mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-25 10:24:38 +08:00
Martin Cech
bedf599779
when no library import configuration is set; thanks to Carl for reporting this
1314 lines
54 KiB
JavaScript
1314 lines
54 KiB
JavaScript
define([
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"galaxy.masthead",
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"utils/utils",
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"libs/toastr",
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"mvc/library/library-model",
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"mvc/ui/ui-select"
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],
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function( mod_masthead,
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mod_utils,
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mod_toastr,
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mod_library_model,
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mod_select
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){
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var FolderToolbarView = Backbone.View.extend({
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el: '#center',
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events: {
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'click #toolbtn_create_folder' : 'createFolderFromModal',
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'click #toolbtn_bulk_import' : 'modalBulkImport',
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'click #include_deleted_datasets_chk' : 'checkIncludeDeleted',
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'click #toolbtn_show_libinfo' : 'showLibInfo',
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'click #toolbtn_bulk_delete' : 'deleteSelectedDatasets',
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'click #page_size_prompt' : 'showPageSizePrompt'
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},
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defaults: {
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'can_add_library_item' : false,
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'contains_file' : false,
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'chain_call_control' : {
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'total_number' : 0,
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'failed_number' : 0
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},
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'disabled_jstree_element' : 'folders'
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},
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modal : null,
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// directory browsing object
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jstree: null,
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// user's histories
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histories : null,
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// genome select
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select_genome : null,
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// extension select
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select_extension : null,
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// extension types
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list_extensions :[],
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// datatype placeholder for extension auto-detection
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auto: {
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id : 'auto',
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text : 'Auto-detect',
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description : 'This system will try to detect the file type automatically.' +
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' If your file is not detected properly as one of the known formats,' +
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' it most likely means that it has some format problems (e.g., different' +
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' number of columns on different rows). You can still coerce the system' +
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' to set your data to the format you think it should be.' +
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' You can also upload compressed files, which will automatically be decompressed.'
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},
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// genomes
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list_genomes : [],
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initialize: function(options){
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this.options = _.defaults( options || {}, this.defaults );
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this.fetchExtAndGenomes();
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this.render();
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},
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render: function(options){
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this.options = _.extend( this.options, options );
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var toolbar_template = this.templateToolBar();
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var template_defaults = {
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id: this.options.id,
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is_admin: false,
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is_anonym: true,
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mutiple_add_dataset_options: false
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}
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if (Galaxy.currUser){
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template_defaults.is_admin = Galaxy.currUser.isAdmin();
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template_defaults.is_anonym = Galaxy.currUser.isAnonymous();
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if ( Galaxy.config.user_library_import_dir !== null || Galaxy.config.allow_library_path_paste !== false || Galaxy.config.library_import_dir !== null ){
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template_defaults.mutiple_add_dataset_options = true;
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}
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}
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this.$el.html(toolbar_template(template_defaults));
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},
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/**
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* Called from FolderListView when needed.
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* @param {object} options common options
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*/
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renderPaginator: function( options ){
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this.options = _.extend( this.options, options );
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var paginator_template = this.templatePaginator();
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this.$el.find( '#folder_paginator' ).html( paginator_template({
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id: this.options.id,
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show_page: parseInt( this.options.show_page ),
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page_count: parseInt( this.options.page_count ),
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total_items_count: this.options.total_items_count,
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items_shown: this.options.items_shown
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}));
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},
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configureElements: function(options){
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this.options = _.extend(this.options, options);
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if (this.options.can_add_library_item === true){
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$('.add-library-items').show();
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} else{
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$('.add-library-items').hide();
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}
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if (this.options.contains_file === true){
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if (Galaxy.currUser){
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if (!Galaxy.currUser.isAnonymous()){
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$('.logged-dataset-manipulation').show();
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$('.dataset-manipulation').show();
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} else {
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$('.dataset-manipulation').show();
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$('.logged-dataset-manipulation').hide();
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}
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} else {
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$('.logged-dataset-manipulation').hide();
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$('.dataset-manipulation').hide();
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}
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} else {
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$('.logged-dataset-manipulation').hide();
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$('.dataset-manipulation').hide();
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}
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this.$el.find('[data-toggle]').tooltip();
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},
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// shows modal for creating folder
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createFolderFromModal: function( event ){
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event.preventDefault();
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event.stopPropagation();
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// create modal
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var self = this;
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var template = this.templateNewFolderInModal();
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this.modal = Galaxy.modal;
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this.modal.show({
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closing_events : true,
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title : 'Create New Folder',
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body : template(),
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buttons : {
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'Create' : function() {self.create_new_folder_event();},
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'Close' : function() {Galaxy.modal.hide();}
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}
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});
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},
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// create the new folder from modal
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create_new_folder_event: function(){
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var folderDetails = this.serialize_new_folder();
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if (this.validate_new_folder(folderDetails)){
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var folder = new mod_library_model.FolderAsModel();
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url_items = Backbone.history.fragment.split('/');
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current_folder_id = url_items[url_items.length-1];
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folder.url = folder.urlRoot + '/' + current_folder_id ;
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folder.save(folderDetails, {
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success: function (folder) {
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Galaxy.modal.hide();
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mod_toastr.success('Folder created.');
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folder.set({'type' : 'folder'});
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Galaxy.libraries.folderListView.collection.add(folder);
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},
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error: function(model, response){
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Galaxy.modal.hide();
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if (typeof response.responseJSON !== "undefined"){
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mod_toastr.error(response.responseJSON.err_msg);
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} else {
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mod_toastr.error('An error ocurred.');
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}
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}
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});
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} else {
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mod_toastr.error('Folder\'s name is missing.');
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}
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return false;
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},
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// serialize data from the modal
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serialize_new_folder : function(){
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return {
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name: $("input[name='Name']").val(),
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description: $("input[name='Description']").val()
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};
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},
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// validate new folder info
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validate_new_folder: function(folderDetails){
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return folderDetails.name !== '';
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},
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// show bulk import modal
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modalBulkImport : function(){
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var checkedValues = $('#folder_table').find(':checked');
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if(checkedValues.length === 0){
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mod_toastr.info('You must select some datasets first.');
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} else {
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this.refreshUserHistoriesList(function(that){
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var template = that.templateBulkImportInModal();
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that.modal = Galaxy.modal;
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that.modal.show({
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closing_events : true,
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title : 'Import into History',
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body : template({histories : that.histories.models}),
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buttons : {
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'Import' : function() {that.importAllIntoHistory();},
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'Close' : function() {Galaxy.modal.hide();}
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}
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});
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});
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}
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},
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refreshUserHistoriesList: function(callback){
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var that = this;
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this.histories = new mod_library_model.GalaxyHistories();
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this.histories.fetch({
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success: function (){
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callback(that);
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},
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error: function(model, response){
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if (typeof response.responseJSON !== "undefined"){
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mod_toastr.error(response.responseJSON.err_msg);
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} else {
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mod_toastr.error('An error ocurred.');
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}
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}
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});
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},
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/**
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* Import all selected datasets into history.
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*/
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importAllIntoHistory : function (){
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this.modal.disableButton('Import');
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var history_id = $("select[name=dataset_import_bulk] option:selected").val();
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var history_name = $("select[name=dataset_import_bulk] option:selected").text();
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// we can save last used history to pre-select it next time
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this.options.last_used_history_id = history_id;
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var dataset_ids = [];
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$('#folder_table').find(':checked').each(function(){
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if (this.parentElement.parentElement.id !== '') {
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dataset_ids.push(this.parentElement.parentElement.id);
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}
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});
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// prepare the dataset objects to be imported
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var datasets_to_import = [];
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for (var i = dataset_ids.length - 1; i >= 0; i--) {
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var library_dataset_id = dataset_ids[i];
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var historyItem = new mod_library_model.HistoryItem();
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historyItem.url = historyItem.urlRoot + history_id + '/contents';
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historyItem.content = library_dataset_id;
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historyItem.source = 'library';
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datasets_to_import.push(historyItem);
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}
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this.initChainCallControl( { length: datasets_to_import.length, action: 'to_history', history_name: history_name } );
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// set the used history as current so user will see the last one
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// that he imported into in the history panel on the 'analysis' page
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jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + history_id );
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this.chainCallImportingIntoHistory( datasets_to_import, history_name );
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},
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/**
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* Update the progress bar in modal window.
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*/
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updateProgress: function(){
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this.progress += this.progressStep;
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$( '.progress-bar-import' ).width( Math.round( this.progress ) + '%' );
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txt_representation = Math.round( this.progress ) + '% Complete';
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$( '.completion_span' ).text( txt_representation );
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},
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/**
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* download selected datasets
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* @param {str} folder_id id of the current folder
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* @param {str} format requested archive format
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*/
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download : function( folder_id, format ){
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var dataset_ids = [];
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$( '#folder_table' ).find( ':checked' ).each( function(){
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if ( this.parentElement.parentElement.id !== '' ) {
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dataset_ids.push( this.parentElement.parentElement.id );
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}
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} );
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var url = '/api/libraries/datasets/download/' + format;
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var data = { 'ld_ids' : dataset_ids };
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this.processDownload( url, data, 'get' );
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},
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/**
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* Create hidden form and submit it through POST
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* to initialize the download.
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* @param {str} url url to call
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* @param {obj} data data to include in the request
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* @param {str} method method of the request
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*/
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processDownload: function( url, data, method ){
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if ( url && data ){
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// data can be string of parameters or array/object
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data = typeof data === 'string' ? data : $.param( data );
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// split params into form inputs
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var inputs = '';
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$.each( data.split( '&' ), function(){
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var pair = this.split( '=' );
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inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />';
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});
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// send request
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$('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>')
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.appendTo( 'body' ).submit().remove();
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mod_toastr.info( 'Your download will begin soon.' );
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} else {
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mod_toastr.error( 'An error occurred.' );
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}
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},
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addFilesFromHistoryModal: function(){
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this.refreshUserHistoriesList( function( self ){
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self.modal = Galaxy.modal;
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var template_modal = self.templateAddFilesFromHistory();
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var folder_name = self.options.full_path[self.options.full_path.length - 1][1]
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self.modal.show({
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closing_events : true,
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title : 'Adding datasets from your history to folder ' + folder_name,
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body : template_modal({histories: self.histories.models}),
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buttons : {
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'Add' : function() {self.addAllDatasetsFromHistory();},
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'Close' : function() {Galaxy.modal.hide();}
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},
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closing_callback: function(){
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Galaxy.libraries.library_router.back();
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}
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});
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// user should always have a history, even anonymous user
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if (self.histories.models.length > 0){
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self.fetchAndDisplayHistoryContents(self.histories.models[0].id);
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$( "#dataset_add_bulk" ).change(function(event) {
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self.fetchAndDisplayHistoryContents(event.target.value);
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});
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} else {
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mod_toastr.error( 'An error ocurred.' );
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}
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});
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},
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/**
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* Create modal for importing from Galaxy path.
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* This feature is admin-only.
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*/
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importFilesFromPathModal: function(){
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var that = this;
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this.modal = Galaxy.modal;
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var template_modal = this.templateImportPathModal();
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this.modal.show({
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closing_events : true,
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title : 'Please enter paths to import',
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body : template_modal({}),
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buttons : {
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'Import' : function() { that.importFromPathsClicked(that); },
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'Close' : function() { Galaxy.modal.hide(); }
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},
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closing_callback: function(){
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// TODO: should not trigger routes outside of the router
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Galaxy.libraries.library_router.navigate( 'folders/' + that.id, { trigger: true } );
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}
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});
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this.renderSelectBoxes();
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},
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/**
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* Request all extensions and genomes from Galaxy
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* and save them sorted in arrays.
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*/
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fetchExtAndGenomes: function(){
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var that = this;
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mod_utils.get({
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url : galaxy_config.root + "api/datatypes?extension_only=False",
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success : function( datatypes ) {
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for (key in datatypes) {
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that.list_extensions.push({
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id : datatypes[key].extension,
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text : datatypes[key].extension,
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description : datatypes[key].description,
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description_url : datatypes[key].description_url
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});
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}
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that.list_extensions.sort(function(a, b) {
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return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
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});
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that.list_extensions.unshift(that.auto);
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}
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});
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mod_utils.get({
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url: galaxy_config.root + "api/genomes",
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success: function( genomes ) {
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for ( key in genomes ) {
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that.list_genomes.push({
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id : genomes[key][1],
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text : genomes[key][0]
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});
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}
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that.list_genomes.sort(function(a, b) {
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return a.id > b.id ? 1 : a.id < b.id ? -1 : 0;
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});
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}
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});
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},
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renderSelectBoxes: function(){
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// This won't work properly unlesss we already have the data fetched.
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// See this.fetchExtAndGenomes()
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// TODO switch to common resources:
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// https://trello.com/c/dIUE9YPl/1933-ui-common-resources-and-data-into-galaxy-object
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var that = this;
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this.select_genome = new mod_select.View( {
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css: 'library-genome-select',
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data: that.list_genomes,
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container: Galaxy.modal.$el.find( '#library_genome_select' ),
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value: '?'
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} );
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this.select_extension = new mod_select.View({
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css: 'library-extension-select',
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data: that.list_extensions,
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container: Galaxy.modal.$el.find( '#library_extension_select' ),
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value: 'auto'
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});
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},
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/**
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* Create modal for importing from given directory
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* on Galaxy. Bind jQuery events.
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*/
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importFilesFromGalaxyFolderModal: function( options ){
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var that = this;
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var template_modal = this.templateBrowserModal();
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this.modal = Galaxy.modal;
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this.modal.show({
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closing_events : true,
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title : 'Please select folders or files',
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body : template_modal({}),
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buttons : {
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'Import' : function() {
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that.importFromJstreePath( that, options );
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},
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'Close' : function() {
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Galaxy.modal.hide();
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}
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},
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closing_callback: function(){
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// TODO: should not trigger routes outside of the router
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Galaxy.libraries.library_router.navigate('folders/' + that.id, {trigger: true});
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}
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});
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this.renderSelectBoxes();
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options.disabled_jstree_element = 'folders';
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this.renderJstree( options );
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$( 'input[type=radio]' ).change( function( event ){
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if (event.target.value ==='jstree-disable-folders') {
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options.disabled_jstree_element = 'folders';
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that.renderJstree( options );
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$('.jstree-folders-message').hide();
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$('.jstree-preserve-structure').hide();
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$('.jstree-link-files').hide();
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$('.jstree-files-message').show();
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} else if ( event.target.value ==='jstree-disable-files' ){
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$('.jstree-files-message').hide();
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$('.jstree-folders-message').show();
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$('.jstree-link-files').show();
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$('.jstree-preserve-structure').show();
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options.disabled_jstree_element = 'files';
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that.renderJstree( options );
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}
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}
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);
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},
|
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/**
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* Fetch the contents of user directory on Galaxy
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* and render jstree component based on received
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* data.
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* @param {[type]} options [description]
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*/
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renderJstree: function( options ){
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var that = this;
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this.options = _.extend( this.options, options );
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var target = options.source || 'userdir';
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var disabled_jstree_element = this.options.disabled_jstree_element;
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this.jstree = new mod_library_model.Jstree();
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this.jstree.url = this.jstree.urlRoot +
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'?target=' + target +
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'&format=jstree' +
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'&disable=' + disabled_jstree_element;
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this.jstree.fetch({
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success: function(model, response){
|
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// This is to prevent double jquery load. I think. Carl is magician.
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|
define( 'jquery', function(){ return jQuery; });
|
|
// Now we need jstree, time to lazy load it.
|
|
require([ 'libs/jquery/jstree' ], function(jstree){
|
|
$('#jstree_browser').jstree("destroy");
|
|
$('#jstree_browser').jstree({
|
|
'core':{
|
|
'data': model
|
|
},
|
|
'plugins': ['types', 'checkbox'],
|
|
'types': {
|
|
"folder": {
|
|
"icon": "jstree-folder"
|
|
},
|
|
"file": {
|
|
"icon": "jstree-file"
|
|
}
|
|
},
|
|
'checkbox': {
|
|
three_state: false
|
|
}
|
|
});
|
|
});
|
|
},
|
|
error: function(model, response){
|
|
if (typeof response.responseJSON !== "undefined"){
|
|
mod_toastr.error(response.responseJSON.err_msg);
|
|
} else {
|
|
mod_toastr.error('An error ocurred.');
|
|
}
|
|
}
|
|
})
|
|
},
|
|
|
|
/**
|
|
* Take the paths from the textarea, split it, create
|
|
* a request queue and call a function that starts sending
|
|
* one by one to be imported on the server.
|
|
*/
|
|
importFromPathsClicked: function(){
|
|
var preserve_dirs = this.modal.$el.find('.preserve-checkbox').is(':checked');
|
|
var link_data = this.modal.$el.find('.link-checkbox').is(':checked');
|
|
var file_type = this.select_extension.value();
|
|
var dbkey = this.select_genome.value();
|
|
var paths = $('textarea#import_paths').val();
|
|
var valid_paths = [];
|
|
if (!paths){
|
|
mod_toastr.info('Please enter a path relative to Galaxy root.');
|
|
} else {
|
|
this.modal.disableButton('Import');
|
|
paths = paths.split('\n');
|
|
for (var i = paths.length - 1; i >= 0; i--) {
|
|
trimmed = paths[i].trim();
|
|
if (trimmed.length!==0){
|
|
valid_paths.push(trimmed);
|
|
}
|
|
};
|
|
this.initChainCallControl( { length: valid_paths.length, action: 'adding_datasets' } );
|
|
this.chainCallImportingFolders( { paths: valid_paths,
|
|
preserve_dirs: preserve_dirs,
|
|
link_data: link_data,
|
|
source: 'admin_path',
|
|
file_type: file_type,
|
|
dbkey: dbkey } );
|
|
}
|
|
},
|
|
|
|
/**
|
|
* Initialize the control of chaining requests
|
|
* in the current modal.
|
|
* @param {int} length The number of items in the chain call.
|
|
*/
|
|
initChainCallControl: function( options ){
|
|
var template;
|
|
switch( options.action ){
|
|
case "adding_datasets":
|
|
template = this.templateAddingDatasetsProgressBar();
|
|
this.modal.$el.find( '.modal-body' ).html( template( { folder_name : this.options.folder_name } ) );
|
|
break;
|
|
case "deleting_datasets":
|
|
template = this.templateDeletingDatasetsProgressBar();
|
|
this.modal.$el.find( '.modal-body' ).html( template() );
|
|
break;
|
|
case "to_history":
|
|
template = this.templateImportIntoHistoryProgressBar();
|
|
this.modal.$el.find( '.modal-body' ).html( template( { history_name : options.history_name } ) );
|
|
break;
|
|
default:
|
|
console.error( 'Wrong action specified.')
|
|
break;
|
|
}
|
|
|
|
// var progress_bar_tmpl = this.templateAddingDatasetsProgressBar();
|
|
// this.modal.$el.find( '.modal-body' ).html( progress_bar_tmpl( { folder_name : this.options.folder_name } ) );
|
|
this.progress = 0;
|
|
this.progressStep = 100 / options.length;
|
|
this.options.chain_call_control.total_number = options.length;
|
|
this.options.chain_call_control.failed_number = 0;
|
|
},
|
|
|
|
/**
|
|
* Take the selected items from the jstree, create a request queue
|
|
* and send them one by one to the server for importing into
|
|
* the current folder.
|
|
*
|
|
* jstree.js has to be loaded before
|
|
* @see renderJstree
|
|
*/
|
|
importFromJstreePath: function ( that, options ){
|
|
var selected_nodes = $( '#jstree_browser' ).jstree().get_selected( true );
|
|
var preserve_dirs = this.modal.$el.find( '.preserve-checkbox' ).is( ':checked' );
|
|
var link_data = this.modal.$el.find( '.link-checkbox' ).is( ':checked' );
|
|
var file_type = this.select_extension.value();
|
|
var dbkey = this.select_genome.value();
|
|
var selection_type = selected_nodes[0].type;
|
|
var paths = [];
|
|
if ( selected_nodes.length < 1 ){
|
|
mod_toastr.info( 'Please select some items first.' );
|
|
} else {
|
|
this.modal.disableButton( 'Import' );
|
|
for ( var i = selected_nodes.length - 1; i >= 0; i-- ){
|
|
if ( selected_nodes[i].li_attr.full_path !== undefined ){
|
|
paths.push( selected_nodes[i].li_attr.full_path );
|
|
}
|
|
}
|
|
this.initChainCallControl( { length: paths.length, action: 'adding_datasets' } );
|
|
if ( selection_type === 'folder' ){
|
|
var full_source = options.source + '_folder';
|
|
this.chainCallImportingFolders( { paths: paths,
|
|
preserve_dirs: preserve_dirs,
|
|
link_data: link_data,
|
|
source: full_source,
|
|
file_type: file_type,
|
|
dbkey: dbkey } );
|
|
} else if ( selection_type === 'file' ){
|
|
var full_source = options.source + '_file';
|
|
this.chainCallImportingUserdirFiles( { paths : paths,
|
|
file_type: file_type,
|
|
dbkey: dbkey,
|
|
source: full_source } );
|
|
}
|
|
}
|
|
},
|
|
|
|
fetchAndDisplayHistoryContents: function(history_id){
|
|
var history_contents = new mod_library_model.HistoryContents({id:history_id});
|
|
var self = this;
|
|
history_contents.fetch({
|
|
success: function(history_contents){
|
|
var history_contents_template = self.templateHistoryContents();
|
|
self.histories.get(history_id).set({'contents' : history_contents});
|
|
self.modal.$el.find('#selected_history_content').html(history_contents_template({history_contents: history_contents.models.reverse()}));
|
|
},
|
|
error: function(model, response){
|
|
if (typeof response.responseJSON !== "undefined"){
|
|
mod_toastr.error(response.responseJSON.err_msg);
|
|
} else {
|
|
mod_toastr.error('An error ocurred.');
|
|
}
|
|
}
|
|
});
|
|
},
|
|
|
|
/**
|
|
* Import all selected datasets from history into the current folder.
|
|
*/
|
|
addAllDatasetsFromHistory : function (){
|
|
var checked_hdas = this.modal.$el.find( '#selected_history_content' ).find( ':checked' );
|
|
var history_dataset_ids = [];
|
|
var hdas_to_add = [];
|
|
if ( checked_hdas.length < 1 ){
|
|
mod_toastr.info( 'You must select some datasets first.' );
|
|
} else {
|
|
this.modal.disableButton( 'Add' );
|
|
checked_hdas.each(function(){
|
|
var hid = $( this.parentElement ).data( 'id' );
|
|
if ( hid ) {
|
|
history_dataset_ids.push( hid );
|
|
}
|
|
});
|
|
for ( var i = history_dataset_ids.length - 1; i >= 0; i-- ) {
|
|
history_dataset_id = history_dataset_ids[i];
|
|
var folder_item = new mod_library_model.Item();
|
|
folder_item.url = '/api/folders/' + this.options.id + '/contents';
|
|
folder_item.set( { 'from_hda_id':history_dataset_id } );
|
|
hdas_to_add.push( folder_item );
|
|
}
|
|
this.initChainCallControl( { length: hdas_to_add.length, action: 'adding_datasets' } );
|
|
this.chainCallAddingHdas( hdas_to_add );
|
|
}
|
|
},
|
|
|
|
/**
|
|
* Take array of empty history items and make request for each of them
|
|
* to create it on server. Update progress in between calls.
|
|
* @param {array} history_item_set array of empty history items
|
|
* @param {str} history_name name of the history to import to
|
|
*/
|
|
chainCallImportingIntoHistory: function( history_item_set, history_name ){
|
|
var self = this;
|
|
var popped_item = history_item_set.pop();
|
|
if ( typeof popped_item == "undefined" ) {
|
|
if ( this.options.chain_call_control.failed_number === 0 ){
|
|
mod_toastr.success( 'Selected datasets imported into history. Click this to start analysing it.', '', { onclick: function() { window.location='/' } } );
|
|
} else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
|
|
mod_toastr.error( 'There was an error and no datasets were imported into history.' );
|
|
} else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
|
|
mod_toastr.warning( 'Some of the datasets could not be imported into history. Click this to see what was imported.', '', { onclick: function() { window.location='/' } } );
|
|
}
|
|
Galaxy.modal.hide();
|
|
return true;
|
|
}
|
|
var promise = $.when( popped_item.save( { content: popped_item.content, source: popped_item.source } ) );
|
|
|
|
promise.done( function(){
|
|
self.updateProgress();
|
|
self.chainCallImportingIntoHistory( history_item_set, history_name );
|
|
} )
|
|
.fail( function(){
|
|
self.options.chain_call_control.failed_number += 1;
|
|
self.updateProgress();
|
|
self.chainCallImportingIntoHistory( history_item_set, history_name );
|
|
} );
|
|
},
|
|
|
|
/**
|
|
* Take the array of paths and createa request for each of them
|
|
* calling them in chain. Update the progress bar in between each.
|
|
* @param {array} paths paths relative to user folder on Galaxy
|
|
*/
|
|
chainCallImportingUserdirFiles: function( options ){
|
|
|
|
var that = this;
|
|
var popped_item = options.paths.pop();
|
|
if ( typeof popped_item === "undefined" ) {
|
|
if ( this.options.chain_call_control.failed_number === 0 ){
|
|
mod_toastr.success( 'Selected files imported into the current folder' );
|
|
Galaxy.modal.hide();
|
|
} else {
|
|
mod_toastr.error( 'An error occured.' );
|
|
}
|
|
return true;
|
|
}
|
|
var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id +
|
|
'&source=' + options.source +
|
|
'&path=' + popped_item +
|
|
'&file_type=' + options.file_type +
|
|
'&dbkey=' + options.dbkey ) )
|
|
promise.done( function( response ){
|
|
that.updateProgress();
|
|
that.chainCallImportingUserdirFiles( options );
|
|
} )
|
|
.fail( function(){
|
|
that.options.chain_call_control.failed_number += 1;
|
|
that.updateProgress();
|
|
that.chainCallImportingUserdirFiles( options );
|
|
} );
|
|
},
|
|
|
|
/**
|
|
* Take the array of paths and createa request for each of them
|
|
* calling them in chain. Update the progress bar in between each.
|
|
* @param {array} paths paths relative to Galaxy root folder
|
|
* @param {boolean} preserve_dirs indicates whether to preserve folder structure
|
|
* @param {boolean} link_data copy files to Galaxy or link instead
|
|
* @param {str} source string representing what type of folder
|
|
* is the source of import
|
|
*/
|
|
chainCallImportingFolders: function( options ){
|
|
// TODO need to check which paths to call
|
|
var that = this;
|
|
var popped_item = options.paths.pop();
|
|
if (typeof popped_item == "undefined") {
|
|
if (this.options.chain_call_control.failed_number === 0){
|
|
mod_toastr.success('Selected folders and their contents imported into the current folder.');
|
|
Galaxy.modal.hide();
|
|
} else {
|
|
// TODO better error report
|
|
mod_toastr.error('An error occured.');
|
|
}
|
|
return true;
|
|
}
|
|
var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id +
|
|
'&source=' + options.source +
|
|
'&path=' + popped_item +
|
|
'&preserve_dirs=' + options.preserve_dirs +
|
|
'&link_data=' + options.link_data +
|
|
'&file_type=' + options.file_type +
|
|
'&dbkey=' + options.dbkey ) )
|
|
promise.done(function(response){
|
|
that.updateProgress();
|
|
that.chainCallImportingFolders( options );
|
|
})
|
|
.fail(function(){
|
|
that.options.chain_call_control.failed_number += 1;
|
|
that.updateProgress();
|
|
that.chainCallImportingFolders( options );
|
|
});
|
|
},
|
|
|
|
/**
|
|
* Take the array of hdas and create a request for each.
|
|
* Call them in chain and update progress bar in between each.
|
|
* @param {array} hdas_set array of empty hda objects
|
|
*/
|
|
chainCallAddingHdas: function( hdas_set ){
|
|
var self = this;
|
|
this.added_hdas = new mod_library_model.Folder();
|
|
var popped_item = hdas_set.pop();
|
|
if ( typeof popped_item == "undefined" ) {
|
|
if ( this.options.chain_call_control.failed_number === 0 ){
|
|
mod_toastr.success( 'Selected datasets from history added to the folder' );
|
|
} else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
|
|
mod_toastr.error( 'There was an error and no datasets were added to the folder.' );
|
|
} else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
|
|
mod_toastr.warning( 'Some of the datasets could not be added to the folder' );
|
|
}
|
|
Galaxy.modal.hide();
|
|
return this.added_hdas;
|
|
}
|
|
var promise = $.when( popped_item.save( { from_hda_id: popped_item.get( 'from_hda_id' ) } ) );
|
|
|
|
promise.done( function( model ){
|
|
Galaxy.libraries.folderListView.collection.add( model );
|
|
self.updateProgress();
|
|
self.chainCallAddingHdas( hdas_set );
|
|
})
|
|
.fail( function(){
|
|
self.options.chain_call_control.failed_number += 1;
|
|
self.updateProgress();
|
|
self.chainCallAddingHdas( hdas_set );
|
|
});
|
|
},
|
|
|
|
/**
|
|
* Take the array of lddas, create request for each and
|
|
* call them in chain. Update progress bar in between each.
|
|
* @param {array} lddas_set array of lddas to delete
|
|
*/
|
|
chainCallDeletingHdas: function( lddas_set ){
|
|
var self = this;
|
|
this.deleted_lddas = new mod_library_model.Folder();
|
|
var popped_item = lddas_set.pop();
|
|
if ( typeof popped_item === "undefined" ) {
|
|
if ( this.options.chain_call_control.failed_number === 0 ){
|
|
mod_toastr.success( 'Selected datasets were deleted.' );
|
|
} else if ( this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number ){
|
|
mod_toastr.error( 'There was an error and no datasets were deleted. Please make sure you have sufficient permissions.' );
|
|
} else if ( this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number ){
|
|
mod_toastr.warning( 'Some of the datasets could not be deleted. Please make sure you have sufficient permissions.' );
|
|
}
|
|
Galaxy.modal.hide();
|
|
return this.deleted_lddas;
|
|
}
|
|
var promise = $.when( popped_item.destroy() );
|
|
|
|
promise.done( function( dataset ){
|
|
Galaxy.libraries.folderListView.collection.remove( popped_item.id );
|
|
self.updateProgress();
|
|
// add the deleted dataset to collection, triggers rendering
|
|
if ( Galaxy.libraries.folderListView.options.include_deleted ){
|
|
var updated_dataset = new mod_library_model.Item( dataset );
|
|
Galaxy.libraries.folderListView.collection.add( updated_dataset );
|
|
}
|
|
self.chainCallDeletingHdas( lddas_set );
|
|
})
|
|
.fail( function(){
|
|
self.options.chain_call_control.failed_number += 1;
|
|
self.updateProgress();
|
|
self.chainCallDeletingHdas( lddas_set );
|
|
});
|
|
},
|
|
|
|
/**
|
|
* Handles the click on 'show deleted' checkbox
|
|
*/
|
|
checkIncludeDeleted: function(event){
|
|
if (event.target.checked){
|
|
Galaxy.libraries.folderListView.fetchFolder({include_deleted: true});
|
|
} else{
|
|
Galaxy.libraries.folderListView.fetchFolder({include_deleted: false});
|
|
}
|
|
},
|
|
|
|
/**
|
|
* Deletes the selected datasets. Atomic. One by one.
|
|
*/
|
|
deleteSelectedDatasets: function(){
|
|
var checkedValues = $('#folder_table').find(':checked');
|
|
if(checkedValues.length === 0){
|
|
mod_toastr.info('You must select at least one dataset for deletion.');
|
|
} else {
|
|
var template = this.templateDeletingDatasetsProgressBar();
|
|
this.modal = Galaxy.modal;
|
|
this.modal.show({
|
|
closing_events : true,
|
|
title : 'Deleting selected datasets',
|
|
body : template({}),
|
|
buttons : {
|
|
'Close' : function() {Galaxy.modal.hide();}
|
|
}
|
|
});
|
|
// init the control counters
|
|
this.options.chain_call_control.total_number = 0;
|
|
this.options.chain_call_control.failed_number = 0;
|
|
|
|
var dataset_ids = [];
|
|
checkedValues.each(function(){
|
|
if (this.parentElement.parentElement.id !== '') {
|
|
dataset_ids.push(this.parentElement.parentElement.id);
|
|
}
|
|
});
|
|
// init the progress bar
|
|
this.progressStep = 100 / dataset_ids.length;
|
|
this.progress = 0;
|
|
|
|
// prepare the dataset items to be added
|
|
var lddas_to_delete = [];
|
|
for (var i = dataset_ids.length - 1; i >= 0; i--) {
|
|
var dataset = new mod_library_model.Item({id:dataset_ids[i]});
|
|
lddas_to_delete.push(dataset);
|
|
}
|
|
|
|
this.options.chain_call_control.total_number = dataset_ids.length;
|
|
// call the recursive function to call ajax one after each other (request FIFO queue)
|
|
this.chainCallDeletingHdas(lddas_to_delete);
|
|
}
|
|
},
|
|
|
|
|
|
showLibInfo: function(){
|
|
var library_id = Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;
|
|
var library = null;
|
|
var that = this;
|
|
if (Galaxy.libraries.libraryListView !== null){
|
|
library = Galaxy.libraries.libraryListView.collection.get(library_id);
|
|
this.showLibInfoModal(library);
|
|
} else {
|
|
library = new mod_library_model.Library({id: library_id});
|
|
library.fetch({
|
|
success: function(){
|
|
that.showLibInfoModal(library);
|
|
},
|
|
error: function(model, response){
|
|
if (typeof response.responseJSON !== "undefined"){
|
|
mod_toastr.error(response.responseJSON.err_msg);
|
|
} else {
|
|
mod_toastr.error('An error ocurred.');
|
|
}
|
|
}
|
|
})
|
|
}
|
|
},
|
|
|
|
showLibInfoModal: function(library){
|
|
var template = this.templateLibInfoInModal();
|
|
this.modal = Galaxy.modal;
|
|
this.modal.show({
|
|
closing_events : true,
|
|
title : 'Library Information',
|
|
body : template({library:library}),
|
|
buttons : {
|
|
'Close' : function() {Galaxy.modal.hide();}
|
|
}
|
|
});
|
|
},
|
|
|
|
showImportModal: function(options){
|
|
switch(options.source){
|
|
case "history":
|
|
this.addFilesFromHistoryModal();
|
|
break;
|
|
case "importdir":
|
|
this.importFilesFromGalaxyFolderModal( { source: 'importdir' } );
|
|
break;
|
|
case "path":
|
|
this.importFilesFromPathModal();
|
|
break;
|
|
case "userdir":
|
|
this.importFilesFromGalaxyFolderModal( { source: 'userdir' } );
|
|
break;
|
|
default:
|
|
Galaxy.libraries.library_router.back();
|
|
mod_toastr.error('Invalid import source.');
|
|
break;
|
|
}
|
|
},
|
|
|
|
showPageSizePrompt: function(){
|
|
var folder_page_size = prompt( 'How many items per page do you want to see?', Galaxy.libraries.preferences.get( 'folder_page_size' ) );
|
|
if ( ( folder_page_size != null ) && ( folder_page_size == parseInt( folder_page_size ) ) ) {
|
|
Galaxy.libraries.preferences.set( { 'folder_page_size': parseInt( folder_page_size ) } );
|
|
Galaxy.libraries.folderListView.render( { id: this.options.id, show_page: 1 } );
|
|
}
|
|
},
|
|
|
|
templateToolBar: function(){
|
|
tmpl_array = [];
|
|
|
|
// CONTAINER START
|
|
tmpl_array.push('<div class="library_style_container">');
|
|
// TOOLBAR START
|
|
tmpl_array.push(' <div id="library_toolbar">');
|
|
tmpl_array.push(' <span><strong>DATA LIBRARIES</strong></span>');
|
|
tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');
|
|
tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span> <span class="fa fa-folder"></span></button>');
|
|
|
|
tmpl_array.push('<% if(mutiple_add_dataset_options) { %>');
|
|
tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');
|
|
tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');
|
|
tmpl_array.push(' <span class="fa fa-plus"></span> <span class="fa fa-file"></span> <span class="caret"></span>');
|
|
tmpl_array.push(' </button>');
|
|
tmpl_array.push(' <ul class="dropdown-menu" role="menu">');
|
|
tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');
|
|
tmpl_array.push('<% if(Galaxy.config.user_library_import_dir !== null) { %>');
|
|
tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');
|
|
tmpl_array.push('<% } %>');
|
|
tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>');
|
|
|
|
tmpl_array.push(' <li class="divider"></li>');
|
|
tmpl_array.push(' <li class="dropdown-header">Admins only</li>');
|
|
|
|
tmpl_array.push('<% if(Galaxy.config.library_import_dir !== null) { %>');
|
|
tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>');
|
|
tmpl_array.push('<% } %>');
|
|
|
|
tmpl_array.push('<% if(Galaxy.config.allow_library_path_paste) { %>');
|
|
tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');
|
|
tmpl_array.push('<% } %>');
|
|
tmpl_array.push('<% } %>');
|
|
tmpl_array.push(' </ul>');
|
|
tmpl_array.push(' </div>');
|
|
tmpl_array.push('<% } else { %>');
|
|
tmpl_array.push(' <a data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button"><span class="fa fa-plus"></span> <span class="fa fa-file"></span></span></a>');
|
|
tmpl_array.push('<% } %>');
|
|
|
|
tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');
|
|
tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');
|
|
tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');
|
|
tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');
|
|
tmpl_array.push(' </button>');
|
|
tmpl_array.push(' <ul class="dropdown-menu" role="menu">');
|
|
tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');
|
|
tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');
|
|
tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');
|
|
tmpl_array.push(' </ul>');
|
|
tmpl_array.push(' </div>');
|
|
tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');
|
|
tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');
|
|
tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');
|
|
|
|
tmpl_array.push(' <span id="folder_paginator" class="library-paginator">');
|
|
// paginator will append here
|
|
tmpl_array.push(' </span>');
|
|
|
|
tmpl_array.push(' </div>');
|
|
// TOOLBAR END
|
|
tmpl_array.push(' <div id="folder_items_element">');
|
|
tmpl_array.push(' </div>');
|
|
tmpl_array.push('</div>');
|
|
// CONTAINER END
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
templateLibInfoInModal: function(){
|
|
tmpl_array = [];
|
|
|
|
tmpl_array.push('<div id="lif_info_modal">');
|
|
tmpl_array.push('<h2>Library name:</h2>');
|
|
tmpl_array.push('<p><%- library.get("name") %></p>');
|
|
tmpl_array.push('<h3>Library description:</h3>');
|
|
tmpl_array.push('<p><%- library.get("description") %></p>');
|
|
tmpl_array.push('<h3>Library synopsis:</h3>');
|
|
tmpl_array.push('<p><%- library.get("synopsis") %></p>');
|
|
|
|
tmpl_array.push('</div>');
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
templateNewFolderInModal: function(){
|
|
tmpl_array = [];
|
|
|
|
tmpl_array.push('<div id="new_folder_modal">');
|
|
tmpl_array.push('<form>');
|
|
tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');
|
|
tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');
|
|
tmpl_array.push('</form>');
|
|
tmpl_array.push('</div>');
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
|
|
templateBulkImportInModal : function(){
|
|
var tmpl_array = [];
|
|
|
|
tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');
|
|
tmpl_array.push('Select history: ');
|
|
tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');
|
|
tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box
|
|
tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');
|
|
tmpl_array.push(' <% }); %>');
|
|
tmpl_array.push('</select>');
|
|
tmpl_array.push('</span>');
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
templateImportIntoHistoryProgressBar : function (){
|
|
var tmpl_array = [];
|
|
|
|
tmpl_array.push('<div class="import_text">');
|
|
tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>');
|
|
tmpl_array.push('</div>');
|
|
tmpl_array.push('<div class="progress">');
|
|
tmpl_array.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');
|
|
tmpl_array.push(' <span class="completion_span">0% Complete</span>');
|
|
tmpl_array.push(' </div>');
|
|
tmpl_array.push('</div>');
|
|
tmpl_array.push('');
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
templateAddingDatasetsProgressBar: function (){
|
|
var tmpl_array = [];
|
|
|
|
tmpl_array.push('<div class="import_text">');
|
|
tmpl_array.push('Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>');
|
|
tmpl_array.push('</div>');
|
|
tmpl_array.push('<div class="progress">');
|
|
tmpl_array.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');
|
|
tmpl_array.push(' <span class="completion_span">0% Complete</span>');
|
|
tmpl_array.push(' </div>');
|
|
tmpl_array.push('</div>');
|
|
tmpl_array.push('');
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
templateDeletingDatasetsProgressBar: function (){
|
|
var tmpl_array = [];
|
|
|
|
tmpl_array.push('<div class="import_text">');
|
|
tmpl_array.push('</div>');
|
|
tmpl_array.push('<div class="progress">');
|
|
tmpl_array.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');
|
|
tmpl_array.push(' <span class="completion_span">0% Complete</span>');
|
|
tmpl_array.push(' </div>');
|
|
tmpl_array.push('</div>');
|
|
tmpl_array.push('');
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
templateBrowserModal: function(){
|
|
var tmpl_array = [];
|
|
|
|
tmpl_array.push('<div id="file_browser_modal">');
|
|
tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
|
|
tmpl_array.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');
|
|
|
|
|
|
tmpl_array.push('<div style="margin-bottom:1em;">');
|
|
tmpl_array.push('<label class="radio-inline">');
|
|
tmpl_array.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');
|
|
tmpl_array.push('</label>');
|
|
tmpl_array.push('<label class="radio-inline">');
|
|
tmpl_array.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');
|
|
tmpl_array.push('</label>');
|
|
tmpl_array.push('</div>');
|
|
tmpl_array.push('<div style="margin-bottom:1em;">');
|
|
tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');
|
|
tmpl_array.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
|
|
tmpl_array.push('Preserve directory structure');
|
|
tmpl_array.push(' </label>');
|
|
tmpl_array.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');
|
|
tmpl_array.push(' <input class="link-checkbox" type="checkbox" value="link_files">');
|
|
tmpl_array.push('Link files instead of copying');
|
|
tmpl_array.push(' </label>');
|
|
tmpl_array.push('</div>');
|
|
tmpl_array.push('<div id="jstree_browser">');
|
|
tmpl_array.push('</div>');
|
|
|
|
tmpl_array.push('<hr />');
|
|
tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
|
|
tmpl_array.push('<div>');
|
|
tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />');
|
|
tmpl_array.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');
|
|
tmpl_array.push('</div>');
|
|
tmpl_array.push('</div>');
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
templateImportPathModal: function(){
|
|
var tmpl_array = [];
|
|
|
|
tmpl_array.push('<div id="file_browser_modal">');
|
|
tmpl_array.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');
|
|
|
|
tmpl_array.push('<div style="margin-bottom: 0.5em;">');
|
|
tmpl_array.push('<label class="checkbox-inline jstree-preserve-structure">');
|
|
tmpl_array.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');
|
|
tmpl_array.push('Preserve directory structure');
|
|
tmpl_array.push(' </label>');
|
|
tmpl_array.push('<label class="checkbox-inline jstree-link-files">');
|
|
tmpl_array.push(' <input class="link-checkbox" type="checkbox" value="link_files">');
|
|
tmpl_array.push('Link files instead of copying');
|
|
tmpl_array.push(' </label>');
|
|
tmpl_array.push('</div>');
|
|
|
|
tmpl_array.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');
|
|
|
|
tmpl_array.push('<hr />');
|
|
tmpl_array.push('<p>You can set extension type and genome for all imported datasets at once:</p>');
|
|
tmpl_array.push('<div>');
|
|
tmpl_array.push('Type: <span id="library_extension_select" class="library-extension-select" />');
|
|
tmpl_array.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');
|
|
tmpl_array.push('</div>');
|
|
|
|
tmpl_array.push('</div>');
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
templateAddFilesFromHistory: function (){
|
|
var tmpl_array = [];
|
|
|
|
tmpl_array.push('<div id="add_files_modal">');
|
|
tmpl_array.push('<div id="history_modal_combo_bulk">');
|
|
tmpl_array.push('Select history: ');
|
|
tmpl_array.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');
|
|
tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box
|
|
tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');
|
|
tmpl_array.push(' <% }); %>');
|
|
tmpl_array.push('</select>');
|
|
tmpl_array.push('</div>');
|
|
tmpl_array.push('<br/>');
|
|
tmpl_array.push('<div id="selected_history_content">');
|
|
|
|
tmpl_array.push('</div>');
|
|
tmpl_array.push('</div>');
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
templateHistoryContents: function (){
|
|
var tmpl_array = [];
|
|
|
|
tmpl_array.push('<strong>Choose the datasets to import:</strong>');
|
|
tmpl_array.push('<ul>');
|
|
tmpl_array.push(' <% _.each(history_contents, function(history_item) { %>');
|
|
tmpl_array.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');
|
|
tmpl_array.push(' <input style="margin: 0;" type="checkbox"> <%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');
|
|
tmpl_array.push(' </li>');
|
|
tmpl_array.push(' <% }); %>');
|
|
tmpl_array.push('</ul>');
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
templatePaginator: function(){
|
|
tmpl_array = [];
|
|
|
|
tmpl_array.push(' <ul class="pagination pagination-sm">');
|
|
tmpl_array.push(' <% if ( ( show_page - 1 ) > 0 ) { %>');
|
|
tmpl_array.push(' <% if ( ( show_page - 1 ) > page_count ) { %>'); // we are on higher page than total page count
|
|
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');
|
|
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');
|
|
tmpl_array.push(' <% } else { %>');
|
|
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');
|
|
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');
|
|
tmpl_array.push(' <% } %>');
|
|
tmpl_array.push(' <% } else { %>'); // we are on the first page
|
|
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');
|
|
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');
|
|
tmpl_array.push(' <% } %>');
|
|
tmpl_array.push(' <li class="active">');
|
|
tmpl_array.push(' <a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page ) %></a>');
|
|
tmpl_array.push(' </li>');
|
|
tmpl_array.push(' <% if ( ( show_page ) < page_count ) { %>');
|
|
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');
|
|
tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');
|
|
tmpl_array.push(' <% } else { %>');
|
|
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');
|
|
tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');
|
|
tmpl_array.push(' <% } %>');
|
|
tmpl_array.push(' </ul>');
|
|
tmpl_array.push(' <span>');
|
|
tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of items on page" id="page_size_prompt"><%- items_shown %></a> of <%- total_items_count %> items');
|
|
tmpl_array.push(' </span>');
|
|
|
|
return _.template(tmpl_array.join(''));
|
|
},
|
|
|
|
});
|
|
|
|
return {
|
|
FolderToolbarView: FolderToolbarView
|
|
};
|
|
|
|
});
|