mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge branch 'release_15.10' into dev
This commit is contained in:
@@ -66,7 +66,7 @@ var FolderRowView = Backbone.View.extend({
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var dataset_id = $(event.target).closest('tr')[0].id;
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var dataset = Galaxy.libraries.folderListView.collection.get(dataset_id);
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dataset.url = dataset.urlRoot + dataset.id + '?undelete=true';
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dataset.destroy({
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dataset.destroy({
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success : function(model, response){
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Galaxy.libraries.folderListView.collection.remove(dataset_id);
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var updated_dataset = new mod_library_model.Item(response);
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@@ -76,7 +76,7 @@ var FolderRowView = Backbone.View.extend({
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var folder_id = that.model.get('folder_id');
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window.location='#folders/' + folder_id + '/datasets/' + that.id;
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}});
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},
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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('Dataset was not undeleted. ' + response.responseJSON.err_msg);
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@@ -103,7 +103,7 @@ var FolderRowView = Backbone.View.extend({
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Galaxy.libraries.folderListView.collection.add(updated_folder);
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Galaxy.libraries.folderListView.collection.sortByNameAsc();
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mod_toastr.success('Folder undeleted.');
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},
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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('Folder was not undeleted. ' + response.responseJSON.err_msg);
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@@ -157,7 +157,7 @@ var FolderRowView = Backbone.View.extend({
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tmpl_array.push('</tr>');
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return _.template(tmpl_array.join(''));
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},
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},
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templateRowDeletedFile: function(){
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tmpl_array = [];
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@@ -180,7 +180,7 @@ var FolderRowView = Backbone.View.extend({
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templateRowDeletedFolder: function(){
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tmpl_array = [];
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tmpl_array.push('<tr class="active folder_row light library-row" id="<%- content_item.id %>">');
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tmpl_array.push('<tr class="active deleted_folder light library-row" id="<%- content_item.id %>">');
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tmpl_array.push(' <td>');
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tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');
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tmpl_array.push(' </td>');
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@@ -196,7 +196,7 @@ var FolderRowView = Backbone.View.extend({
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return _.template(tmpl_array.join(''));
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}
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});
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return {
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@@ -63,7 +63,7 @@ var FolderToolbarView = Backbone.View.extend({
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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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@@ -99,7 +99,7 @@ var FolderToolbarView = Backbone.View.extend({
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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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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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@@ -163,7 +163,7 @@ var FolderToolbarView = Backbone.View.extend({
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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.url = folder.urlRoot + current_folder_id ;
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folder.save(folderDetails, {
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success: function (folder) {
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@@ -281,7 +281,7 @@ var FolderToolbarView = Backbone.View.extend({
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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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// 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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@@ -360,7 +360,7 @@ var FolderToolbarView = Backbone.View.extend({
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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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@@ -393,7 +393,7 @@ var FolderToolbarView = Backbone.View.extend({
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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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});
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this.renderSelectBoxes();
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},
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@@ -439,7 +439,7 @@ var FolderToolbarView = Backbone.View.extend({
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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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// 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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@@ -469,7 +469,7 @@ var FolderToolbarView = Backbone.View.extend({
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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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'Import' : function() {
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that.importFromJstreePath( that, options );
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},
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'Close' : function() {
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@@ -503,7 +503,7 @@ var FolderToolbarView = Backbone.View.extend({
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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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/**
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@@ -518,9 +518,9 @@ var FolderToolbarView = Backbone.View.extend({
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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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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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@@ -583,8 +583,8 @@ var FolderToolbarView = Backbone.View.extend({
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};
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this.initChainCallControl( { length: valid_paths.length, action: 'adding_datasets' } );
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this.chainCallImportingFolders( { paths: valid_paths,
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preserve_dirs: preserve_dirs,
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link_data: link_data,
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preserve_dirs: preserve_dirs,
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link_data: link_data,
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source: 'admin_path',
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file_type: file_type,
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dbkey: dbkey } );
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@@ -626,9 +626,9 @@ var FolderToolbarView = Backbone.View.extend({
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/**
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* Take the selected items from the jstree, create a request queue
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* and send them one by one to the server for importing into
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* the current folder.
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*
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* and send them one by one to the server for importing into
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* the current folder.
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*
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* jstree.js has to be loaded before
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* @see renderJstree
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*/
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@@ -653,8 +653,8 @@ var FolderToolbarView = Backbone.View.extend({
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if ( selection_type === 'folder' ){
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var full_source = options.source + '_folder';
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this.chainCallImportingFolders( { paths: paths,
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preserve_dirs: preserve_dirs,
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link_data: link_data,
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preserve_dirs: preserve_dirs,
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link_data: link_data,
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source: full_source,
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file_type: file_type,
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dbkey: dbkey } );
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@@ -767,7 +767,7 @@ var FolderToolbarView = Backbone.View.extend({
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}
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return true;
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}
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var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id +
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var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id +
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'&source=' + options.source +
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'&path=' + popped_item +
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'&file_type=' + options.file_type +
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@@ -789,7 +789,7 @@ var FolderToolbarView = Backbone.View.extend({
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* @param {array} paths paths relative to Galaxy root folder
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* @param {boolean} preserve_dirs indicates whether to preserve folder structure
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* @param {boolean} link_data copy files to Galaxy or link instead
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* @param {str} source string representing what type of folder
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* @param {str} source string representing what type of folder
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* is the source of import
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*/
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chainCallImportingFolders: function( options ){
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@@ -825,7 +825,7 @@ var FolderToolbarView = Backbone.View.extend({
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},
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/**
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* Take the array of hdas and create a request for each.
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* Take the array of hdas and create a request for each.
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* Call them in chain and update progress bar in between each.
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* @param {array} hdas_set array of empty hda objects
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*/
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@@ -859,7 +859,7 @@ var FolderToolbarView = Backbone.View.extend({
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},
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/**
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* Take the array of lddas, create request for each and
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* Take the array of lddas, create request for each and
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* call them in chain. Update progress bar in between each.
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* @param {array} lddas_set array of lddas to delete
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*/
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@@ -953,7 +953,7 @@ var FolderToolbarView = Backbone.View.extend({
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var items_total = dataset_ids.length + folder_ids.length
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this.progressStep = 100 / items_total;
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this.progress = 0;
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// prepare the dataset items to be added
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var items_to_delete = [];
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for (var i = dataset_ids.length - 1; i >= 0; i--) {
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@@ -1017,7 +1017,7 @@ var FolderToolbarView = Backbone.View.extend({
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case "importdir":
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this.importFilesFromGalaxyFolderModal( { source: 'importdir' } );
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break;
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case "path":
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case "path":
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this.importFilesFromPathModal();
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break;
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case "userdir":
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@@ -1215,7 +1215,7 @@ var FolderToolbarView = Backbone.View.extend({
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tmpl_array.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');
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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>');
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tmpl_array.push('<div style="margin-bottom:1em;">');
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tmpl_array.push('<label class="radio-inline">');
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tmpl_array.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');
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@@ -427,6 +427,8 @@
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<datatype extension="vtkbinary" type="galaxy.datatypes.constructive_solid_geometry:VtkBinary" display_in_upload="true" />
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<!-- Metagenomic Datatype -->
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<datatype extension="biom1" type="galaxy.datatypes.text:Biom1" display_in_upload="True" subclass="True" mimetype="application/json" />
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<!-- Strand-specific Coordinate Count Datatype used by the Center for Eukaryotic Gene Regulation labs at Penn State -->
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<datatype extension="scidx" type="galaxy.datatypes.interval:ScIdx" display_in_upload="true" />
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</registration>
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<sniffers>
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<!--
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@@ -440,6 +442,7 @@
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyBinary"/>
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkAscii"/>
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:VtkBinary"/>
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<sniffer type="galaxy.datatypes.interval:ScIdx"/>
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<sniffer type="galaxy.datatypes.tabular:Vcf"/>
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<sniffer type="galaxy.datatypes.binary:TwoBit"/>
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<sniffer type="galaxy.datatypes.binary:GeminiSQLite"/>
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@@ -1482,6 +1482,78 @@ class ChromatinInteractions( Interval ):
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return False
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class ScIdx(Tabular):
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"""
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ScIdx files are 1-based and consist of strand-specific coordinate counts.
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They always have 5 columns, and the first row is the column labels:
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'chrom', 'index', 'forward', 'reverse', 'value'.
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Each line following the first consists of data:
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chromosome name (type str), peak index (type int), Forward strand peak
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count (type int), Reverse strand peak count (type int) and value (type int).
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The value of the 5th 'value' column is the sum of the forward and reverse
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peak count values.
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"""
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file_ext = "scidx"
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MetadataElement(name="columns", default=0, desc="Number of columns", readonly=True, visible=False)
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MetadataElement(name="column_types", default=[], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False, no_value=[])
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def __init__(self, **kwd):
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"""
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Initialize scidx datatype.
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"""
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Tabular.__init__(self, **kwd)
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# Don't set column names since the first
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# line of the dataset displays them.
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self.column_names = ['chrom', 'index', 'forward', 'reverse', 'value']
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def sniff(self, filename):
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"""
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Checks for 'scidx-ness.'
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"""
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try:
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count = 0
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fh = open(filename, "r")
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while True:
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line = fh.readline()
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line = line.strip()
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if not line:
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# EOF
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if count > 1:
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# We need at least the column labels and a data line.
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return True
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return False
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# Skip first line.
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if count > 0:
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items = line.split('\t')
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if len(items) != 5:
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return False
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index = items[1]
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if not index.isdigit():
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return False
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forward = items[2]
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if not forward.isdigit():
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return False
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reverse = items[3]
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if not reverse.isdigit():
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return False
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value = items[4]
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if not value.isdigit():
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return False
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if int(forward) + int(reverse) != int(value):
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return False
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if count == 100:
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return True
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count += 1
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if count < 100 and count > 0:
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return True
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except:
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return False
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finally:
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fh.close()
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return False
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if __name__ == '__main__':
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import doctest
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doctest.testmod(sys.modules[__name__])
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@@ -1 +1 @@
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