser":!1,"Saved Visualizations":!1,"Interactive Environments":!1,Admin:!1,Help:!1,Support:!1,Search:!1,"Mailing Lists":!1,Videos:!1,Wiki:!1,"How to Cite Galaxy":!1,"Interactive Tours":!1,User:!1,Login:!1,Register:!1,"Login or Register":!1,"Logged in as":!1,Preferences:!1,"Custom Builds":!1,Logout:!1,"Saved Histories":!1,"Saved Datasets":!1,"Saved Pages":!1,"History Lists":!1,"Histories Shared with Me":!1,"Current History":!1,"Create New":!1,"Copy History":!1,"Share or Publish":!1,"Show Structure":!1,"Extract Workflow":!1,"Delete Permanently":!1,"Dataset Actions":!1,"Copy Datasets":!1,"Dataset Security":!1,"Resume Paused Jobs":!1,"Collapse Expanded Datasets":!1,"Unhide Hidden Datasets":!1,"Delete Hidden Datasets":!1,"Purge Deleted Datasets":!1,Downloads:!1,"Export Tool Citations":!1,"Export History to File":!1,"Other Actions":!1,"Import from File":!1,Webhooks:!1,"This history is empty":!1,"No matching datasets found":!1,"An error occurred while getting updates from the server":!1,"Please contact a Galaxy administrator if the problem persists":!1,"search datasets":!1,"You are currently viewing a deleted history!":!1,"You are over your disk quota":!1,"Tool execution is on hold until your disk usage drops below your allocated quota":!1,All:!1,None:!1,"For all selected":!1,"Edit history tags":!1,"Edit history Annotation":!1,"Click to rename history":!1,"Operations on multiple datasets":!1,"Hide datasets":!1,"Unhide datasets":!1,"Delete datasets":!1,"Undelete datasets":!1,"Permanently delete datasets":!1,"This will permanently remove the data in your datasets. Are you sure?":!1,Dataset:!1,Annotation:!1,"This history is empty. Click 'Get Data' on the left tool menu to start":!1,"You must be logged in to create histories":!1,"Unable to purge dataset":!1,"Cannot display datasets removed from disk":!1,"This dataset must finish uploading before it can be viewed":!1,"This dataset is not yet viewable":!1,"View data":!1,Download:!1,"Download dataset":!1,"Additional files":!1,"View details":!1,"This is a new dataset and not all of its data are available yet":!1,"You do not have permission to view this dataset":!1,"The job creating this dataset was cancelled before completion":!1,"This job is waiting to run":!1,"This dataset is currently uploading":!1,"Metadata is being auto-detected":!1,"This job is currently running":!1,'This job is paused. Use the "Resume Paused Jobs" in the history menu to resume':!1,"An error occurred with this dataset":!1,"No data":!1,"An error occurred setting the metadata for this dataset":!1,"There was an error getting the data for this dataset":!1,"This dataset has been deleted and removed from disk":!1,"This dataset has been deleted":!1,"This dataset has been hidden":!1,format:!1,database:!1,"Edit attributes":!1,"Cannot edit attributes of datasets removed from disk":!1,"Undelete dataset to edit attributes":!1,"This dataset must finish uploading before it can be edited":!1,"This dataset is not yet editable":!1,Delete:!1,"Dataset is already deleted":!1,"View or report this error":!1,"Run this job again":!1,Visualize:!1,"Visualize in":!1,"Undelete it":!1,"Permanently remove it from disk":!1,"Unhide it":!1,"You may be able to":!1,"set it manually or retry auto-detection":!1,"Edit dataset tags":!1,"Edit dataset annotation":!1,Tags:!1,"Edit annotation":!1},ja:!0,fr:!0,zh:!0});
|
||||
define({root:{"Analyze Data":!1,Workflow:!1,"Shared Data":!1,"Data Libraries":!1,Histories:!1,Workflows:!1,Visualizations:!1,Pages:!1,Visualization:!1,"New Track Browser":!1,"Saved Visualizations":!1,"Interactive Environments":!1,Admin:!1,Help:!1,Support:!1,Search:!1,"Mailing Lists":!1,Videos:!1,Wiki:!1,"How to Cite Galaxy":!1,"Interactive Tours":!1,User:!1,Login:!1,Register:!1,"Login or Register":!1,"Logged in as":!1,Preferences:!1,"Custom Builds":!1,Logout:!1,"Saved Histories":!1,"Saved Datasets":!1,"Saved Pages":!1,"Account and saved data":!1,"Account registration or login":!1,"Support, contact, and community":!1,"Administer this Galaxy":!1,"Visualize datasets":!1,"Access published resources":!1,"Chain tools into workflows":!1,"Analysis home view":!1,"History Lists":!1,"Histories Shared with Me":!1,"Current History":!1,"Create New":!1,"Copy History":!1,"Share or Publish":!1,"Show Structure":!1,"Extract Workflow":!1,"Delete Permanently":!1,"Dataset Actions":!1,"Copy Datasets":!1,"Dataset Security":!1,"Resume Paused Jobs":!1,"Collapse Expanded Datasets":!1,"Unhide Hidden Datasets":!1,"Delete Hidden Datasets":!1,"Purge Deleted Datasets":!1,Downloads:!1,"Export Tool Citations":!1,"Export History to File":!1,"Other Actions":!1,"Import from File":!1,Webhooks:!1,"This history is empty":!1,"No matching datasets found":!1,"An error occurred while getting updates from the server":!1,"Please contact a Galaxy administrator if the problem persists":!1,"search datasets":!1,"You are currently viewing a deleted history!":!1,"You are over your disk quota":!1,"Tool execution is on hold until your disk usage drops below your allocated quota":!1,All:!1,None:!1,"For all selected":!1,"Edit history tags":!1,"Edit history Annotation":!1,"Click to rename history":!1,"Operations on multiple datasets":!1,"Hide datasets":!1,"Unhide datasets":!1,"Delete datasets":!1,"Undelete datasets":!1,"Permanently delete datasets":!1,"This will permanently remove the data in your datasets. Are you sure?":!1,Dataset:!1,Annotation:!1,"This history is empty. Click 'Get Data' on the left tool menu to start":!1,"You must be logged in to create histories":!1,"Unable to purge dataset":!1,"Cannot display datasets removed from disk":!1,"This dataset must finish uploading before it can be viewed":!1,"This dataset is not yet viewable":!1,"View data":!1,Download:!1,"Download dataset":!1,"Additional files":!1,"View details":!1,"This is a new dataset and not all of its data are available yet":!1,"You do not have permission to view this dataset":!1,"The job creating this dataset was cancelled before completion":!1,"This job is waiting to run":!1,"This dataset is currently uploading":!1,"Metadata is being auto-detected":!1,"This job is currently running":!1,'This job is paused. Use the "Resume Paused Jobs" in the history menu to resume':!1,"An error occurred with this dataset":!1,"No data":!1,"An error occurred setting the metadata for this dataset":!1,"There was an error getting the data for this dataset":!1,"This dataset has been deleted and removed from disk":!1,"This dataset has been deleted":!1,"This dataset has been hidden":!1,format:!1,database:!1,"Edit attributes":!1,"Cannot edit attributes of datasets removed from disk":!1,"Undelete dataset to edit attributes":!1,"This dataset must finish uploading before it can be edited":!1,"This dataset is not yet editable":!1,Delete:!1,"Dataset is already deleted":!1,"View or report this error":!1,"Run this job again":!1,Visualize:!1,"Visualize in":!1,"Undelete it":!1,"Permanently remove it from disk":!1,"Unhide it":!1,"You may be able to":!1,"set it manually or retry auto-detection":!1,"Edit dataset tags":!1,"Edit dataset annotation":!1,Tags:!1,"Edit annotation":!1},ja:!0,fr:!0,zh:!0});
|
||||
//# sourceMappingURL=../../maps/nls/locale.js.map
|
||||
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|
||||
<%inherit file="/webapps/galaxy/base_panels.mako"/>
|
||||
|
||||
<%def name="init()">
|
||||
<%
|
||||
self.has_left_panel=False
|
||||
self.has_right_panel=False
|
||||
self.active_view="workflow"
|
||||
self.message_box_visible=False
|
||||
%>
|
||||
</%def>
|
||||
|
||||
<%def name="title()">Workflow home</%def>
|
||||
|
||||
<%def name="center_panel()">
|
||||
<div style="overflow: auto; height: 100%;">
|
||||
<div class="page-container" style="padding: 10px;">
|
||||
%if message:
|
||||
<%
|
||||
try:
|
||||
status
|
||||
except:
|
||||
status = "done"
|
||||
%>
|
||||
<p />
|
||||
<div class="${status}message">
|
||||
${h.to_unicode( message )}
|
||||
</div>
|
||||
%endif
|
||||
|
||||
<h2>Your workflows</h2>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" id="new-workflow" href="${h.url_for( controller='workflow', action='create' )}">
|
||||
<img src="${h.url_for('/static/images/silk/add.png')}" />
|
||||
<span>Create new workflow</span>
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a class="action-button" id="import-workflow" href="${h.url_for( controller='workflow', action='import_workflow' )}">
|
||||
<img src="${h.url_for('/static/images/fugue/arrow-090.png')}" />
|
||||
<span>Upload or import workflow</span>
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
%if workflows:
|
||||
<table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" style="width:100%;">
|
||||
<tr class="header">
|
||||
<th>Name</th>
|
||||
<th># of Steps</th>
|
||||
## <th>Last Updated</th>
|
||||
<th></th>
|
||||
</tr>
|
||||
%for i, workflow in enumerate( workflows ):
|
||||
<tr>
|
||||
<td>
|
||||
<div class="menubutton" style="float: left;" id="wf-${i}-popup">
|
||||
${h.to_unicode( workflow.name ) | h}
|
||||
</div>
|
||||
</td>
|
||||
<td>${len(workflow.latest_workflow.steps)}</td>
|
||||
## <td>${str(workflow.update_time)[:19]}</td>
|
||||
<td>
|
||||
<div popupmenu="wf-${i}-popup">
|
||||
<a class="action-button" href="${h.url_for( controller='workflow', action='editor', id=trans.security.encode_id( workflow.id ) )}" target="_parent">Edit</a>
|
||||
<a class="action-button" href="${h.url_for( controller='root', action='index', workflow_id=trans.security.encode_id( workflow.id ) )}" target="_parent">Run</a>
|
||||
<a class="action-button" href="${h.url_for( controller='workflow', action='sharing', id=trans.security.encode_id( workflow.id ) )}">Share or Download</a>
|
||||
<a class="action-button" href="${h.url_for( controller='workflow', action='copy', id=trans.security.encode_id( workflow.id ) )}">Copy</a>
|
||||
<a class="action-button" href="${h.url_for( controller='workflow', action='rename', id=trans.security.encode_id( workflow.id ) )}">Rename</a>
|
||||
<a class="action-button" href="${h.url_for( controller='workflow', action='display_by_id', id=trans.security.encode_id( workflow.id ) )}" target="_top">View</a>
|
||||
<a class="action-button" confirm="Are you sure you want to delete workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='delete', id=trans.security.encode_id( workflow.id ) )}">Delete</a>
|
||||
</div>
|
||||
</td>
|
||||
</tr>
|
||||
%endfor
|
||||
</table>
|
||||
%else:
|
||||
You have no workflows.
|
||||
%endif
|
||||
|
||||
<h2>Workflows shared with you by others</h2>
|
||||
|
||||
%if shared_by_others:
|
||||
<table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%">
|
||||
<tr class="header">
|
||||
<th>Name</th>
|
||||
<th>Owner</th>
|
||||
<th># of Steps</th>
|
||||
<th></th>
|
||||
</tr>
|
||||
%for i, association in enumerate( shared_by_others ):
|
||||
<% workflow = association.stored_workflow %>
|
||||
<tr>
|
||||
<td>
|
||||
<a class="menubutton" id="shared-${i}-popup" href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${h.to_unicode( workflow.name ) | h}</a>
|
||||
</td>
|
||||
<td>${workflow.user.email}</td>
|
||||
<td>${len(workflow.latest_workflow.steps)}</td>
|
||||
<td>
|
||||
<div popupmenu="shared-${i}-popup">
|
||||
<a class="action-button" href="${h.url_for( controller='workflow', action='display_by_username_and_slug', username=workflow.user.username, slug=workflow.slug )}" target="_top">View</a>
|
||||
<a class="action-button" href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id( workflow.id ) )}">Run</a>
|
||||
<a class="action-button" href="${h.url_for( controller='workflow', action='copy', id=trans.security.encode_id( workflow.id ) )}">Copy</a>
|
||||
<a class="action-button" confirm="Are you sure you want to remove the shared workflow '${h.to_unicode( workflow.name ) | h}'?" href="${h.url_for( controller='workflow', action='sharing', unshare_me=True, id=trans.security.encode_id( workflow.id ))}">Remove</a>
|
||||
</div>
|
||||
</td>
|
||||
</tr>
|
||||
%endfor
|
||||
</table>
|
||||
%else:
|
||||
No workflows have been shared with you.
|
||||
%endif
|
||||
|
||||
<h2>Other options</h2>
|
||||
|
||||
<a class="action-button" href="${h.url_for( controller='workflow', action='configure_menu' )}">
|
||||
<span>Configure your workflow menu</span>
|
||||
</a>
|
||||
</div>
|
||||
</div>
|
||||
</%def>
|
||||
@@ -1,66 +0,0 @@
|
||||
<%inherit file="/base.mako"/>
|
||||
|
||||
<%def name="title()">Workflow home</%def>
|
||||
|
||||
<h2>Your workflows</h2>
|
||||
|
||||
<ul class="manage-table-actions">
|
||||
<li>
|
||||
<a class="action-button" href="${h.url_for( controller='workflow', action='index' )}" target="_parent">
|
||||
<span>Switch to workflow management view</span>
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
%if workflows:
|
||||
<table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%">
|
||||
<tr class="header">
|
||||
<th>Name</th>
|
||||
<th># of Steps</th>
|
||||
## <th>Last Updated</th>
|
||||
<th></th>
|
||||
</tr>
|
||||
%for i, workflow in enumerate( workflows ):
|
||||
<tr>
|
||||
<td>
|
||||
<a href="${h.url_for(controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${h.to_unicode( workflow.name ) | h}</a>
|
||||
<a id="wf-${i}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
</td>
|
||||
<td>${len(workflow.latest_workflow.steps)}</td>
|
||||
## <td>${str(workflow.update_time)[:19]}</td>
|
||||
</tr>
|
||||
%endfor
|
||||
</table>
|
||||
%else:
|
||||
|
||||
You have no workflows.
|
||||
|
||||
%endif
|
||||
|
||||
<h2>Workflows shared with you by others</h2>
|
||||
|
||||
%if shared_by_others:
|
||||
<table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%">
|
||||
<tr class="header">
|
||||
<th>Name</th>
|
||||
<th>Owner</th>
|
||||
<th># of Steps</th>
|
||||
<th></th>
|
||||
</tr>
|
||||
%for i, association in enumerate( shared_by_others ):
|
||||
<% workflow = association.stored_workflow %>
|
||||
<tr>
|
||||
<td>
|
||||
<a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name | h}</a>
|
||||
<a id="shared-${i}-popup" class="popup-arrow" style="display: none;">▼</a>
|
||||
</td>
|
||||
<td>${workflow.user.email | h}</td>
|
||||
<td>${len(workflow.latest_workflow.steps)}</td>
|
||||
</tr>
|
||||
%endfor
|
||||
</table>
|
||||
%else:
|
||||
|
||||
No workflows have been shared with you.
|
||||
|
||||
%endif
|
||||
@@ -1295,6 +1295,37 @@ test_data:
|
||||
content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True )
|
||||
assert content[ "name" ] == "foo was replaced"
|
||||
|
||||
@skip_without_tool( "cat" )
|
||||
def test_run_rename_collection_element( self ):
|
||||
history_id = self.dataset_populator.new_history()
|
||||
self._run_jobs("""
|
||||
class: GalaxyWorkflow
|
||||
inputs:
|
||||
- id: input1
|
||||
type: data_collection_input
|
||||
collection_type: list
|
||||
steps:
|
||||
- tool_id: cat
|
||||
label: first_cat
|
||||
state:
|
||||
input1:
|
||||
$link: input1
|
||||
outputs:
|
||||
out_file1:
|
||||
rename: "my new name"
|
||||
test_data:
|
||||
input1:
|
||||
type: list
|
||||
name: the_dataset_list
|
||||
elements:
|
||||
- identifier: el1
|
||||
value: 1.fastq
|
||||
type: File
|
||||
""", history_id=history_id)
|
||||
content = self.dataset_populator.get_history_dataset_details( history_id, hid=3, wait=True, assert_ok=True )
|
||||
name = content[ "name" ]
|
||||
assert name == "my new name", name
|
||||
|
||||
@skip_without_tool( "cat" )
|
||||
def test_run_rename_based_on_input( self ):
|
||||
history_id = self.dataset_populator.new_history()
|
||||
|
||||
@@ -394,17 +394,16 @@ class NavigatesGalaxy(HasDriver):
|
||||
self.click_masthead_workflow()
|
||||
|
||||
def workflow_index_table_elements(self):
|
||||
self.wait_for_selector_visible(".manage-table tbody")
|
||||
table_elements = self.driver.find_elements_by_css_selector(".manage-table tbody > tr")
|
||||
# drop header
|
||||
return table_elements[1:]
|
||||
self.wait_for_selector_visible("tbody.workflow-search")
|
||||
table_elements = self.driver.find_elements_by_css_selector("tbody.workflow-search > tr")
|
||||
return table_elements
|
||||
|
||||
def workflow_index_click_option(self, option_title, workflow_index=0):
|
||||
table_elements = self.workflow_index_table_elements()
|
||||
workflow_row = table_elements[workflow_index]
|
||||
workflow_button = workflow_row.find_element_by_css_selector(".menubutton")
|
||||
workflow_button.click()
|
||||
menu_element = self.wait_for_selector_visible(".popmenu-wrapper .dropdown-menu")
|
||||
menu_element = self.wait_for_selector_visible("ul.action-dpd")
|
||||
menu_options = menu_element.find_elements_by_css_selector("li a")
|
||||
found_option = False
|
||||
for menu_option in menu_options:
|
||||
|
||||
@@ -71,6 +71,8 @@ def selenium_test(f):
|
||||
def func_wrapper(self, *args, **kwds):
|
||||
retry_attempts = 0
|
||||
while True:
|
||||
if retry_attempts > 0:
|
||||
self.reset_driver_and_session()
|
||||
try:
|
||||
return f(self, *args, **kwds)
|
||||
except Exception:
|
||||
@@ -118,11 +120,7 @@ class SeleniumTestCase(FunctionalTestCase, NavigatesGalaxy):
|
||||
self.target_url_from_selenium = GALAXY_TEST_EXTERNAL_FROM_SELENIUM
|
||||
else:
|
||||
self.target_url_from_selenium = self.url
|
||||
self.display = driver_factory.virtual_display_if_enabled(headless_selenium())
|
||||
self.driver = get_driver()
|
||||
|
||||
if self.ensure_registered:
|
||||
self.register()
|
||||
self.setup_driver_and_session()
|
||||
|
||||
def tearDown(self):
|
||||
exception = None
|
||||
@@ -131,6 +129,27 @@ class SeleniumTestCase(FunctionalTestCase, NavigatesGalaxy):
|
||||
except Exception as e:
|
||||
exception = e
|
||||
|
||||
try:
|
||||
self.tear_down_driver()
|
||||
except Exception as e:
|
||||
exception = e
|
||||
|
||||
if exception is not None:
|
||||
raise exception
|
||||
|
||||
def reset_driver_and_session(self):
|
||||
self.tear_down_driver()
|
||||
self.setup_driver_and_session()
|
||||
|
||||
def setup_driver_and_session(self):
|
||||
self.display = driver_factory.virtual_display_if_enabled(headless_selenium())
|
||||
self.driver = get_driver()
|
||||
|
||||
if self.ensure_registered:
|
||||
self.register()
|
||||
|
||||
def tear_down_driver(self):
|
||||
exception = None
|
||||
try:
|
||||
self.driver.close()
|
||||
except Exception as e:
|
||||
|
||||
@@ -31,22 +31,23 @@ class ToolFormTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
|
||||
hda = self.latest_history_item()
|
||||
self._check_dataset_details_for_inttest_value(1)
|
||||
|
||||
dataset_details_key_value_pairs = self._table_to_key_value_elements("table#dataset-details")
|
||||
number_found = name_found = format_found = False
|
||||
for key, value in dataset_details_key_value_pairs:
|
||||
if "Number:" in key.text:
|
||||
assert str(hda["hid"]) in value.text
|
||||
number_found = True
|
||||
if "Name:" in key.text:
|
||||
assert hda["name"] in value.text
|
||||
name_found = True
|
||||
if "Format:" in key.text:
|
||||
assert hda["extension"] in value.text
|
||||
format_found = True
|
||||
with self.main_panel():
|
||||
dataset_details_key_value_pairs = self._table_to_key_value_elements("table#dataset-details")
|
||||
number_found = name_found = format_found = False
|
||||
for key, value in dataset_details_key_value_pairs:
|
||||
if "Number:" in key.text:
|
||||
assert str(hda["hid"]) in value.text
|
||||
number_found = True
|
||||
if "Name:" in key.text:
|
||||
assert hda["name"] in value.text
|
||||
name_found = True
|
||||
if "Format:" in key.text:
|
||||
assert hda["extension"] in value.text
|
||||
format_found = True
|
||||
|
||||
assert number_found
|
||||
assert name_found
|
||||
assert format_found
|
||||
assert number_found
|
||||
assert name_found
|
||||
assert format_found
|
||||
|
||||
def _table_to_key_value_elements(self, table_selector):
|
||||
tool_parameters_table = self.wait_for_selector_visible(table_selector)
|
||||
|
||||
@@ -45,7 +45,8 @@ class WorkflowManagementTestCase(SeleniumTestCase):
|
||||
assert 'CoolNewName' in renamed_workflow_button.text, renamed_workflow_button.text
|
||||
|
||||
def _workflow_import_from_url(self):
|
||||
self.click_selector(self.test_data["selectors"]["workflows"]["import_button"])
|
||||
element = self.wait_for_selector_clickable(self.test_data["selectors"]["workflows"]["import_button"])
|
||||
element.click()
|
||||
url = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test/base/data/test_workflow_1.ga"
|
||||
form_element = self.driver.find_element_by_css_selector("#center form")
|
||||
url_element = form_element.find_element_by_css_selector("input[type='text']")
|
||||
|
||||
Reference in New Issue
Block a user