commit/galaxy-central: martenson: libraries: refactor into separate files for model/views/main+router, showing infoicon for public libraries
by commits-noreply＠bitbucket.org 24 Mar '14
by commits-noreply＠bitbucket.org 24 Mar '14
24 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/68d35caf407f/
Changeset: 68d35caf407f
User: martenson
Date: 2014-03-24 20:12:48
Summary: libraries: refactor into separate files for model/views/main+router, showing infoicon for public libraries
Affected #: 12 files
diff -r 33cc6056d83760e5e3b98999b01ecb260423d33c -r 68d35caf407f367c3447a1a6675d6705c8daacf4 lib/galaxy/webapps/galaxy/api/libraries.py
--- a/lib/galaxy/webapps/galaxy/api/libraries.py
+++ b/lib/galaxy/webapps/galaxy/api/libraries.py
@@ -55,10 +55,12 @@
libraries = []
for library in query:
item = library.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id , 'root_folder_id' : trans.security.encode_id } )
+ if trans.app.security_agent.library_is_public( library, contents=False ):
+ item[ 'public' ] = True
libraries.append( item )
return libraries
- @expose_api
+ @expose_api_anonymous
def show( self, trans, id, deleted='False', **kwd ):
"""
show( self, trans, id, deleted='False', **kwd )
@@ -139,6 +141,9 @@
.. note:: Currently, only admin users can update libraries. Also the library must not be `deleted`.
+ :param id: the encoded id of the library
+ :type id: an encoded id string
+
:param payload: (required) dictionary structure containing::
'name': new library's name, cannot be empty
'description': new library's description
@@ -192,7 +197,7 @@
.. note:: Currently, only admin users can un/delete libraries.
:param id: the encoded id of the library to un/delete
- :type id: str
+ :type id: an encoded id string
:param undelete: (optional) flag specifying whether the item should be deleted or undeleted, defaults to false:
:type undelete: bool
diff -r 33cc6056d83760e5e3b98999b01ecb260423d33c -r 68d35caf407f367c3447a1a6675d6705c8daacf4 static/scripts/galaxy.library.js
--- a/static/scripts/galaxy.library.js
+++ b/static/scripts/galaxy.library.js
@@ -1,1192 +1,26 @@
-// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
-// === GALAXY LIBRARY MODULE ====
-// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
+// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
+// === MAIN GALAXY LIBRARY MODULE ====
+// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
// global variables
-var view = null;
var library_router = null;
-var responses = [];
// dependencies
define([
"galaxy.masthead",
"utils/utils",
- "libs/toastr"], function(mod_masthead, mod_utils, mod_toastr) {
-
-// MMMMMMMMMMMMMMM
-// === Models ====
-// MMMMMMMMMMMMMMM
-
- // LIBRARY
- var Library = Backbone.Model.extend({
- urlRoot: '/api/libraries/'
- });
-
- // FOLDER AS MODEL
- var FolderAsModel = Backbone.Model.extend({
- urlRoot: '/api/folders'
- });
-
- // LIBRARIES
- var Libraries = Backbone.Collection.extend({
- url: '/api/libraries',
-
- model: Library,
-
- sort_key: 'name', // default
-
- sort_order: null, // default
-
- });
-
- // ITEM
- var Item = Backbone.Model.extend({
- urlRoot : '/api/libraries/datasets'
- });
-
- // FOLDER AS COLLECTION
- var Folder = Backbone.Collection.extend({
- model: Item
- });
-
- // CONTAINER for folder contents (folders, items and metadata).
- var FolderContainer = Backbone.Model.extend({
- defaults : {
- folder : new Folder(),
- full_path : "unknown",
- urlRoot : "/api/folders/",
- id : "unknown"
- },
- parse : function(obj) {
- this.full_path = obj[0].full_path;
- // update the inner collection
- this.get("folder").reset(obj[1].folder_contents);
- return obj;
- }
- });
-
- // HISTORY ITEM
- var HistoryItem = Backbone.Model.extend({
- urlRoot : '/api/histories/'
- });
-
- // HISTORY
- var GalaxyHistory = Backbone.Model.extend({
- url : '/api/histories/'
- });
-
- // HISTORIES
- var GalaxyHistories = Backbone.Collection.extend({
- url : '/api/histories',
- model : GalaxyHistory
- });
-
-// MMMMMMMMMMMMMM
-// === VIEWS ====
-// MMMMMMMMMMMMMM
-
-//main view for folder browsing
-var FolderContentView = Backbone.View.extend({
- // main element definition
- el : '#center',
- // progress percentage
- progress: 0,
- // progress rate per one item
- progressStep: 1,
- // last selected history in modal for UX
- lastSelectedHistory: '',
- // self modal
- modal : null,
- // loaded folders
- folders : null,
-
- // initialize
- initialize : function(){
- this.folders = [];
- this.queue = jQuery.Deferred();
- this.queue.resolve();
- },
-
-// MMMMMMMMMMMMMMMMMM
-// === TEMPLATES ====
-// MMMMMMMMMMMMMMMMMM
-
- // main template for folder browsing
- templateFolder : function (){
- var tmpl_array = [];
-
- // CONTAINER
- tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');
- tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');
-
- // TOOLBAR
- tmpl_array.push('<div id="library_folder_toolbar" >');
- tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');
- tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-book"></span> to history</button>');
- tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');
- tmpl_array.push(' <button title="Download selected datasets" 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('</div>');
-
- // BREADCRUMBS
- tmpl_array.push('<ol class="breadcrumb">');
- tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');
- tmpl_array.push(' <% _.each(path, function(path_item) { %>');
- tmpl_array.push(' <% if (path_item[0] != id) { %>');
- tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');
- tmpl_array.push( '<% } else { %>');
- tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');
- tmpl_array.push(' <% } %>');
- tmpl_array.push(' <% }); %>');
- tmpl_array.push('</ol>');
-
-
- // FOLDER CONTENT
- tmpl_array.push('<table id="folder_table" class="grid table table-condensed">');
- tmpl_array.push(' <thead>');
- tmpl_array.push(' <th class="button_heading"></th>');
- tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');
- tmpl_array.push(' <th>name</th>');
- tmpl_array.push(' <th>data type</th>');
- tmpl_array.push(' <th>size</th>');
- tmpl_array.push(' <th>date (UTC)</th>');
- tmpl_array.push(' </thead>');
- tmpl_array.push(' <tbody>');
- tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');
- tmpl_array.push(' <td></td>');
- tmpl_array.push(' <td></td>');
- tmpl_array.push(' <td></td>');
- tmpl_array.push(' <td></td>');
- tmpl_array.push(' <td></td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <% _.each(items, function(content_item) { %>');
- tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder
- tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">');
- tmpl_array.push(' <td>');
- tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');
- tmpl_array.push(' </td>');
- tmpl_array.push(' <td></td>');
- tmpl_array.push(' <td>');
- tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');
- tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder
- tmpl_array.push(' <span class="muted">(empty folder)</span>');
- tmpl_array.push(' <% } %>');
- tmpl_array.push(' </td>');
- tmpl_array.push(' <td>folder</td>');
- tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size
- tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <% } else { %>');
- tmpl_array.push(' <tr class="dataset_row light" id="<%- content_item.id %>">');
- tmpl_array.push(' <td>');
- tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');
- tmpl_array.push(' </td>');
- tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');
- tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset
- tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type
- tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size
- tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <% } %> ');
- tmpl_array.push(' <% }); %>');
- tmpl_array.push(' ');
- tmpl_array.push(' </tbody>');
- tmpl_array.push('</table>');
-
- tmpl_array.push('</div>');
- return tmpl_array.join('');
- },
- templateDatasetModal : function(){
- var tmpl_array = [];
-
- tmpl_array.push('<div class="modal_table">');
- tmpl_array.push(' <table class="grid table table-striped table-condensed">');
- tmpl_array.push(' <tr>');
- tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');
- tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <tr>');
- tmpl_array.push(' <th scope="row">Data type</th>');
- tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <tr>');
- tmpl_array.push(' <th scope="row">Genome build</th>');
- tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <th scope="row">Size</th>');
- tmpl_array.push(' <td><%= _.escape(size) %></td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <tr>');
- tmpl_array.push(' <th scope="row">Date uploaded (UTC)</th>');
- tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <tr>');
- tmpl_array.push(' <th scope="row">Uploaded by</th>');
- tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <tr scope="row">');
- tmpl_array.push(' <th scope="row">Data Lines</th>');
- tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <th scope="row">Comment Lines</th>');
- tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>');
- tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');
- tmpl_array.push(' <% } else { %>');
- tmpl_array.push(' <td scope="row">unknown</td>');
- tmpl_array.push(' <% } %>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <tr>');
- tmpl_array.push(' <th scope="row">Number of Columns</th>');
- tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <tr>');
- tmpl_array.push(' <th scope="row">Column Types</th>');
- tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <tr>');
- tmpl_array.push(' <th scope="row">Miscellaneous information</th>');
- tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' </table>');
- tmpl_array.push(' <pre class="peek">');
- tmpl_array.push(' </pre>');
- tmpl_array.push('</div>');
-
- return tmpl_array.join('');
- },
-
- templateHistorySelectInModal : function(){
- var tmpl_array = [];
-
- tmpl_array.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');
- tmpl_array.push('Select history: ');
- tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; 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 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 tmpl_array.join('');
- },
-
- templateProgressBar : 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 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 tmpl_array.join('');
- },
-
-// MMMMMMMMMMMMMMM
-// === EVENTS ====
-// MMMMMMMMMMMMMMM
-
- // event binding
- events: {
- 'click #select-all-checkboxes' : 'selectAll',
- 'click #toolbtn_bulk_import' : 'modalBulkImport',
- 'click #toolbtn_dl' : 'bulkDownload',
- 'click #toolbtn_create_folder' : 'createFolderFromModal',
- 'click .library-dataset' : 'showDatasetDetails',
- 'click .dataset_row' : 'selectClickedRow'
- },
-
-// MMMMMMMMMMMMMMMMMM
-// === FUNCTIONS ====
-// MMMMMMMMMMMMMMMMMM
-
- //render the folder view
- render: function (options) {
- //hack to show scrollbars
- $("#center").css('overflow','auto');
-
- view = this;
- var that = this;
-
- var folderContainer = new FolderContainer({id: options.id});
- folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents';
-
- folderContainer.fetch({
- success: function (container) {
-
- // prepare nice size strings
- for (var i = 0; i < folderContainer.attributes.folder.models.length; i++) {
- var model = folderContainer.attributes.folder.models[i]
- if (model.get('type') === 'file'){
- model.set('readable_size', that.size_to_string(model.get('file_size')))
- }
- };
-
- // find the upper id
- var path = folderContainer.full_path;
- var upper_folder_id;
- if (path.length === 1){ // library is above us
- upper_folder_id = 0;
- } else {
- upper_folder_id = path[path.length-2][0];
- }
-
- var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id });
- // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id });
- that.$el.html(template);
-
- },
- error: function(){
- mod_toastr.error('An error occured :(');
- }
- })
- },
-
- // convert size to nice string
- size_to_string : function (size)
- {
- // identify unit
- var unit = "";
- if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else
- if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else
- if (size >= 100000) { size = size / 100000; unit = "MB"; } else
- if (size >= 100) { size = size / 100; unit = "KB"; } else
- { size = size * 10; unit = "b"; }
- // return formatted string
- return (Math.round(size) / 10) + unit;
- },
-
- //show modal with current dataset info
- showDatasetDetails : function(event){
- // prevent default
- event.preventDefault();
-
- //TODO check whether we already have the data
-
- //load the ID of the row
- var id = $(event.target).parent().parent().parent().attr('id');
- if (typeof id === 'undefined'){
- id = $(event.target).parent().attr('id');
- }
- if (typeof id === 'undefined'){
- id = $(event.target).parent().parent().attr('id')
- }
-
- //create new item
- var item = new Item();
- var histories = new GalaxyHistories();
- item.id = id;
- var self = this;
-
- //fetch the dataset info
- item.fetch({
- success: function (item) {
- // TODO can render here already
- //fetch user histories for import purposes
- histories.fetch({
- success: function (histories){
- self.renderModalAfterFetch(item, histories)
- },
- error: function(){
- mod_toastr.error('An error occured during fetching histories:(');
- self.renderModalAfterFetch(item)
- }
- });
- },
- error: function(){
- mod_toastr.error('An error occured during loading dataset details :(');
- }
- });
- },
-
- // show the current dataset in a modal
- renderModalAfterFetch : function(item, histories){
- var size = this.size_to_string(item.get('file_size'));
- var template = _.template(this.templateDatasetModal(), { item : item, size : size });
- // make modal
- var self = this;
- this.modal = Galaxy.modal;
- this.modal.show({
- closing_events : true,
- title : 'Dataset Details',
- body : template,
- buttons : {
- 'Import' : function() { self.importCurrentIntoHistory() },
- 'Download' : function() { self.downloadCurrent() },
- 'Close' : function() { self.modal.hide() }
- }
- });
-
- $(".peek").html('Peek:' + item.get("peek"));
-
- // show the import-into-history footer only if the request for histories succeeded
- if (typeof history.models !== undefined){
- var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models});
- $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl);
- // preset last selected history if we know it
- if (self.lastSelectedHistory.length > 0) {
- $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory);
- }
- }
- },
-
- // download dataset shown currently in modal
- downloadCurrent : function(){
- //disable the buttons
- this.modal.disableButton('Import');
- this.modal.disableButton('Download');
-
- var library_dataset_id = [];
- library_dataset_id.push($('#id_row').attr('data-id'));
- var url = '/api/libraries/datasets/download/uncompressed';
- var data = {'ldda_ids' : library_dataset_id};
-
- // we assume the view is existent
- folderContentView.processDownload(url, data);
- this.modal.enableButton('Import');
- this.modal.enableButton('Download');
- },
-
- // import dataset shown currently in modal into selected history
- importCurrentIntoHistory : function(){
- //disable the buttons
- this.modal.disableButton('Import');
- this.modal.disableButton('Download');
-
- var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val();
- this.lastSelectedHistory = history_id; //save selected history for further use
-
- var library_dataset_id = $('#id_row').attr('data-id');
- var historyItem = new HistoryItem();
- var self = this;
- historyItem.url = historyItem.urlRoot + history_id + '/contents';
-
- // save the dataset into selected history
- historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){
- mod_toastr.success('Dataset imported');
- //enable the buttons
- self.modal.enableButton('Import');
- self.modal.enableButton('Download');
- }, error : function(){
- mod_toastr.error('An error occured! Dataset not imported. Please try again.')
- //enable the buttons
- self.modal.enableButton('Import');
- self.modal.enableButton('Download');
- }
- });
- },
-
- // select all datasets
- selectAll : function (event) {
- var selected = event.target.checked;
- that = this;
- // Iterate each checkbox
- $(':checkbox').each(function () {
- this.checked = selected;
- $row = $(this.parentElement.parentElement);
- // Change color of selected/unselected
- (selected) ? that.makeDarkRow($row) : that.makeWhiteRow($row);
- });
- // Show the tools in menu
- this.checkTools();
- },
-
- // Check checkbox on row itself or row checkbox click
- selectClickedRow : function (event) {
- var checkbox = '';
- var $row;
- var source;
- if (event.target.localName === 'input'){
- checkbox = event.target;
- $row = $(event.target.parentElement.parentElement);
- source = 'input';
- } else if (event.target.localName === 'td') {
- checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0];
- $row = $(event.target.parentElement);
- source = 'td';
- }
-
- if (checkbox.checked){
- if (source==='td'){
- checkbox.checked = '';
- this.makeWhiteRow($row);
- } else if (source==='input') {
- this.makeDarkRow($row);
- }
- } else {
- if (source==='td'){
- checkbox.checked = 'selected';
- this.makeDarkRow($row);
- } else if (source==='input') {
- this.makeWhiteRow($row);
- }
- }
- this.checkTools();
- },
-
- makeDarkRow: function($row){
- $row.removeClass('light');
- $row.find('a').removeClass('light');
- $row.addClass('dark');
- $row.find('a').addClass('dark');
- $row.find('span').removeClass('fa-file-o');
- $row.find('span').addClass('fa-file');
-
- },
-
- makeWhiteRow: function($row){
- $row.removeClass('dark');
- $row.find('a').removeClass('dark');
- $row.addClass('light');
- $row.find('a').addClass('light');
- $row.find('span').addClass('fa-file-o');
- $row.find('span').removeClass('fa-file');
- },
-
- // show toolbar in case something is selected
- checkTools : function(){
- var checkedValues = $('#folder_table').find(':checked');
- if(checkedValues.length > 0){
- $('#toolbtn_bulk_import').show();
- $('#toolbtn_dl').show();
- } else {
- $('#toolbtn_bulk_import').hide();
- $('#toolbtn_dl').hide();
- }
- },
-
- // show bulk import modal
- modalBulkImport : function(){
- var self = this;
- // fetch histories
- var histories = new GalaxyHistories();
- histories.fetch({
- success: function (histories){
- // make modal
- var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models});
- self.modal = Galaxy.modal;
- self.modal.show({
- closing_events : true,
- title : 'Import into History',
- body : history_modal_tmpl,
- buttons : {
- 'Import' : function() {self.importAllIntoHistory()},
- 'Close' : function() {self.modal.hide();}
- }
- });
- },
- error: function(){
- mod_toastr.error('An error occured :(');
- }
- });
- },
-
- // import all selected datasets into history
- importAllIntoHistory : function (){
- //disable the button to prevent multiple submission
- this.modal.disableButton('Import');
-
- var history_id = $("select[name=dataset_import_bulk] option:selected").val();
- var history_name = $("select[name=dataset_import_bulk] option:selected").text();
-
- var dataset_ids = [];
- $('#folder_table').find(':checked').each(function(){
- if (this.parentElement.parentElement.id != '') {
- dataset_ids.push(this.parentElement.parentElement.id);
- }
- });
- var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name });
- $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl);
-
- // init the progress bar
- var progressStep = 100 / dataset_ids.length;
- this.initProgress(progressStep);
-
- // prepare the dataset objects to be imported
- var datasets_to_import = [];
- for (var i = dataset_ids.length - 1; i >= 0; i--) {
- library_dataset_id = dataset_ids[i];
- var historyItem = new HistoryItem();
- var self = this;
- historyItem.url = historyItem.urlRoot + history_id + '/contents';
- historyItem.content = library_dataset_id;
- historyItem.source = 'library';
- datasets_to_import.push(historyItem);
- };
-
- // call the recursive function to call ajax one after each other (request FIFO queue)
- this.chainCall(datasets_to_import);
- },
-
- chainCall: function(history_item_set){
- var self = this;
- var popped_item = history_item_set.pop();
- if (typeof popped_item === "undefined") {
- mod_toastr.success('All datasets imported');
- this.modal.hide();
- return
- }
- var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){
- self.updateProgress();
- responses.push(a1);
- self.chainCall(history_item_set);
- });
- },
-
- initProgress: function(progressStep){
- this.progress = 0;
- this.progressStep = progressStep;
- },
- updateProgress: function(){
- this.progress += this.progressStep;
- $('.progress-bar-import').width(Math.round(this.progress) + '%');
- txt_representation = Math.round(this.progress) + '% Complete';
- $('.completion_span').text(txt_representation);
- },
-
-
-
- // download selected datasets
- download : function(folder_id, format){
- var dataset_ids = [];
- $('#folder_table').find(':checked').each(function(){
- if (this.parentElement.parentElement.id != '') {
- dataset_ids.push(this.parentElement.parentElement.id);
- }
- });
-
- var url = '/api/libraries/datasets/download/' + format;
- var data = {'ldda_ids' : dataset_ids};
- this.processDownload(url, data, 'get');
- },
-
- // create hidden form and submit through POST to initialize download
- processDownload: function(url, data, method){
- //url and data options required
- if( url && data ){
- //data can be string of parameters or array/object
- data = typeof data == 'string' ? data : $.param(data);
- //split params into form inputs
- var inputs = '';
- $.each(data.split('&'), function(){
- var pair = this.split('=');
- inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />';
- });
- //send request
- $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>')
- .appendTo('body').submit().remove();
-
- mod_toastr.info('Your download will begin soon');
- };
- },
-
- // shows modal for creating folder
- createFolderFromModal: function(){
- event.preventDefault();
- event.stopPropagation();
-
- // create modal
- var self = this;
- this.modal = Galaxy.modal;
- this.modal.show({
- closing_events : true,
- title : 'Create New Folder',
- body : this.templateNewFolderInModal(),
- buttons : {
- 'Create' : function() {self.create_new_folder_event()},
- 'Close' : function() {self.modal.hide(); self.modal = null;}
- }
- });
- },
-
- // create the new folder from modal
- create_new_folder_event: function(){
- var folderDetails = this.serialize_new_folder();
- if (this.validate_new_folder(folderDetails)){
- var folder = new FolderAsModel();
-
- url_items = Backbone.history.fragment.split('/');
- current_folder_id = url_items[url_items.length-1];
- folder.url = folder.urlRoot + '/' + current_folder_id ;
-
- var self = this;
- folder.save(folderDetails, {
- success: function (folder) {
- self.modal.hide();
- mod_toastr.success('Folder created');
- self.render({id: current_folder_id});
- },
- error: function(){
- mod_toastr.error('An error occured :(');
- }
- });
- } else {
- mod_toastr.error('Folder\'s name is missing');
- }
- return false;
- },
-
- // serialize data from the form
- serialize_new_folder : function(){
- return {
- name: $("input[name='Name']").val(),
- description: $("input[name='Description']").val()
- };
- },
-
- // validate new library info
- validate_new_folder: function(folderDetails){
- return folderDetails.name !== '';
- }
-
- });
-
-// galaxy library view
-var GalaxyLibraryview = Backbone.View.extend({
- el: '#libraries_element',
-
- events: {
- 'click .edit_library_btn' : 'edit_button_event',
- 'click .save_library_btn' : 'save_library_modification',
- 'click .cancel_library_btn' : 'cancel_library_modification',
- 'click .delete_library_btn' : 'delete_library',
- 'click .undelete_library_btn' : 'undelete_library'
- },
-
- modal: null,
-
- collection: null,
-
- // initialize
- initialize : function(){
- var viewContext = this;
- this.collection = new Libraries();
-
- this.collection.fetch({
- success: function(libraries){
- viewContext.render();
- // initialize the library tooltips
- $("#center [data-toggle]").tooltip();
- // modification of upper DOM element to show scrollbars due to the #center element inheritance
- $("#center").css('overflow','auto');
- },
- error: function(model, response){
- mod_toastr.error('An error occured. Please try again.');
- }
- })
- },
-
- /** Renders the libraries table either from the object's own collection,
- or from a given array of library models,
- or renders an empty list in case no data is given. */
- render: function (options) {
- var template = this.templateLibraryList();
- var libraries_to_render = null;
- var include_deleted = false;
- var models = null
- if (typeof options !== 'undefined'){
- include_deleted = typeof options.with_deleted !== 'undefined' ? options.with_deleted : false;
- models = typeof options.models !== 'undefined' ? options.models : null;
- }
-
- if (this.collection !== null && models === null){
- if (include_deleted){ // show all the libraries
- libraries_to_render = this.collection.models;
- } else{ // show only undeleted libraries
- libraries_to_render = this.collection.where({deleted: false});;
- }
- } else if (models !== null){
- libraries_to_render = models;
- } else {
- libraries_to_render = [];
- }
-
- this.$el.html(template({libraries: libraries_to_render, order: this.collection.sort_order}));
- },
-
- /** Sorts the underlying collection according to the parameters received through URL.
- Currently supports only sorting by name. */
- sortLibraries: function(sort_by, order){
- if (sort_by === 'name'){
- if (order === 'asc'){
- this.collection.sort_order = 'asc';
- this.collection.comparator = function(libraryA, libraryB){
- if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) return 1; // after
- if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) return -1; // before
- return 0; // equal
- }
- } else if (order === 'desc'){
- this.collection.sort_order = 'desc';
- this.collection.comparator = function(libraryA, libraryB){
- if (libraryA.get('name').toLowerCase() > libraryB.get('name').toLowerCase()) return -1; // before
- if (libraryB.get('name').toLowerCase() > libraryA.get('name').toLowerCase()) return 1; // after
- return 0; // equal
- }
- }
- this.collection.sort();
- }
-
- },
-
-// MMMMMMMMMMMMMMMMMM
-// === TEMPLATES ====
-// MMMMMMMMMMMMMMMMMM
-
- templateLibraryList: function(){
- tmpl_array = [];
-
- tmpl_array.push('<div class="library_container table-responsive">');
- tmpl_array.push('<% if(libraries.length === 0) { %>');
- tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>");
- tmpl_array.push('<% } else{ %>');
- tmpl_array.push('<table class="grid table table-condensed">');
- tmpl_array.push(' <thead>');
- tmpl_array.push(' <th style="width:30%;"><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
- tmpl_array.push(' <th style="width:22%;">description</th>');
- tmpl_array.push(' <th style="width:22%;">synopsis</th> ');
- tmpl_array.push(' <th style="width:26%;"></th> ');
- tmpl_array.push(' </thead>');
- tmpl_array.push(' <tbody>');
- tmpl_array.push(' <% _.each(libraries, function(library) { %>');
- tmpl_array.push(' <tr class="<% if(library.get("deleted") === true){print("active");}%>" data-id="<%- library.get("id") %>">');
- tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');
- tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');
- tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');
- tmpl_array.push(' <td class="right-center">');
- tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button"><span class="fa fa-pencil"></span></button>');
- tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="display:none;"><span class="fa fa-floppy-o"> Save</span></button>');
- tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="display:none;"><span class="fa fa-times"> Cancel</span></button>');
- tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="display:none;"><span class="fa fa-trash-o"> Delete</span></button>');
- tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button>');
- tmpl_array.push(' </td>');
- tmpl_array.push(' </tr>');
- tmpl_array.push(' <% }); %>');
- tmpl_array.push(' </tbody>');
- tmpl_array.push('</table>');
- tmpl_array.push('<% }%>');
- tmpl_array.push('</div>');
-
- return _.template(tmpl_array.join(''));
- },
-
- templateNewLibraryInModal: function(){
- tmpl_array = [];
-
- tmpl_array.push('<div id="new_library_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(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');
- tmpl_array.push(' </form>');
- tmpl_array.push('</div>');
-
- return tmpl_array.join('');
- },
-
- save_library_modification: function(event){
- var $library_row = $(event.target).closest('tr');
- var library = this.collection.get($library_row.data('id'));
-
- var is_changed = false;
-
- var new_name = $library_row.find('.input_library_name').val();
- if (typeof new_name !== 'undefined' && new_name !== library.get('name') ){
- if (new_name.length > 2){
- library.set("name", new_name);
- is_changed = true;
- } else{
- mod_toastr.warning('Library name has to be at least 3 characters long');
- return
- }
- }
-
- var new_description = $library_row.find('.input_library_description').val();
- if (typeof new_description !== 'undefined' && new_description !== library.get('description') ){
- library.set("description", new_description);
- is_changed = true;
- }
-
- var new_synopsis = $library_row.find('.input_library_synopsis').val();
- if (typeof new_synopsis !== 'undefined' && new_synopsis !== library.get('synopsis') ){
- library.set("synopsis", new_synopsis);
- is_changed = true;
- }
-
- if (is_changed){
- library.save(null, {
- patch: true,
- success: function(library) {
- mod_toastr.success('Changes to library saved');
- galaxyLibraryview.toggle_library_modification($library_row);
- },
- error: function(model, response){
- mod_toastr.error('An error occured during updating the library :(');
- }
- });
- }
- },
-
- edit_button_event: function(event){
- this.toggle_library_modification($(event.target).closest('tr'));
- },
-
- toggle_library_modification: function($library_row){
- var library = this.collection.get($library_row.data('id'));
-
- $library_row.find('.edit_library_btn').toggle();
- $library_row.find('.save_library_btn').toggle();
- $library_row.find('.cancel_library_btn').toggle();
- if (library.get('deleted')){
- $library_row.find('.undelete_library_btn').toggle();
- } else {
- $library_row.find('.delete_library_btn').toggle();
- }
-
- if ($library_row.find('.edit_library_btn').is(':hidden')){
- // library name
- var current_library_name = library.get('name');
- var new_html = '<input type="text" class="form-control input_library_name" placeholder="name">';
- $library_row.children('td').eq(0).html(new_html);
- if (typeof current_library_name !== undefined){
- $library_row.find('.input_library_name').val(current_library_name);
- }
- // library description
- var current_library_description = library.get('description');
- var new_html = '<input type="text" class="form-control input_library_description" placeholder="description">';
- $library_row.children('td').eq(1).html(new_html);
- if (typeof current_library_description !== undefined){
- $library_row.find('.input_library_description').val(current_library_description);
- }
- // library synopsis
- var current_library_synopsis = library.get('synopsis');
- var new_html = '<input type="text" class="form-control input_library_synopsis" placeholder="synopsis">';
- $library_row.children('td').eq(2).html(new_html);
- if (typeof current_library_synopsis !== undefined){
- $library_row.find('.input_library_synopsis').val(current_library_synopsis);
- }
- } else {
- $library_row.children('td').eq(0).html(library.get('name'));
- $library_row.children('td').eq(1).html(library.get('description'));
- $library_row.children('td').eq(2).html(library.get('synopsis'));
- }
-
- },
-
- cancel_library_modification: function(event){
- var $library_row = $(event.target).closest('tr');
- var library = this.collection.get($library_row.data('id'));
- this.toggle_library_modification($library_row);
-
- $library_row.children('td').eq(0).html(library.get('name'));
- $library_row.children('td').eq(1).html(library.get('description'));
- $library_row.children('td').eq(2).html(library.get('synopsis'));
- },
-
- undelete_library: function(event){
- var $library_row = $(event.target).closest('tr');
- var library = this.collection.get($library_row.data('id'));
- this.toggle_library_modification($library_row);
-
- // mark the library undeleted
- library.url = library.urlRoot + library.id + '?undelete=true';
- library.destroy({
- success: function (library) {
- // add the newly undeleted library back to the collection
- // backbone does not accept changes through destroy, so update it too
- library.set('deleted', false);
- galaxyLibraryview.collection.add(library);
- $library_row.removeClass('active');
- mod_toastr.success('Library has been undeleted');
- },
- error: function(){
- mod_toastr.error('An error occured while undeleting the library :(');
- }
- });
- },
-
- delete_library: function(event){
- var $library_row = $(event.target).closest('tr');
- var library = this.collection.get($library_row.data('id'));
- this.toggle_library_modification($library_row);
-
- // mark the library deleted
- library.destroy({
- success: function (library) {
- // add the new deleted library back to the collection
- $library_row.remove();
- library.set('deleted', true);
- galaxyLibraryview.collection.add(library);
- mod_toastr.success('Library has been marked deleted');
- },
- error: function(){
- mod_toastr.error('An error occured during deleting the library :(');
- }
- });
-
- },
-
- redirectToHome: function(){
- window.location = '../';
- },
- redirectToLogin: function(){
- window.location = '/user/login';
- },
-
- // show/hide create library modal
- show_library_modal : function (event){
- event.preventDefault();
- event.stopPropagation();
-
- // create modal
- var self = this;
- this.modal = Galaxy.modal;
- this.modal.show({
- closing_events : true,
- title : 'Create New Library',
- body : this.templateNewLibraryInModal(),
- buttons : {
- 'Create' : function() {self.create_new_library_event()},
- 'Close' : function() {self.modal.hide();}
- }
- });
- },
-
- // create the new library from modal
- create_new_library_event: function(){
- var libraryDetails = this.serialize_new_library();
- if (this.validate_new_library(libraryDetails)){
- var library = new Library();
- var self = this;
- library.save(libraryDetails, {
- success: function (library) {
- self.collection.add(library);
- self.modal.hide();
- self.clear_library_modal();
- self.render();
- mod_toastr.success('Library created');
- },
- error: function(){
- mod_toastr.error('An error occured :(');
- }
- });
- } else {
- mod_toastr.error('Library\'s name is missing');
- }
- return false;
- },
-
- // clear the library modal once saved
- clear_library_modal : function(){
- $("input[name='Name']").val('');
- $("input[name='Description']").val('');
- $("input[name='Synopsis']").val('');
- },
-
- // serialize data from the form
- serialize_new_library : function(){
- return {
- name: $("input[name='Name']").val(),
- description: $("input[name='Description']").val(),
- synopsis: $("input[name='Synopsis']").val()
- };
- },
-
- // validate new library info
- validate_new_library: function(libraryDetails){
- return libraryDetails.name !== '';
- }
-});
-
-var ToolbarView = Backbone.View.extend({
- el: '#center',
-
- events: {
- 'click #create_new_library_btn' : 'delegate_modal',
- 'click #include_deleted_chk' : 'check_include_deleted'
- },
-
- initialize: function(){
- this.render();
- },
-
- delegate_modal: function(event){
- // probably should refactor to have this functionality in this view, not in the library view
- galaxyLibraryview.show_library_modal(event);
- },
-
- // include or exclude deleted libraries from the view
- check_include_deleted: function(event){
- if (event.target.checked){
- galaxyLibraryview.render( {'with_deleted': true} );
- } else{
- galaxyLibraryview.render({'with_deleted': false});
- }
- },
-
- render: function(){
- var toolbar_template = this.templateToolBar()
- this.$el.html(toolbar_template())
- },
-
- templateToolBar: function(){
- tmpl_array = [];
-
- tmpl_array.push('<div id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">');
- // TOOLBAR
- tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');
- tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');
- tmpl_array.push(' <div id="library_toolbar">');
- tmpl_array.push(' <input id="include_deleted_chk" style="margin: 0;" type="checkbox">include deleted</input>');
- tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>');
- tmpl_array.push(' </div>');
- tmpl_array.push(' </div>');
- tmpl_array.push(' <div id="libraries_element">');
- tmpl_array.push(' </div>');
- tmpl_array.push('</div>');
-
- return _.template(tmpl_array.join(''));
- }
-})
+ "libs/toastr",
+ "mvc/library/library-model",
+ "mvc/library/library-folderlist-view",
+ "mvc/library/library-librarylist-view",
+ "mvc/library/library-librarytoolbar-view"],
+function(mod_masthead,
+ mod_utils,
+ mod_toastr,
+ mod_library_model,
+ mod_folderlist_view,
+ mod_librarylist_view,
+ mod_librarytoolbar_view) {
//ROUTER
var LibraryRouter = Backbone.Router.extend({
@@ -1202,16 +36,17 @@
var GalaxyLibrary = Backbone.View.extend({
initialize : function(){
- toolbarView = new ToolbarView();
- galaxyLibraryview = new GalaxyLibraryview();
+ toolbarView = new mod_librarytoolbar_view.ToolbarView();
+ galaxyLibraryview = new mod_librarylist_view.GalaxyLibraryview();
library_router = new LibraryRouter();
- folderContentView = new FolderContentView();
+
+ folderContentView = null;
library_router.on('route:libraries', function() {
// initialize and render the toolbar first
- toolbarView = new ToolbarView();
+ toolbarView = new mod_librarytoolbar_view.ToolbarView();
// initialize and render libraries second
- galaxyLibraryview = new GalaxyLibraryview();
+ galaxyLibraryview = new mod_librarylist_view.GalaxyLibraryview();
});
library_router.on('route:sort_libraries', function(sort_by, order) {
@@ -1222,6 +57,7 @@
library_router.on('route:folder_content', function(id) {
// render folder contents
+ if (!folderContentView) {folderContentView = new mod_folderlist_view.FolderContentView();}
folderContentView.render({id: id});
});
diff -r 33cc6056d83760e5e3b98999b01ecb260423d33c -r 68d35caf407f367c3447a1a6675d6705c8daacf4 static/scripts/mvc/library/library-folderlist-view.js
--- /dev/null
+++ b/static/scripts/mvc/library/library-folderlist-view.js
@@ -0,0 +1,713 @@
+// dependencies
+define([
+ "galaxy.masthead",
+ "utils/utils",
+ "libs/toastr",
+ "mvc/library/library-model"],
+function(mod_masthead,
+ mod_utils,
+ mod_toastr,
+ mod_library_model) {
+
+ //main view for folder browsing
+var FolderContentView = Backbone.View.extend({
+ // main element definition
+ el : '#center',
+ // progress percentage
+ progress: 0,
+ // progress rate per one item
+ progressStep: 1,
+ // last selected history in modal for UX
+ lastSelectedHistory: '',
+ // self modal
+ modal : null,
+ // loaded folders
+ folders : null,
+
+ // initialize
+ initialize : function(){
+ this.folders = [];
+ this.queue = jQuery.Deferred();
+ this.queue.resolve();
+ },
+
+// MMMMMMMMMMMMMMMMMM
+// === TEMPLATES ====
+// MMMMMMMMMMMMMMMMMM
+
+ // main template for folder browsing
+ templateFolder : function (){
+ var tmpl_array = [];
+
+ // CONTAINER
+ tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');
+ tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');
+
+ // TOOLBAR
+ tmpl_array.push('<div id="library_folder_toolbar" >');
+ tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');
+ tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-book"></span> to history</button>');
+ tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');
+ tmpl_array.push(' <button title="Download selected datasets" 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('</div>');
+
+ // BREADCRUMBS
+ tmpl_array.push('<ol class="breadcrumb">');
+ tmpl_array.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');
+ tmpl_array.push(' <% _.each(path, function(path_item) { %>');
+ tmpl_array.push(' <% if (path_item[0] != id) { %>');
+ tmpl_array.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');
+ tmpl_array.push( '<% } else { %>');
+ tmpl_array.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');
+ tmpl_array.push(' <% } %>');
+ tmpl_array.push(' <% }); %>');
+ tmpl_array.push('</ol>');
+
+
+ // FOLDER CONTENT
+ tmpl_array.push('<table id="folder_table" class="grid table table-condensed">');
+ tmpl_array.push(' <thead>');
+ tmpl_array.push(' <th class="button_heading"></th>');
+ tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');
+ tmpl_array.push(' <th>name</th>');
+ tmpl_array.push(' <th>data type</th>');
+ tmpl_array.push(' <th>size</th>');
+ tmpl_array.push(' <th>date (UTC)</th>');
+ tmpl_array.push(' </thead>');
+ tmpl_array.push(' <tbody>');
+ tmpl_array.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');
+ tmpl_array.push(' <td></td>');
+ tmpl_array.push(' <td></td>');
+ tmpl_array.push(' <td></td>');
+ tmpl_array.push(' <td></td>');
+ tmpl_array.push(' <td></td>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <% _.each(items, function(content_item) { %>');
+ tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder
+ tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">');
+ tmpl_array.push(' <td>');
+ tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');
+ tmpl_array.push(' </td>');
+ tmpl_array.push(' <td></td>');
+ tmpl_array.push(' <td>');
+ tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');
+ tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder
+ tmpl_array.push(' <span class="muted">(empty folder)</span>');
+ tmpl_array.push(' <% } %>');
+ tmpl_array.push(' </td>');
+ tmpl_array.push(' <td>folder</td>');
+ tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size
+ tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <% } else { %>');
+ tmpl_array.push(' <tr class="dataset_row light" id="<%- content_item.id %>">');
+ tmpl_array.push(' <td>');
+ tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');
+ tmpl_array.push(' </td>');
+ tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');
+ tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset
+ tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type
+ tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size
+ tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <% } %> ');
+ tmpl_array.push(' <% }); %>');
+ tmpl_array.push(' ');
+ tmpl_array.push(' </tbody>');
+ tmpl_array.push('</table>');
+
+ tmpl_array.push('</div>');
+ return tmpl_array.join('');
+ },
+ templateDatasetModal : function(){
+ var tmpl_array = [];
+
+ tmpl_array.push('<div class="modal_table">');
+ tmpl_array.push(' <table class="grid table table-striped table-condensed">');
+ tmpl_array.push(' <tr>');
+ tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');
+ tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <tr>');
+ tmpl_array.push(' <th scope="row">Data type</th>');
+ tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <tr>');
+ tmpl_array.push(' <th scope="row">Genome build</th>');
+ tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <th scope="row">Size</th>');
+ tmpl_array.push(' <td><%= _.escape(size) %></td>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <tr>');
+ tmpl_array.push(' <th scope="row">Date uploaded (UTC)</th>');
+ tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <tr>');
+ tmpl_array.push(' <th scope="row">Uploaded by</th>');
+ tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <tr scope="row">');
+ tmpl_array.push(' <th scope="row">Data Lines</th>');
+ tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <th scope="row">Comment Lines</th>');
+ tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>');
+ tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');
+ tmpl_array.push(' <% } else { %>');
+ tmpl_array.push(' <td scope="row">unknown</td>');
+ tmpl_array.push(' <% } %>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <tr>');
+ tmpl_array.push(' <th scope="row">Number of Columns</th>');
+ tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <tr>');
+ tmpl_array.push(' <th scope="row">Column Types</th>');
+ tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' <tr>');
+ tmpl_array.push(' <th scope="row">Miscellaneous information</th>');
+ tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');
+ tmpl_array.push(' </tr>');
+ tmpl_array.push(' </table>');
+ tmpl_array.push(' <pre class="peek">');
+ tmpl_array.push(' </pre>');
+ tmpl_array.push('</div>');
+
+ return tmpl_array.join('');
+ },
+
+ templateHistorySelectInModal : function(){
+ var tmpl_array = [];
+
+ tmpl_array.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');
+ tmpl_array.push('Select history: ');
+ tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; 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 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 tmpl_array.join('');
+ },
+
+ templateProgressBar : 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 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 tmpl_array.join('');
+ },
+
+// MMMMMMMMMMMMMMM
+// === EVENTS ====
+// MMMMMMMMMMMMMMM
+
+ // event binding
+ events: {
+ 'click #select-all-checkboxes' : 'selectAll',
+ 'click #toolbtn_bulk_import' : 'modalBulkImport',
+ 'click #toolbtn_dl' : 'bulkDownload',
+ 'click #toolbtn_create_folder' : 'createFolderFromModal',
+ 'click .library-dataset' : 'showDatasetDetails',
+ 'click .dataset_row' : 'selectClickedRow'
+ },
+
+// MMMMMMMMMMMMMMMMMM
+// === FUNCTIONS ====
+// MMMMMMMMMMMMMMMMMM
+
+ //render the folder view
+ render: function (options) {
+ //hack to show scrollbars
+ $("#center").css('overflow','auto');
+
+ view = this;
+ var that = this;
+
+ var folderContainer = new mod_library_model.FolderContainer({id: options.id});
+ folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents';
+
+ folderContainer.fetch({
+ success: function (container) {
+
+ // prepare nice size strings
+ for (var i = 0; i < folderContainer.attributes.folder.models.length; i++) {
+ var model = folderContainer.attributes.folder.models[i]
+ if (model.get('type') === 'file'){
+ model.set('readable_size', that.size_to_string(model.get('file_size')))
+ }
+ };
+
+ // find the upper id
+ var path = folderContainer.full_path;
+ var upper_folder_id;
+ if (path.length === 1){ // library is above us
+ upper_folder_id = 0;
+ } else {
+ upper_folder_id = path[path.length-2][0];
+ }
+
+ var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id });
+ // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id });
+ that.$el.html(template);
+
+ },
+ error: function(){
+ mod_toastr.error('An error occured :(');
+ }
+ })
+ },
+
+ // convert size to nice string
+ size_to_string : function (size)
+ {
+ // identify unit
+ var unit = "";
+ if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else
+ if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else
+ if (size >= 100000) { size = size / 100000; unit = "MB"; } else
+ if (size >= 100) { size = size / 100; unit = "KB"; } else
+ { size = size * 10; unit = "b"; }
+ // return formatted string
+ return (Math.round(size) / 10) + unit;
+ },
+
+ //show modal with current dataset info
+ showDatasetDetails : function(event){
+ // prevent default
+ event.preventDefault();
+
+ //TODO check whether we already have the data
+
+ //load the ID of the row
+ var id = $(event.target).parent().parent().parent().attr('id');
+ if (typeof id === 'undefined'){
+ id = $(event.target).parent().attr('id');
+ }
+ if (typeof id === 'undefined'){
+ id = $(event.target).parent().parent().attr('id')
+ }
+
+ //create new item
+ var item = new mod_library_model.Item();
+ var histories = new mod_library_model.GalaxyHistories();
+ item.id = id;
+ var self = this;
+
+ //fetch the dataset info
+ item.fetch({
+ success: function (item) {
+ // TODO can render here already
+ //fetch user histories for import purposes
+ histories.fetch({
+ success: function (histories){
+ self.renderModalAfterFetch(item, histories)
+ },
+ error: function(){
+ mod_toastr.error('An error occured during fetching histories:(');
+ self.renderModalAfterFetch(item)
+ }
+ });
+ },
+ error: function(){
+ mod_toastr.error('An error occured during loading dataset details :(');
+ }
+ });
+ },
+
+ // show the current dataset in a modal
+ renderModalAfterFetch : function(item, histories){
+ var size = this.size_to_string(item.get('file_size'));
+ var template = _.template(this.templateDatasetModal(), { item : item, size : size });
+ // make modal
+ var self = this;
+ this.modal = Galaxy.modal;
+ this.modal.show({
+ closing_events : true,
+ title : 'Dataset Details',
+ body : template,
+ buttons : {
+ 'Import' : function() { self.importCurrentIntoHistory() },
+ 'Download' : function() { self.downloadCurrent() },
+ 'Close' : function() { self.modal.hide() }
+ }
+ });
+
+ $(".peek").html('Peek:' + item.get("peek"));
+
+ // show the import-into-history footer only if the request for histories succeeded
+ if (typeof history.models !== undefined){
+ var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models});
+ $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl);
+ // preset last selected history if we know it
+ if (self.lastSelectedHistory.length > 0) {
+ $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory);
+ }
+ }
+ },
+
+ // download dataset shown currently in modal
+ downloadCurrent : function(){
+ //disable the buttons
+ this.modal.disableButton('Import');
+ this.modal.disableButton('Download');
+
+ var library_dataset_id = [];
+ library_dataset_id.push($('#id_row').attr('data-id'));
+ var url = '/api/libraries/datasets/download/uncompressed';
+ var data = {'ldda_ids' : library_dataset_id};
+
+ // we assume the view is existent
+ folderContentView.processDownload(url, data);
+ this.modal.enableButton('Import');
+ this.modal.enableButton('Download');
+ },
+
+ // import dataset shown currently in modal into selected history
+ importCurrentIntoHistory : function(){
+ //disable the buttons
+ this.modal.disableButton('Import');
+ this.modal.disableButton('Download');
+
+ var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val();
+ this.lastSelectedHistory = history_id; //save selected history for further use
+
+ var library_dataset_id = $('#id_row').attr('data-id');
+ var historyItem = new mod_library_model.HistoryItem();
+ var self = this;
+ historyItem.url = historyItem.urlRoot + history_id + '/contents';
+
+ // save the dataset into selected history
+ historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){
+ mod_toastr.success('Dataset imported');
+ //enable the buttons
+ self.modal.enableButton('Import');
+ self.modal.enableButton('Download');
+ }, error : function(){
+ mod_toastr.error('An error occured! Dataset not imported. Please try again.')
+ //enable the buttons
+ self.modal.enableButton('Import');
+ self.modal.enableButton('Download');
+ }
+ });
+ },
+
+ // select all datasets
+ selectAll : function (event) {
+ var selected = event.target.checked;
+ that = this;
+ // Iterate each checkbox
+ $(':checkbox').each(function () {
+ this.checked = selected;
+ $row = $(this.parentElement.parentElement);
+ // Change color of selected/unselected
+ (selected) ? that.makeDarkRow($row) : that.makeWhiteRow($row);
+ });
+ // Show the tools in menu
+ this.checkTools();
+ },
+
+ // Check checkbox on row itself or row checkbox click
+ selectClickedRow : function (event) {
+ var checkbox = '';
+ var $row;
+ var source;
+ if (event.target.localName === 'input'){
+ checkbox = event.target;
+ $row = $(event.target.parentElement.parentElement);
+ source = 'input';
+ } else if (event.target.localName === 'td') {
+ checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0];
+ $row = $(event.target.parentElement);
+ source = 'td';
+ }
+
+ if (checkbox.checked){
+ if (source==='td'){
+ checkbox.checked = '';
+ this.makeWhiteRow($row);
+ } else if (source==='input') {
+ this.makeDarkRow($row);
+ }
+ } else {
+ if (source==='td'){
+ checkbox.checked = 'selected';
+ this.makeDarkRow($row);
+ } else if (source==='input') {
+ this.makeWhiteRow($row);
+ }
+ }
+ this.checkTools();
+ },
+
+ makeDarkRow: function($row){
+ $row.removeClass('light');
+ $row.find('a').removeClass('light');
+ $row.addClass('dark');
+ $row.find('a').addClass('dark');
+ $row.find('span').removeClass('fa-file-o');
+ $row.find('span').addClass('fa-file');
+
+ },
+
+ makeWhiteRow: function($row){
+ $row.removeClass('dark');
+ $row.find('a').removeClass('dark');
+ $row.addClass('light');
+ $row.find('a').addClass('light');
+ $row.find('span').addClass('fa-file-o');
+ $row.find('span').removeClass('fa-file');
+ },
+
+ // show toolbar in case something is selected
+ checkTools : function(){
+ var checkedValues = $('#folder_table').find(':checked');
+ if(checkedValues.length > 0){
+ $('#toolbtn_bulk_import').show();
+ $('#toolbtn_dl').show();
+ } else {
+ $('#toolbtn_bulk_import').hide();
+ $('#toolbtn_dl').hide();
+ }
+ },
+
+ // show bulk import modal
+ modalBulkImport : function(){
+ var self = this;
+ // fetch histories
+ var histories = new mod_library_model.GalaxyHistories();
+ histories.fetch({
+ success: function (histories){
+ // make modal
+ var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models});
+ self.modal = Galaxy.modal;
+ self.modal.show({
+ closing_events : true,
+ title : 'Import into History',
+ body : history_modal_tmpl,
+ buttons : {
+ 'Import' : function() {self.importAllIntoHistory()},
+ 'Close' : function() {self.modal.hide();}
+ }
+ });
+ },
+ error: function(){
+ mod_toastr.error('An error occured :(');
+ }
+ });
+ },
+
+ // import all selected datasets into history
+ importAllIntoHistory : function (){
+ //disable the button to prevent multiple submission
+ this.modal.disableButton('Import');
+
+ var history_id = $("select[name=dataset_import_bulk] option:selected").val();
+ var history_name = $("select[name=dataset_import_bulk] option:selected").text();
+
+ var dataset_ids = [];
+ $('#folder_table').find(':checked').each(function(){
+ if (this.parentElement.parentElement.id != '') {
+ dataset_ids.push(this.parentElement.parentElement.id);
+ }
+ });
+ var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name });
+ $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl);
+
+ // init the progress bar
+ var progressStep = 100 / dataset_ids.length;
+ this.initProgress(progressStep);
+
+ // prepare the dataset objects to be imported
+ var datasets_to_import = [];
+ for (var i = dataset_ids.length - 1; i >= 0; i--) {
+ library_dataset_id = dataset_ids[i];
+ var historyItem = new mod_library_model.HistoryItem();
+ var self = this;
+ historyItem.url = historyItem.urlRoot + history_id + '/contents';
+ historyItem.content = library_dataset_id;
+ historyItem.source = 'library';
+ datasets_to_import.push(historyItem);
+ };
+
+ // call the recursive function to call ajax one after each other (request FIFO queue)
+ this.chainCall(datasets_to_import);
+ },
+
+ chainCall: function(history_item_set){
+ var self = this;
+ var popped_item = history_item_set.pop();
+ if (typeof popped_item === "undefined") {
+ mod_toastr.success('All datasets imported');
+ this.modal.hide();
+ return
+ }
+ var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){
+ self.updateProgress();
+ // responses.push(a1);
+ self.chainCall(history_item_set);
+ });
+ },
+
+ initProgress: function(progressStep){
+ this.progress = 0;
+ this.progressStep = progressStep;
+ },
+ updateProgress: function(){
+ this.progress += this.progressStep;
+ $('.progress-bar-import').width(Math.round(this.progress) + '%');
+ txt_representation = Math.round(this.progress) + '% Complete';
+ $('.completion_span').text(txt_representation);
+ },
+
+
+
+ // download selected datasets
+ download : function(folder_id, format){
+ var dataset_ids = [];
+ $('#folder_table').find(':checked').each(function(){
+ if (this.parentElement.parentElement.id != '') {
+ dataset_ids.push(this.parentElement.parentElement.id);
+ }
+ });
+
+ var url = '/api/libraries/datasets/download/' + format;
+ var data = {'ldda_ids' : dataset_ids};
+ this.processDownload(url, data, 'get');
+ },
+
+ // create hidden form and submit through POST to initialize download
+ processDownload: function(url, data, method){
+ //url and data options required
+ if( url && data ){
+ //data can be string of parameters or array/object
+ data = typeof data == 'string' ? data : $.param(data);
+ //split params into form inputs
+ var inputs = '';
+ $.each(data.split('&'), function(){
+ var pair = this.split('=');
+ inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />';
+ });
+ //send request
+ $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>')
+ .appendTo('body').submit().remove();
+
+ mod_toastr.info('Your download will begin soon');
+ };
+ },
+
+ // shows modal for creating folder
+ createFolderFromModal: function(){
+ event.preventDefault();
+ event.stopPropagation();
+
+ // create modal
+ var self = this;
+ this.modal = Galaxy.modal;
+ this.modal.show({
+ closing_events : true,
+ title : 'Create New Folder',
+ body : this.templateNewFolderInModal(),
+ buttons : {
+ 'Create' : function() {self.create_new_folder_event()},
+ 'Close' : function() {self.modal.hide(); self.modal = null;}
+ }
+ });
+ },
+
+ // create the new folder from modal
+ create_new_folder_event: function(){
+ var folderDetails = this.serialize_new_folder();
+ if (this.validate_new_folder(folderDetails)){
+ var folder = new mod_library_model.FolderAsModel();
+
+ url_items = Backbone.history.fragment.split('/');
+ current_folder_id = url_items[url_items.length-1];
+ folder.url = folder.urlRoot + '/' + current_folder_id ;
+
+ var self = this;
+ folder.save(folderDetails, {
+ success: function (folder) {
+ self.modal.hide();
+ mod_toastr.success('Folder created');
+ self.render({id: current_folder_id});
+ },
+ error: function(){
+ mod_toastr.error('An error occured :(');
+ }
+ });
+ } else {
+ mod_toastr.error('Folder\'s name is missing');
+ }
+ return false;
+ },
+
+ // serialize data from the form
+ serialize_new_folder : function(){
+ return {
+ name: $("input[name='Name']").val(),
+ description: $("input[name='Description']").val()
+ };
+ },
+
+ // validate new library info
+ validate_new_folder: function(folderDetails){
+ return folderDetails.name !== '';
+ }
+
+ });
+
+// return
+return {
+ FolderContentView: FolderContentView
+};
+
+});
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: libraries - exposed to anonymous users, allowed editing, deleting, undeleting, improved 'include deleted' filter, refactoring toolbar to have its own view
by commits-noreply＠bitbucket.org 24 Mar '14
by commits-noreply＠bitbucket.org 24 Mar '14
24 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/33cc6056d837/
Changeset: 33cc6056d837
User: martenson
Date: 2014-03-24 16:16:36
Summary: libraries - exposed to anonymous users, allowed editing, deleting, undeleting, improved 'include deleted' filter, refactoring toolbar to have its own view
Affected #: 6 files
diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -209,7 +209,7 @@
'/api/libraries/:id',
controller='libraries',
action='update',
- conditions=dict( method=[ "PATCH" ] ) )
+ conditions=dict( method=[ "PATCH", 'PUT' ] ) )
webapp.mapper.connect( 'show_lda_item',
'/api/libraries/datasets/:id',
diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c static/scripts/galaxy.library.js
--- a/static/scripts/galaxy.library.js
+++ b/static/scripts/galaxy.library.js
@@ -19,7 +19,7 @@
// LIBRARY
var Library = Backbone.Model.extend({
- urlRoot: '/api/libraries'
+ urlRoot: '/api/libraries/'
});
// FOLDER AS MODEL
@@ -122,7 +122,7 @@
// TOOLBAR
tmpl_array.push('<div id="library_folder_toolbar" >');
tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');
- tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');
+ tmpl_array.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-book"></span> to history</button>');
tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');
tmpl_array.push(' <button title="Download selected datasets" 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>');
@@ -208,7 +208,7 @@
var tmpl_array = [];
tmpl_array.push('<div class="modal_table">');
- tmpl_array.push(' <table class="table table-striped table-condensed">');
+ tmpl_array.push(' <table class="grid table table-striped table-condensed">');
tmpl_array.push(' <tr>');
tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');
tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>');
@@ -266,9 +266,9 @@
templateHistorySelectInModal : function(){
var tmpl_array = [];
- tmpl_array.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');
+ tmpl_array.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');
tmpl_array.push('Select history: ');
- tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');
+ tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; 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(' <% }); %>');
@@ -457,7 +457,7 @@
}
});
- $(".peek").html(item.get("peek"));
+ $(".peek").html('Peek:' + item.get("peek"));
// show the import-into-history footer only if the request for histories succeeded
if (typeof history.models !== undefined){
@@ -783,10 +783,14 @@
// galaxy library view
var GalaxyLibraryview = Backbone.View.extend({
- el: '#center',
+ el: '#libraries_element',
events: {
- 'click #create_new_library_btn' : 'show_library_modal'
+ 'click .edit_library_btn' : 'edit_button_event',
+ 'click .save_library_btn' : 'save_library_modification',
+ 'click .cancel_library_btn' : 'cancel_library_modification',
+ 'click .delete_library_btn' : 'delete_library',
+ 'click .undelete_library_btn' : 'undelete_library'
},
modal: null,
@@ -801,19 +805,15 @@
this.collection.fetch({
success: function(libraries){
viewContext.render();
+ // initialize the library tooltips
+ $("#center [data-toggle]").tooltip();
+ // modification of upper DOM element to show scrollbars due to the #center element inheritance
+ $("#center").css('overflow','auto');
},
error: function(model, response){
-
- if (response.statusCode().status === 403){ //TODO open to public
- mod_toastr.info('Please log in first. Redirecting to login page in 3s.');
- setTimeout(that.redirectToLogin, 3000);
- } else {
- mod_toastr.error('An error occured. Please try again.');
- }
+ mod_toastr.error('An error occured. Please try again.');
}
})
- // modification of upper DOM element to show scrollbars due to the #center element inheritance
- $("#center").css('overflow','auto');
},
/** Renders the libraries table either from the object's own collection,
@@ -875,39 +875,40 @@
templateLibraryList: function(){
tmpl_array = [];
- tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');
-
- tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');
- tmpl_array.push('<div id="library_toolbar">');
- tmpl_array.push(' <button title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>');
- tmpl_array.push('</div>');
-
+ tmpl_array.push('<div class="library_container table-responsive">');
tmpl_array.push('<% if(libraries.length === 0) { %>');
tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>");
tmpl_array.push('<% } else{ %>');
tmpl_array.push('<table class="grid table table-condensed">');
tmpl_array.push(' <thead>');
- tmpl_array.push(' <th><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
- tmpl_array.push(' <th>description</th>');
- tmpl_array.push(' <th>synopsis</th> ');
+ tmpl_array.push(' <th style="width:30%;"><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');
+ tmpl_array.push(' <th style="width:22%;">description</th>');
+ tmpl_array.push(' <th style="width:22%;">synopsis</th> ');
+ tmpl_array.push(' <th style="width:26%;"></th> ');
tmpl_array.push(' </thead>');
tmpl_array.push(' <tbody>');
tmpl_array.push(' <% _.each(libraries, function(library) { %>');
- tmpl_array.push(' <tr>');
+ tmpl_array.push(' <tr class="<% if(library.get("deleted") === true){print("active");}%>" data-id="<%- library.get("id") %>">');
tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');
tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');
tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');
+ tmpl_array.push(' <td class="right-center">');
+ tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button"><span class="fa fa-pencil"></span></button>');
+ tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="display:none;"><span class="fa fa-floppy-o"> Save</span></button>');
+ tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="display:none;"><span class="fa fa-times"> Cancel</span></button>');
+ tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="display:none;"><span class="fa fa-trash-o"> Delete</span></button>');
+ tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button>');
+ tmpl_array.push(' </td>');
tmpl_array.push(' </tr>');
tmpl_array.push(' <% }); %>');
tmpl_array.push(' </tbody>');
tmpl_array.push('</table>');
tmpl_array.push('<% }%>');
-
tmpl_array.push('</div>');
return _.template(tmpl_array.join(''));
},
-
+
templateNewLibraryInModal: function(){
tmpl_array = [];
@@ -922,6 +923,148 @@
return tmpl_array.join('');
},
+ save_library_modification: function(event){
+ var $library_row = $(event.target).closest('tr');
+ var library = this.collection.get($library_row.data('id'));
+
+ var is_changed = false;
+
+ var new_name = $library_row.find('.input_library_name').val();
+ if (typeof new_name !== 'undefined' && new_name !== library.get('name') ){
+ if (new_name.length > 2){
+ library.set("name", new_name);
+ is_changed = true;
+ } else{
+ mod_toastr.warning('Library name has to be at least 3 characters long');
+ return
+ }
+ }
+
+ var new_description = $library_row.find('.input_library_description').val();
+ if (typeof new_description !== 'undefined' && new_description !== library.get('description') ){
+ library.set("description", new_description);
+ is_changed = true;
+ }
+
+ var new_synopsis = $library_row.find('.input_library_synopsis').val();
+ if (typeof new_synopsis !== 'undefined' && new_synopsis !== library.get('synopsis') ){
+ library.set("synopsis", new_synopsis);
+ is_changed = true;
+ }
+
+ if (is_changed){
+ library.save(null, {
+ patch: true,
+ success: function(library) {
+ mod_toastr.success('Changes to library saved');
+ galaxyLibraryview.toggle_library_modification($library_row);
+ },
+ error: function(model, response){
+ mod_toastr.error('An error occured during updating the library :(');
+ }
+ });
+ }
+ },
+
+ edit_button_event: function(event){
+ this.toggle_library_modification($(event.target).closest('tr'));
+ },
+
+ toggle_library_modification: function($library_row){
+ var library = this.collection.get($library_row.data('id'));
+
+ $library_row.find('.edit_library_btn').toggle();
+ $library_row.find('.save_library_btn').toggle();
+ $library_row.find('.cancel_library_btn').toggle();
+ if (library.get('deleted')){
+ $library_row.find('.undelete_library_btn').toggle();
+ } else {
+ $library_row.find('.delete_library_btn').toggle();
+ }
+
+ if ($library_row.find('.edit_library_btn').is(':hidden')){
+ // library name
+ var current_library_name = library.get('name');
+ var new_html = '<input type="text" class="form-control input_library_name" placeholder="name">';
+ $library_row.children('td').eq(0).html(new_html);
+ if (typeof current_library_name !== undefined){
+ $library_row.find('.input_library_name').val(current_library_name);
+ }
+ // library description
+ var current_library_description = library.get('description');
+ var new_html = '<input type="text" class="form-control input_library_description" placeholder="description">';
+ $library_row.children('td').eq(1).html(new_html);
+ if (typeof current_library_description !== undefined){
+ $library_row.find('.input_library_description').val(current_library_description);
+ }
+ // library synopsis
+ var current_library_synopsis = library.get('synopsis');
+ var new_html = '<input type="text" class="form-control input_library_synopsis" placeholder="synopsis">';
+ $library_row.children('td').eq(2).html(new_html);
+ if (typeof current_library_synopsis !== undefined){
+ $library_row.find('.input_library_synopsis').val(current_library_synopsis);
+ }
+ } else {
+ $library_row.children('td').eq(0).html(library.get('name'));
+ $library_row.children('td').eq(1).html(library.get('description'));
+ $library_row.children('td').eq(2).html(library.get('synopsis'));
+ }
+
+ },
+
+ cancel_library_modification: function(event){
+ var $library_row = $(event.target).closest('tr');
+ var library = this.collection.get($library_row.data('id'));
+ this.toggle_library_modification($library_row);
+
+ $library_row.children('td').eq(0).html(library.get('name'));
+ $library_row.children('td').eq(1).html(library.get('description'));
+ $library_row.children('td').eq(2).html(library.get('synopsis'));
+ },
+
+ undelete_library: function(event){
+ var $library_row = $(event.target).closest('tr');
+ var library = this.collection.get($library_row.data('id'));
+ this.toggle_library_modification($library_row);
+
+ // mark the library undeleted
+ library.url = library.urlRoot + library.id + '?undelete=true';
+ library.destroy({
+ success: function (library) {
+ // add the newly undeleted library back to the collection
+ // backbone does not accept changes through destroy, so update it too
+ library.set('deleted', false);
+ galaxyLibraryview.collection.add(library);
+ $library_row.removeClass('active');
+ mod_toastr.success('Library has been undeleted');
+ },
+ error: function(){
+ mod_toastr.error('An error occured while undeleting the library :(');
+ }
+ });
+ },
+
+ delete_library: function(event){
+ var $library_row = $(event.target).closest('tr');
+ var library = this.collection.get($library_row.data('id'));
+ this.toggle_library_modification($library_row);
+
+ // mark the library deleted
+ library.destroy({
+ success: function (library) {
+ // add the new deleted library back to the collection
+ $library_row.remove();
+ library.set('deleted', true);
+ galaxyLibraryview.collection.add(library);
+ mod_toastr.success('Library has been marked deleted');
+ },
+ error: function(){
+ mod_toastr.error('An error occured during deleting the library :(');
+ }
+ });
+
+ },
+
redirectToHome: function(){
window.location = '../';
},
@@ -994,6 +1137,56 @@
}
});
+var ToolbarView = Backbone.View.extend({
+ el: '#center',
+
+ events: {
+ 'click #create_new_library_btn' : 'delegate_modal',
+ 'click #include_deleted_chk' : 'check_include_deleted'
+ },
+
+ initialize: function(){
+ this.render();
+ },
+
+ delegate_modal: function(event){
+ // probably should refactor to have this functionality in this view, not in the library view
+ galaxyLibraryview.show_library_modal(event);
+ },
+
+ // include or exclude deleted libraries from the view
+ check_include_deleted: function(event){
+ if (event.target.checked){
+ galaxyLibraryview.render( {'with_deleted': true} );
+ } else{
+ galaxyLibraryview.render({'with_deleted': false});
+ }
+ },
+
+ render: function(){
+ var toolbar_template = this.templateToolBar()
+ this.$el.html(toolbar_template())
+ },
+
+ templateToolBar: function(){
+ tmpl_array = [];
+
+ tmpl_array.push('<div id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">');
+ // TOOLBAR
+ tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');
+ tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');
+ tmpl_array.push(' <div id="library_toolbar">');
+ tmpl_array.push(' <input id="include_deleted_chk" style="margin: 0;" type="checkbox">include deleted</input>');
+ tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>');
+ tmpl_array.push(' </div>');
+ tmpl_array.push(' </div>');
+ tmpl_array.push(' <div id="libraries_element">');
+ tmpl_array.push(' </div>');
+ tmpl_array.push('</div>');
+
+ return _.template(tmpl_array.join(''));
+ }
+})
//ROUTER
var LibraryRouter = Backbone.Router.extend({
@@ -1007,18 +1200,18 @@
// galaxy library wrapper View
var GalaxyLibrary = Backbone.View.extend({
- // folderContentView : null,
- // galaxyLibraryview : null,
initialize : function(){
-
+ toolbarView = new ToolbarView();
galaxyLibraryview = new GalaxyLibraryview();
library_router = new LibraryRouter();
folderContentView = new FolderContentView();
library_router.on('route:libraries', function() {
- // render libraries list
- galaxyLibraryview.render();
+ // initialize and render the toolbar first
+ toolbarView = new ToolbarView();
+ // initialize and render libraries second
+ galaxyLibraryview = new GalaxyLibraryview();
});
library_router.on('route:sort_libraries', function(sort_by, order) {
@@ -1028,9 +1221,7 @@
});
library_router.on('route:folder_content', function(id) {
- // if (this.folderContentView === null){
- // }
- // render folder's contents
+ // render folder contents
folderContentView.render({id: id});
});
diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c static/scripts/packed/galaxy.library.js
--- a/static/scripts/packed/galaxy.library.js
+++ b/static/scripts/packed/galaxy.library.js
@@ -1,1 +1,1 @@
-var view=null;var library_router=null;var responses=[];define(["galaxy.masthead","utils/utils","libs/toastr"],function(k,h,m){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var n=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(q){this.full_path=q[0].full_path;this.get("folder").reset(q[1].folder_contents);return q}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var o=Backbone.Collection.extend({url:"/api/histories",model:j});var l=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var q=[];q.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');q.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');q.push('<div id="library_folder_toolbar" >');q.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');q.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');q.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');q.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');q.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');q.push(" </button>");q.push(' <ul class="dropdown-menu" role="menu">');q.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');q.push(" </ul>");q.push(" </div>");q.push("</div>");q.push('<ol class="breadcrumb">');q.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');q.push(" <% _.each(path, function(path_item) { %>");q.push(" <% if (path_item[0] != id) { %>");q.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');q.push("<% } else { %>");q.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');q.push(" <% } %>");q.push(" <% }); %>");q.push("</ol>");q.push('<table id="folder_table" class="grid table table-condensed">');q.push(" <thead>");q.push(' <th class="button_heading"></th>');q.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');q.push(" <th>name</th>");q.push(" <th>data type</th>");q.push(" <th>size</th>");q.push(" <th>date (UTC)</th>");q.push(" </thead>");q.push(" <tbody>");q.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" </tr>");q.push(" <% _.each(items, function(content_item) { %>");q.push(' <% if (content_item.get("type") === "folder") { %>');q.push(' <tr class="folder_row light" id="<%- content_item.id %>">');q.push(" <td>");q.push(' <span title="Folder" class="fa fa-folder-o"></span>');q.push(" </td>");q.push(" <td></td>");q.push(" <td>");q.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');q.push(' <% if (content_item.get("item_count") === 0) { %>');q.push(' <span class="muted">(empty folder)</span>');q.push(" <% } %>");q.push(" </td>");q.push(" <td>folder</td>");q.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% } else { %>");q.push(' <tr class="dataset_row light" id="<%- content_item.id %>">');q.push(" <td>");q.push(' <span title="Dataset" class="fa fa-file-o"></span>');q.push(" </td>");q.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');q.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');q.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');q.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% } %> ");q.push(" <% }); %>");q.push(" ");q.push(" </tbody>");q.push("</table>");q.push("</div>");return q.join("")},templateDatasetModal:function(){var q=[];q.push('<div class="modal_table">');q.push(' <table class="table table-striped table-condensed">');q.push(" <tr>");q.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');q.push(' <td><%= _.escape(item.get("name")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Data type</th>');q.push(' <td><%= _.escape(item.get("data_type")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Genome build</th>');q.push(' <td><%= _.escape(item.get("genome_build")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Size</th>');q.push(" <td><%= _.escape(size) %></td>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Date uploaded (UTC)</th>');q.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Uploaded by</th>');q.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');q.push(" </tr>");q.push(' <tr scope="row">');q.push(' <th scope="row">Data Lines</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Comment Lines</th>');q.push(' <% if (item.get("metadata_comment_lines") === "") { %>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');q.push(" <% } else { %>");q.push(' <td scope="row">unknown</td>');q.push(" <% } %>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Number of Columns</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Column Types</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Miscellaneous information</th>');q.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');q.push(" </tr>");q.push(" </table>");q.push(' <pre class="peek">');q.push(" </pre>");q.push("</div>");return q.join("")},templateHistorySelectInModal:function(){var q=[];q.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},templateBulkImportInModal:function(){var q=[];q.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},templateProgressBar:function(){var q=[];q.push('<div class="import_text">');q.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");q.push("</div>");q.push('<div class="progress">');q.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');q.push(' <span class="completion_span">0% Complete</span>');q.push(" </div>");q.push("</div>");q.push("");return q.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 tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click #toolbtn_create_folder":"createFolderFromModal","click .library-dataset":"showDatasetDetails","click .dataset_row":"selectClickedRow"},render:function(q){$("#center").css("overflow","auto");view=this;var s=this;var r=new e({id:q.id});r.url=r.attributes.urlRoot+q.id+"/contents";r.fetch({success:function(t){for(var v=0;v<r.attributes.folder.models.length;v++){var u=r.attributes.folder.models[v];if(u.get("type")==="file"){u.set("readable_size",s.size_to_string(u.get("file_size")))}}var x=r.full_path;var y;if(x.length===1){y=0}else{y=x[x.length-2][0]}var w=_.template(s.templateFolder(),{path:r.full_path,items:r.attributes.folder.models,id:q.id,upper_folder_id:y});s.$el.html(w)},error:function(){m.error("An error occured :(")}})},size_to_string:function(q){var r="";if(q>=100000000000){q=q/100000000000;r="TB"}else{if(q>=100000000){q=q/100000000;r="GB"}else{if(q>=100000){q=q/100000;r="MB"}else{if(q>=100){q=q/100;r="KB"}else{q=q*10;r="b"}}}}return(Math.round(q)/10)+r},showDatasetDetails:function(t){t.preventDefault();var u=$(t.target).parent().parent().parent().attr("id");if(typeof u==="undefined"){u=$(t.target).parent().attr("id")}if(typeof u==="undefined"){u=$(t.target).parent().parent().attr("id")}var s=new i();var r=new o();s.id=u;var q=this;s.fetch({success:function(v){r.fetch({success:function(w){q.renderModalAfterFetch(v,w)},error:function(){m.error("An error occured during fetching histories:(");q.renderModalAfterFetch(v)}})},error:function(){m.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(v,s){var t=this.size_to_string(v.get("file_size"));var u=_.template(this.templateDatasetModal(),{item:v,size:t});var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:u,buttons:{Import:function(){r.importCurrentIntoHistory()},Download:function(){r.downloadCurrent()},Close:function(){r.modal.hide()}}});$(".peek").html(v.get("peek"));if(typeof history.models!==undefined){var q=_.template(this.templateHistorySelectInModal(),{histories:s.models});$(this.modal.elMain).find(".buttons").prepend(q);if(r.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(r.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var q=[];q.push($("#id_row").attr("data-id"));var r="/api/libraries/datasets/download/uncompressed";var s={ldda_ids:q};folderContentView.processDownload(r,s);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var s=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=s;var q=$("#id_row").attr("data-id");var t=new b();var r=this;t.url=t.urlRoot+s+"/contents";t.save({content:q,source:"library"},{success:function(){m.success("Dataset imported");r.modal.enableButton("Import");r.modal.enableButton("Download")},error:function(){m.error("An error occured! Dataset not imported. Please try again.");r.modal.enableButton("Import");r.modal.enableButton("Download")}})},selectAll:function(r){var q=r.target.checked;that=this;$(":checkbox").each(function(){this.checked=q;$row=$(this.parentElement.parentElement);(q)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(r){var t="";var q;var s;if(r.target.localName==="input"){t=r.target;q=$(r.target.parentElement.parentElement);s="input"}else{if(r.target.localName==="td"){t=$("#"+r.target.parentElement.id).find(":checkbox")[0];q=$(r.target.parentElement);s="td"}}if(t.checked){if(s==="td"){t.checked="";this.makeWhiteRow(q)}else{if(s==="input"){this.makeDarkRow(q)}}}else{if(s==="td"){t.checked="selected";this.makeDarkRow(q)}else{if(s==="input"){this.makeWhiteRow(q)}}}this.checkTools()},makeDarkRow:function(q){q.removeClass("light");q.find("a").removeClass("light");q.addClass("dark");q.find("a").addClass("dark");q.find("span").removeClass("fa-file-o");q.find("span").addClass("fa-file")},makeWhiteRow:function(q){q.removeClass("dark");q.find("a").removeClass("dark");q.addClass("light");q.find("a").addClass("light");q.find("span").addClass("fa-file-o");q.find("span").removeClass("fa-file")},checkTools:function(){var q=$("#folder_table").find(":checked");if(q.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var r=this;var q=new o();q.fetch({success:function(s){var t=_.template(r.templateBulkImportInModal(),{histories:s.models});r.modal=Galaxy.modal;r.modal.show({closing_events:true,title:"Import into History",body:t,buttons:{Import:function(){r.importAllIntoHistory()},Close:function(){r.modal.hide()}}})},error:function(){m.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var s=$("select[name=dataset_import_bulk] option:selected").val();var w=$("select[name=dataset_import_bulk] option:selected").text();var y=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){y.push(this.parentElement.parentElement.id)}});var x=_.template(this.templateProgressBar(),{history_name:w});$(this.modal.elMain).find(".modal-body").html(x);var t=100/y.length;this.initProgress(t);var q=[];for(var r=y.length-1;r>=0;r--){library_dataset_id=y[r];var u=new b();var v=this;u.url=u.urlRoot+s+"/contents";u.content=library_dataset_id;u.source="library";q.push(u)}this.chainCall(q)},chainCall:function(r){var q=this;var s=r.pop();if(typeof s==="undefined"){m.success("All datasets imported");this.modal.hide();return}var t=$.when(s.save({content:s.content,source:s.source})).done(function(u){q.updateProgress();responses.push(u);q.chainCall(r)})},initProgress:function(q){this.progress=0;this.progressStep=q},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(q,u){var s=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){s.push(this.parentElement.parentElement.id)}});var r="/api/libraries/datasets/download/"+u;var t={ldda_ids:s};this.processDownload(r,t,"get")},processDownload:function(r,s,t){if(r&&s){s=typeof s=="string"?s:$.param(s);var q="";$.each(s.split("&"),function(){var u=this.split("=");q+='<input type="hidden" name="'+u[0]+'" value="'+u[1]+'" />'});$('<form action="'+r+'" method="'+(t||"post")+'">'+q+"</form>").appendTo("body").submit().remove();m.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var q=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){q.create_new_folder_event()},Close:function(){q.modal.hide();q.modal=null}}})},create_new_folder_event:function(){var q=this.serialize_new_folder();if(this.validate_new_folder(q)){var s=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];s.url=s.urlRoot+"/"+current_folder_id;var r=this;s.save(q,{success:function(t){r.modal.hide();m.success("Folder created");r.render({id:current_folder_id})},error:function(){m.error("An error occured :(")}})}else{m.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(q){return q.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},modal:null,collection:null,initialize:function(){var q=this;this.collection=new n();this.collection.fetch({success:function(r){q.render()},error:function(s,r){if(r.statusCode().status===403){m.info("Please log in first. Redirecting to login page in 3s.");setTimeout(that.redirectToLogin,3000)}else{m.error("An error occured. Please try again.")}}});$("#center").css("overflow","auto")},render:function(r){var s=this.templateLibraryList();var t=null;var q=false;var u=null;if(typeof r!=="undefined"){q=typeof r.with_deleted!=="undefined"?r.with_deleted:false;u=typeof r.models!=="undefined"?r.models:null}if(this.collection!==null&&u===null){if(q){t=this.collection.models}else{t=this.collection.where({deleted:false})}}else{if(u!==null){t=u}else{t=[]}}this.$el.html(s({libraries:t,order:this.collection.sort_order}))},sortLibraries:function(r,q){if(r==="name"){if(q==="asc"){this.collection.sort_order="asc";this.collection.comparator=function(t,s){if(t.get("name").toLowerCase()>s.get("name").toLowerCase()){return 1}if(s.get("name").toLowerCase()>t.get("name").toLowerCase()){return -1}return 0}}else{if(q==="desc"){this.collection.sort_order="desc";this.collection.comparator=function(t,s){if(t.get("name").toLowerCase()>s.get("name").toLowerCase()){return -1}if(s.get("name").toLowerCase()>t.get("name").toLowerCase()){return 1}return 0}}}this.collection.sort()}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<div id="library_toolbar">');tmpl_array.push(' <button title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>');tmpl_array.push("</div>");tmpl_array.push("<% if(libraries.length === 0) { %>");tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>");tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_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(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(r){r.preventDefault();r.stopPropagation();var q=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){q.create_new_library_event()},Close:function(){q.modal.hide()}}})},create_new_library_event:function(){var s=this.serialize_new_library();if(this.validate_new_library(s)){var r=new f();var q=this;r.save(s,{success:function(t){q.collection.add(t);q.modal.hide();q.clear_library_modal();q.render();m.success("Library created")},error:function(){m.error("An error occured :(")}})}else{m.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(q){return q.name!==""}});var p=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var g=Backbone.View.extend({initialize:function(){galaxyLibraryview=new a();library_router=new p();folderContentView=new l();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:sort_libraries",function(r,q){galaxyLibraryview.sortLibraries(r,q);galaxyLibraryview.render()});library_router.on("route:folder_content",function(q){folderContentView.render({id:q})});library_router.on("route:download",function(q,r){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+q,{trigger:true,replace:true})}else{folderContentView.download(q,r);library_router.navigate("folders/"+q,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}});
\ No newline at end of file
+var view=null;var library_router=null;var responses=[];define(["galaxy.masthead","utils/utils","libs/toastr"],function(l,i,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries/"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,});var j=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:j});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var k=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:k});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div class="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="primary-button" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');r.push(' <button title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-book"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<ol class="breadcrumb">');r.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');r.push(" <% _.each(path, function(path_item) { %>");r.push(" <% if (path_item[0] != id) { %>");r.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');r.push("<% } else { %>");r.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');r.push(" <% } %>");r.push(" <% }); %>");r.push("</ol>");r.push('<table id="folder_table" class="grid table table-condensed">');r.push(" <thead>");r.push(' <th class="button_heading"></th>');r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(" <td>");r.push(' <span title="Folder" class="fa fa-folder-o"></span>');r.push(" </td>");r.push(" <td></td>");r.push(" <td>");r.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% } else { %>");r.push(' <tr class="dataset_row light" id="<%- content_item.id %>">');r.push(" <td>");r.push(' <span title="Dataset" class="fa fa-file-o"></span>');r.push(" </td>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% } %> ");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div class="modal_table">');r.push(' <table class="grid table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.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 tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click #toolbtn_create_folder":"createFolderFromModal","click .library-dataset":"showDatasetDetails","click .dataset_row":"selectClickedRow"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().parent().attr("id");if(typeof v==="undefined"){v=$(u.target).parent().attr("id")}if(typeof v==="undefined"){v=$(u.target).parent().parent().attr("id")}var t=new j();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hide()}}});$(".peek").html("Peek:"+w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark");r.find("span").removeClass("fa-file-o");r.find("span").addClass("fa-file")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light");r.find("span").addClass("fa-file-o");r.find("span").removeClass("fa-file")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=Galaxy.modal;s.modal.show({closing_events:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hide()}}})},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hide();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hide();r.modal=null}}})},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hide();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#libraries_element",events:{"click .edit_library_btn":"edit_button_event","click .save_library_btn":"save_library_modification","click .cancel_library_btn":"cancel_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library"},modal:null,collection:null,initialize:function(){var r=this;this.collection=new o();this.collection.fetch({success:function(s){r.render();$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},error:function(t,s){n.error("An error occured. Please try again.")}})},render:function(s){var t=this.templateLibraryList();var u=null;var r=false;var v=null;if(typeof s!=="undefined"){r=typeof s.with_deleted!=="undefined"?s.with_deleted:false;v=typeof s.models!=="undefined"?s.models:null}if(this.collection!==null&&v===null){if(r){u=this.collection.models}else{u=this.collection.where({deleted:false})}}else{if(v!==null){u=v}else{u=[]}}this.$el.html(t({libraries:u,order:this.collection.sort_order}))},sortLibraries:function(s,r){if(s==="name"){if(r==="asc"){this.collection.sort_order="asc";this.collection.comparator=function(u,t){if(u.get("name").toLowerCase()>t.get("name").toLowerCase()){return 1}if(t.get("name").toLowerCase()>u.get("name").toLowerCase()){return -1}return 0}}else{if(r==="desc"){this.collection.sort_order="desc";this.collection.comparator=function(u,t){if(u.get("name").toLowerCase()>t.get("name").toLowerCase()){return -1}if(t.get("name").toLowerCase()>u.get("name").toLowerCase()){return 1}return 0}}}this.collection.sort()}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(libraries.length === 0) { %>");tmpl_array.push("<div>I see no libraries. Why don't you create one?</div>");tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a title="Click to reverse order" href="#sort/name/<% if(order==="desc"||order===null){print("asc")}else{print("desc")} %>">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(' <tr class="<% if(library.get("deleted") === true){print("active");}%>" data-id="<%- library.get("id") %>">');tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="display:none;"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="display:none;"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="display:none;"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_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(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},save_library_modification:function(u){var t=$(u.target).closest("tr");var r=this.collection.get(t.data("id"));var s=false;var w=t.find(".input_library_name").val();if(typeof w!=="undefined"&&w!==r.get("name")){if(w.length>2){r.set("name",w);s=true}else{n.warning("Library name has to be at least 3 characters long");return}}var v=t.find(".input_library_description").val();if(typeof v!=="undefined"&&v!==r.get("description")){r.set("description",v);s=true}var x=t.find(".input_library_synopsis").val();if(typeof x!=="undefined"&&x!==r.get("synopsis")){r.set("synopsis",x);s=true}if(s){r.save(null,{patch:true,success:function(y){n.success("Changes to library saved");galaxyLibraryview.toggle_library_modification(t)},error:function(z,y){n.error("An error occured during updating the library :(")}})}},edit_button_event:function(r){this.toggle_library_modification($(r.target).closest("tr"))},toggle_library_modification:function(u){var r=this.collection.get(u.data("id"));u.find(".edit_library_btn").toggle();u.find(".save_library_btn").toggle();u.find(".cancel_library_btn").toggle();if(r.get("deleted")){u.find(".undelete_library_btn").toggle()}else{u.find(".delete_library_btn").toggle()}if(u.find(".edit_library_btn").is(":hidden")){var s=r.get("name");var w='<input type="text" class="form-control input_library_name" placeholder="name">';u.children("td").eq(0).html(w);if(typeof s!==undefined){u.find(".input_library_name").val(s)}var t=r.get("description");var w='<input type="text" class="form-control input_library_description" placeholder="description">';u.children("td").eq(1).html(w);if(typeof t!==undefined){u.find(".input_library_description").val(t)}var v=r.get("synopsis");var w='<input type="text" class="form-control input_library_synopsis" placeholder="synopsis">';u.children("td").eq(2).html(w);if(typeof v!==undefined){u.find(".input_library_synopsis").val(v)}}else{u.children("td").eq(0).html(r.get("name"));u.children("td").eq(1).html(r.get("description"));u.children("td").eq(2).html(r.get("synopsis"))}},cancel_library_modification:function(t){var s=$(t.target).closest("tr");var r=this.collection.get(s.data("id"));this.toggle_library_modification(s);s.children("td").eq(0).html(r.get("name"));s.children("td").eq(1).html(r.get("description"));s.children("td").eq(2).html(r.get("synopsis"))},undelete_library:function(t){var s=$(t.target).closest("tr");var r=this.collection.get(s.data("id"));this.toggle_library_modification(s);r.url=r.urlRoot+r.id+"?undelete=true";r.destroy({success:function(u){u.set("deleted",false);galaxyLibraryview.collection.add(u);s.removeClass("active");n.success("Library has been undeleted")},error:function(){n.error("An error occured while undeleting the library :(")}})},delete_library:function(t){var s=$(t.target).closest("tr");var r=this.collection.get(s.data("id"));this.toggle_library_modification(s);r.destroy({success:function(u){s.remove();u.set("deleted",true);galaxyLibraryview.collection.add(u);n.success("Library has been marked deleted")},error:function(){n.error("An error occured during deleting the library :(")}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hide()}}})},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.collection.add(u);r.modal.hide();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var h=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"delegate_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},delegate_modal:function(r){galaxyLibraryview.show_library_modal(r)},check_include_deleted:function(r){if(r.target.checked){galaxyLibraryview.render({with_deleted:true})}else{galaxyLibraryview.render({with_deleted:false})}},render:function(){var r=this.templateToolBar();this.$el.html(r())},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div id="libraries_container" style="width: 90%; margin: auto; margin-top:2em; overflow: auto !important; ">');tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <input id="include_deleted_chk" style="margin: 0;" type="checkbox">include deleted</input>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Library" id="create_new_library_btn" class="primary-button" type="button"><span class="fa fa-plus"></span> New Library</button>');tmpl_array.push(" </div>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))}});var q=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var g=Backbone.View.extend({initialize:function(){toolbarView=new h();galaxyLibraryview=new a();library_router=new q();folderContentView=new m();library_router.on("route:libraries",function(){toolbarView=new h();galaxyLibraryview=new a()});library_router.on("route:sort_libraries",function(s,r){galaxyLibraryview.sortLibraries(s,r);galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}});
\ No newline at end of file
diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1295,6 +1295,7 @@
div.libraryItemBody{padding:4px 4px 2px 4px}
li.folderRow,li.datasetRow{border-top:solid 1px #c6bfa8}
li.folderRow:hover,li.datasetRow:hover{background-color:#f9f9f9}
+td.right-center{vertical-align:middle !important;text-align:right}
.library_table td{border-top:1px solid #5f6990 !important}
.library_table th{border-bottom:2px solid #5f6990 !important}
.library_table a{color:#0A143D}.library_table a:hover{color:maroon}
diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c static/style/blue/library.css
--- a/static/style/blue/library.css
+++ b/static/style/blue/library.css
@@ -6,6 +6,7 @@
div.libraryItemBody{padding:4px 4px 2px 4px}
li.folderRow,li.datasetRow{border-top:solid 1px #c6bfa8}
li.folderRow:hover,li.datasetRow:hover{background-color:#f9f9f9}
+td.right-center{vertical-align:middle !important;text-align:right}
.library_table td{border-top:1px solid #5f6990 !important}
.library_table th{border-bottom:2px solid #5f6990 !important}
.library_table a{color:#0A143D}.library_table a:hover{color:maroon}
diff -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 -r 33cc6056d83760e5e3b98999b01ecb260423d33c static/style/src/less/library.less
--- a/static/style/src/less/library.less
+++ b/static/style/src/less/library.less
@@ -29,6 +29,11 @@
background-color: @table-bg-accent;
}
+td.right-center{
+ vertical-align: middle !important;
+ text-align: right;
+
+}
.library_table{
td {
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: UI: Modularize scratch book and make it reusable as regular ui element, refactor charts
by commits-noreply＠bitbucket.org 24 Mar '14
by commits-noreply＠bitbucket.org 24 Mar '14
24 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fa0968cfe3c3/
Changeset: fa0968cfe3c3
User: guerler
Date: 2014-03-24 09:50:52
Summary: UI: Modularize scratch book and make it reusable as regular ui element, refactor charts
Affected #: 16 files
diff -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -1,10 +1,10 @@
// dependencies
-define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils', 'plugin/library/jobs', 'plugin/library/datasets',
- 'plugin/views/charts', 'plugin/views/chart',
- 'plugin/models/config', 'plugin/models/chart', 'plugin/models/charts', 'plugin/charts/types'],
- function( Modal, Portlet, Ui, Utils, Jobs, Datasets,
- ChartsView, ChartView,
- Config, Chart, Charts, Types
+define(['mvc/ui/ui-modal', 'mvc/ui/ui-portlet', 'plugin/library/ui', 'utils/utils', 'plugin/library/jobs', 'plugin/library/datasets', 'plugin/library/storage',
+ 'plugin/views/viewer', 'plugin/views/editor',
+ 'plugin/models/config', 'plugin/models/chart', 'plugin/charts/types'],
+ function( Modal, Portlet, Ui, Utils, Jobs, Datasets, Storage,
+ ViewerView, EditorView,
+ Config, Chart, Types
) {
// widget
@@ -23,91 +23,61 @@
this.modal = new Modal.View();
}
- // create configuration model
+ //
+ // models
+ //
this.config = new Config();
-
- // job/data /processor
- this.jobs = new Jobs(this);
-
- // create chart models
this.types = new Types();
this.chart = new Chart();
- this.charts = new Charts(null, this);
- // create dataset handler
+ //
+ // libraries
+ //
+ this.jobs = new Jobs(this);
this.datasets = new Datasets(this);
-
- // create views
- this.charts_view = new ChartsView(this);
- this.chart_view = new ChartView(this);
-
- // create portlet
- if (!this.options.config.widget) {
- this.portlet = new Portlet.View({icon : 'fa-bar-chart-o'});
- } else {
- this.portlet = $('<div></div>');
- }
+ this.storage = new Storage(this);
+
+ //
+ // views
+ //
+ this.viewer_view = new ViewerView(this);
+ this.editor_view = new EditorView(this);
// append views
- this.portlet.append(this.charts_view.$el);
- this.portlet.append(this.chart_view.$el);
+ this.$el.append(this.viewer_view.$el);
+ this.$el.append(this.editor_view.$el);
- // set element
- if (!this.options.config.widget) {
- this.setElement(this.portlet.$el);
+ // pick start screen
+ if (!this.storage.load()) {
+ // show editor
+ this.go('editor');
} else {
- this.setElement(this.portlet);
- }
-
- // events
- var self = this;
- this.config.on('change:title', function() {
- self._refreshTitle();
- });
-
- // render
- this.render();
-
- // load charts
- this.charts.load();
-
- // start with chart view
- if (this.charts.length == 0) {
- this.go('chart_view');
- } else {
- this.go('charts_view');
+ // show viewport
+ this.go('viewer');
+
+ // redraw chart
+ this.chart.trigger('redraw');
}
},
// loads a view and makes sure that all others are hidden
go: function(view_id) {
+ // hide all tooltips
+ $('.tooltip').hide();
+
// pick view
switch (view_id) {
- case 'chart_view' :
- this.chart_view.show();
- this.charts_view.hide();
+ case 'editor' :
+ this.editor_view.show();
+ this.viewer_view.hide();
break;
- case 'charts_view' :
- this.chart_view.hide();
- this.charts_view.show();
+ case 'viewer' :
+ this.editor_view.hide();
+ this.viewer_view.show();
break;
}
},
- // render
- render: function() {
- this._refreshTitle();
- },
-
- // refresh title
- _refreshTitle: function() {
- var title = this.config.get('title');
- if (title) {
- title = ' - ' + title;
- }
- this.portlet.title('Charts' + title);
- },
-
// execute command
execute: function(options) {
},
diff -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore may be freely distributed under the MIT license.
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n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()})}},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}},s.cleanup(t),t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{s._refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({list:{},optionsDefault:{height:300},initialize:function(t,r){this.app=t,this.options=n.merge(r,this.optionsDefault),this.portlet=new e.View({title:"title",height:this.options.height,overflow:"hidden"}),this.setElement(this.portlet.$el);var i=this;this.app.charts.on("remove",function(e){i._removeChart(e.id)}),this.app.charts.on("redraw",function(e){i._drawChart(e)})},showChart:function(e){this.show(),this.hideCharts();var t=this.list[e];if(t){var n=this.app.charts.get(e);this.portlet.title(n.get("title")),t.$el.show(),$(window).trigger("resize")}},hideCharts:function(){this.$el.find(".item").hide()},show:function(){$(".tooltip").hide(),this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_drawChart:function(e){var t=this;if(!e.ready()){t.app.log("viewport:_drawChart()","Invalid attempt to draw chart before completion.");return}var n=e.id;this._removeChart(n);var r="#"+n,i=$(this._template({id:r}));this.portlet.append(i);var s=d3.select(i.find("svg")[0]);this.list[n]={svg:s,$el:i},e.off("change:state"),e.on("change:state",function(){var t=i.find("#info"),n=t.find("#icon");n.removeClass(),t.show(),t.find("#text").html(e.get("state_info"));var r=e.get("state");switch(r){case"ok":t.hide();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var o=e.get("type"),u=this.app.types.get(o),t=this;require(["plugin/charts/"+o+"/"+o],function(n){var r=new n(t.app,{svg:s});u.execute?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){r.draw(e,t._defaultRequestDictionary(e))}):r.draw(e,t._defaultRequestDictionary(e))})},_removeChart:function(e){var t=this.list[e];t&&(t.svg.remove(),t.$el.remove())},_template:function(e){return'<div id="'+e.id.substr(1)+'" class="item">'+'<span id="info">'+'<span id="icon" style="font-size: 1.2em; display: inline-block;"/>'+'<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>'+"</span>"+'<svg style="height: auto;"/>'+"</div>"},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/charts",["mvc/ui/ui-portlet","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(i,o){this.app=i,this.viewport_view=new s(i),this.table=new t.View({content:"Add charts to this table.",ondblclick:function(e){u._showChartView(e)},onchange:function(e){var t=u.app.charts.get(e);u.app.config.set("title",t.get("title")),u.viewport_view.showChart(e)}});var u=this;this.portlet=new e.View({icon:"fa-list",title:"List of created charts:",height:100,operations:{"new":new n.ButtonIcon({icon:"fa-magic",tooltip:"Create a new Chart",title:"New",onclick:function(){u.app.go("chart_view"),u.app.chart.reset()}}),edit:new n.ButtonIcon({icon:"fa-gear",tooltip:"Customize this Chart",title:"Customize",onclick:function(){var e=u.table.value();if(!e)return;u._showChartView(e)}}),"delete":new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this Chart",title:"Delete",onclick:function(){var e=u.table.value();if(!e)return;var t=u.app.charts.get(e);u._wait(t,function(){u.app.modal.show({title:"Are you sure?",body:'The selected chart "'+t.get("title")+'" will be irreversibly deleted.',buttons:{Cancel:function(){u.app.modal.hide()},Delete:function(){u.app.modal.hide(),u.app.charts.remove(e),u.app.jobs.cleanup(t)}}})})}})}}),this.portlet.append(this.table.$el),this.app.options.config.widget||this.$el.append(this.portlet.$el),this.$el.append(r.wrap("")),this.$el.append(this.viewport_view.$el);var u=this;this.app.charts.on("add",function(e){u._addChart(e)}),this.app.charts.on("remove",function(e){u._removeChart(e)}),this.app.charts.on("change",function(e){u._changeChart(e)})},show:function(){this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_addChart:function(e){var t=e.get("title");t==""&&(t="Untitled"),this.table.add(t);var n=this.app.types.get(e.get("type"));this.table.add(n.title),this.table.add("Last change: "+e.get("date")),this.table.prepend(e.get("id")),this.table.value(e.get("id"))},_removeChart:function(e){this.table.remove(e.id),this.app.charts.save(),this.table.size()==0?(this.app.go("chart_view"),this.app.chart.reset()):this.table.value(this.app.charts.last().id)},_changeChart:function(e){e.get("type")&&(this._addChart(e),this.table.value(e.id))},_showChartView:function(e){var t=this,n=this.app.charts.get(e);this._wait(n,function(){t.app.go("chart_view"),t.app.chart.copy(n)})},_wait:function(e,t){if(e.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:'The selected chart "'+e.get("title")+'" is currently being processed. 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t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" 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Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},ready:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a 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t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show()})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/chart",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault);var o=this;this.table=new t.View({header:!1,onconfirm:function(e){o.chart.groups.length>0?o.app.modal.show({title:"Switching to another chart type?",body:"If you continue 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title",onchange:function(){o.app.config.set("title",o.title.value())}});var h=$("<div/>");h.append(r.wrap((new n.Label({title:"Provide a chart title:"})).$el)),h.append(r.wrap(this.title.$el)),h.append(r.wrap((new n.Label({title:"Select a chart type:"})).$el)),h.append(r.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:h}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.setElement(this.tabs.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o.title.value(e.get("title")),o.app.config.set("title",e.get("title"))}),this.chart.on("change:type",function(e){o.table.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.charts.on("add",function(e){o.tabs.showOperation("back")}),this.app.charts.on("remove",function(e){o.app.charts.length==0&&o.tabs.hideOperation("back")}),this.app.charts.on("reset",function(e){o.tabs.hideOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey()},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this.app.charts.get(this.chart.id);e?e.copy(this.chart):(e=this.chart.clone(),e.copy(this.chart),this.app.charts.add(e)),e.trigger("redraw",e),this.app.charts.save()}})}),define("plugin/models/config",[],function(){return 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n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&(this.options.buttons.Pause||$(document).on("keyup",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:t}}),define("mvc/ui/ui-portlet",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$content=this.$el.find("#content"),this.$title=this.$el.find("#title-text"),this.options.height&&(this.$el.find("#body").css("height",this.options.height),this.$el.find("#content").css("overflow",this.options.overflow)),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var n=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),n.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var n=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),n.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="toolForm portlet-view no-highlight">';if(e.title||e.icon)t+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">',e.icon&&(t+='<div class="portlet-title-icon fa '+e.icon+'"> </div>'),t+='<div id="title-text" class="portlet-title-text">'+e.title+"</div>",t+="</div></div>";return t+='<div id="body" class="toolFormBody portlet-body">',e.placement=="top"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+='<div id="content" class="portlet-content"/>',e.placement=="bottom"&&(t+='<div id="buttons" class="portlet-buttons"/>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon"),this.selected=this.options.value;var n=this;this.options.onchange&&this.$select.on("change",function(){n.value(n.$select.val())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()})}},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}},s.cleanup(t),t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{s._refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"ok",state_info:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},ready:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n),alert("Error loading data:\n"+e.responseText)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;this.chart.set(e.attributes),this.chart.settings.set(e.settings);for(var t in e.groups)this.chart.groups.add(new n(e.groups[t]));return this.chart.state("ok","Loaded previously saved visualization."),!0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({height:300,initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template()));var r=this;this.chart.on("redraw",function(){r._draw(r.chart)})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_draw:function(e){var t=this;if(!e.ready()){this.app.log("viewport:_drawChart()","Invalid attempt to draw chart before completion.");return}this.svg&&this.svg.remove(),this.svg=document.createElementNS("http://www.w3.org/2000/svg","svg"),this.svg.setAttribute("height",this.height),this.$el.append(this.svg),this.svg=d3.select(this.$el.find("svg")[0]),e.off("change:state"),e.on("change:state",function(){var n=t.$el.find("#info"),r=n.find("#icon");r.removeClass(),n.show(),n.find("#text").html(e.get("state_info"));var i=e.get("state");switch(i){case"ok":n.hide();break;case"failed":r.addClass("fa fa-warning");break;default:r.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var n=e.get("type"),r=this.app.types.get(n),t=this;require(["plugin/charts/"+n+"/"+n],function(n){var i=new n(t.app,{svg:t.svg});r.execute?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){i.draw(e,t._defaultRequestDictionary(e))}):i.draw(e,t._defaultRequestDictionary(e))})},_template:function(){return'<div><div id="info" style="text-align: center; margin-top: 20px;"><span id="icon" style="font-size: 1.2em; display: inline-block;"/><span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/></div></div>'},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,r){this.app=e,this.chart=this.app.chart,this.viewport_view=new i(e);var s=this;this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",operations:{edit_button:new t.ButtonIcon({icon:"fa-gear",tooltip:"Customize Chart",title:"Customize",onclick:function(){s._wait(s.app.chart,function(){s.app.go("editor")})}})}}),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var s=this;this.chart.on("change:title",function(){s._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");e&&(e=" - "+e),this.portlet.title("Charts"+e)},_wait:function(e,t){if(e.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:"Your chart is currently being processed. Please wait...",buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show()})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(s,o){this.app=s,this.chart=this.app.chart,this.options=i.merge(o,this.optionsDefault),this.portlet=new r.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){u.app.go("viewer"),u._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){u.app.go("viewer"),u.app.storage.load()}})}});var u=this;this.table=new t.View({header:!1,onconfirm:function(e){u.chart.groups.length>0?u.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){u.app.modal.hide()},Continue:function(){u.app.modal.hide(),u.table.value(e)}}}):u.table.value(e)},onchange:function(e){u.chart.groups.reset(),u.chart.settings.clear(),u.chart.set({type:e})},ondblclick:function(e){u.tabs.show("settings")},content:"No chart types available"});var f=0,l=s.types.attributes;for(var c in l){var h=l[c];this.table.add(++f+"."),h.execute?this.table.add(h.title+" (requires processing)"):this.table.add(h.title),this.table.append(c)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=u._addGroupModel();u.tabs.show(e.id)}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){u.app.config.set("title",u.title.value())}});var p=$("<div/>");p.append(i.wrap((new n.Label({title:"Provide a chart title:"})).$el)),p.append(i.wrap(this.title.$el)),p.append(i.wrap((new n.Label({title:"Select a chart type:"})).$el)),p.append(i.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:p}),this.settings=new a(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var u=this;this.chart.on("change:title",function(e){u._refreshTitle()}),this.chart.on("change:type",function(e){u.table.value(e.get("type"))}),this.chart.on("reset",function(e){u._resetChart()}),this.app.chart.on("redraw",function(e){u.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){u._addGroup(e)}),this.app.chart.groups.on("remove",function(e){u._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){u._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){u._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");e&&(e=" - "+e),this.portlet.title("Charts"+e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new o({id:i.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new u(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey()},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",i.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:i.time()}),this.chart.groups.length==0&&this._addGroupModel(),this.chart.trigger("redraw"),this.app.storage.save()}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_tick:{init:".3"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/library/storage","plugin/views/viewer","plugin/views/editor","plugin/models/config","plugin/models/chart","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(t){this.options=t,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new f,this.types=new c,this.chart=new l,this.jobs=new i(this),this.datasets=new s(this),this.storage=new o(this),this.viewer_view=new u(this),this.editor_view=new a(this),this.$el.append(this.viewer_view.$el),this.$el.append(this.editor_view.$el),this.storage.load()?(this.go("viewer"),this.chart.trigger("redraw")):this.go("editor")},go:function(e){$(".tooltip").hide();switch(e){case"editor":this.editor_view.show(),this.viewer_view.hide();break;case"viewer":this.editor_view.hide(),this.viewer_view.show()}},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 config/plugins/visualizations/charts/static/library/storage.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/library/storage.js
@@ -0,0 +1,118 @@
+// dependencies
+define(['utils/utils', 'plugin/models/chart', 'plugin/models/group'], function(Utils, Chart, Group) {
+
+// collection
+return Backbone.Model.extend(
+{
+ // viz model
+ vis: null,
+
+ // initialize
+ initialize: function(app) {
+ // link app
+ this.app = app;
+
+ // link chart
+ this.chart = this.app.chart;
+
+ // link options
+ this.options = this.app.options;
+
+ // initialize parameters
+ this.id = this.options.id;
+
+ // create visualization
+ this.vis = new Visualization({
+ type : 'charts',
+ config : {
+ dataset_id : this.options.config.dataset_id,
+ chart_dict : {}
+ }
+ });
+
+ // add visualization id
+ if (this.id) {
+ this.vis.id = this.id;
+ }
+
+ // add charts
+ var chart_dict = this.options.config.chart_dict;
+ if (chart_dict) {
+ this.vis.get('config').chart_dict = chart_dict;
+ }
+ },
+
+ // pack and save nested chart model
+ save: function() {
+
+ // link chart
+ var chart = this.app.chart;
+
+ // reset
+ this.vis.get('config').chart_dict = {};
+
+ // set title
+ var title = chart.get('title');
+ if (title != '') {
+ this.vis.set('title', title);
+ }
+
+ // create chart dictionary
+ var chart_dict = {
+ attributes : chart.attributes,
+ settings : chart.settings.attributes,
+ groups : []
+ };
+
+ // append groups
+ chart.groups.each(function(group) {
+ chart_dict.groups.push(group.attributes);
+ });
+
+ // add chart to charts array
+ this.vis.get('config').chart_dict = chart_dict;
+
+ // save visualization
+ var self = this;
+ this.vis.save()
+ .fail(function(xhr, status, message) {
+ console.error(xhr, status, message);
+ alert( 'Error loading data:\n' + xhr.responseText );
+ })
+ .then(function(response) {
+ if (response && response.id) {
+ self.id = response.id;
+ }
+ });
+ },
+
+ // load nested models/collections from packed dictionary
+ load: function() {
+ // get charts array
+ var chart_dict = this.vis.get('config').chart_dict;
+
+ // check
+ if (!chart_dict.attributes) {
+ return false;
+ }
+
+ // main
+ this.chart.set(chart_dict.attributes);
+
+ // get settings
+ this.chart.settings.set(chart_dict.settings);
+
+ // get groups
+ for (var j in chart_dict.groups) {
+ this.chart.groups.add(new Group(chart_dict.groups[j]));
+ }
+
+ // reset status
+ this.chart.state('ok', 'Loaded previously saved visualization.');
+
+ // return
+ return true;
+ }
+});
+
+});
\ No newline at end of file
diff -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 config/plugins/visualizations/charts/static/models/charts.js
--- a/config/plugins/visualizations/charts/static/models/charts.js
+++ /dev/null
@@ -1,114 +0,0 @@
-// dependencies
-define(['plugin/models/chart', 'plugin/models/group'], function(Chart, Group) {
-
-// collection
-return Backbone.Collection.extend(
-{
- // nested chart model contains collections
- model : Chart,
-
- // viz model
- vis: null,
-
- // initialize
- initialize: function(options, app) {
- // initialize parameters
- this.app = app;
- this.id = this.app.options.id;
-
- // create visualization
- this.vis = new Visualization({
- type : 'charts',
- config : {
- dataset_id : this.app.options.config.dataset_id,
- charts : []
- }
- });
-
- // add visualization id
- if (this.id) {
- this.vis.id = this.id;
- }
-
- // add charts
- var charts_array = this.app.options.config.charts;
- if (charts_array) {
- this.vis.get('config').charts = charts_array;
- }
- },
-
- // pack and save nested chart models
- save: function() {
- // reset
- this.vis.get('config').charts = [];
-
- // pack nested chart models into arrays attributes
- var self = this;
- this.each(function(chart) {
- // create chart dictionary
- var chart_dict = {
- attributes : chart.attributes,
- settings : chart.settings.attributes,
- groups : []
- };
-
- // append groups
- chart.groups.each(function(group) {
- chart_dict.groups.push(group.attributes);
- });
-
- // add chart to charts array
- self.vis.get('config').charts.push(chart_dict);
- });
-
- // save visualization
- var self = this;
- this.vis.save()
- .fail(function(xhr, status, message) {
- console.error(xhr, status, message);
- alert( 'Error loading data:\n' + xhr.responseText );
- })
- .then(function(response) {
- if (response && response.id) {
- self.id = response.id;
- }
- });
- },
-
- // load nested models/collections from packed dictionary
- load: function() {
- // get charts array
- var charts_array = this.vis.get('config').charts;
-
- // unpack chart models
- for (var i in charts_array) {
- // get chart details
- var chart_dict = charts_array[i];
-
- // construct chart model
- var chart = new Chart();
-
- // main
- chart.set(chart_dict.attributes);
-
- // get settings
- chart.settings.set(chart_dict.settings);
-
- // get groups
- for (var j in chart_dict.groups) {
- chart.groups.add(new Group(chart_dict.groups[j]));
- }
-
- // reset status
- chart.state('ok', 'Loaded previously saved visualization.');
-
- // add to collection
- this.add(chart);
-
- // trigger
- chart.trigger('redraw', chart);
- }
- }
-});
-
-});
\ No newline at end of file
diff -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 config/plugins/visualizations/charts/static/models/config.js
--- a/config/plugins/visualizations/charts/static/models/config.js
+++ b/config/plugins/visualizations/charts/static/models/config.js
@@ -7,8 +7,7 @@
// options
defaults : {
query_limit : 1000,
- query_timeout : 500,
- title : 'Create a new chart'
+ query_timeout : 500
}
});
diff -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 config/plugins/visualizations/charts/static/views/chart.js
--- a/config/plugins/visualizations/charts/static/views/chart.js
+++ /dev/null
@@ -1,321 +0,0 @@
-// dependencies
-define(['mvc/ui/ui-tabs', 'plugin/library/ui-table', 'plugin/library/ui', 'utils/utils',
- 'plugin/models/chart', 'plugin/models/group',
- 'plugin/views/group', 'plugin/views/settings'],
- function(Tabs, Table, Ui, Utils, Chart, Group, GroupView, SettingsView) {
-
-// widget
-return Backbone.View.extend(
-{
- // defaults options
- optionsDefault: {
- header : true,
- content : 'No content available.'
- },
-
- // initialize
- initialize: function(app, options)
- {
- // link application
- this.app = app;
-
- // get current chart object
- this.chart = this.app.chart;
-
- // configure options
- this.options = Utils.merge(options, this.optionsDefault);
-
- //
- // table with chart types
- //
- var self = this;
- this.table = new Table.View({
- header : false,
- onconfirm : function(type) {
- if (self.chart.groups.length > 0) {
- // show modal
- self.app.modal.show({
- title : 'Switching to another chart type?',
- body : 'If you continue your settings and selections will be cleared.',
- buttons : {
- 'Cancel' : function() {
- // hide modal
- self.app.modal.hide();
- },
- 'Continue' : function() {
- // hide modal
- self.app.modal.hide();
-
- // confirm
- self.table.value(type);
- }
- }
- });
- } else {
- // confirm
- self.table.value(type);
- }
- },
- onchange : function(type) {
- // reset type relevant chart content
- self.chart.groups.reset();
- self.chart.settings.clear();
-
- // update chart type
- self.chart.set({type: type});
- },
- ondblclick : function(chart_id) {
- self.tabs.show('settings');
- },
- content: 'No chart types available'
- });
-
- // load chart types into table
- var types_n = 0;
- var types = app.types.attributes;
- for (var id in types){
- var chart_type = types[id];
- this.table.add (++types_n + '.');
- if (chart_type.execute) {
- this.table.add(chart_type.title + ' (requires processing)');
- } else {
- this.table.add (chart_type.title);
- }
- this.table.append(id);
- }
-
- //
- // tabs
- //
- this.tabs = new Tabs.View({
- title_new : 'Add Data',
- onnew : function() {
- var group = self._addGroupModel();
- self.tabs.show(group.id);
- },
- operations : {
- 'save' : new Ui.ButtonIcon({
- icon : 'fa-save',
- tooltip : 'Draw Chart',
- title : 'Draw',
- onclick : function() {
- // show charts
- self.app.go('charts_view');
-
- // save chart
- self._saveChart();
- }
- }),
- 'back' : new Ui.ButtonIcon({
- icon : 'fa-caret-left',
- tooltip : 'Return to Viewer',
- title : 'Return',
- onclick : function() {
- self.app.go('charts_view');
- }
- })
- }
- });
-
- //
- // main/default tab
- //
-
- // construct elements
- this.title = new Ui.Input({
- placeholder: 'Chart title',
- onchange: function() {
- self.app.config.set('title', self.title.value());
- }
- });
-
- // append element
- var $main = $('<div/>');
- $main.append(Utils.wrap((new Ui.Label({ title : 'Provide a chart title:'})).$el));
- $main.append(Utils.wrap(this.title.$el));
- $main.append(Utils.wrap((new Ui.Label({ title : 'Select a chart type:'})).$el));
- $main.append(Utils.wrap(this.table.$el));
-
- // add tab
- this.tabs.add({
- id : 'main',
- title : 'Start',
- $el : $main
- });
-
- //
- // main settings tab
- //
-
- // create settings view
- this.settings = new SettingsView(this.app);
-
- // add tab
- this.tabs.add({
- id : 'settings',
- title : 'Configuration',
- $el : this.settings.$el
- });
-
- // elements
- this.setElement(this.tabs.$el);
-
- // hide back button on startup
- this.tabs.hideOperation('back');
-
- // chart events
- var self = this;
- this.chart.on('change:title', function(chart) {
- self.title.value(chart.get('title'));
- self.app.config.set('title', chart.get('title'));
- });
- this.chart.on('change:type', function(chart) {
- self.table.value(chart.get('type'));
- });
- this.chart.on('reset', function(chart) {
- self._resetChart();
- });
-
- // charts events
- this.app.charts.on('add', function(chart) {
- self.tabs.showOperation('back');
- });
- this.app.charts.on('remove', function(chart) {
- if (self.app.charts.length == 0) {
- self.tabs.hideOperation('back');
- }
- });
- this.app.charts.on('reset', function(chart) {
- self.tabs.hideOperation('back');
- });
-
- // groups events
- this.app.chart.groups.on('add', function(group) {
- self._addGroup(group);
- });
- this.app.chart.groups.on('remove', function(group) {
- self._removeGroup(group);
- });
- this.app.chart.groups.on('reset', function(group) {
- self._removeAllGroups();
- });
- this.app.chart.groups.on('change:key', function(group) {
- self._refreshGroupKey();
- });
-
- // reset
- this._resetChart();
- },
-
- // hide
- show: function() {
- this.$el.show();
- },
-
- // hide
- hide: function() {
- $('.tooltip').hide();
- this.$el.hide();
- },
-
- // update
- _refreshGroupKey: function() {
- var self = this;
- var counter = 0;
- this.chart.groups.each(function(group) {
- var title = group.get('key', '');
- if (title == '') {
- title = 'Chart data';
- }
- self.tabs.title(group.id, ++counter + ': ' + title);
- });
- },
-
- // new group
- _addGroupModel: function() {
- var group = new Group({
- id : Utils.uuid()
- });
- this.chart.groups.add(group);
- return group;
- },
-
- // add group
- _addGroup: function(group) {
- // link this
- var self = this;
-
- // create view
- var group_view = new GroupView(this.app, {group: group});
-
- // number of groups
- var count = self.chart.groups.length;
-
- // add new tab
- this.tabs.add({
- id : group.id,
- $el : group_view.$el,
- ondel : function() {
- self.chart.groups.remove(group.id);
- }
- });
-
- // update titles
- this._refreshGroupKey();
- },
-
- // remove group
- _removeGroup: function(group) {
- this.tabs.del(group.id);
-
- // update titles
- this._refreshGroupKey();
- },
-
- // remove group
- _removeAllGroups: function(group) {
- this.tabs.delRemovable();
- },
-
- // reset
- _resetChart: function() {
- // reset chart details
- this.chart.set('id', Utils.uuid());
- this.chart.set('type', 'bardiagram');
- this.chart.set('dataset_id', this.app.options.config.dataset_id);
- this.chart.set('title', 'New Chart');
- },
-
- // create chart
- _saveChart: function() {
- // update chart data
- this.chart.set({
- type : this.table.value(),
- title : this.title.value(),
- date : Utils.time()
- });
-
- // ensure that data group is available
- if (this.chart.groups.length == 0) {
- this._addGroupModel();
- }
-
- // create/get chart
- var current = this.app.charts.get(this.chart.id);
- if (!current) {
- current = this.chart.clone();
- current.copy(this.chart);
- this.app.charts.add(current);
- } else {
- current.copy(this.chart);
- }
-
- // trigger redraw
- current.trigger('redraw', current);
-
- // save
- this.app.charts.save();
- }
-});
-
-});
\ No newline at end of file
diff -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 config/plugins/visualizations/charts/static/views/charts.js
--- a/config/plugins/visualizations/charts/static/views/charts.js
+++ /dev/null
@@ -1,227 +0,0 @@
-// dependencies
-define(['mvc/ui/ui-portlet', 'plugin/library/ui-table', 'plugin/library/ui', 'utils/utils', 'plugin/models/group', 'plugin/views/viewport',], function(Portlet, Table, Ui, Utils, Group, ViewportView) {
-
-// widget
-return Backbone.View.extend(
-{
- // initialize
- initialize: function(app, options)
- {
- // link app
- this.app = app;
-
- // create viewport
- this.viewport_view = new ViewportView(app);
-
- // table
- this.table = new Table.View({
- content : 'Add charts to this table.',
- ondblclick : function(chart_id) {
- // attempt to load chart editor
- self._showChartView(chart_id);
- },
- onchange : function(chart_id) {
- // get chart
- var chart = self.app.charts.get(chart_id);
-
- // update main title
- self.app.config.set('title', chart.get('title'));
-
- // show viewport
- self.viewport_view.showChart(chart_id);
- }
- });
-
- // add table to portlet
- var self = this;
- this.portlet = new Portlet.View({
- icon : 'fa-list',
- title : 'List of created charts:',
- height : 100,
- operations : {
- 'new' : new Ui.ButtonIcon({
- icon : 'fa-magic',
- tooltip : 'Create a new Chart',
- title : 'New',
- onclick : function() {
- self.app.go('chart_view');
- self.app.chart.reset();
- }
- }),
- 'edit' : new Ui.ButtonIcon({
- icon : 'fa-gear',
- tooltip : 'Customize this Chart',
- title : 'Customize',
- onclick : function() {
- // check if element has been selected
- var chart_id = self.table.value();
- if (!chart_id) {
- return;
- }
-
- // attempt to load chart editor
- self._showChartView(chart_id);
- }
- }),
- 'delete' : new Ui.ButtonIcon({
- icon : 'fa-trash-o',
- tooltip : 'Delete this Chart',
- title : 'Delete',
- onclick : function() {
-
- // check if element has been selected
- var chart_id = self.table.value();
- if (!chart_id) {
- return;
- }
-
- // title
- var chart = self.app.charts.get(chart_id);
-
- // make sure that chart is ready
- self._wait (chart, function() {
- self.app.modal.show({
- title : 'Are you sure?',
- body : 'The selected chart "' + chart.get('title') + '" will be irreversibly deleted.',
- buttons : {
- 'Cancel' : function() {self.app.modal.hide();},
- 'Delete' : function() {
- // hide modal
- self.app.modal.hide();
-
- // remove chart
- self.app.charts.remove(chart_id);
-
- // cleanup
- self.app.jobs.cleanup(chart);
- }
- }
- });
- });
- }
- }),
- }
- });
- this.portlet.append(this.table.$el);
-
- // append portlet with table
- if (!this.app.options.config.widget) {
- this.$el.append(this.portlet.$el);
- }
-
- // append view port
- this.$el.append(Utils.wrap(''));
- this.$el.append(this.viewport_view.$el);
-
- // events
- var self = this;
- this.app.charts.on('add', function(chart) {
- // add
- self._addChart(chart);
- });
- this.app.charts.on('remove', function(chart) {
- // remove
- self._removeChart(chart);
- });
- this.app.charts.on('change', function(chart) {
- // replace
- self._changeChart(chart);
- });
- },
-
- // show
- show: function() {
- this.$el.show();
- },
-
- // hide
- hide: function() {
- $('.tooltip').hide();
- this.$el.hide();
- },
-
- // add
- _addChart: function(chart) {
- // add title to table
- var title = chart.get('title');
- if (title == '') {
- title = 'Untitled';
- }
- this.table.add(title);
-
- // get chart type
- var type = this.app.types.get(chart.get('type'));
- this.table.add(type.title);
-
- // add additional columns
- this.table.add('Last change: ' + chart.get('date'));
- this.table.prepend(chart.get('id'));
- this.table.value(chart.get('id'));
- },
-
- // remove
- _removeChart: function(chart) {
- // remove from to table
- this.table.remove(chart.id);
-
- // save
- this.app.charts.save();
-
- // check if table is empty
- if (this.table.size() == 0) {
- this.app.go('chart_view');
- this.app.chart.reset();
- } else {
- // select available chart
- this.table.value(this.app.charts.last().id);
- }
- },
-
- // change
- _changeChart: function(chart) {
- if (chart.get('type')) {
- // add chart
- this._addChart(chart);
-
- // select available chart
- this.table.value(chart.id);
- }
- },
-
- // show chart editor
- _showChartView: function(chart_id) {
- var self = this;
- var chart = this.app.charts.get(chart_id);
- this._wait (chart, function() {
- self.app.go('chart_view');
- self.app.chart.copy(chart);
- });
- },
-
- // wait for chart to be ready
- _wait: function(chart, callback) {
- // get chart
- if (chart.ready()) {
- callback();
- } else {
- // show modal
- var self = this;
- this.app.modal.show({
- title : 'Please wait!',
- body : 'The selected chart "' + chart.get('title') + '" is currently being processed. Please wait...',
- buttons : {
- 'Close' : function() {self.app.modal.hide();},
- 'Retry' : function() {
- // hide modal
- self.app.modal.hide();
-
- // retry
- setTimeout(function() { self._wait(chart, callback); }, self.app.config.get('query_timeout'));
- }
- }
- });
- }
- }
-});
-
-});
\ No newline at end of file
diff -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 config/plugins/visualizations/charts/static/views/editor.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/views/editor.js
@@ -0,0 +1,324 @@
+// dependencies
+define(['mvc/ui/ui-tabs', 'plugin/library/ui-table', 'plugin/library/ui', 'mvc/ui/ui-portlet', 'utils/utils',
+ 'plugin/models/chart', 'plugin/models/group',
+ 'plugin/views/group', 'plugin/views/settings'],
+ function(Tabs, Table, Ui, Portlet, Utils, Chart, Group, GroupView, SettingsView) {
+
+// widget
+return Backbone.View.extend(
+{
+ // defaults options
+ optionsDefault: {
+ header : true,
+ content : 'No content available.'
+ },
+
+ // initialize
+ initialize: function(app, options)
+ {
+ // link application
+ this.app = app;
+
+ // get current chart object
+ this.chart = this.app.chart;
+
+ // configure options
+ this.options = Utils.merge(options, this.optionsDefault);
+
+ // create portlet
+ this.portlet = new Portlet.View({
+ icon : 'fa-bar-chart-o',
+ title: 'Editor',
+ operations : {
+ 'save' : new Ui.ButtonIcon({
+ icon : 'fa-save',
+ tooltip : 'Draw Chart',
+ title : 'Draw',
+ onclick : function() {
+ // show viewport
+ self.app.go('viewer');
+
+ // save chart
+ self._saveChart();
+ }
+ }),
+ 'back' : new Ui.ButtonIcon({
+ icon : 'fa-caret-left',
+ tooltip : 'Return to Viewer',
+ title : 'Return',
+ onclick : function() {
+ // show viewport
+ self.app.go('viewer');
+
+ // reset chart
+ self.app.storage.load();
+ }
+ })
+ }
+ });
+
+ //
+ // table with chart types
+ //
+ var self = this;
+ this.table = new Table.View({
+ header : false,
+ onconfirm : function(type) {
+ if (self.chart.groups.length > 0) {
+ // show modal
+ self.app.modal.show({
+ title : 'Switching to another chart type?',
+ body : 'If you continue your settings and selections will be cleared.',
+ buttons : {
+ 'Cancel' : function() {
+ // hide modal
+ self.app.modal.hide();
+ },
+ 'Continue' : function() {
+ // hide modal
+ self.app.modal.hide();
+
+ // confirm
+ self.table.value(type);
+ }
+ }
+ });
+ } else {
+ // confirm
+ self.table.value(type);
+ }
+ },
+ onchange : function(type) {
+ // reset type relevant chart content
+ self.chart.groups.reset();
+ self.chart.settings.clear();
+
+ // update chart type
+ self.chart.set({type: type});
+ },
+ ondblclick : function(chart_id) {
+ self.tabs.show('settings');
+ },
+ content: 'No chart types available'
+ });
+
+ // load chart types into table
+ var types_n = 0;
+ var types = app.types.attributes;
+ for (var id in types){
+ var chart_type = types[id];
+ this.table.add (++types_n + '.');
+ if (chart_type.execute) {
+ this.table.add(chart_type.title + ' (requires processing)');
+ } else {
+ this.table.add (chart_type.title);
+ }
+ this.table.append(id);
+ }
+
+ //
+ // tabs
+ //
+ this.tabs = new Tabs.View({
+ title_new : 'Add Data',
+ onnew : function() {
+ var group = self._addGroupModel();
+ self.tabs.show(group.id);
+ }
+ });
+
+ //
+ // main/default tab
+ //
+
+ // construct elements
+ this.title = new Ui.Input({
+ placeholder: 'Chart title',
+ onchange: function() {
+ self.app.config.set('title', self.title.value());
+ }
+ });
+
+ // append element
+ var $main = $('<div/>');
+ $main.append(Utils.wrap((new Ui.Label({ title : 'Provide a chart title:'})).$el));
+ $main.append(Utils.wrap(this.title.$el));
+ $main.append(Utils.wrap((new Ui.Label({ title : 'Select a chart type:'})).$el));
+ $main.append(Utils.wrap(this.table.$el));
+
+ // add tab
+ this.tabs.add({
+ id : 'main',
+ title : 'Start',
+ $el : $main
+ });
+
+ //
+ // main settings tab
+ //
+
+ // create settings view
+ this.settings = new SettingsView(this.app);
+
+ // add tab
+ this.tabs.add({
+ id : 'settings',
+ title : 'Configuration',
+ $el : this.settings.$el
+ });
+
+ // append tabs
+ this.portlet.append(this.tabs.$el);
+
+ // elements
+ this.setElement(this.portlet.$el);
+
+ // hide back button on startup
+ this.tabs.hideOperation('back');
+
+ // chart events
+ var self = this;
+ this.chart.on('change:title', function(chart) {
+ self._refreshTitle();
+ });
+ this.chart.on('change:type', function(chart) {
+ self.table.value(chart.get('type'));
+ });
+ this.chart.on('reset', function(chart) {
+ self._resetChart();
+ });
+ this.app.chart.on('redraw', function(chart) {
+ self.portlet.showOperation('back');
+ });
+
+ // groups events
+ this.app.chart.groups.on('add', function(group) {
+ self._addGroup(group);
+ });
+ this.app.chart.groups.on('remove', function(group) {
+ self._removeGroup(group);
+ });
+ this.app.chart.groups.on('reset', function(group) {
+ self._removeAllGroups();
+ });
+ this.app.chart.groups.on('change:key', function(group) {
+ self._refreshGroupKey();
+ });
+
+ // reset
+ this._resetChart();
+ },
+
+ // hide
+ show: function() {
+ this.$el.show();
+ },
+
+ // hide
+ hide: function() {
+ this.$el.hide();
+ },
+
+ // refresh title
+ _refreshTitle: function() {
+ var title = this.chart.get('title');
+ if (title) {
+ title = ' - ' + title;
+ }
+ this.portlet.title('Charts' + title);
+ },
+
+ // update
+ _refreshGroupKey: function() {
+ var self = this;
+ var counter = 0;
+ this.chart.groups.each(function(group) {
+ var title = group.get('key', '');
+ if (title == '') {
+ title = 'Chart data';
+ }
+ self.tabs.title(group.id, ++counter + ': ' + title);
+ });
+ },
+
+ // new group
+ _addGroupModel: function() {
+ var group = new Group({
+ id : Utils.uuid()
+ });
+ this.chart.groups.add(group);
+ return group;
+ },
+
+ // add group
+ _addGroup: function(group) {
+ // link this
+ var self = this;
+
+ // create view
+ var group_view = new GroupView(this.app, {group: group});
+
+ // number of groups
+ var count = self.chart.groups.length;
+
+ // add new tab
+ this.tabs.add({
+ id : group.id,
+ $el : group_view.$el,
+ ondel : function() {
+ self.chart.groups.remove(group.id);
+ }
+ });
+
+ // update titles
+ this._refreshGroupKey();
+ },
+
+ // remove group
+ _removeGroup: function(group) {
+ this.tabs.del(group.id);
+
+ // update titles
+ this._refreshGroupKey();
+ },
+
+ // remove group
+ _removeAllGroups: function(group) {
+ this.tabs.delRemovable();
+ },
+
+ // reset
+ _resetChart: function() {
+ // reset chart details
+ this.chart.set('id', Utils.uuid());
+ this.chart.set('type', 'bardiagram');
+ this.chart.set('dataset_id', this.app.options.config.dataset_id);
+ this.chart.set('title', 'New Chart');
+
+ // reset back button
+ this.portlet.hideOperation('back');
+ },
+
+ // create chart
+ _saveChart: function() {
+ // update chart data
+ this.chart.set({
+ type : this.table.value(),
+ title : this.title.value(),
+ date : Utils.time()
+ });
+
+ // ensure that data group is available
+ if (this.chart.groups.length == 0) {
+ this._addGroupModel();
+ }
+
+ // trigger redraw
+ this.chart.trigger('redraw');
+
+ // save
+ this.app.storage.save();
+ }
+});
+
+});
\ No newline at end of file
diff -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 config/plugins/visualizations/charts/static/views/viewer.js
--- /dev/null
+++ b/config/plugins/visualizations/charts/static/views/viewer.js
@@ -0,0 +1,106 @@
+// dependencies
+define(['utils/utils', 'plugin/library/ui', 'mvc/ui/ui-portlet',
+ 'plugin/models/group', 'plugin/views/viewport',],
+ function(Utils, Ui, Portlet, Group, ViewportView) {
+
+// widget
+return Backbone.View.extend(
+{
+ // initialize
+ initialize: function(app, options)
+ {
+ // link app
+ this.app = app;
+
+ // link chart
+ this.chart = this.app.chart;
+
+ // create viewport
+ this.viewport_view = new ViewportView(app);
+
+ // link this
+ var self = this;
+
+ // create portlet
+ this.portlet = new Portlet.View({
+ icon : 'fa-bar-chart-o',
+ title: 'Viewport',
+ operations: {
+ edit_button: new Ui.ButtonIcon({
+ icon : 'fa-gear',
+ tooltip : 'Customize Chart',
+ title : 'Customize',
+ onclick : function() {
+ // attempt to load chart editor
+ self._wait (self.app.chart, function() {
+ self.app.go('editor');
+ });
+ }
+ })
+
+ }
+ });
+
+ // append view port
+ this.portlet.append(this.viewport_view.$el);
+
+ // set element
+ this.setElement(this.portlet.$el);
+
+ // events
+ var self = this;
+ this.chart.on('change:title', function() {
+ self._refreshTitle();
+ });
+ },
+
+ // show
+ show: function() {
+ // show element
+ this.$el.show();
+
+ // trigger resize to refresh d3 element
+ $(window).trigger('resize');
+ },
+
+ // hide
+ hide: function() {
+ this.$el.hide();
+ },
+
+ // refresh title
+ _refreshTitle: function() {
+ var title = this.chart.get('title');
+ if (title) {
+ title = ' - ' + title;
+ }
+ this.portlet.title('Charts' + title);
+ },
+
+ // wait for chart to be ready
+ _wait: function(chart, callback) {
+ // get chart
+ if (chart.ready()) {
+ callback();
+ } else {
+ // show modal
+ var self = this;
+ this.app.modal.show({
+ title : 'Please wait!',
+ body : 'Your chart is currently being processed. Please wait...',
+ buttons : {
+ 'Close' : function() {self.app.modal.hide();},
+ 'Retry' : function() {
+ // hide modal
+ self.app.modal.hide();
+
+ // retry
+ setTimeout(function() { self._wait(chart, callback); }, self.app.config.get('query_timeout'));
+ }
+ }
+ });
+ }
+ }
+});
+
+});
\ No newline at end of file
diff -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 -r fa0968cfe3c3fec5869168bd7dd68829024f1ec3 config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -5,14 +5,8 @@
// widget
return Backbone.View.extend(
{
- // list
- list: {},
-
- // options
- optionsDefault :
- {
- height : 300
- },
+ // height
+ height : 300,
// initialize
initialize: function(app, options)
@@ -20,117 +14,63 @@
// link app
this.app = app;
+ // link chart
+ this.chart = this.app.chart;
+
// link options
this.options = Utils.merge(options, this.optionsDefault);
- // add table to portlet
- this.portlet = new Portlet.View({
- title : 'title',
- height : this.options.height,
- overflow : 'hidden'
- });
-
- // set this element
- this.setElement(this.portlet.$el);
+ // create element
+ this.setElement($(this._template()));
// events
var self = this;
-
- // remove
- this.app.charts.on('remove', function(chart) {
- self._removeChart(chart.id);
- });
-
- // redraw
- this.app.charts.on('redraw', function(chart) {
- self._drawChart(chart);
+ this.chart.on('redraw', function() {
+ self._draw(self.chart);
});
},
// show
- showChart: function(chart_id) {
- // show
- this.show();
-
- // hide all
- this.hideCharts();
-
- // identify selected item from list
- var item = this.list[chart_id];
- if (item) {
- // get chart
- var chart = this.app.charts.get(chart_id);
-
- // update portlet
- this.portlet.title(chart.get('title'));
-
- // show selected chart
- item.$el.show();
-
- // this trigger d3 update events
- $(window).trigger('resize');
- }
- },
-
- // hide charts
- hideCharts: function() {
- this.$el.find('.item').hide();
- },
-
- // show
show: function() {
- $('.tooltip').hide();
this.$el.show();
},
// hide
hide: function() {
- $('.tooltip').hide();
this.$el.hide();
},
// add
- _drawChart: function(chart) {
+ _draw: function(chart) {
// link this
var self = this;
// check
if (!chart.ready()) {
- self.app.log('viewport:_drawChart()', 'Invalid attempt to draw chart before completion.');
+ this.app.log('viewport:_drawChart()', 'Invalid attempt to draw chart before completion.');
return;
}
-
- // backup chart details
- var chart_id = chart.id;
-
- // make sure that svg does not exist already
- this._removeChart(chart_id);
-
- // create id
- var id = '#' + chart_id;
- // create element
- var $chart_el = $(this._template({id: id}));
+ // clear svg
+ if (this.svg) {
+ this.svg.remove();
+ }
- // add to portlet
- this.portlet.append($chart_el);
+ // create
+ this.svg = document.createElementNS('http://www.w3.org/2000/svg', 'svg');
+ this.svg.setAttribute('height', this.height);
+ this.$el.append(this.svg);
// find svg element
- var svg = d3.select($chart_el.find('svg')[0]);
-
- // add chart to list
- this.list[chart_id] = {
- svg : svg,
- $el : $chart_el
- }
-
+ this.svg = d3.select(this.$el.find('svg')[0]);
+
// clear all previous handlers (including redraw listeners)
chart.off('change:state');
// link status handler
chart.on('change:state', function() {
// get info element
- var $info = $chart_el.find('#info');
+ var $info = self.$el.find('#info');
// get icon
var $icon = $info.find('#icon');
@@ -168,7 +108,7 @@
var self = this;
require(['plugin/charts/' + chart_type + '/' + chart_type], function(ChartView) {
// create chart
- var view = new ChartView(self.app, {svg : svg});
+ var view = new ChartView(self.app, {svg : self.svg});
// request data
if (chart_settings.execute) {
@@ -181,31 +121,18 @@
});
},
- // remove
- _removeChart: function(id) {
- var item = this.list[id];
- if (item) {
- // remove svg element
- item.svg.remove();
-
- // find div element (if any)
- item.$el.remove();
- }
- },
-
// template
- _template: function(options) {
- return '<div id="' + options.id.substr(1) + '" class="item">' +
- '<span id="info">' +
+ _template: function() {
+ return '<div>' +
+ '<div id="info" style="text-align: center; margin-top: 20px;">' +
'<span id="icon" style="font-size: 1.2em; display: inline-block;"/>' +
'<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>' +
- '</span>' +
- '<svg style="height: auto;"/>' +
+ '</div>' +
'</div>';
},
// create default chart request
- _defaultRequestString : function(chart) {
+ _defaultRequestString: function(chart) {
// get chart settings
var chart_settings = this.app.types.get(chart.get('type'));
@@ -226,7 +153,7 @@
},
// create default chart request
- _defaultSettingsString : function(chart) {
+ _defaultSettingsString: function(chart) {
// configure settings
var settings_string = '';
@@ -241,7 +168,7 @@
},
// create default chart request
- _defaultRequestDictionary : function(chart) {
+ _defaultRequestDictionary: function(chart) {
// get chart settings
var chart_settings = this.app.types.get(chart.get('type'));
This diff is so big that we needed to truncate the remainder.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Charts: Save/read from backend
by commits-noreply＠bitbucket.org 22 Mar '14
by commits-noreply＠bitbucket.org 22 Mar '14
22 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e7dfb71eeb79/
Changeset: e7dfb71eeb79
User: guerler
Date: 2014-03-22 18:38:48
Summary: Charts: Save/read from backend
Affected #: 8 files
diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -32,7 +32,7 @@
// create chart models
this.types = new Types();
this.chart = new Chart();
- this.charts = new Charts();
+ this.charts = new Charts(null, this);
// create dataset handler
this.datasets = new Datasets(this);
@@ -59,9 +59,6 @@
this.setElement(this.portlet);
}
- // start with chart view
- this.go('chart_view');
-
// events
var self = this;
this.config.on('change:title', function() {
@@ -70,6 +67,16 @@
// render
this.render();
+
+ // load charts
+ this.charts.load();
+
+ // start with chart view
+ if (this.charts.length == 0) {
+ this.go('chart_view');
+ } else {
+ this.go('charts_view');
+ }
},
// loads a view and makes sure that all others are hidden
diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
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options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}};var f=t.get("dataset_id_job");f&&e.request("PUT",config.root+"api/histories/"+t.get("history_id")+"/contents/"+f,{deleted:!0}),t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({list:{},optionsDefault:{height:300},initialize:function(t,r){this.app=t,this.options=n.merge(r,this.optionsDefault),this.portlet=new e.View({title:"title",height:this.options.height,overflow:"hidden"}),this.setElement(this.portlet.$el);var i=this;this.app.charts.on("remove",function(e){i._removeChart(e.id)}),this.app.charts.on("redraw",function(e){e.ready()?i._refreshChart(e):e.on("change:state",function(){e.ready()&&i._refreshChart(e)})})},showChart:function(e){this.show(),this.hideCharts();var t=this.list[e];if(t){var n=self.app.charts.get(e);this.portlet.title(n.get("title")),t.$el.show(),$(window).trigger("resize")}},hideCharts:function(){this.$el.find(".item").hide()},show:function(){$(".tooltip").hide(),this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshChart:function(e){var t=this;if(!e.ready()){t.app.log("viewport:_refreshChart()","Invalid attempt to refresh chart before completion.");return}var n=e.id;this._removeChart(n);var r="#"+n,i=$(this._template({id:r}));this.portlet.append(i);var s=d3.select(r+" svg");this.list[n]={svg:s,$el:i},this.showChart(n),e.off("change:state"),e.on("change:state",function(){var t=i.find("#info"),n=t.find("#icon");n.removeClass(),t.show(),t.find("#text").html(e.get("state_info"));var r=e.get("state");switch(r){case"ok":t.hide();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var o=e.get("type"),u=this.app.types.get(o),t=this;require(["plugin/charts/"+o+"/"+o],function(n){var r=new n(t.app,{svg:s});u.execute?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){r.draw(e,t._defaultRequestDictionary(e))}):r.draw(e,t._defaultRequestDictionary(e))})},_removeChart:function(e){var t=this.list[e];t&&(t.svg.remove(),t.$el.remove())},_template:function(e){return'<div id="'+e.id.substr(1)+'" class="item">'+'<span id="info">'+'<span id="icon" style="font-size: 1.2em; display: inline-block;"/>'+'<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>'+"</span>"+'<svg style="height: auto;"/>'+"</div>"},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/charts",["mvc/ui/ui-portlet","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(i,o){this.app=i,this.viewport_view=new s(i),this.table=new t.View({content:"Add charts to this table.",ondblclick:function(e){u._showChartView(e)},onchange:function(e){var t=u.app.charts.get(e);u.app.config.set("title",t.get("title")),u.viewport_view.showChart(e)}});var u=this;this.portlet=new e.View({icon:"fa-list",title:"List of created charts:",height:100,operations:{"new":new n.ButtonIcon({icon:"fa-magic",tooltip:"Create a new Chart",title:"New",onclick:function(){u.app.go("chart_view"),u.app.chart.reset()}}),edit:new n.ButtonIcon({icon:"fa-gear",tooltip:"Customize this Chart",title:"Customize",onclick:function(){var e=u.table.value();if(!e)return;u._showChartView(e)}}),"delete":new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this Chart",title:"Delete",onclick:function(){var e=u.table.value();if(!e)return;var t=u.app.charts.get(e);u.app.modal.show({title:"Are you sure?",body:'The selected chart "'+t.get("title")+'" will be irreversibly deleted.',buttons:{Cancel:function(){u.app.modal.hide()},Delete:function(){u.app.modal.hide(),u.app.charts.remove(e)}}})}})}}),this.portlet.append(this.table.$el),this.app.options.config.widget||this.$el.append(this.portlet.$el),this.$el.append(r.wrap("")),this.$el.append(this.viewport_view.$el);var u=this;this.app.charts.on("add",function(e){u._addChart(e)}),this.app.charts.on("remove",function(e){u._removeChart(e)}),this.app.charts.on("change",function(e){u._changeChart(e)})},show:function(){this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_addChart:function(e){var t=e.get("title");t==""&&(t="Untitled"),this.table.add(t);var n=this.app.types.get(e.get("type"));this.table.add(n.title),this.table.add("Last change: "+e.get("date")),this.table.prepend(e.get("id")),this.table.value(e.get("id"))},_removeChart:function(e){this.table.remove(e.id),this.app.charts.save(),this.table.size()==0?(this.app.go("chart_view"),this.app.chart.reset()):this.table.value(this.app.charts.last().id)},_changeChart:function(e){e.get("type")&&(this._addChart(e),this.table.value(e.id))},_showChartView:function(e){var t=this.app.charts.get(e);if(t.ready())this.app.go("chart_view"),this.app.chart.copy(t);else{var n=this;this.app.modal.show({title:"Please wait!",body:'The selected chart "'+t.get("title")+'" is currently being processed. Please wait...',buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),n._showChartView(e)}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"ok",state_info:""},initialize:function(t){this.groups=new e,this.settings=new 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this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));!this.selected&&e.length>0&&this.value(e[0].value),this._refresh()},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.$select.append(this._templateOption({value:"null",label:this.options.empty})),this.disable()):(this.enable(),this.selected&&this.$select.val(this.selected))},_exists:function(e){return 0!=this.$select.find("option[value="+e+"]").length},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="styled-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select"],function(e,t){var n=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.find("b").html(e)},_template:function(e){return"<label><b>"+e.title+"</b></label>"},value:function(){return options.title}}),r=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="margin-right: 5px; float: '+e.float+';" type="button" class="btn '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),i=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" style="font-size: 1.2em;"/> '+e.title+"</div>"}}),s=Backbone.View.extend({optionsDefault:{title:"",id:null,"float":"right",cls:"icon-btn",icon:"",tooltip:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="margin-right: 5px; float: '+e.float+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div style="margin-right: 5px; margin-left: 5px;"><i class="icon fa '+e.icon+'"/> '+'<span style="position: relative; font-size: 0.8em; font-weight: normal; top: -1px;">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),o=Backbone.View.extend({optionsDefault:{title:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)">'+e.title+"</a></div>"}}),u=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="alert alert-'+e.status+'" style="padding: 2px 2px 2px 10px;">'+e.message+"</div>"}}),a=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),f=Backbone.View.extend({optionsDefault:{title:"Unlabeled",body:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.body&&this.$el.find(".body").append(this.options.body)},_template:function(e){return'<div id="title" class="title">'+e.title+":"+"</div>"}}),l=Backbone.View.extend({optionsDefault:{id:"",title:"",target:"",href:"",onunload:null,onclick:null,visible:!0,icon:null,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide()},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t='<div id="'+e.id+'" class="button-menu btn-group">'+'<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),"</button></div>",t}}),c=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.options.onchange&&this.$el.on("input",function(){n.options.onchange()})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="form-control">'}});return{Label:n,Button:r,Icon:i,ButtonIcon:s,Input:c,Anchor:o,Message:u,Searchbox:a,Title:f,Select:t,ButtonMenu:l}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},cleanup:function(t){var n=t.get("dataset_id_job");if(n){var r=this;e.request("PUT",config.root+"api/histories/none/contents/"+n,{deleted:!0},function(){r._refreshHdas()})}},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}},s.cleanup(t),t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{s._refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({list:{},optionsDefault:{height:300},initialize:function(t,r){this.app=t,this.options=n.merge(r,this.optionsDefault),this.portlet=new e.View({title:"title",height:this.options.height,overflow:"hidden"}),this.setElement(this.portlet.$el);var i=this;this.app.charts.on("remove",function(e){i._removeChart(e.id)}),this.app.charts.on("redraw",function(e){i._drawChart(e)})},showChart:function(e){this.show(),this.hideCharts();var t=this.list[e];if(t){var n=this.app.charts.get(e);this.portlet.title(n.get("title")),t.$el.show(),$(window).trigger("resize")}},hideCharts:function(){this.$el.find(".item").hide()},show:function(){$(".tooltip").hide(),this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_drawChart:function(e){var t=this;if(!e.ready()){t.app.log("viewport:_drawChart()","Invalid attempt to draw chart before completion.");return}var n=e.id;this._removeChart(n);var r="#"+n,i=$(this._template({id:r}));this.portlet.append(i);var s=d3.select(i.find("svg")[0]);this.list[n]={svg:s,$el:i},e.off("change:state"),e.on("change:state",function(){var t=i.find("#info"),n=t.find("#icon");n.removeClass(),t.show(),t.find("#text").html(e.get("state_info"));var r=e.get("state");switch(r){case"ok":t.hide();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var o=e.get("type"),u=this.app.types.get(o),t=this;require(["plugin/charts/"+o+"/"+o],function(n){var r=new n(t.app,{svg:s});u.execute?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){r.draw(e,t._defaultRequestDictionary(e))}):r.draw(e,t._defaultRequestDictionary(e))})},_removeChart:function(e){var t=this.list[e];t&&(t.svg.remove(),t.$el.remove())},_template:function(e){return'<div id="'+e.id.substr(1)+'" class="item">'+'<span id="info">'+'<span id="icon" style="font-size: 1.2em; display: inline-block;"/>'+'<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>'+"</span>"+'<svg style="height: auto;"/>'+"</div>"},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/charts",["mvc/ui/ui-portlet","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(i,o){this.app=i,this.viewport_view=new s(i),this.table=new t.View({content:"Add charts to this table.",ondblclick:function(e){u._showChartView(e)},onchange:function(e){var t=u.app.charts.get(e);u.app.config.set("title",t.get("title")),u.viewport_view.showChart(e)}});var u=this;this.portlet=new e.View({icon:"fa-list",title:"List of created charts:",height:100,operations:{"new":new n.ButtonIcon({icon:"fa-magic",tooltip:"Create a new Chart",title:"New",onclick:function(){u.app.go("chart_view"),u.app.chart.reset()}}),edit:new n.ButtonIcon({icon:"fa-gear",tooltip:"Customize this Chart",title:"Customize",onclick:function(){var e=u.table.value();if(!e)return;u._showChartView(e)}}),"delete":new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this Chart",title:"Delete",onclick:function(){var e=u.table.value();if(!e)return;var t=u.app.charts.get(e);u._wait(t,function(){u.app.modal.show({title:"Are you sure?",body:'The selected chart "'+t.get("title")+'" will be irreversibly deleted.',buttons:{Cancel:function(){u.app.modal.hide()},Delete:function(){u.app.modal.hide(),u.app.charts.remove(e),u.app.jobs.cleanup(t)}}})})}})}}),this.portlet.append(this.table.$el),this.app.options.config.widget||this.$el.append(this.portlet.$el),this.$el.append(r.wrap("")),this.$el.append(this.viewport_view.$el);var u=this;this.app.charts.on("add",function(e){u._addChart(e)}),this.app.charts.on("remove",function(e){u._removeChart(e)}),this.app.charts.on("change",function(e){u._changeChart(e)})},show:function(){this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_addChart:function(e){var t=e.get("title");t==""&&(t="Untitled"),this.table.add(t);var n=this.app.types.get(e.get("type"));this.table.add(n.title),this.table.add("Last change: "+e.get("date")),this.table.prepend(e.get("id")),this.table.value(e.get("id"))},_removeChart:function(e){this.table.remove(e.id),this.app.charts.save(),this.table.size()==0?(this.app.go("chart_view"),this.app.chart.reset()):this.table.value(this.app.charts.last().id)},_changeChart:function(e){e.get("type")&&(this._addChart(e),this.table.value(e.id))},_showChartView:function(e){var t=this,n=this.app.charts.get(e);this._wait(n,function(){t.app.go("chart_view"),t.app.chart.copy(n)})},_wait:function(e,t){if(e.ready())t();else{var n=this;this.app.modal.show({title:"Please wait!",body:'The selected chart "'+e.get("title")+'" is currently being processed. Please wait...',buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),setTimeout(function(){n._wait(e,t)},n.app.config.get("query_timeout"))}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"ok",state_info:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},ready:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show()})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/chart",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault);var o=this;this.table=new t.View({header:!1,onconfirm:function(e){o.chart.groups.length>0?o.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o.table.value(e)}}}):o.table.value(e)},onchange:function(e){o.chart.groups.reset(),o.chart.settings.clear(),o.chart.set({type:e})},ondblclick:function(e){o.tabs.show("settings")},content:"No chart types available"});var a=0,f=i.types.attributes;for(var l in f){var c=f[l];this.table.add(++a+"."),c.execute?this.table.add(c.title+" (requires processing)"):this.table.add(c.title),this.table.append(l)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)},operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("charts_view"),o._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("charts_view")}})}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){o.app.config.set("title",o.title.value())}});var h=$("<div/>");h.append(r.wrap((new n.Label({title:"Provide a chart title:"})).$el)),h.append(r.wrap(this.title.$el)),h.append(r.wrap((new n.Label({title:"Select a chart type:"})).$el)),h.append(r.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:h}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.setElement(this.tabs.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o.title.value(e.get("title")),o.app.config.set("title",e.get("title"))}),this.chart.on("change:type",function(e){o.table.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.charts.on("add",function(e){o.tabs.showOperation("back")}),this.app.charts.on("remove",function(e){o.app.charts.length==0&&o.tabs.hideOperation("back")}),this.app.charts.on("reset",function(e){o.tabs.hideOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey()},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this.app.charts.get(this.chart.id);e?e.copy(this.chart):(e=this.chart.clone(),e.copy(this.chart),this.app.charts.add(e)),e.trigger("redraw",e),this.app.charts.save()}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500,title:"Create a new chart"}})}),define("plugin/models/charts",["plugin/models/chart","plugin/models/group"],function(e,t){return Backbone.Collection.extend({model:e,vis:null,initialize:function(e,t){this.app=t,this.id=this.app.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.app.options.config.dataset_id,charts:[]}}),this.id&&(this.vis.id=this.id);var n=this.app.options.config.charts;n&&(this.vis.get("config").charts=n)},save:function(){this.vis.get("config").charts=[];var e=this;this.each(function(t){var n={attributes:t.attributes,settings:t.settings.attributes,groups:[]};t.groups.each(function(e){n.groups.push(e.attributes)}),e.vis.get("config").charts.push(n)});var e=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n),alert("Error loading data:\n"+e.responseText)}).then(function(t){t&&t.id&&(e.id=t.id)})},load:function(){var n=this.vis.get("config").charts;for(var r in n){var i=n[r],s=new e;s.set(i.attributes),s.settings.set(i.settings);for(var o in i.groups)s.groups.add(new t(i.groups[o]));s.state("ok","Loaded previously saved visualization."),this.add(s),s.trigger("redraw",s)}}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_tick:{init:".3"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/views/charts","plugin/views/chart","plugin/models/config","plugin/models/chart","plugin/models/charts","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(n){this.options=n,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new a,this.jobs=new i(this),this.types=new c,this.chart=new f,this.charts=new l(null,this),this.datasets=new s(this),this.charts_view=new o(this),this.chart_view=new u(this),this.options.config.widget?this.portlet=$("<div></div>"):this.portlet=new t.View({icon:"fa-bar-chart-o"}),this.portlet.append(this.charts_view.$el),this.portlet.append(this.chart_view.$el),this.options.config.widget?this.setElement(this.portlet):this.setElement(this.portlet.$el);var r=this;this.config.on("change:title",function(){r._refreshTitle()}),this.render(),this.charts.load(),this.charts.length==0?this.go("chart_view"):this.go("charts_view")},go:function(e){switch(e){case"chart_view":this.chart_view.show(),this.charts_view.hide();break;case"charts_view":this.chart_view.hide(),this.charts_view.show()}},render:function(){this._refreshTitle()},_refreshTitle:function(){var e=this.config.get("title");e&&(e=" - "+e),this.portlet.title("Charts"+e)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
--- a/config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
+++ b/config/plugins/visualizations/charts/static/charts/_nvd3/nvd3.js
@@ -65,7 +65,7 @@
nv.utils.windowResize(nvd3_model.update);
// set chart state
- chart.set('state', 'ok');
+ chart.state('ok', 'Chart has been drawn.');
});
});
}
diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/static/library/jobs.js
--- a/config/plugins/visualizations/charts/static/library/jobs.js
+++ b/config/plugins/visualizations/charts/static/library/jobs.js
@@ -13,6 +13,20 @@
this.options = Utils.merge(options, this.optionsDefault);
},
+ // clean
+ cleanup: function(chart) {
+ // cleanup previous dataset file
+ var previous = chart.get('dataset_id_job');
+ if (previous) {
+ var self = this;
+ Utils.request('PUT', config.root + 'api/histories/none/contents/' + previous, { deleted: true }, function() {
+ // update galaxy history
+ self._refreshHdas();
+ });
+ }
+
+ },
+
// create job
submit: function(chart, settings_string, columns_string, callback) {
// link this
@@ -39,11 +53,8 @@
}
}
- // cleanup previous dataset file
- var previous = chart.get('dataset_id_job');
- if (previous) {
- Utils.request('PUT', config.root + 'api/histories/' + chart.get('history_id') + '/contents/' + previous, { deleted: true });
- }
+ // cleanup
+ self.cleanup(chart);
// set chart state
chart.state('submit', 'Sending job request...');
@@ -56,9 +67,7 @@
chart.state('failed', 'Job submission failed. No response.');
} else {
// update galaxy history
- if (Galaxy && Galaxy.currHistoryPanel) {
- Galaxy.currHistoryPanel.refreshHdas();
- }
+ self._refreshHdas();
// get dataset
var job = response.outputs[0];
@@ -105,6 +114,14 @@
setTimeout(function() { self._loop(id, callback); }, self.app.config.get('query_timeout'));
}
});
+ },
+
+ // refresh history panel
+ _refreshHdas: function() {
+ // update galaxy history
+ if (Galaxy && Galaxy.currHistoryPanel) {
+ Galaxy.currHistoryPanel.refreshHdas();
+ }
}
});
diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/static/models/charts.js
--- a/config/plugins/visualizations/charts/static/models/charts.js
+++ b/config/plugins/visualizations/charts/static/models/charts.js
@@ -1,30 +1,113 @@
// dependencies
-define(['plugin/models/chart'], function(Chart) {
+define(['plugin/models/chart', 'plugin/models/group'], function(Chart, Group) {
// collection
return Backbone.Collection.extend(
{
- model: Chart,
+ // nested chart model contains collections
+ model : Chart,
- // save charts
- save: function() {
+ // viz model
+ vis: null,
+
+ // initialize
+ initialize: function(options, app) {
+ // initialize parameters
+ this.app = app;
+ this.id = this.app.options.id;
+
// create visualization
- var vis = new Visualization({
- type : 'charts',
+ this.vis = new Visualization({
+ type : 'charts',
config : {
- charts : []
+ dataset_id : this.app.options.config.dataset_id,
+ charts : []
}
});
- // copy attributes
- //vis.set(this.attributes);
+ // add visualization id
+ if (this.id) {
+ this.vis.id = this.id;
+ }
+
+ // add charts
+ var charts_array = this.app.options.config.charts;
+ if (charts_array) {
+ this.vis.get('config').charts = charts_array;
+ }
+ },
+
+ // pack and save nested chart models
+ save: function() {
+ // reset
+ this.vis.get('config').charts = [];
+
+ // pack nested chart models into arrays attributes
+ var self = this;
+ this.each(function(chart) {
+ // create chart dictionary
+ var chart_dict = {
+ attributes : chart.attributes,
+ settings : chart.settings.attributes,
+ groups : []
+ };
+
+ // append groups
+ chart.groups.each(function(group) {
+ chart_dict.groups.push(group.attributes);
+ });
+
+ // add chart to charts array
+ self.vis.get('config').charts.push(chart_dict);
+ });
// save visualization
- vis.save()
- .fail( function( xhr, status, message ){
- console.error( xhr, status, message );
- alert( 'Error loading data:\n' + xhr.responseText );
+ var self = this;
+ this.vis.save()
+ .fail(function(xhr, status, message) {
+ console.error(xhr, status, message);
+ alert( 'Error loading data:\n' + xhr.responseText );
+ })
+ .then(function(response) {
+ if (response && response.id) {
+ self.id = response.id;
+ }
});
+ },
+
+ // load nested models/collections from packed dictionary
+ load: function() {
+ // get charts array
+ var charts_array = this.vis.get('config').charts;
+
+ // unpack chart models
+ for (var i in charts_array) {
+ // get chart details
+ var chart_dict = charts_array[i];
+
+ // construct chart model
+ var chart = new Chart();
+
+ // main
+ chart.set(chart_dict.attributes);
+
+ // get settings
+ chart.settings.set(chart_dict.settings);
+
+ // get groups
+ for (var j in chart_dict.groups) {
+ chart.groups.add(new Group(chart_dict.groups[j]));
+ }
+
+ // reset status
+ chart.state('ok', 'Loaded previously saved visualization.');
+
+ // add to collection
+ this.add(chart);
+
+ // trigger
+ chart.trigger('redraw', chart);
+ }
}
});
diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/static/views/charts.js
--- a/config/plugins/visualizations/charts/static/views/charts.js
+++ b/config/plugins/visualizations/charts/static/views/charts.js
@@ -78,20 +78,25 @@
// title
var chart = self.app.charts.get(chart_id);
- // show modal
- self.app.modal.show({
- title : 'Are you sure?',
- body : 'The selected chart "' + chart.get('title') + '" will be irreversibly deleted.',
- buttons : {
- 'Cancel' : function() {self.app.modal.hide();},
- 'Delete' : function() {
- // hide modal
- self.app.modal.hide();
-
- // remove chart
- self.app.charts.remove(chart_id);
+ // make sure that chart is ready
+ self._wait (chart, function() {
+ self.app.modal.show({
+ title : 'Are you sure?',
+ body : 'The selected chart "' + chart.get('title') + '" will be irreversibly deleted.',
+ buttons : {
+ 'Cancel' : function() {self.app.modal.hide();},
+ 'Delete' : function() {
+ // hide modal
+ self.app.modal.hide();
+
+ // remove chart
+ self.app.charts.remove(chart_id);
+
+ // cleanup
+ self.app.jobs.cleanup(chart);
+ }
}
- }
+ });
});
}
}),
@@ -185,14 +190,19 @@
// show chart editor
_showChartView: function(chart_id) {
+ var self = this;
+ var chart = this.app.charts.get(chart_id);
+ this._wait (chart, function() {
+ self.app.go('chart_view');
+ self.app.chart.copy(chart);
+ });
+ },
+
+ // wait for chart to be ready
+ _wait: function(chart, callback) {
// get chart
- var chart = this.app.charts.get(chart_id);
if (chart.ready()) {
- // show chart view
- this.app.go('chart_view');
-
- // load chart into view
- this.app.chart.copy(chart);
+ callback();
} else {
// show modal
var self = this;
@@ -206,7 +216,7 @@
self.app.modal.hide();
// retry
- self._showChartView(chart_id);
+ setTimeout(function() { self._wait(chart, callback); }, self.app.config.get('query_timeout'));
}
}
});
diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -43,17 +43,7 @@
// redraw
this.app.charts.on('redraw', function(chart) {
- // redraw if chart is not currently processed
- if (chart.ready()) {
- self._refreshChart(chart);
- } else {
- // redraw once current drawing process has finished
- chart.on('change:state', function() {
- if (chart.ready()) {
- self._refreshChart(chart);
- }
- });
- }
+ self._drawChart(chart);
});
},
@@ -69,7 +59,7 @@
var item = this.list[chart_id];
if (item) {
// get chart
- var chart = self.app.charts.get(chart_id);
+ var chart = this.app.charts.get(chart_id);
// update portlet
this.portlet.title(chart.get('title'));
@@ -100,13 +90,13 @@
},
// add
- _refreshChart: function(chart) {
+ _drawChart: function(chart) {
// link this
var self = this;
// check
if (!chart.ready()) {
- self.app.log('viewport:_refreshChart()', 'Invalid attempt to refresh chart before completion.');
+ self.app.log('viewport:_drawChart()', 'Invalid attempt to draw chart before completion.');
return;
}
@@ -126,7 +116,7 @@
this.portlet.append($chart_el);
// find svg element
- var svg = d3.select(id + ' svg');
+ var svg = d3.select($chart_el.find('svg')[0]);
// add chart to list
this.list[chart_id] = {
@@ -134,9 +124,6 @@
$el : $chart_el
}
- // show chart from list
- this.showChart(chart_id);
-
// clear all previous handlers (including redraw listeners)
chart.off('change:state');
@@ -172,7 +159,7 @@
// set chart state
chart.state('wait', 'Please wait...');
-
+
// identify chart type
var chart_type = chart.get('type');
var chart_settings = this.app.types.get(chart_type);
diff -r dec159841d670560582aadc1327bec0673f7003a -r e7dfb71eeb796d0cf560ffa48445d243aeb37a67 config/plugins/visualizations/charts/templates/charts.mako
--- a/config/plugins/visualizations/charts/templates/charts.mako
+++ b/config/plugins/visualizations/charts/templates/charts.mako
@@ -71,9 +71,10 @@
require(['plugin/app'], function(App) {
// load options
var options = {
+ id : ${h.to_json_string( visualization_id )} || undefined,
config : ${h.to_json_string( config )}
}
- console.log(options);
+
// create application
app = new App(options);
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: guerler: Charts/Ui: Improvements and fixes
by commits-noreply＠bitbucket.org 21 Mar '14
by commits-noreply＠bitbucket.org 21 Mar '14
21 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/dec159841d67/
Changeset: dec159841d67
User: guerler
Date: 2014-03-21 05:05:21
Summary: Charts/Ui: Improvements and fixes
Affected #: 17 files
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/app.js
--- a/config/plugins/visualizations/charts/static/app.js
+++ b/config/plugins/visualizations/charts/static/app.js
@@ -59,8 +59,8 @@
this.setElement(this.portlet);
}
- // hide views
- this.charts_view.$el.hide();
+ // start with chart view
+ this.go('chart_view');
// events
var self = this;
@@ -72,6 +72,21 @@
this.render();
},
+ // loads a view and makes sure that all others are hidden
+ go: function(view_id) {
+ // pick view
+ switch (view_id) {
+ case 'chart_view' :
+ this.chart_view.show();
+ this.charts_view.hide();
+ break;
+ case 'charts_view' :
+ this.chart_view.hide();
+ this.charts_view.show();
+ break;
+ }
+ },
+
// render
render: function() {
this._refreshTitle();
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/build-app.js
--- a/config/plugins/visualizations/charts/static/build-app.js
+++ b/config/plugins/visualizations/charts/static/build-app.js
@@ -3,4 +3,4 @@
// (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc.
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Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}};var f=t.get("dataset_id_job");f&&e.request("PUT",config.root+"api/histories/"+t.get("history_id")+"/contents/"+f,{deleted:!0}),t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires processing by the R-kit. Please make sure that it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/library/ui-table",["utils/utils"],function(e){return Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({list:{},optionsDefault:{height:300},initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.portlet=new e.View({title:"title",height:this.options.height,overflow:"hidden",operations:{edit:new t.ButtonIcon({icon:"fa-gear",tooltip:"Customize Chart",title:"Customize"})}}),this.setElement(this.portlet.$el);var s=this;this.app.charts.on("remove",function(e){s._removeChart(e.id)}),this.app.charts.on("redraw",function(e){e.ready()?s._refreshChart(e):e.on("change:state",function(){e.ready()&&s._refreshChart(e)})})},showChart:function(e){this.show(),this.hideCharts();var t=this.list[e];if(t){var n=self.app.charts.get(e);this.portlet.title(n.get("title")),this.portlet.setOperation("edit",function(){self.app.chart.copy(n),self.app.charts_view.hide(),self.app.chart_view.$el.show()}),t.$el.show(),$(window).trigger("resize")}},hideCharts:function(){this.$el.find(".item").hide()},show:function(){$(".tooltip").hide(),this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshChart:function(e){var t=this;if(!e.ready()){t.app.log("viewport:_refreshChart()","Invalid attempt to refresh chart before completion.");return}var n=e.id;this._removeChart(n);var r="#"+n,i=$(this._template({id:r}));this.portlet.append(i);var s=d3.select(r+" svg");this.list[n]={svg:s,$el:i},this.showChart(n),e.off("change:state"),e.on("change:state",function(){var t=i.find("#info"),n=t.find("#icon");n.removeClass(),t.show(),t.find("#text").html(e.get("state_info"));var r=e.get("state");switch(r){case"ok":t.hide();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var o=e.get("type"),u=this.app.types.get(o),t=this;require(["plugin/charts/"+o+"/"+o],function(n){var r=new n(t.app,{svg:s});u.execute?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){r.draw(e,t._defaultRequestDictionary(e))}):r.draw(e,t._defaultRequestDictionary(e))})},_removeChart:function(e){var t=this.list[e];t&&(t.svg.remove(),t.$el.remove())},_template:function(e){return'<div id="'+e.id.substr(1)+'" class="item">'+'<span id="info">'+'<span id="icon" style="font-size: 1.2em; display: inline-block;"/>'+'<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>'+"</span>"+'<svg style="height: auto;"/>'+"</div>"},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/charts",["mvc/ui/ui-portlet","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(i,o){this.app=i,this.viewport_view=new s(i),this.table=new t({content:"Add charts to this table.",ondblclick:function(e){var t=u.app.charts.get(e);u.app.chart.copy(t),u.hide(),u.app.chart_view.$el.show()},onchange:function(e){var t=u.app.charts.get(e);u.app.config.set("title",t.get("title")),u.viewport_view.showChart(e)}});var u=this;this.portlet=new e.View({icon:"fa-list",title:"List of created charts:",height:100,operations:{"new":new n.ButtonIcon({icon:"fa-magic",tooltip:"Create a new Chart",title:"New",onclick:function(){u.hide(),u.app.chart.reset(),u.app.chart_view.$el.show()}}),"delete":new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this Chart",title:"Delete",onclick:function(){var e=u.table.value();if(!e)return;var t=u.app.charts.get(e);u.app.modal.show({title:"Are you sure?",body:'The selected chart "'+t.get("title")+'" will be irreversibly deleted.',buttons:{Cancel:function(){u.app.modal.hide()},Delete:function(){u.app.modal.hide(),u.app.charts.remove(e)}}})}})}}),this.portlet.append(this.table.$el),this.app.options.config.widget||this.$el.append(this.portlet.$el),this.$el.append(r.wrap("")),this.$el.append(this.viewport_view.$el);var u=this;this.app.charts.on("add",function(e){u._addChart(e)}),this.app.charts.on("remove",function(e){u._removeChart(e)}),this.app.charts.on("change",function(e){u._changeChart(e)})},hide:function(){$(".tooltip").hide(),this.$el.hide()},_addChart:function(e){var t=e.get("title");t==""&&(t="Untitled"),this.table.add(t);var n=this.app.types.get(e.get("type"));this.table.add(n.title),this.table.add("Last change: "+e.get("date")),this.table.prepend(e.get("id")),this.table.value(e.get("id"))},_removeChart:function(e){this.table.remove(e.id),this.table.size()==0?(this.hide(),this.app.chart.reset(),this.app.chart_view.$el.show()):this.table.value(this.app.charts.last().id)},_changeChart:function(e){e.get("type")&&(this._addChart(e),this.table.value(e.id))}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});var Visualization=Backbone.Model.extend(LoggableMixin).extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){this.log(this+".initialize",e,this.attributes),_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend(LoggableMixin).extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"ok",state_info:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},ready:function(){return this.get("state")=="ok"||this.get("state")=="failed"},save:function(){}})}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show()})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/chart",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault);var o=this;this.table=new t({header:!1,onconfirm:function(e){o.chart.groups.length>0?o.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be reseted.",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o.table.value(e)}}}):o.table.value(e)},onchange:function(e){o.chart.groups.reset(),o.chart.settings.clear(),o.chart.set({type:e})},ondblclick:function(e){o.tabs.show("settings")},content:"No chart types available"});var a=0,f=i.types.attributes;for(var l in f){var c=f[l];this.table.add(++a+"."),c.execute?this.table.add(c.title+" (requires processing)"):this.table.add(c.title),this.table.append(l)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)},operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.chart.groups.length==0&&o._addGroupModel(),o._saveChart(),o.hide(),o.app.charts_view.$el.show()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.hide(),o.app.charts_view.$el.show()}})}}),this.title=new 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Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},submit:function(t,n,r,i){var s=this,o=t.id,u=t.get("type"),a=this.app.types.get(u);data={tool_id:"rkit",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:u,columns:r,settings:n}};var f=t.get("dataset_id_job");f&&e.request("PUT",config.root+"api/histories/"+t.get("history_id")+"/contents/"+f,{deleted:!0}),t.state("submit","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response.");else{Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshHdas();var n=e.outputs[0];t.state("queued","Job has been queued..."),t.set("dataset_id_job",n.id),s._loop(n.id,function(e){switch(e.state){case"ok":return t.state("success","Job completed successfully..."),i(e),!0;case"error":return t.state("failed","Job has failed. Please check the history for details."),!0;case"running":return t.state("running","Job is running..."),!1}})}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the R-kit. Please make sure it is installed. "+n)})},_loop:function(t,n){var r=this;e.request("GET",config.root+"api/jobs/"+t,{},function(e){n(e)||setTimeout(function(){r._loop(t,n)},r.app.config.get("query_timeout"))})}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(t,n,r){var i=this;if(t.groups)this._fetch(t,n);else{var s=this.list[t.id];if(s){n(s);return}e.request("GET",config.root+"api/datasets/"+t.id,{},function(e){switch(e.state){case"error":r&&r(e);break;default:i.list[t.id]=e,n(e)}})}},_fetch:function(t,n){var r=t.start?t.start:0,i=Math.abs(t.end-t.start),s=this.app.config.get("query_limit");if(!i||i>s)i=s;var o="",u={},a=0;for(var f in t.groups){var l=t.groups[f];for(var c in l.columns){var h=l.columns[c];o+=h+",",u[h]=a,a++}}if(a==0){n({});return}o=o.substring(0,o.length-1);var p=t.groups.slice(0);for(var f in p)p[f].values=[];var d=this;e.request("GET",config.root+"api/datasets/"+t.id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){for(var i in e.data){var s=e.data[i];for(var o in t.groups){var a=t.groups[o],f={x:parseInt(i)+r};for(var l in a.columns){var c=a.columns[l],h=u[c],d=s[h];if(isNaN(d)||!d)d=0;f[l]=d}p[o].values.push(f)}}n(p)})}})}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null},events:{click:"_onclick",dblclick:"_ondblclick"},first:!0,initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t){var n=$("<td></td>");t&&n.css("width",t),n.append(e),this.row.append(n)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},remove:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},removeAll:function(){this.$tbody.html(""),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.remove(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="grid"><thead></thead><tbody style="cursor: pointer;"></tbody></table><tmessage>'+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({list:{},optionsDefault:{height:300},initialize:function(t,r){this.app=t,this.options=n.merge(r,this.optionsDefault),this.portlet=new e.View({title:"title",height:this.options.height,overflow:"hidden"}),this.setElement(this.portlet.$el);var i=this;this.app.charts.on("remove",function(e){i._removeChart(e.id)}),this.app.charts.on("redraw",function(e){e.ready()?i._refreshChart(e):e.on("change:state",function(){e.ready()&&i._refreshChart(e)})})},showChart:function(e){this.show(),this.hideCharts();var t=this.list[e];if(t){var n=self.app.charts.get(e);this.portlet.title(n.get("title")),t.$el.show(),$(window).trigger("resize")}},hideCharts:function(){this.$el.find(".item").hide()},show:function(){$(".tooltip").hide(),this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshChart:function(e){var t=this;if(!e.ready()){t.app.log("viewport:_refreshChart()","Invalid attempt to refresh chart before completion.");return}var n=e.id;this._removeChart(n);var r="#"+n,i=$(this._template({id:r}));this.portlet.append(i);var s=d3.select(r+" svg");this.list[n]={svg:s,$el:i},this.showChart(n),e.off("change:state"),e.on("change:state",function(){var t=i.find("#info"),n=t.find("#icon");n.removeClass(),t.show(),t.find("#text").html(e.get("state_info"));var r=e.get("state");switch(r){case"ok":t.hide();break;case"failed":n.addClass("fa fa-warning");break;default:n.addClass("fa fa-spinner fa-spin")}}),e.state("wait","Please wait...");var o=e.get("type"),u=this.app.types.get(o),t=this;require(["plugin/charts/"+o+"/"+o],function(n){var r=new n(t.app,{svg:s});u.execute?t.app.jobs.submit(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){r.draw(e,t._defaultRequestDictionary(e))}):r.draw(e,t._defaultRequestDictionary(e))})},_removeChart:function(e){var t=this.list[e];t&&(t.svg.remove(),t.$el.remove())},_template:function(e){return'<div id="'+e.id.substr(1)+'" class="item">'+'<span id="info">'+'<span id="icon" style="font-size: 1.2em; display: inline-block;"/>'+'<span id="text" style="position: relative; margin-left: 5px; top: -1px; font-size: 1.0em;"/>'+"</span>"+'<svg style="height: auto;"/>'+"</div>"},_defaultRequestString:function(e){var t=this.app.types.get(e.get("type")),n="",r=0;return e.groups.each(function(e){for(var i in t.columns)n+=i+"_"+ ++r+":"+(parseInt(e.get(i))+1)+", "}),n.substring(0,n.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t=this.app.types.get(e.get("type")),n={id:e.get("dataset_id"),groups:[]},r=0;return e.groups.each(function(e){var i={};for(var s in t.columns)i[s]=e.get(s);n.groups.push({key:++r+":"+e.get("key"),columns:i})}),n}})}),define("plugin/views/charts",["mvc/ui/ui-portlet","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/group","plugin/views/viewport"],function(e,t,n,r,i,s){return Backbone.View.extend({initialize:function(i,o){this.app=i,this.viewport_view=new s(i),this.table=new t.View({content:"Add charts to this table.",ondblclick:function(e){u._showChartView(e)},onchange:function(e){var t=u.app.charts.get(e);u.app.config.set("title",t.get("title")),u.viewport_view.showChart(e)}});var u=this;this.portlet=new e.View({icon:"fa-list",title:"List of created charts:",height:100,operations:{"new":new n.ButtonIcon({icon:"fa-magic",tooltip:"Create a new Chart",title:"New",onclick:function(){u.app.go("chart_view"),u.app.chart.reset()}}),edit:new n.ButtonIcon({icon:"fa-gear",tooltip:"Customize this Chart",title:"Customize",onclick:function(){var e=u.table.value();if(!e)return;u._showChartView(e)}}),"delete":new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this Chart",title:"Delete",onclick:function(){var e=u.table.value();if(!e)return;var t=u.app.charts.get(e);u.app.modal.show({title:"Are you sure?",body:'The selected chart "'+t.get("title")+'" will be irreversibly deleted.',buttons:{Cancel:function(){u.app.modal.hide()},Delete:function(){u.app.modal.hide(),u.app.charts.remove(e)}}})}})}}),this.portlet.append(this.table.$el),this.app.options.config.widget||this.$el.append(this.portlet.$el),this.$el.append(r.wrap("")),this.$el.append(this.viewport_view.$el);var u=this;this.app.charts.on("add",function(e){u._addChart(e)}),this.app.charts.on("remove",function(e){u._removeChart(e)}),this.app.charts.on("change",function(e){u._changeChart(e)})},show:function(){this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_addChart:function(e){var t=e.get("title");t==""&&(t="Untitled"),this.table.add(t);var n=this.app.types.get(e.get("type"));this.table.add(n.title),this.table.add("Last change: "+e.get("date")),this.table.prepend(e.get("id")),this.table.value(e.get("id"))},_removeChart:function(e){this.table.remove(e.id),this.app.charts.save(),this.table.size()==0?(this.app.go("chart_view"),this.app.chart.reset()):this.table.value(this.app.charts.last().id)},_changeChart:function(e){e.get("type")&&(this._addChart(e),this.table.value(e.id))},_showChartView:function(e){var t=this.app.charts.get(e);if(t.ready())this.app.go("chart_view"),this.app.chart.copy(t);else{var n=this;this.app.modal.show({title:"Please wait!",body:'The selected chart "'+t.get("title")+'" is currently being processed. Please wait...',buttons:{Close:function(){n.app.modal.hide()},Retry:function(){n.app.modal.hide(),n._showChartView(e)}}})}}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({visible:!1,list:{},$nav:null,$content:null,first_tab:null,optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=e.id,n={$title:$(this._template_tab(e)),$content:$(this._template_tab_content(e)),removable:e.ondel?!0:!1};this.list[t]=n,this.options.onnew?this.$nav.find("#new-tab").before(n.$title):this.$nav.append(n.$title),n.$content.append(e.$el),this.$content.append(n.$content),_.size(this.list)==1&&(n.$title.addClass("active"),n.$content.addClass("active"),this.first_tab=t);if(e.ondel){var r=this,i=n.$title.find("#delete");i.tooltip({title:"Delete this tab",placement:"bottom",container:r.$el}),i.on("click",function(){return i.tooltip("destroy"),r.$el.find(".tooltip").remove(),e.ondel(),!1})}e.onclick&&n.$title.on("click",function(){e.onclick()})},del:function(e){var t=this.list[e];t.$title.remove(),t.$content.remove(),delete t,this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list){var t=this.list[e];t.removable&&this.del(e)}},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&this.list[e].$title.find("a").tab("show")},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.list[e].$title.find("#text");return t&&n.html(t),n.html()},_template:function(e){return'<div class="tabbable tabs-left"><ul class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i style="font-size: 0.8em; margin-right: 5px;" class="fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="title-'+e.id+'">'+'<a title="" href="#tab-'+e.id+'" data-toggle="tab" data-original-title="">'+'<span id="text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" style="font-size: 0.8em; margin-left: 5px; cursor: pointer;" class="fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/models/chart",["plugin/models/groups","mvc/visualization/visualization-model"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"ok",state_info:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state_info",t),this.set("state",e)},ready:function(){return this.get("state")=="ok"||this.get("state")=="failed"}})}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({columns:[],initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(){s.group.set("key",s.group_key.value())}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.app.types.get(n);this.table.removeAll();var s={};for(var o in i.columns){var u=this.group.get(o);u||this.group.set(o,0);var a=i.columns[o],f=new t.Select.View({id:"select_"+o,gid:o,onchange:function(e){r.group.set(this.gid,e)},value:u,wait:!0});this.table.add(a.title,"25%"),this.table.add(f.$el),this.table.append(o),s[o]=f}this.app.datasets.request({id:e},function(e){r.columns=[];var t=e.metadata_column_types;for(var n in t)(t[n]=="int"||t[n]=="float")&&r.columns.push({label:"Column: "+(parseInt(n)+1)+" ["+t[n]+"]",value:n});for(var n in s)s[n].update(r.columns),s[n].show()})},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({initialize:function(r){this.table_title=new t.Label({title:r.title}),this.table=new e.View({content:r.content});var i=$("<div/>");i.append(n.wrap(this.table_title.$el)),i.append(n.wrap(this.table.$el)),this.setElement(i)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.removeAll();for(var n in e)this._add(n,e[n],t)},_add:function(e,n,r){var i=null,s=n.type;switch(s){case"text":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"select":i=new t.Select.View({data:n.data,onchange:function(){r.set(e,i.value())}});break;case"slider":i=new t.Input({placeholder:n.placeholder,onchange:function(){r.set(e,i.value())}});break;case"separator":i=$("<div/>");break;default:console.log("ui-table-form:_add","Unknown setting type ("+n.type+")");return}if(s!="separator"){r.get(e)||r.set(e,n.init),i.value(r.get(e));var o=$("<div/>");o.append(i.$el),o.append('<div class="toolParamHelp" style="font-size: 0.9em;">'+n.info+"</div>"),this.table.add('<span style="white-space: nowrap;">'+n.title+"</span>","25%"),this.table.add(o)}else this.table.add('<h6 style="white-space: nowrap;">'+n.title+":<h6/>"),this.table.add($("<div/>"));this.table.append(e)}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View({title:"Chart options:",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refreshTable()})},_refreshTable:function(){var e=this.chart.get("type");if(!e)return;var t=this.app.types.get(e);this.form.title(t.title+":"),this.form.update(t.settings,this.chart.settings)}})}),define("plugin/views/chart",["mvc/ui/ui-tabs","plugin/library/ui-table","plugin/library/ui","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings"],function(e,t,n,r,i,s,o,u){return Backbone.View.extend({optionsDefault:{header:!0,content:"No content available."},initialize:function(i,s){this.app=i,this.chart=this.app.chart,this.options=r.merge(s,this.optionsDefault);var o=this;this.table=new t.View({header:!1,onconfirm:function(e){o.chart.groups.length>0?o.app.modal.show({title:"Switching to another chart type?",body:"If you continue your settings and selections will be cleared.",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o.table.value(e)}}}):o.table.value(e)},onchange:function(e){o.chart.groups.reset(),o.chart.settings.clear(),o.chart.set({type:e})},ondblclick:function(e){o.tabs.show("settings")},content:"No chart types available"});var a=0,f=i.types.attributes;for(var l in f){var c=f[l];this.table.add(++a+"."),c.execute?this.table.add(c.title+" (requires processing)"):this.table.add(c.title),this.table.append(l)}this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)},operations:{save:new n.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o.app.go("charts_view"),o._saveChart()}}),back:new n.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Return",onclick:function(){o.app.go("charts_view")}})}}),this.title=new n.Input({placeholder:"Chart title",onchange:function(){o.app.config.set("title",o.title.value())}});var h=$("<div/>");h.append(r.wrap((new n.Label({title:"Provide a chart title:"})).$el)),h.append(r.wrap(this.title.$el)),h.append(r.wrap((new n.Label({title:"Select a chart type:"})).$el)),h.append(r.wrap(this.table.$el)),this.tabs.add({id:"main",title:"Start",$el:h}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.setElement(this.tabs.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o.title.value(e.get("title")),o.app.config.set("title",e.get("title"))}),this.chart.on("change:type",function(e){o.table.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.charts.on("add",function(e){o.tabs.showOperation("back")}),this.app.charts.on("remove",function(e){o.app.charts.length==0&&o.tabs.hideOperation("back")}),this.app.charts.on("reset",function(e){o.tabs.hideOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){$(".tooltip").hide(),this.$el.hide()},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Chart data"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e}),r=t.chart.groups.length;this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey()},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey()},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","bardiagram"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart")},_saveChart:function(){this.chart.set({type:this.table.value(),title:this.title.value(),date:r.time()}),this.chart.groups.length==0&&this._addGroupModel();var e=this.app.charts.get(this.chart.id);e?e.copy(this.chart):(e=this.chart.clone(),e.copy(this.chart),this.app.charts.add(e)),e.trigger("redraw",e),this.app.charts.save()}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:1e3,query_timeout:500,title:"Create a new chart"}})}),define("plugin/models/charts",["plugin/models/chart"],function(e){return Backbone.Collection.extend({model:e,save:function(){var e=new Visualization({type:"charts",config:{charts:[]}});e.save().fail(function(e,t,n){console.error(e,t,n),alert("Error loading data:\n"+e.responseText)})}})}),define("plugin/charts/_nvd3/config",[],function(){return{title:"",columns:{y:{title:"Values for y-axis"}},settings:{separator_label:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},x_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_tick:{title:"Y axis",type:"separator"},y_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"Y-axis",placeholder:"Axis label"},y_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"f",data:[{label:"-- Do not show values --",value:"hide"},{label:"Float",value:"f"},{label:"Exponent",value:"e"},{label:"Integer",value:"d"},{label:"Percentage",value:"p"},{label:"Rounded",value:"r"},{label:"SI-prefix",value:"s"}]},y_axis_tick:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:".1",data:[{label:"0.00001",value:".5"},{label:"0.0001",value:".4"},{label:"0.001",value:".3"},{label:"0.01",value:".2"},{label:"0.1",value:".1"},{label:"1",value:"1"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"select",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),define("plugin/charts/bardiagram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram"})}),define("plugin/charts/histogram/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Histogram",execute:!0,columns:{y:{title:"Observations"}},settings:{x_axis_label:{init:"Breaks"},y_axis_label:{init:"Density"},y_axis_tick:{init:".3"}}})}),define("plugin/charts/horizontal/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Bar diagram (horizontal)",settings:{x_axis_type:{init:"hide"}}})}),define("plugin/charts/line/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line chart"})}),define("plugin/charts/linewithfocus/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Line with focus"})}),define("plugin/charts/piechart/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Pie chart"})}),define("plugin/charts/scatterplot/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Scatter plot",columns:{x:{title:"Values for x-axis"}}})}),define("plugin/charts/stackedarea/config",["plugin/charts/_nvd3/config"],function(e){return $.extend(!0,{},e,{title:"Stacked area"})}),define("plugin/charts/types",["plugin/charts/bardiagram/config","plugin/charts/histogram/config","plugin/charts/horizontal/config","plugin/charts/line/config","plugin/charts/linewithfocus/config","plugin/charts/piechart/config","plugin/charts/scatterplot/config","plugin/charts/stackedarea/config"],function(e,t,n,r,i,s,o,u){return Backbone.Model.extend({defaults:{bardiagram:e,horizontal:n,histogram:t,line:r,linewithfocus:i,piechart:s,scatterplot:o,stackedarea:u}})}),define("plugin/app",["mvc/ui/ui-modal","mvc/ui/ui-portlet","plugin/library/ui","utils/utils","plugin/library/jobs","plugin/library/datasets","plugin/views/charts","plugin/views/chart","plugin/models/config","plugin/models/chart","plugin/models/charts","plugin/charts/types"],function(e,t,n,r,i,s,o,u,a,f,l,c){return Backbone.View.extend({initialize:function(n){this.options=n,Galaxy&&Galaxy.modal?this.modal=Galaxy.modal:this.modal=new e.View,this.config=new a,this.jobs=new i(this),this.types=new c,this.chart=new f,this.charts=new l,this.datasets=new s(this),this.charts_view=new o(this),this.chart_view=new u(this),this.options.config.widget?this.portlet=$("<div></div>"):this.portlet=new t.View({icon:"fa-bar-chart-o"}),this.portlet.append(this.charts_view.$el),this.portlet.append(this.chart_view.$el),this.options.config.widget?this.setElement(this.portlet):this.setElement(this.portlet.$el),this.go("chart_view");var r=this;this.config.on("change:title",function(){r._refreshTitle()}),this.render()},go:function(e){switch(e){case"chart_view":this.chart_view.show(),this.charts_view.hide();break;case"charts_view":this.chart_view.hide(),this.charts_view.show()}},render:function(){this._refreshTitle()},_refreshTitle:function(){var e=this.config.get("title");e&&(e=" - "+e),this.portlet.title("Charts"+e)},execute:function(e){},onunload:function(){},log:function(e,t){console.log(e+" "+t)}})});
\ No newline at end of file
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/charts/histogram/config.js
--- a/config/plugins/visualizations/charts/static/charts/histogram/config.js
+++ b/config/plugins/visualizations/charts/static/charts/histogram/config.js
@@ -17,46 +17,6 @@
},
y_axis_tick : {
init : '.3'
- },
- separator_custom : {
- title : 'Advanced',
- type : 'separator'
- },
- bin_size : {
- title : 'Bin size',
- info : 'Provide the bin size for the histogram.',
- type : 'select',
- init : 1,
- data : [
- {
- label : '0.001',
- value : '0.001'
- },
- {
- label : '0.01',
- value : '0.01'
- },
- {
- label : '0.1',
- value : '0.1'
- },
- {
- label : '1',
- value : '1'
- },
- {
- label : '10',
- value : '10'
- },
- {
- label : '100',
- value : '100'
- },
- {
- label : '1000',
- value : '1000'
- }
- ]
}
}
});
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/library/jobs.js
--- a/config/plugins/visualizations/charts/static/library/jobs.js
+++ b/config/plugins/visualizations/charts/static/library/jobs.js
@@ -92,7 +92,7 @@
if (response && response.message && response.message.data && response.message.data.input) {
message = response.message.data.input + '.';
}
- chart.state('failed', 'This visualization requires processing by the R-kit. Please make sure that it is installed. ' + message);
+ chart.state('failed', 'This visualization requires the R-kit. Please make sure it is installed. ' + message);
}
);
},
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/library/ui-table-form.js
--- a/config/plugins/visualizations/charts/static/library/ui-table-form.js
+++ b/config/plugins/visualizations/charts/static/library/ui-table-form.js
@@ -9,7 +9,7 @@
initialize: function(options) {
// ui elements
this.table_title = new Ui.Label({title: options.title});
- this.table = new Table({content: options.content});
+ this.table = new Table.View({content: options.content});
// create element
var $view = $('<div/>');
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/library/ui-table.js
--- a/config/plugins/visualizations/charts/static/library/ui-table.js
+++ b/config/plugins/visualizations/charts/static/library/ui-table.js
@@ -1,8 +1,6 @@
-// dependencies
define(['utils/utils'], function(Utils) {
-// return
-return Backbone.View.extend(
+var View = Backbone.View.extend(
{
// current row
row: null,
@@ -202,4 +200,8 @@
}
});
+return {
+ View: View
+}
+
});
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/models/chart.js
--- a/config/plugins/visualizations/charts/static/models/chart.js
+++ b/config/plugins/visualizations/charts/static/models/chart.js
@@ -58,25 +58,6 @@
ready: function() {
return (this.get('state') == 'ok') || (this.get('state') == 'failed');
- },
-
- // save charts
- save: function() {
- /*/ create visualization
- var vis = new Visualization({
- type : 'charts',
- config : this.attributes
- });
-
- // copy attributes
- //vis.set(this.attributes);
-
- // save visualization
- vis.save()
- .fail( function( xhr, status, message ){
- console.error( xhr, status, message );
- alert( 'Error loading data:\n' + xhr.responseText );
- });*/
}
});
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/models/charts.js
--- a/config/plugins/visualizations/charts/static/models/charts.js
+++ b/config/plugins/visualizations/charts/static/models/charts.js
@@ -4,7 +4,28 @@
// collection
return Backbone.Collection.extend(
{
- model: Chart
+ model: Chart,
+
+ // save charts
+ save: function() {
+ // create visualization
+ var vis = new Visualization({
+ type : 'charts',
+ config : {
+ charts : []
+ }
+ });
+
+ // copy attributes
+ //vis.set(this.attributes);
+
+ // save visualization
+ vis.save()
+ .fail( function( xhr, status, message ){
+ console.error( xhr, status, message );
+ alert( 'Error loading data:\n' + xhr.responseText );
+ });
+ }
});
});
\ No newline at end of file
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/views/chart.js
--- a/config/plugins/visualizations/charts/static/views/chart.js
+++ b/config/plugins/visualizations/charts/static/views/chart.js
@@ -29,14 +29,14 @@
// table with chart types
//
var self = this;
- this.table = new Table({
+ this.table = new Table.View({
header : false,
onconfirm : function(type) {
if (self.chart.groups.length > 0) {
// show modal
self.app.modal.show({
title : 'Switching to another chart type?',
- body : 'If you continue your settings and selections will be reseted.',
+ body : 'If you continue your settings and selections will be cleared.',
buttons : {
'Cancel' : function() {
// hide modal
@@ -99,17 +99,11 @@
tooltip : 'Draw Chart',
title : 'Draw',
onclick : function() {
- // ensure that data group is available
- if (self.chart.groups.length == 0) {
- self._addGroupModel();
- }
+ // show charts
+ self.app.go('charts_view');
// save chart
self._saveChart();
-
- // show charts
- self.hide();
- self.app.charts_view.$el.show();
}
}),
'back' : new Ui.ButtonIcon({
@@ -117,8 +111,7 @@
tooltip : 'Return to Viewer',
title : 'Return',
onclick : function() {
- self.hide();
- self.app.charts_view.$el.show();
+ self.app.go('charts_view');
}
})
}
@@ -215,6 +208,11 @@
},
// hide
+ show: function() {
+ this.$el.show();
+ },
+
+ // hide
hide: function() {
$('.tooltip').hide();
this.$el.hide();
@@ -297,6 +295,11 @@
date : Utils.time()
});
+ // ensure that data group is available
+ if (this.chart.groups.length == 0) {
+ this._addGroupModel();
+ }
+
// create/get chart
var current = this.app.charts.get(this.chart.id);
if (!current) {
@@ -307,11 +310,11 @@
current.copy(this.chart);
}
- // save
- current.save();
-
// trigger redraw
current.trigger('redraw', current);
+
+ // save
+ this.app.charts.save();
}
});
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/views/charts.js
--- a/config/plugins/visualizations/charts/static/views/charts.js
+++ b/config/plugins/visualizations/charts/static/views/charts.js
@@ -14,18 +14,11 @@
this.viewport_view = new ViewportView(app);
// table
- this.table = new Table({
+ this.table = new Table.View({
content : 'Add charts to this table.',
ondblclick : function(chart_id) {
- // get chart
- var chart = self.app.charts.get(chart_id);
- self.app.chart.copy(chart);
-
- // hide this element
- self.hide();
-
- // show chart view
- self.app.chart_view.$el.show();
+ // attempt to load chart editor
+ self._showChartView(chart_id);
},
onchange : function(chart_id) {
// get chart
@@ -47,32 +40,46 @@
height : 100,
operations : {
'new' : new Ui.ButtonIcon({
- icon : 'fa-magic',
- tooltip: 'Create a new Chart',
- title: 'New',
- onclick: function() {
- self.hide();
- self.app.chart.reset();
- self.app.chart_view.$el.show();
- }
- }),
+ icon : 'fa-magic',
+ tooltip : 'Create a new Chart',
+ title : 'New',
+ onclick : function() {
+ self.app.go('chart_view');
+ self.app.chart.reset();
+ }
+ }),
+ 'edit' : new Ui.ButtonIcon({
+ icon : 'fa-gear',
+ tooltip : 'Customize this Chart',
+ title : 'Customize',
+ onclick : function() {
+ // check if element has been selected
+ var chart_id = self.table.value();
+ if (!chart_id) {
+ return;
+ }
+
+ // attempt to load chart editor
+ self._showChartView(chart_id);
+ }
+ }),
'delete' : new Ui.ButtonIcon({
- icon : 'fa-trash-o',
- tooltip: 'Delete this Chart',
- title: 'Delete',
- onclick: function() {
+ icon : 'fa-trash-o',
+ tooltip : 'Delete this Chart',
+ title : 'Delete',
+ onclick : function() {
- // check if element has been selected
- var chart_id = self.table.value();
- if (!chart_id) {
- return;
- }
-
- // title
- var chart = self.app.charts.get(chart_id);
-
- // show modal
- self.app.modal.show({
+ // check if element has been selected
+ var chart_id = self.table.value();
+ if (!chart_id) {
+ return;
+ }
+
+ // title
+ var chart = self.app.charts.get(chart_id);
+
+ // show modal
+ self.app.modal.show({
title : 'Are you sure?',
body : 'The selected chart "' + chart.get('title') + '" will be irreversibly deleted.',
buttons : {
@@ -116,7 +123,12 @@
self._changeChart(chart);
});
},
-
+
+ // show
+ show: function() {
+ this.$el.show();
+ },
+
// hide
hide: function() {
$('.tooltip').hide();
@@ -147,11 +159,13 @@
// remove from to table
this.table.remove(chart.id);
+ // save
+ this.app.charts.save();
+
// check if table is empty
if (this.table.size() == 0) {
- this.hide();
+ this.app.go('chart_view');
this.app.chart.reset();
- this.app.chart_view.$el.show();
} else {
// select available chart
this.table.value(this.app.charts.last().id);
@@ -167,6 +181,36 @@
// select available chart
this.table.value(chart.id);
}
+ },
+
+ // show chart editor
+ _showChartView: function(chart_id) {
+ // get chart
+ var chart = this.app.charts.get(chart_id);
+ if (chart.ready()) {
+ // show chart view
+ this.app.go('chart_view');
+
+ // load chart into view
+ this.app.chart.copy(chart);
+ } else {
+ // show modal
+ var self = this;
+ this.app.modal.show({
+ title : 'Please wait!',
+ body : 'The selected chart "' + chart.get('title') + '" is currently being processed. Please wait...',
+ buttons : {
+ 'Close' : function() {self.app.modal.hide();},
+ 'Retry' : function() {
+ // hide modal
+ self.app.modal.hide();
+
+ // retry
+ self._showChartView(chart_id);
+ }
+ }
+ });
+ }
}
});
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/views/group.js
--- a/config/plugins/visualizations/charts/static/views/group.js
+++ b/config/plugins/visualizations/charts/static/views/group.js
@@ -29,7 +29,7 @@
self.group.set('key', self.group_key.value());
}
});
- this.table = new Table({content: 'No data column.'});
+ this.table = new Table.View({content: 'No data column.'});
// create element
var $view = $('<div/>');
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/static/views/viewport.js
--- a/config/plugins/visualizations/charts/static/views/viewport.js
+++ b/config/plugins/visualizations/charts/static/views/viewport.js
@@ -27,14 +27,7 @@
this.portlet = new Portlet.View({
title : 'title',
height : this.options.height,
- overflow : 'hidden',
- operations : {
- 'edit' : new Ui.ButtonIcon({
- icon : 'fa-gear',
- tooltip : 'Customize Chart',
- title : 'Customize'
- })
- }
+ overflow : 'hidden'
});
// set this element
@@ -80,15 +73,7 @@
// update portlet
this.portlet.title(chart.get('title'));
- this.portlet.setOperation('edit', function() {
- // get chart
- self.app.chart.copy(chart);
-
- // show edit
- self.app.charts_view.hide();
- self.app.chart_view.$el.show();
- });
-
+
// show selected chart
item.$el.show();
@@ -124,7 +109,7 @@
self.app.log('viewport:_refreshChart()', 'Invalid attempt to refresh chart before completion.');
return;
}
-
+
// backup chart details
var chart_id = chart.id;
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a config/plugins/visualizations/charts/templates/charts.mako
--- a/config/plugins/visualizations/charts/templates/charts.mako
+++ b/config/plugins/visualizations/charts/templates/charts.mako
@@ -15,8 +15,7 @@
'libs/require',
'libs/underscore',
'libs/backbone/backbone',
- 'libs/d3',
- 'mvc/base-mvc')}
+ 'libs/d3')}
## css
${h.css( 'base' )}
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a static/scripts/mvc/ui/ui-portlet.js
--- a/static/scripts/mvc/ui/ui-portlet.js
+++ b/static/scripts/mvc/ui/ui-portlet.js
@@ -141,31 +141,31 @@
// fill template
_template: function(options) {
- var tmpl = '<div class="toolForm">';
+ var tmpl = '<div class="toolForm portlet-view no-highlight">';
if (options.title || options.icon) {
- tmpl += '<div id="title" class="toolFormTitle" style="overflow: hidden;">' +
- '<div id="operations" style="float: right;"></div>' +
+ tmpl += '<div id="title" class="toolFormTitle portlet-title">' +
+ '<div id="operations" class="portlet-operations"/>' +
'<div style="overflow: hidden;">';
if (options.icon)
- tmpl += '<i style="padding-top: 3px; float: left; font-size: 1.2em" class="icon fa ' + options.icon + '"> </i>';
+ tmpl += '<div class="portlet-title-icon fa ' + options.icon + '"> </div>';
- tmpl += '<div id="title-text" style="padding-top: 2px; float: left;">' + options.title + '</div>';
+ tmpl += '<div id="title-text" class="portlet-title-text">' + options.title + '</div>';
tmpl += '</div>' +
'</div>';
}
- tmpl += '<div id="body" class="toolFormBody">';
+ tmpl += '<div id="body" class="toolFormBody portlet-body">';
if (options.placement == 'top') {
- tmpl += '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>';
+ tmpl += '<div id="buttons" class="portlet-buttons"/>';
}
- tmpl += '<div id="content" class="content" style="height: inherit; padding: 10px;"></div>';
+ tmpl += '<div id="content" class="portlet-content"/>';
if (options.placement == 'bottom') {
- tmpl += '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>';
+ tmpl += '<div id="buttons" class="portlet-buttons"/>';
}
tmpl += '</div>' +
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a static/scripts/packed/mvc/ui/ui-portlet.js
--- a/static/scripts/packed/mvc/ui/ui-portlet.js
+++ b/static/scripts/packed/mvc/ui/ui-portlet.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$content=this.$el.find("#content");this.$title=this.$el.find("#title-text");if(this.options.height){this.$el.find("#body").css("height",this.options.height);this.$el.find("#content").css("overflow",this.options.overflow)}this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var c=this;$.each(this.options.buttons,function(e,f){f.$el.prop("id",e);c.$buttons.append(f.$el)})}else{this.$buttons.remove()}this.$operations=$(this.el).find("#operations");if(this.options.operations){var c=this;$.each(this.options.operations,function(e,f){f.$el.prop("id",e);c.$operations.append(f.$el)})}if(this.options.body){this.append(this.options.body)}},append:function(c){this.$content.append(a.wrap(c))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast");this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},enableButton:function(c){this.$buttons.find("#"+c).prop("disabled",false)},disableButton:function(c){this.$buttons.find("#"+c).prop("disabled",true)},hideOperation:function(c){this.$operations.find("#"+c).hide()},showOperation:function(c){this.$operations.find("#"+c).show()},setOperation:function(e,d){var c=this.$operations.find("#"+e);c.off("click");c.on("click",d)},title:function(d){var c=this.$title;if(d){c.html(d)}return c.html()},_template:function(d){var c='<div class="toolForm">';if(d.title||d.icon){c+='<div id="title" class="toolFormTitle" style="overflow: hidden;"><div id="operations" style="float: right;"></div><div style="overflow: hidden;">';if(d.icon){c+='<i style="padding-top: 3px; float: left; font-size: 1.2em" class="icon fa '+d.icon+'"> </i>'}c+='<div id="title-text" style="padding-top: 2px; float: left;">'+d.title+"</div>";c+="</div></div>"}c+='<div id="body" class="toolFormBody">';if(d.placement=="top"){c+='<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'}c+='<div id="content" class="content" style="height: inherit; padding: 10px;"></div>';if(d.placement=="bottom"){c+='<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'}c+="</div></div>";return c}});return{View:b}});
\ No newline at end of file
+define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,optionsDefault:{title:"",icon:"",buttons:null,body:null,height:null,operations:null,placement:"bottom",overflow:"auto"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$content=this.$el.find("#content");this.$title=this.$el.find("#title-text");if(this.options.height){this.$el.find("#body").css("height",this.options.height);this.$el.find("#content").css("overflow",this.options.overflow)}this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var c=this;$.each(this.options.buttons,function(e,f){f.$el.prop("id",e);c.$buttons.append(f.$el)})}else{this.$buttons.remove()}this.$operations=$(this.el).find("#operations");if(this.options.operations){var c=this;$.each(this.options.operations,function(e,f){f.$el.prop("id",e);c.$operations.append(f.$el)})}if(this.options.body){this.append(this.options.body)}},append:function(c){this.$content.append(a.wrap(c))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast");this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},enableButton:function(c){this.$buttons.find("#"+c).prop("disabled",false)},disableButton:function(c){this.$buttons.find("#"+c).prop("disabled",true)},hideOperation:function(c){this.$operations.find("#"+c).hide()},showOperation:function(c){this.$operations.find("#"+c).show()},setOperation:function(e,d){var c=this.$operations.find("#"+e);c.off("click");c.on("click",d)},title:function(d){var c=this.$title;if(d){c.html(d)}return c.html()},_template:function(d){var c='<div class="toolForm portlet-view no-highlight">';if(d.title||d.icon){c+='<div id="title" class="toolFormTitle portlet-title"><div id="operations" class="portlet-operations"/><div style="overflow: hidden;">';if(d.icon){c+='<div class="portlet-title-icon fa '+d.icon+'"> </div>'}c+='<div id="title-text" class="portlet-title-text">'+d.title+"</div>";c+="</div></div>"}c+='<div id="body" class="toolFormBody portlet-body">';if(d.placement=="top"){c+='<div id="buttons" class="portlet-buttons"/>'}c+='<div id="content" class="portlet-content"/>';if(d.placement=="bottom"){c+='<div id="buttons" class="portlet-buttons"/>'}c+="</div></div>";return c}});return{View:b}});
\ No newline at end of file
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1278,6 +1278,13 @@
.upload-ftp .upload-ftp-help{margin-bottom:10px}
.upload-ftp .upload-ftp-warning{text-align:center;margin-top:20px}
.upload-settings .upload-settings-cover{position:absolute;width:100%;height:100%;top:0px;left:0px;background:#fff;opacity:0.4;cursor:no-drop}
+.no-highlight{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;}
+.portlet-view{min-width:300px}.portlet-view .portlet-title-icon{float:left;font-size:1.2em;padding-top:3px}
+.portlet-view .portlet-title{overflow:hidden}
+.portlet-view .portlet-title-text{float:left;padding-top:1px}
+.portlet-view .portlet-operations{float:right;cursor:pointer}
+.portlet-view .portlet-buttons{height:50px;padding:10px}
+.portlet-view .portlet-content{height:inherit;padding:10px}
.popover-view{max-width:700px;display:none}.popover-view .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer}
.popover-view .popover-title{padding:4px 10px}
.styled-select{position:relative;height:27px;overflow:hidden;border:1px solid #bfbfbf;-moz-border-radius:3px;border-radius:3px}.styled-select .button{position:relative;width:25px;height:100%;float:right;border-left:1px solid #bfbfbf;padding-left:9px;padding-top:4px;background:#f2f2f2}
diff -r aa1eee2bd24a4ba449449f16659701eb7481f301 -r dec159841d670560582aadc1327bec0673f7003a static/style/src/less/ui.less
--- a/static/style/src/less/ui.less
+++ b/static/style/src/less/ui.less
@@ -1,3 +1,44 @@
+.no-highlight {
+ -webkit-user-select: none; /* webkit (safari, chrome) browsers */
+ -moz-user-select: none; /* mozilla browsers */
+ -khtml-user-select: none; /* webkit (konqueror) browsers */
+ -ms-user-select: none; /* IE10+ */
+}
+
+.portlet-view {
+ min-width: 300px;
+
+ .portlet-title-icon {
+ float: left;
+ font-size: 1.2em;
+ padding-top: 3px;
+ }
+
+ .portlet-title {
+ overflow: hidden;
+ }
+
+ .portlet-title-text {
+ float: left;
+ padding-top: 1px;
+ }
+
+ .portlet-operations {
+ float: right;
+ cursor: pointer;
+ }
+
+ .portlet-buttons {
+ height: 50px;
+ padding: 10px;
+ }
+
+ .portlet-content {
+ height: inherit;
+ padding: 10px;
+ }
+}
+
.popover-view {
max-width: 700px;
display: none;
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: libraries - removal of id-encoding related bug in API commited in f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 and identified by jmchilton in https://bitbucket.org/galaxy/galaxy-central/commits/f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900#comment-825140
by commits-noreply＠bitbucket.org 21 Mar '14
by commits-noreply＠bitbucket.org 21 Mar '14
21 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/aa1eee2bd24a/
Changeset: aa1eee2bd24a
User: martenson
Date: 2014-03-21 00:26:45
Summary: libraries - removal of id-encoding related bug in API commited in f7ebd14c2f9b260cdb6627e4abfd5c03f14c4900 and identified by jmchilton in https://bitbucket.org/galaxy/galaxy-central/commits/f7ebd14c2f9b260cdb6627e…
Affected #: 2 files
diff -r 29a9d6d904f3506f141253e2b1e97cf1aa55a081 -r aa1eee2bd24a4ba449449f16659701eb7481f301 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2078,8 +2078,8 @@
# This needs to be a list
return [ ld for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.dataset.deleted ]
- def to_dict( self, view='collection' ):
- rval = super( LibraryFolder, self ).to_dict( view=view )
+ def to_dict( self, view='collection', value_mapper=None ):
+ rval = super( LibraryFolder, self ).to_dict( view=view, value_mapper=value_mapper )
info_association, inherited = self.get_info_association()
if info_association:
if inherited:
diff -r 29a9d6d904f3506f141253e2b1e97cf1aa55a081 -r aa1eee2bd24a4ba449449f16659701eb7481f301 lib/galaxy/webapps/galaxy/api/library_contents.py
--- a/lib/galaxy/webapps/galaxy/api/library_contents.py
+++ b/lib/galaxy/webapps/galaxy/api/library_contents.py
@@ -123,11 +123,18 @@
class_name, content_id = self.__decode_library_content_id( trans, id )
if class_name == 'LibraryFolder':
content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True )
+ rval = content.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id } )
+ rval[ 'id' ] = 'F' + str( rval[ 'id' ] )
+ rval[ 'parent_id' ] = 'F' + str( trans.security.encode_id( rval[ 'parent_id' ] ) )
+ rval[ 'parent_library_id' ] = trans.security.encode_id( rval[ 'parent_library_id' ] )
else:
content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessible=True )
-
- return content.to_dict( view='element', value_mapper={ 'id' : trans.security.encode_id } )
- # return self.encode_all_ids( trans, content.to_dict( view='element' ) )
+ rval = content.to_dict( view='element')
+ rval[ 'id' ] = trans.security.encode_id( rval[ 'id' ] )
+ rval[ 'ldda_id' ] = trans.security.encode_id( rval[ 'ldda_id' ] )
+ rval[ 'folder_id' ] = 'F' + str( trans.security.encode_id( rval[ 'folder_id' ] ) )
+ rval[ 'parent_library_id' ] = trans.security.encode_id( rval[ 'parent_library_id' ] )
+ return rval
@web.expose_api
def create( self, trans, library_id, payload, **kwd ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: martenson: biostar: moved icon tooltips placement to the bottom for readability
by commits-noreply＠bitbucket.org 20 Mar '14
by commits-noreply＠bitbucket.org 20 Mar '14
20 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/29a9d6d904f3/
Changeset: 29a9d6d904f3
User: martenson
Date: 2014-03-20 22:30:47
Summary: biostar: moved icon tooltips placement to the bottom for readability
Affected #: 1 file
diff -r 86ea88b98bb7b2f2eb1fad554307d3e5d055d9ce -r 29a9d6d904f3506f141253e2b1e97cf1aa55a081 templates/webapps/galaxy/tool_form.mako
--- a/templates/webapps/galaxy/tool_form.mako
+++ b/templates/webapps/galaxy/tool_form.mako
@@ -327,9 +327,9 @@
Help from Biostar
<div class="icon-btn-group"><a href="${h.url_for( controller='biostar', action='biostar_tool_tag_redirect', tool_id=tool.id )}"
- target="_blank" class="icon-btn" title="Search for this tool"><span class="fa fa-search"></span></a>
+ target="_blank" class="icon-btn" title="Search for this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-search"></span></a><a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}"
- target="_blank" class="icon-btn" title="Ask a question about this tool"><span class="fa fa-question-circle"></a>
+ target="_blank" class="icon-btn" title="Ask a question about this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-question-circle"></a></div></span>
%endif
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: dan: Refactor Biostar interaction code. Add the ability to search for previously asked questions about a tool from the tool form. Allow logging out of biostar.
by commits-noreply＠bitbucket.org 20 Mar '14
by commits-noreply＠bitbucket.org 20 Mar '14
20 Mar '14
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/86ea88b98bb7/
Changeset: 86ea88b98bb7
User: dan
Date: 2014-03-20 22:23:41
Summary: Refactor Biostar interaction code. Add the ability to search for previously asked questions about a tool from the tool form. Allow logging out of biostar.
Affected #: 5 files
diff -r f830918df15be11380a4628c9c3aad860547e092 -r 86ea88b98bb7b2f2eb1fad554307d3e5d055d9ce lib/galaxy/util/biostar.py
--- /dev/null
+++ b/lib/galaxy/util/biostar.py
@@ -0,0 +1,121 @@
+"""
+Support for integration with the Biostar application
+"""
+
+import hmac
+import urlparse
+import re
+from unicodedata import normalize
+from galaxy.web.base.controller import url_for
+
+_punct_re = re.compile(r'[\t !"#$%&\'()*\-/<=>?(a)\[\\\]^_`{|},.]+')
+
+DEFAULT_GALAXY_TAG = 'galaxy'
+
+BIOSTAR_ACTIONS = {
+ None: { 'url': lambda x: '', 'uses_payload': False },
+ 'new_post': { 'url': lambda x: 'p/new/post/', 'uses_payload': True },
+ 'show_tags': { 'url': lambda x: 't/%s/' % ( "+".join( ( x.get( 'tag_val' ) or DEFAULT_GALAXY_TAG ).split( ',' ) ) ), 'uses_payload':False },
+ 'log_out': { 'url': lambda x: 'site/logout/', 'uses_payload': False }
+}
+
+DEFAULT_BIOSTAR_COOKIE_AGE = 1
+
+def biostar_enabled( app ):
+ return bool( app.config.biostar_url )
+
+# Slugifying from Armin Ronacher (http://flask.pocoo.org/snippets/5/)
+def slugify(text, delim=u'-'):
+ """Generates an slightly worse ASCII-only slug."""
+ result = []
+ for word in _punct_re.split(text.lower()):
+ word = normalize('NFKD', word).encode('ascii', 'ignore')
+ if word:
+ result.append(word)
+ return unicode(delim.join(result))
+
+# Default values for new posts to Biostar
+DEFAULT_PAYLOAD = {
+ 'title': '',
+ 'tag_val': DEFAULT_GALAXY_TAG,
+ 'content': '',
+}
+
+def get_biostar_url( app, payload=None, biostar_action=None ):
+ # Ensure biostar integration is enabled
+ if not biostar_enabled( app ):
+ raise Exception( "Biostar integration is not enabled" )
+ if biostar_action not in BIOSTAR_ACTIONS:
+ raise Exception( "Invalid action specified (%s)." % ( biostar_action ) )
+ biostar_action = BIOSTAR_ACTIONS[ biostar_action ]
+ # Start building up the payload
+ payload = payload or {}
+ payload = dict( DEFAULT_PAYLOAD, **payload )
+ #generate url, can parse payload info
+ url = str( urlparse.urljoin( app.config.biostar_url, biostar_action.get( 'url' )( payload ) ) )
+ if not biostar_action.get( 'uses_payload' ):
+ payload = {}
+ url = url_for( url, **payload )
+ return url
+
+def tag_for_tool( tool ):
+ """
+ Generate a reasonable biostar tag for a tool.
+ """
+ #Biostar can now handle tags with spaces, do we want to generate tags differently now?
+ return slugify( unicode( tool.name ), delim='-' )
+
+def populate_tag_payload( payload=None, tool=None ):
+ if payload is None:
+ payload = {}
+ tag_val = [ DEFAULT_GALAXY_TAG ]
+ if tool:
+ tag_val.append( tag_for_tool( tool ) )
+ payload[ 'tag_val' ] = ','.join( tag_val )
+ return payload
+
+def populate_tool_payload( payload=None, tool=None ):
+ payload = populate_tag_payload( payload=payload, tool=tool )
+ payload[ 'title' ] = 'Need help with "%s" tool' % ( tool.name )
+ payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id )
+ return payload
+
+def determine_cookie_domain( galaxy_hostname, biostar_hostname ):
+ if galaxy_hostname == biostar_hostname:
+ return galaxy_hostname
+
+ sub_biostar_hostname = biostar_hostname.split( '.', 1 )[-1]
+ if sub_biostar_hostname == galaxy_hostname:
+ return galaxy_hostname
+
+ sub_galaxy_hostname = galaxy_hostname.split( '.', 1 )[-1]
+ if sub_biostar_hostname == sub_galaxy_hostname:
+ return sub_galaxy_hostname
+
+ return galaxy_hostname
+
+def create_cookie( trans, key_name, key, email, age=DEFAULT_BIOSTAR_COOKIE_AGE ):
+ digest = hmac.new( key, email ).hexdigest()
+ value = "%s:%s" % (email, digest)
+ trans.set_cookie( value, name=key_name, path='/', age=age, version='1' )
+ #We need to explicitly set the domain here, in order to allow for biostar in a subdomain to work
+ galaxy_hostname = urlparse.urlsplit( url_for( '/', qualified=True ) ).hostname
+ biostar_hostname = urlparse.urlsplit( trans.app.config.biostar_url ).hostname
+ trans.response.cookies[ key_name ][ 'domain' ] = determine_cookie_domain( galaxy_hostname, biostar_hostname )
+
+def delete_cookie( trans, key_name ):
+ #Set expiration of Cookie to time in past, to cause browser to delete
+ if key_name in trans.request.cookies:
+ create_cookie( trans, trans.app.config.biostar_key_name, '', '', age=-90 )
+
+def biostar_logged_in( trans ):
+ if biostar_enabled( trans.app ):
+ if trans.app.config.biostar_key_name in trans.request.cookies:
+ return True
+ return False
+
+def biostar_logout( trans ):
+ if biostar_enabled( trans.app ):
+ delete_cookie( trans, trans.app.config.biostar_key_name )
+ return get_biostar_url( trans.app, biostar_action='log_out' )
+ return None
diff -r f830918df15be11380a4628c9c3aad860547e092 -r 86ea88b98bb7b2f2eb1fad554307d3e5d055d9ce lib/galaxy/webapps/galaxy/controllers/biostar.py
--- a/lib/galaxy/webapps/galaxy/controllers/biostar.py
+++ b/lib/galaxy/webapps/galaxy/controllers/biostar.py
@@ -1,84 +1,10 @@
"""
-Support for integration with the Biostar Q&A application
+Controller for integration with the Biostar application
"""
from galaxy.web.base.controller import BaseUIController, url_for, error, web
+from galaxy.util import biostar
-import base64
-from galaxy.util import json
-import hmac
-import urlparse
-
-# Slugifying from Armin Ronacher (http://flask.pocoo.org/snippets/5/)
-
-import re
-from unicodedata import normalize
-
-_punct_re = re.compile(r'[\t !"#$%&\'()*\-/<=>?(a)\[\\\]^_`{|},.]+')
-
-BIOSTAR_ACTIONS = {
- None: '',
- 'new': 'p/new/post/',
- 'show_tag_galaxy': 't/galaxy/'
-}
-
-
-def slugify(text, delim=u'-'):
- """Generates an slightly worse ASCII-only slug."""
- result = []
- for word in _punct_re.split(text.lower()):
- word = normalize('NFKD', word).encode('ascii', 'ignore')
- if word:
- result.append(word)
- return unicode(delim.join(result))
-
-
-# Biostar requires all keys to be present, so we start with a template
-DEFAULT_PAYLOAD = {
- 'title': '',
- 'tag_val': 'galaxy',
- 'content': '',
-}
-
-
-def encode_data( key, data ):
- """
- Encode data to send a question to Biostar
- """
- text = json.to_json_string(data)
- text = base64.urlsafe_b64encode(text)
- digest = hmac.new(key, text).hexdigest()
- return text, digest
-
-
-def tag_for_tool( tool ):
- """
- Generate a reasonable biostar tag for a tool.
- """
- return slugify( unicode( tool.name ) )
-
-def determine_cookie_domain( galaxy_hostname, biostar_hostname ):
- if galaxy_hostname == biostar_hostname:
- return galaxy_hostname
-
- sub_biostar_hostname = biostar_hostname.split( '.', 1 )[-1]
- if sub_biostar_hostname == galaxy_hostname:
- return galaxy_hostname
-
- sub_galaxy_hostname = galaxy_hostname.split( '.', 1 )[-1]
- if sub_biostar_hostname == sub_galaxy_hostname:
- return sub_galaxy_hostname
-
- return galaxy_hostname
-
-def create_cookie( trans, key_name, key, email ):
- digest = hmac.new( key, email ).hexdigest()
- value = "%s:%s" % (email, digest)
- trans.set_cookie( value, name=key_name, path='/', age=90, version='1' )
- #We need to explicitly set the domain here, in order to allow for biostar in a subdomain to work
- galaxy_hostname = urlparse.urlsplit( url_for( '/', qualified=True ) ).hostname
- biostar_hostname = urlparse.urlsplit( trans.app.config.biostar_url ).hostname
- trans.response.cookies[ key_name ][ 'domain' ] = determine_cookie_domain( galaxy_hostname, biostar_hostname )
class BiostarController( BaseUIController ):
"""
@@ -89,24 +15,35 @@
def biostar_redirect( self, trans, payload=None, biostar_action=None ):
"""
Generate a redirect to a Biostar site using external authentication to
- pass Galaxy user information and information about a specific tool.
+ pass Galaxy user information and optional information about a specific tool.
"""
- # Ensure biostar integration is enabled
- if not trans.app.config.biostar_url:
- return error( "Biostar integration is not enabled" )
- if biostar_action not in BIOSTAR_ACTIONS:
- return error( "Invalid action specified (%s)." % ( biostar_action ) )
-
- # Start building up the payload
- payload = payload or {}
- payload = dict( DEFAULT_PAYLOAD, **payload )
- # Do the best we can of providing user information for the payload
+ try:
+ url = biostar.get_biostar_url( trans.app, payload=payload, biostar_action=biostar_action )
+ except Exception, e:
+ return error( str( e ) )
+ # Only create/log in biostar user if is registered Galaxy user
if trans.user:
- email = trans.user.email
- else:
- email = "anon-%s" % ( trans.security.encode_id( trans.galaxy_session.id ) )
- create_cookie( trans, trans.app.config.biostar_key_name, trans.app.config.biostar_key, email )
- return trans.response.send_redirect( url_for( urlparse.urljoin( trans.app.config.biostar_url, BIOSTAR_ACTIONS[ biostar_action ] ), **payload ) )
+ biostar.create_cookie( trans, trans.app.config.biostar_key_name, trans.app.config.biostar_key, trans.user.email )
+ return trans.response.send_redirect( url )
+
+ @web.expose
+ def biostar_tool_tag_redirect( self, trans, tool_id=None ):
+ """
+ Generate a redirect to a Biostar site using tag for tool.
+ """
+ # tool_id is required
+ if tool_id is None:
+ return error( "No tool_id provided" )
+ # Load the tool
+ tool_version_select_field, tools, tool = \
+ self.app.toolbox.get_tool_components( tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True )
+ # No matching tool, unlikely
+ if not tool:
+ return error( "No tool found matching '%s'" % tool_id )
+ # Tool specific information for payload
+ payload = biostar.populate_tag_payload( tool=tool )
+ # Pass on to standard redirect method
+ return self.biostar_redirect( trans, payload=payload, biostar_action='show_tags' )
@web.expose
def biostar_question_redirect( self, trans, payload=None ):
@@ -114,8 +51,8 @@
Generate a redirect to a Biostar site using external authentication to
pass Galaxy user information and information about a specific tool.
"""
- payload = payload or {}
- return self.biostar_redirect( trans, payload=payload, biostar_action='new' )
+ # Pass on to standard redirect method
+ return self.biostar_redirect( trans, payload=payload, biostar_action='new_post' )
@web.expose
def biostar_tool_question_redirect( self, trans, tool_id=None ):
@@ -133,8 +70,19 @@
if not tool:
return error( "No tool found matching '%s'" % tool_id )
# Tool specific information for payload
- payload = { 'title':'Need help with "%s" tool' % ( tool.name ),
- 'content': '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id ),
- 'tag_val': ','.join( [ 'galaxy', tag_for_tool( tool ) ] ) }
+ payload = biostar.populate_tool_payload( tool=tool )
# Pass on to regular question method
return self.biostar_question_redirect( trans, payload )
+
+ @web.expose
+ def biostar_logout( self, trans ):
+ """
+ Log out of biostar
+ """
+ try:
+ url = biostar.biostar_log_out( trans )
+ except Exception, e:
+ return error( str( e ) )
+ if url:
+ return trans.response.send_redirect( url )
+ return error( "Could not determine Biostar logout URL." )
diff -r f830918df15be11380a4628c9c3aad860547e092 -r 86ea88b98bb7b2f2eb1fad554307d3e5d055d9ce lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -30,7 +30,7 @@
from galaxy.web.form_builder import build_select_field
from galaxy.web.framework.helpers import time_ago, grids
from datetime import datetime, timedelta
-from galaxy.util import hash_util
+from galaxy.util import hash_util, biostar
log = logging.getLogger( __name__ )
@@ -600,6 +600,11 @@
trans.handle_user_logout( logout_all=logout_all )
message = 'You have been logged out.<br>You can log in again, <a target="_top" href="%s">go back to the page you were visiting</a> or <a target="_top" href="%s">go to the home page</a>.' % \
( trans.request.referer, url_for( '/' ) )
+ if biostar.biostar_logged_in( trans ):
+ biostar_url = biostar.biostar_logout( trans )
+ if biostar_url:
+ #TODO: It would be better if we automatically logged this user out of biostar
+ message += '<br>To logout of Biostar, please click <a href="%s" target="_blank">here</a>.' % ( biostar_url )
return trans.fill_template( '/user/logout.mako',
refresh_frames=refresh_frames,
message=message,
diff -r f830918df15be11380a4628c9c3aad860547e092 -r 86ea88b98bb7b2f2eb1fad554307d3e5d055d9ce templates/webapps/galaxy/galaxy.masthead.mako
--- a/templates/webapps/galaxy/galaxy.masthead.mako
+++ b/templates/webapps/galaxy/galaxy.masthead.mako
@@ -40,7 +40,7 @@
'enable_cloud_launch' : app.config.get_bool('enable_cloud_launch', False),
'lims_doc_url' : app.config.get("lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts"),
'biostar_url' : app.config.biostar_url,
- 'biostar_url_redirect' : h.url_for( controller='biostar', action='biostar_redirect', biostar_action='show_tag_galaxy', qualified=True ),
+ 'biostar_url_redirect' : h.url_for( controller='biostar', action='biostar_redirect', biostar_action='show_tags', qualified=True ),
'support_url' : app.config.get("support_url", "http://wiki.galaxyproject.org/Support"),
'search_url' : app.config.get("search_url", "http://galaxyproject.org/search/usegalaxy/"),
'mailing_lists' : app.config.get("mailing_lists", "http://wiki.galaxyproject.org/MailingLists"),
diff -r f830918df15be11380a4628c9c3aad860547e092 -r 86ea88b98bb7b2f2eb1fad554307d3e5d055d9ce templates/webapps/galaxy/tool_form.mako
--- a/templates/webapps/galaxy/tool_form.mako
+++ b/templates/webapps/galaxy/tool_form.mako
@@ -324,8 +324,13 @@
%if trans.app.config.biostar_url:
## BioStar links
<span class="pull-right">
- <span class="fa fa-question-circle"> </span><a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}"
- target="_blank">Ask a question about this tool</a> <span class="fa fa-external-link"></span>
+ Help from Biostar
+ <div class="icon-btn-group">
+ <a href="${h.url_for( controller='biostar', action='biostar_tool_tag_redirect', tool_id=tool.id )}"
+ target="_blank" class="icon-btn" title="Search for this tool"><span class="fa fa-search"></span></a>
+ <a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}"
+ target="_blank" class="icon-btn" title="Ask a question about this tool"><span class="fa fa-question-circle"></a>
+ </div></span>
%endif
</div>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5996738d71ac/
Changeset: 5996738d71ac
User: jmchilton
Date: 2014-03-20 22:12:52
Summary: Drop unit incorrect unit tests added in 410a13e and 01933aa.
Workflow run template was causing these methods to be called wrong (and has been for a LONG time), this in turn caused me to misunderstand what the spec for how other_values in tool parameters should operate when writing the tests.
The real underlying bug should be fixed with 55cf8bb.
Affected #: 1 file
diff -r 1285d07792b31e6c1ce9d66f559afc3f49a054a8 -r 5996738d71ace34df5bee3452b8f2cdeda3e230f test/unit/tools/test_select_parameters.py
--- a/test/unit/tools/test_select_parameters.py
+++ b/test/unit/tools/test_select_parameters.py
@@ -35,19 +35,6 @@
# Data ref currently must be same level, if not at top level.
assert not self.param.need_late_validation( self.trans, { "reference_source": { "my_name": "42", "input_bam": model.HistoryDatasetAssociation() } } )
- # Following test will fail due to bug in Galaxy.
- def test_nested_context_validation_needed_in_repeat( self ):
- self.type = "data_column"
- self.set_ref_text = True
- self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
- assert not self.param.need_late_validation( self.trans, { "series": [ { "my_name": "42", "input_bam": model.HistoryDatasetAssociation() } ] } )
-
- def test_nested_context_validation_not_needed_in_repeat( self ):
- self.type = "data_column"
- self.set_ref_text = True
- self.options_xml = '''<options><filter type="data_meta" ref="input_bam" key="dbkey"/></options>'''
- assert self.param.need_late_validation( self.trans, { "series": [ { "my_name": "42", "input_bam": basic.RuntimeValue() } ] } )
-
def test_filter_param_value( self ):
self.options_xml = '''<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="0" /></options>'''
assert ("testname1", "testpath1", False) in self.param.get_options( self.trans, { "input_bam": "testname1" } )
@@ -61,11 +48,6 @@
assert ("testname2", "testpath2", False) in self.param.get_options( self.trans, { "input_bam": "testpath2" } )
assert len( self.param.get_options( self.trans, { "input_bam": "testpath3" } ) ) == 0
- def test_filter_nested( self ):
- # Test filtering a parameter inside a conditional (not currently supported.)
- self.options_xml = '''<options from_data_table="test_table"><filter type="param_value" ref="input_bam" column="1" /></options>'''
- assert ("testname1", "testpath1", False) in self.param.get_options( self.trans, {"condtional1" : { "input_bam": "testpath1", "my_name": 42 } } )
-
# TODO: Good deal of overlap here with DataToolParameterTestCase,
# refactor.
def setUp( self ):
https://bitbucket.org/galaxy/galaxy-central/commits/f830918df15b/
Changeset: f830918df15b
User: jmchilton
Date: 2014-03-20 22:15:20
Summary: Drop functional test for jobs that fails randomly.
Affected #: 1 file
diff -r 5996738d71ace34df5bee3452b8f2cdeda3e230f -r f830918df15be11380a4628c9c3aad860547e092 test/functional/api/test_jobs.py
--- a/test/functional/api/test_jobs.py
+++ b/test/functional/api/test_jobs.py
@@ -84,28 +84,6 @@
self.__assert_one_search_result( search_payload )
- def test_search_param( self ):
- history_id, dataset_id = self.__history_with_ok_dataset()
-
- inputs = json.dumps(
- dict(
- input=dict(
- src='hda',
- id=dataset_id,
- ),
- num_lines=1,
- )
- )
- search_payload = dict(
- tool_id="random_lines1",
- inputs=inputs,
- state="ok",
- )
-
- self.__run_randomlines_tool( 1, history_id, dataset_id )
- self._wait_for_history( history_id, assert_ok=True )
- self.__assert_one_search_result( search_payload )
-
def __assert_one_search_result( self, search_payload ):
search_response = self._post( "jobs/search", data=search_payload )
self._assert_status_code_is( search_response, 200 )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/55cf8bb06007/
Changeset: 55cf8bb06007
User: jmchilton
Date: 2014-03-18 17:33:05
Summary: Bring workflow parameter context inline with tool.
When tool parameters are passed other_values when rendering tool forms - other_values is the context of other tools at their position in the tree, when rendering workflows other_values is the global state of the tool. The result is different handling of say parameter value filtering for tools and workflows. This changeset switches workflows/run.mako to use the same recursive calculation of context/other_values as tool_form.mako uses.
Affected #: 1 file
diff -r 0a9263af45ec678bea82a6d128f49cf5372d370d -r 55cf8bb0600772d4508cd725677725611e4d78d0 templates/webapps/galaxy/workflow/run.mako
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -313,9 +313,10 @@
%><%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None, already_used = None )">
- %if other_values is None:
- <% other_values = values %>
- %endif
+ <%
+ from galaxy.util.expressions import ExpressionContext
+ other_values = ExpressionContext( values, other_values )
+ %>
%for input_index, input in enumerate( inputs.itervalues() ):
%if input.type == "repeat":
<div class="repeat-group">
https://bitbucket.org/galaxy/galaxy-central/commits/1285d07792b3/
Changeset: 1285d07792b3
User: jmchilton
Date: 2014-03-20 22:05:49
Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #349)
Bring workflow parameter context calculation in line with that of tools.
Affected #: 1 file
diff -r 7f7b154608e3e1c54d921d1e23277379f54293d9 -r 1285d07792b31e6c1ce9d66f559afc3f49a054a8 templates/webapps/galaxy/workflow/run.mako
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -313,9 +313,10 @@
%><%def name="do_inputs( inputs, values, errors, prefix, step, other_values = None, already_used = None )">
- %if other_values is None:
- <% other_values = values %>
- %endif
+ <%
+ from galaxy.util.expressions import ExpressionContext
+ other_values = ExpressionContext( values, other_values )
+ %>
%for input_index, input in enumerate( inputs.itervalues() ):
%if input.type == "repeat":
<div class="repeat-group">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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