diff --git a/ui/nG6/res/js/tx_nG6_pi5.js b/ui/nG6/res/js/tx_nG6_pi5.js
index 3080a2a512bb8c9aa69257055e1509ba047bfe82..d323a83ff42ea6f983271d8f14a07a584bea60e9 100644
--- a/ui/nG6/res/js/tx_nG6_pi5.js
+++ b/ui/nG6/res/js/tx_nG6_pi5.js
@@ -1,555 +1,480 @@
-/***************************************************************
-* Copyright notice
-*
-* (c) 2009 PF bioinformatique de Toulouse <>
-* All rights reserved
-*
-* This script is part of the TYPO3 project. The TYPO3 project is
-* free software; you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation; either version 2 of the License, or
-* (at your option) any later version.
-*
-* The GNU General Public License can be found at
-* http://www.gnu.org/copyleft/gpl.html.
-*
-* This script is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* This copyright notice MUST APPEAR in all copies of the script!
-***************************************************************/
-/**
- * Plugin 'nG6' for the 'nG6' extension.
- *
- * @author PF bioinformatique de Toulouse <>
- */
-
-$.validator.setDefaults({
- highlight: function (element, errorClass, validClass) {
- var $element;
- if ( element.type === "radio" ) {
- $element = this.findByName(element.name);
- } else {
- $element = $(element);
- }
- // add the bootstrap error class
- $element.parents("div.form-group").addClass("has-error");
- if ($element.parent("div.input-append").find(".btn").length > 0) {
- $element.parent("div.input-append").find(".btn").addClass("btn-danger");
- $element.parent("div.input-append").find(".glyphicon-wrench").addClass("icon-white");
- }
- },
- unhighlight: function (element, errorClass, validClass) {
- var $element;
- if (element.type === 'radio') {
- $element = this.findByName(element.name);
- } else {
- $element = $(element);
- }
- $element.removeClass(errorClass).addClass(validClass);
- // remove the bootstrap error class
- if ($element.parents("div.form-group").find("." + errorClass).length == 0) {
- // Only remove the class if there are no other errors
- $element.parents("div.form-group").removeClass(errorClass).addClass(validClass);
- }
- if ($element.parent("div.input-append").find(".btn").length > 0) {
- $element.parent("div.input-append").find(".btn").removeClass("btn-danger");
- $element.parent("div.input-append").find(".glyphicon-wrench").removeClass("icon-white");
- }
- },
- errorPlacement: function(error, element) {}
-});
-
-$(function () {
-
- var _get_workflow_status = function(workflow_id, callback, error_callback){
- $.ajax({
- url : $("#server_url").val() + '/get_workflow_status?display=list&workflow_id=' + workflow_id ,
- dataType : 'jsonp',
- timeout: 20000 ,
- success : function(data){
- if (callback){
- callback(data);
- }
- },
- error : function(jqXHR, textStatus, errorThrown){
- if (error_callback){
- error_callback(jqXHR, textStatus, errorThrown);
- }
- }
- });
- };
-
- var _retrieve_data = function(workflow_id, callback, error_callback){
- console.log("IN _retrieve_data, workflow_id=" + workflow_id);
- $.ajax({
- url : $("#server_url").val() + '/get_workflow_outputs?workflow_id=' + workflow_id,
- dataType : 'jsonp',
- success : function(data){
- if (callback) {
- callback(data);
- }
- },
- error : function(jqXHR, textStatus, errorThrown){
- if (error_callback){
- error_callback(jqXHR, textStatus, errorThrown);
- }
- }
- });
- };
-
- var _display_file_content = function(filepath, $elmt, process_data){
- $.get(filepath, function(data){
- if (process_data) {
- data = process_data(data);
- }
- $elmt.html([
- '<div class="alert">',
- ' <p>',
- ' <strong>Success !</strong> You will find bellow the list of paths for all your datas.',
- ' Use the <i class="glyphicon glyphicon-floppy-save"></i> button to copy all paths to the clipboard.<br/>',
- ' </p>',
- '</div>',
- '<div>',
- ' <button id="copy_urls" class="btn btn-default btn-sm pull-right" data-clipboard-target="url_filelist">',
- ' <i class="glyphicon glyphicon-floppy-save"></i> ',
- ' </button><br/>',
- ' <textarea readonly id="url_filelist" rows="25" style="resize:none;white-space: pre; word-wrap: normal; overflow-x: scroll; width: 100%">',
- data.trim(),
- ' </textarea>',
- '</div>'
- ].join(''));
- var client = new ZeroClipboard($("#copy_urls"));
- });
- };
-
- // urls and links
- var _retrieve_url_list = function(modal, running_wf, ufilename , process_data){
- modal.$body.html([
- '<div>',
- ' <div class="alert alert-info">',
- ' <p>',
- ' <strong>Your data</strong> are being created. Use the refresh button to get the status and retrieve them.',
- ' </p>',
- ' </div>',
- ' <div id="wfstatus">',
- ' </div>',
- '</div>'
- ].join(''));
-
- modal.$footer.html([
- ' <div class="btn-group">',
- ' <button id="refresh_workflow" class="btn btn-default"><i class="glyphicon glyphicon-refresh"></i> Get data</button>',
- ' </div>',
- ' <div class="btn-group">',
- ' <button id="close" class="btn btn-default" data-dismiss="modal"><i class="glyphicon glyphicon-remove"></i> Close</button>',
- ' </div>',
- ].join(''));
-
-
- $('#wfstatus').wfstatus({
- workflowID : running_wf.id,
- display : 'list',
- serverURL: $("#server_url").val(),
- })
-
- $("#refresh_workflow").click(function(){
- modal.$body.html("<div class='tx-nG6-wait'> <strong>Please</strong> wait...</div>");
- button = this;
- button.disabled = true;
-
- _get_workflow_status(running_wf.id ,
- // successcb
- function(statusdata){
- if (statusdata.status == "completed"){
- _retrieve_data(running_wf.id, function(data){
- $(button).hide();
- $.each(data, function(i, component) {
- $.each(component, function(filename, file) {
- if (filename == ufilename){
- _display_file_content(file.url, modal.$body, process_data);
- }
- });
- });
- },
- //errorcb
- function(jqXHR, textStatus, errorThrown){
- modal.$body.html([
- '<div class="alert alert-danger">',
- ' <p><strong>Failed !</strong> to get outputs from ' + $("#server_url").val() + ' </p>',
- '</div>',
- ].join(''));
- }
- );
- }
- else if (statusdata.status == "failed") {
- modal.$body.html([
- '<div class="alert alert-danger">',
- ' <p>The workflow has failed, either the login or password is incorrect. </p> <p>You must provide the credentials you use to connect to the GenoToul bioinformatics infrastructure.</p>',
- '</div>',
- ].join(''));
-
- }
- else {
- $('#wfstatus').wfstatus('reload');
- button.disabled = false;
- }
- },
- // errorcb
- function(){
- $('#wfstatus').wfstatus('reload');
- button.disabled = false;
- }
- );
- });
- };
-
- // List of available downloads
- var download_options = {
-
- // archive on server
- "download_archive" : {
- label : "archive",
- id : "download_archive",
- wfName : "DownloadArchive",
- run : function(form_options, modal){
- // display modal box
- modal.$modal.modal();
- modal.$modal.find('#wfform').wfform(form_options);
- modal.$modal.find('#wfform').on('run.wfform', function(event, running_wf) {
- modal.$body.html([
- '<div>',
- ' <div class="alert alert-info">',
- ' <p>',
- ' <strong>The creation</strong> of your archive is in progress. You will recieve an email with a downloadable link of your archive when the process is done.',
- ' You can either close this window, or use the refresh button to view the status. The process can <strong>take a long time</strong> depending on the size of your data.',
- ' Either way you will recieve an email with the downloadable link.',
- ' </p>',
- ' </div>',
- ' <div id="wfstatus">',
- ' </div>',
- '</div>'
- ].join(''));
-
- modal.$footer.html([
- ' <div class="btn-group">',
- ' <button id="refresh_workflow" class="btn btn-default"><i class="glyphicon glyphicon-refresh"></i> Get archive</button>',
- ' </div>',
- ' <div class="btn-group">',
- ' <button id="close" class="btn btn-default" data-dismiss="modal"><i class="glyphicon glyphicon-remove"></i> Close</button>',
- ' </div>',
- ].join(''));
-
- $('#wfstatus').wfstatus({
- workflowID : running_wf.id,
- display : 'list',
- serverURL: $("#server_url").val(),
- })
-
- $("#refresh_workflow").click(function(){
- button = this;
- button.disabled = true;
-
- _get_workflow_status(running_wf.id ,
- // successcb
- function(statusdata){
- if (statusdata.status == "completed"){
- // get outputs
- _retrieve_data(running_wf.id, function(data){
- modal.$body.html("<div class='tx-nG6-wait'>Please wait while retrieving your archive</div>");
- $.each(data, function(i, component) {
- $.each(component, function(i, file) {
- if (file.extension == '.gz'){
- modal.$modal.modal('hide');
- location.href = file.url;
- return;
- }
- });
- });
- });
- }
- else{
- $('#wfstatus').wfstatus('reload');
- button.disabled = false;
- }
- },
- // errorcb
- function(){
- $('#wfstatus').wfstatus('reload');
- button.disabled = false;
- }
- );
- });
- });
- }
- },
- // symlink
- "download_symlink" : {
- label : "symbolic link",
- id : "download_symlink",
- wfName : "DownloadSymlink",
- run : function(form_options, modal){
- // display modal box
- modal.$modal.modal();
- modal.$modal.find('#wfform').wfform(form_options);
- modal.$modal.find('#wfform').on('run.wfform', function(event, running_wf) {
- _retrieve_url_list(modal, running_wf, 'output_list.txt');
- });
- },
- },
- // urls
- "download_url" : {
- label : "url",
- id : "download_url",
- wfName : "DownloadURL",
- run : function(form_options, modal){
- form_options.parameters['url_base'] = location.href.replace(/download/, "" ) + 'fileadmin';
- // display modal box
- modal.$modal.modal();
- modal.$modal.find('#wfform').wfform(form_options);
- modal.$modal.find('#wfform').on('run.wfform', function(event, running_wf) {
- _retrieve_url_list(modal, running_wf, 'output_urls.txt', function(filedata){
- var link_prefix = location.href.replace(/download/, "" ) + 'fileadmin' ;
- var file_list = [];
- $.each(filedata.trim().split('\n'), function(i, path){
- file_list.push(link_prefix + path);
- });
- return file_list.join('\n');
- });
- });
-
- },
- }
- };
-
- // Add download options to the dropdown list
- $.each(download_options, function(id, val){
- $("#available-download-types").append($('<option id="' + val.id + '" >' + val.label + '</option>'));
- });
-
- var get_selected_ids = function (){
- var run_ids = [],
- data_ids = [],
- analysis_ids = [];
-
- $(".jstree-checked > ul > .jstree-checked, .jstree-undetermined > ul > .jstree-checked").each(function(){
- var parts = $(this).attr("id").split('_');
- if (parts[0] == 'analyse') {
- analysis_ids.push(parts[1]);
- }
- else if (parts [0] == 'data'){
- data_ids.push(parts[1]);
- }
- else if (parts[0] == 'run'){
- run_ids.push(parts[1]);
- }
- });
-
- return [run_ids, data_ids, analysis_ids];
- };
-
- var check_data_size = function(){
- var selected_ids = get_selected_ids(),
- run_ids = selected_ids[0],
- data_ids = selected_ids[1],
- analysis_ids = selected_ids[2];
-
- $.ajax({
- url: "index.php?eID=tx_nG6&type=get_data_size&run_ids=" + run_ids.join(',') + '&data_ids=' + data_ids.join(',') +'&analysis_ids=' + analysis_ids.join(',') ,
- success: function (data) {
- var sp = data.split(':::'),
- octets = sp [0],
- string_representation = sp[1];
-
- if ( parseInt(octets) > 0 ){
- $('#total_data_size').html('<small>(' + string_representation + ')</small>');
-
- if ( $("#available-download-types option:selected" ).attr('id') == 'download_archive' ){
- if (parseInt(octets) > 104857600){
- $('#warning_message').html("The total size of selected data cannot exceed 100 Mo for archive downloading").show();
- $("#download_btn").addClass("disabled");
- }
- else{
- $('#warning_message').hide();
- $("#download_btn").removeClass("disabled");
- }
- }
- else {
- $('#warning_message').fadeOut(500);
- $("#download_btn").removeClass("disabled");
- }
- }
- else {
- $("#download_btn").addClass("disabled");
- $('#total_data_size').html('');
- $('#warning_message').fadeOut(500);
- }
- }
- });
- };
-
-
- $("#download_tree").jstree({
- "themes" : {
- "theme" : "default",
- "icons" : false
- },
- "html_data" : {
- "data" : $("#html_tree").attr("value"),
- "ajax" : {
- "url" : "index.php?eID=tx_nG6",
- "data" : function (n) {
- return {
- raw_data_description : "Raw data",
- run_short_description : "Run ###SPAN_NAME### (###SPAN_DATE###)",
- run_description : "Run ###SPAN_NAME### (###SPAN_SPECIES###) - (###SPAN_DATE###) produced ###SPAN_NB_SEQ### reads",
- analyse_description : "Analyse ###SPAN_NAME###",
- user_id : $("#user_id").val(),
- object_id : n.attr("id").split("_")[1],
- type : n.attr("id").split("_")[0]
- };
- }
- }
- },
- "plugins" : [ "themes", "html_data", "ui", "checkbox" ]
- }).bind("change_state.jstree", function(event, data) {
-
- var nb_selected = 0;
- var runs_list = new Array();
- var download_list = new Array();
- $("#download_list").html("");
-
- $(".jstree-checked > ul > .jstree-checked, .jstree-undetermined > ul > .jstree-checked").each(function(){
- nb_selected += 1;
- var tmp = $(this).attr("id").split("_");
-
- if (tmp[0] == "run") {
- runs_list.push($(this).attr("id"));
- download_list[$(this).attr("id")] = $(this).attr("name") + " : <br /> Raw data + all analyses";
- } else if (tmp[0] == "analyse") {
- var tmp2 = $(this).attr("name").split("_");
- if (tmp2.length > 1) {
- var is_in = false;
- for (var i = 0; i < runs_list.length; i++){
- if (tmp2[0]+"_"+tmp2[1] == runs_list[i]) {
- is_in = true;
- }
- }
- if (!is_in) {
- if (tmp2[0]+"_"+tmp2[1] in download_list) {
- download_list[tmp2[0]+"_"+tmp2[1]] += ", " + tmp2[2];
- } else {
- download_list[tmp2[0]+"_"+tmp2[1]] = $("#"+tmp2[0]+"_"+tmp2[1]).attr("name") + " : <br /> " + tmp2[2];
- }
- }
- } else {
- download_list[$(this).attr("id")] = $(this).attr("name");
- }
- } else if (tmp[0] == "data") {
- var tmp2 = $(this).attr("name").split("_");
- var is_in = false;
- for (var i = 0; i < runs_list.length; i++){
- if (tmp2[0]+"_"+tmp2[1] == runs_list[i]) {
- is_in = true;
- }
- }
- if (!is_in) {
- if (tmp2[0]+"_"+tmp2[1] in download_list) {
- download_list[tmp2[0]+"_"+tmp2[1]] += ", " + tmp2[2];
- } else {
- download_list[tmp2[0]+"_"+tmp2[1]] = $("#"+tmp2[0]+"_"+tmp2[1]).attr("name") + " : <br /> " + tmp2[2];
- }
- }
- }
- });
- for (var key in download_list) {
- $("#download_list").append("<p class='bullet'>" + download_list[key] + "</p>");
- }
-
- if (nb_selected == 0) {
- $("#download_list").html("<p>No run neither any analyze selected. <br/>Please select below the data you want to download...</p>");
- check_data_size();
- } else {
- check_data_size();
- }
- });
-
- $('#available-download-types').change(function(){
- check_data_size();
- });
-
- $("#download_btn").click(function(){
- var selected_download_option = download_options[$("#available-download-types option:selected" ).attr('id')];
-
- $('#setAndRunModalLabel').html("Loading");
- $('#setAndRunModalFooter').html([
- ' <div class="btn-group">',
- ' <button id="close" class="btn btn-default" data-dismiss="modal"><i class="glyphicon glyphicon-remove"></i> Close</button>',
- ' </div>',
- ' <div class="btn-group">',
- ' <button id="reset_workflow" class="btn btn-default"><i class="glyphicon glyphicon-refresh"></i> Reset</button>',
- ' <button id="run_workflow" class="btn btn-primary"><i class="glyphicon glyphicon-floppy-save"></i> Start</button>',
- ' </div>'
- ].join(''));
-
- $("#reset_workflow, #run_workflow").hide();
- $("#close").show();
-
- $('#setAndRunModalBody').html([
- '<div >',
- ' <p id="wf-help" class="text-justify"></p><br/><br/>',
- ' <div id="wfform"><div class="tx-nG6-wait">Please wait</div></div>',
- '</div>',
- ].join(''));
-
- var modal = {
- '$label' : $('#setAndRunModalLabel'),
- '$body' : $('#setAndRunModalBody'),
- '$footer' : $('#setAndRunModalFooter'),
- '$modal' : $('#setAndRunModal')
- };
-
- var sel = get_selected_ids(),
- run_ids = sel[0],
- data_ids = sel[1],
- analysis_ids = sel[2];
-
- var wfform_options = {
- workflowClass: selected_download_option.wfName,
- serverURL: $("#server_url").val(),
- displayRunButton: false,
- displayResetButton: false,
- parameters : {
- "admin_login" : $("#user_login").val(),
- "run_id" : sel[0],
- "data_id" : sel[1],
- "analysis_id" : sel[2],
- }
- };
-
- $('#wfform').on("loaded.wfform", function(event, workflow) {
- $("#reset_workflow, #run_workflow").show();
- $("#close").hide();
- if(workflow){
- modal.$label.html(workflow["name"]) ;
- $('#wf-help').html(workflow["help"]);
- }
- else{
- modal.$body.html('<div class="alert alert-warning"> <strong>Warning !</strong> The selected donwload type "' + selected_download_option.label + '" is not available</div>');
- }
- });
-
- $("#reset_workflow").click(function(){
- $('#wfform').wfform('reset');
- });
- $("#run_workflow").click(function(){
- $('#wfform').wfform('run');
- });
- // remove plugin data
- $('#wfform').removeData();
- selected_download_option.run(wfform_options, modal);
- });
-
+/***************************************************************
+* Copyright notice
+*
+* (c) 2009 PF bioinformatique de Toulouse <>
+* All rights reserved
+*
+* This script is part of the TYPO3 project. The TYPO3 project is
+* free software; you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation; either version 2 of the License, or
+* (at your option) any later version.
+*
+* The GNU General Public License can be found at
+* http://www.gnu.org/copyleft/gpl.html.
+*
+* This script is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* This copyright notice MUST APPEAR in all copies of the script!
+***************************************************************/
+/**
+ * Plugin 'nG6' for the 'nG6' extension.
+ *
+ * @author PF bioinformatique de Toulouse <>
+ */
+
+$.validator.setDefaults({
+ highlight: function (element, errorClass, validClass) {
+ var $element;
+ if ( element.type === "radio" ) {
+ $element = this.findByName(element.name);
+ } else {
+ $element = $(element);
+ }
+ // add the bootstrap error class
+ $element.parents("div.form-group").addClass("has-error");
+ if ($element.parent("div.input-append").find(".btn").length > 0) {
+ $element.parent("div.input-append").find(".btn").addClass("btn-danger");
+ $element.parent("div.input-append").find(".glyphicon-wrench").addClass("icon-white");
+ }
+ },
+ unhighlight: function (element, errorClass, validClass) {
+ var $element;
+ if (element.type === 'radio') {
+ $element = this.findByName(element.name);
+ } else {
+ $element = $(element);
+ }
+ $element.removeClass(errorClass).addClass(validClass);
+ // remove the bootstrap error class
+ if ($element.parents("div.form-group").find("." + errorClass).length == 0) {
+ // Only remove the class if there are no other errors
+ $element.parents("div.form-group").removeClass(errorClass).addClass(validClass);
+ }
+ if ($element.parent("div.input-append").find(".btn").length > 0) {
+ $element.parent("div.input-append").find(".btn").removeClass("btn-danger");
+ $element.parent("div.input-append").find(".glyphicon-wrench").removeClass("icon-white");
+ }
+ },
+ errorPlacement: function(error, element) {}
+});
+
+$(function () {
+
+ var _get_workflow_status = function(workflow_id, callback, error_callback){
+ $.ajax({
+ url : $("#server_url").val() + '/get_workflow_status?display=list&workflow_id=' + workflow_id ,
+ dataType : 'jsonp',
+ timeout: 20000 ,
+ success : function(data){
+ if (callback){
+ callback(data);
+ }
+ },
+ error : function(jqXHR, textStatus, errorThrown){
+ if (error_callback){
+ error_callback(jqXHR, textStatus, errorThrown);
+ }
+ }
+ });
+ };
+
+ var _retrieve_data = function(workflow_id, callback, error_callback){
+ console.log("IN _retrieve_data, workflow_id=" + workflow_id);
+ $.ajax({
+ url : $("#server_url").val() + '/get_workflow_outputs?workflow_id=' + workflow_id,
+ dataType : 'jsonp',
+ success : function(data){
+ if (callback) {
+ callback(data);
+ }
+ },
+ error : function(jqXHR, textStatus, errorThrown){
+ if (error_callback){
+ error_callback(jqXHR, textStatus, errorThrown);
+ }
+ }
+ });
+ };
+
+ var _display_file_content = function(filepath, $elmt, process_data){
+ $.get(filepath, function(data){
+ if (process_data) {
+ data = process_data(data);
+ }
+ $elmt.html([
+ '<div class="alert">',
+ ' <p>',
+ ' <strong>Success !</strong> You will find bellow the list of paths for all your datas.',
+ ' Use the <i class="glyphicon glyphicon-floppy-save"></i> button to copy all paths to the clipboard.<br/>',
+ ' </p>',
+ '</div>',
+ '<div>',
+ ' <button id="copy_urls" class="btn btn-default btn-sm pull-right" data-clipboard-target="url_filelist">',
+ ' <i class="glyphicon glyphicon-floppy-save"></i> ',
+ ' </button><br/>',
+ ' <textarea readonly id="url_filelist" rows="25" style="resize:none;white-space: pre; word-wrap: normal; overflow-x: scroll; width: 100%">',
+ data.trim(),
+ ' </textarea>',
+ '</div>'
+ ].join(''));
+ var client = new ZeroClipboard($("#copy_urls"));
+ });
+ };
+
+ // urls and links
+ var _retrieve_url_list = function(modal, running_wf, ufilename , process_data){
+ modal.$body.html([
+ '<div>',
+ ' <div class="alert alert-info">',
+ ' <p>',
+ ' <strong>Your data</strong> are being created. Use the refresh button to get the status and retrieve them.',
+ ' </p>',
+ ' </div>',
+ ' <div id="wfstatus">',
+ ' </div>',
+ '</div>'
+ ].join(''));
+
+ modal.$footer.html([
+ ' <div class="btn-group">',
+ ' <button id="refresh_workflow" class="btn btn-default"><i class="glyphicon glyphicon-refresh"></i> Get data</button>',
+ ' </div>',
+ ' <div class="btn-group">',
+ ' <button id="close" class="btn btn-default" data-dismiss="modal"><i class="glyphicon glyphicon-remove"></i> Close</button>',
+ ' </div>',
+ ].join(''));
+
+
+ $('#wfstatus').wfstatus({
+ workflowID : running_wf.id,
+ display : 'list',
+ serverURL: $("#server_url").val(),
+ })
+
+ $("#refresh_workflow").click(function(){
+ modal.$body.html("<div class='tx-nG6-wait'> <strong>Please</strong> wait...</div>");
+ button = this;
+ button.disabled = true;
+
+ _get_workflow_status(running_wf.id ,
+ // successcb
+ function(statusdata){
+ if (statusdata.status == "completed"){
+ _retrieve_data(running_wf.id, function(data){
+ $(button).hide();
+ $.each(data, function(i, component) {
+ $.each(component, function(filename, file) {
+ if (filename == ufilename){
+ _display_file_content(file.url, modal.$body, process_data);
+ }
+ });
+ });
+ },
+ //errorcb
+ function(jqXHR, textStatus, errorThrown){
+ modal.$body.html([
+ '<div class="alert alert-danger">',
+ ' <p><strong>Failed !</strong> to get outputs from ' + $("#server_url").val() + ' </p>',
+ '</div>',
+ ].join(''));
+ }
+ );
+ }
+ else if (statusdata.status == "failed") {
+ modal.$body.html([
+ '<div class="alert alert-danger">',
+ ' <p>The workflow has failed, either the login or password is incorrect. </p> <p>You must provide the credentials you use to connect to the GenoToul bioinformatics infrastructure.</p>',
+ '</div>',
+ ].join(''));
+
+ }
+ else {
+ $('#wfstatus').wfstatus('reload');
+ button.disabled = false;
+ }
+ },
+ // errorcb
+ function(){
+ $('#wfstatus').wfstatus('reload');
+ button.disabled = false;
+ }
+ );
+ });
+ };
+
+ // List of available downloads
+ var download_options = {
+
+
+ // symlink
+ "download_symlink" : {
+ label : "symbolic link",
+ id : "download_symlink",
+ wfName : "DownloadSymlink",
+ run : function(form_options, modal){
+ // display modal box
+ modal.$modal.modal();
+ modal.$modal.find('#wfform').wfform(form_options);
+ modal.$modal.find('#wfform').on('run.wfform', function(event, running_wf) {
+ _retrieve_url_list(modal, running_wf, 'output_list.txt');
+ });
+ },
+ },
+ // urls
+ "download_url" : {
+ label : "url",
+ id : "download_url",
+ wfName : "DownloadURL",
+ run : function(form_options, modal){
+ form_options.parameters['url_base'] = location.href.replace(/download/, "" ) + 'fileadmin';
+ // display modal box
+ modal.$modal.modal();
+ modal.$modal.find('#wfform').wfform(form_options);
+ modal.$modal.find('#wfform').on('run.wfform', function(event, running_wf) {
+ _retrieve_url_list(modal, running_wf, 'output_urls.txt', function(filedata){
+ var link_prefix = location.href.replace(/download/, "" ) + 'fileadmin' ;
+ var file_list = [];
+ $.each(filedata.trim().split('\n'), function(i, path){
+ file_list.push(link_prefix + path);
+ });
+ return file_list.join('\n');
+ });
+ });
+
+ },
+ }
+ };
+
+ // Add download options to the dropdown list
+ $.each(download_options, function(id, val){
+ $("#available-download-types").append($('<option id="' + val.id + '" >' + val.label + '</option>'));
+ });
+
+ var get_selected_ids = function (){
+ var run_ids = [],
+ data_ids = [],
+ analysis_ids = [];
+
+ $(".jstree-checked > ul > .jstree-checked, .jstree-undetermined > ul > .jstree-checked").each(function(){
+ var parts = $(this).attr("id").split('_');
+ if (parts[0] == 'analyse') {
+ analysis_ids.push(parts[1]);
+ }
+ else if (parts [0] == 'data'){
+ data_ids.push(parts[1]);
+ }
+ else if (parts[0] == 'run'){
+ run_ids.push(parts[1]);
+ }
+ });
+
+ return [run_ids, data_ids, analysis_ids];
+ };
+
+ var check_data_size = function(){
+ var selected_ids = get_selected_ids(),
+ run_ids = selected_ids[0],
+ data_ids = selected_ids[1],
+ analysis_ids = selected_ids[2];
+
+ $.ajax({
+ url: "index.php?eID=tx_nG6&type=get_data_size&run_ids=" + run_ids.join(',') + '&data_ids=' + data_ids.join(',') +'&analysis_ids=' + analysis_ids.join(',') ,
+ success: function (data) {
+ var sp = data.split(':::'),
+ octets = sp [0],
+ string_representation = sp[1];
+
+ if ( parseInt(octets) > 0 ){
+ $('#total_data_size').html('<small>(' + string_representation + ')</small>');
+
+ if ( $("#available-download-types option:selected" ).attr('id') == 'download_archive' ){
+ if (parseInt(octets) > 104857600){
+ $('#warning_message').html("The total size of selected data cannot exceed 100 Mo for archive downloading").show();
+ $("#download_btn").addClass("disabled");
+ }
+ else{
+ $('#warning_message').hide();
+ $("#download_btn").removeClass("disabled");
+ }
+ }
+ else {
+ $('#warning_message').fadeOut(500);
+ $("#download_btn").removeClass("disabled");
+ }
+ }
+ else {
+ $("#download_btn").addClass("disabled");
+ $('#total_data_size').html('');
+ $('#warning_message').fadeOut(500);
+ }
+ }
+ });
+ };
+
+
+ $("#download_tree").jstree({
+ "themes" : {
+ "theme" : "default",
+ "icons" : false
+ },
+ "html_data" : {
+ "data" : $("#html_tree").attr("value"),
+ "ajax" : {
+ "url" : "index.php?eID=tx_nG6",
+ "data" : function (n) {
+ return {
+ raw_data_description : "Raw data",
+ run_short_description : "Run ###SPAN_NAME### (###SPAN_DATE###)",
+ run_description : "Run ###SPAN_NAME### (###SPAN_SPECIES###) - (###SPAN_DATE###) produced ###SPAN_NB_SEQ### reads",
+ analyse_description : "Analyse ###SPAN_NAME###",
+ user_id : $("#user_id").val(),
+ object_id : n.attr("id").split("_")[1],
+ type : n.attr("id").split("_")[0]
+ };
+ }
+ }
+ },
+ "plugins" : [ "themes", "html_data", "ui", "checkbox" ]
+ }).bind("change_state.jstree", function(event, data) {
+
+ var nb_selected = 0;
+ var runs_list = new Array();
+ var download_list = new Array();
+ $("#download_list").html("");
+
+ $(".jstree-checked > ul > .jstree-checked, .jstree-undetermined > ul > .jstree-checked").each(function(){
+ nb_selected += 1;
+ var tmp = $(this).attr("id").split("_");
+
+ if (tmp[0] == "run") {
+ runs_list.push($(this).attr("id"));
+ download_list[$(this).attr("id")] = $(this).attr("name") + " : <br /> Raw data + all analyses";
+ } else if (tmp[0] == "analyse") {
+ var tmp2 = $(this).attr("name").split("_");
+ if (tmp2.length > 1) {
+ var is_in = false;
+ for (var i = 0; i < runs_list.length; i++){
+ if (tmp2[0]+"_"+tmp2[1] == runs_list[i]) {
+ is_in = true;
+ }
+ }
+ if (!is_in) {
+ if (tmp2[0]+"_"+tmp2[1] in download_list) {
+ download_list[tmp2[0]+"_"+tmp2[1]] += ", " + tmp2[2];
+ } else {
+ download_list[tmp2[0]+"_"+tmp2[1]] = $("#"+tmp2[0]+"_"+tmp2[1]).attr("name") + " : <br /> " + tmp2[2];
+ }
+ }
+ } else {
+ download_list[$(this).attr("id")] = $(this).attr("name");
+ }
+ } else if (tmp[0] == "data") {
+ var tmp2 = $(this).attr("name").split("_");
+ var is_in = false;
+ for (var i = 0; i < runs_list.length; i++){
+ if (tmp2[0]+"_"+tmp2[1] == runs_list[i]) {
+ is_in = true;
+ }
+ }
+ if (!is_in) {
+ if (tmp2[0]+"_"+tmp2[1] in download_list) {
+ download_list[tmp2[0]+"_"+tmp2[1]] += ", " + tmp2[2];
+ } else {
+ download_list[tmp2[0]+"_"+tmp2[1]] = $("#"+tmp2[0]+"_"+tmp2[1]).attr("name") + " : <br /> " + tmp2[2];
+ }
+ }
+ }
+ });
+ for (var key in download_list) {
+ $("#download_list").append("<p class='bullet'>" + download_list[key] + "</p>");
+ }
+
+ if (nb_selected == 0) {
+ $("#download_list").html("<p>No run neither any analyze selected. <br/>Please select below the data you want to download...</p>");
+ check_data_size();
+ } else {
+ check_data_size();
+ }
+ });
+
+ $('#available-download-types').change(function(){
+ check_data_size();
+ });
+
+ $("#download_btn").click(function(){
+ var selected_download_option = download_options[$("#available-download-types option:selected" ).attr('id')];
+
+ $('#setAndRunModalLabel').html("Loading");
+ $('#setAndRunModalFooter').html([
+ ' <div class="btn-group">',
+ ' <button id="close" class="btn btn-default" data-dismiss="modal"><i class="glyphicon glyphicon-remove"></i> Close</button>',
+ ' </div>',
+ ' <div class="btn-group">',
+ ' <button id="reset_workflow" class="btn btn-default"><i class="glyphicon glyphicon-refresh"></i> Reset</button>',
+ ' <button id="run_workflow" class="btn btn-primary"><i class="glyphicon glyphicon-floppy-save"></i> Start</button>',
+ ' </div>'
+ ].join(''));
+
+ $("#reset_workflow, #run_workflow").hide();
+ $("#close").show();
+
+ $('#setAndRunModalBody').html([
+ '<div >',
+ ' <p id="wf-help" class="text-justify"></p><br/><br/>',
+ ' <div id="wfform"><div class="tx-nG6-wait">Please wait</div></div>',
+ '</div>',
+ ].join(''));
+
+ var modal = {
+ '$label' : $('#setAndRunModalLabel'),
+ '$body' : $('#setAndRunModalBody'),
+ '$footer' : $('#setAndRunModalFooter'),
+ '$modal' : $('#setAndRunModal')
+ };
+
+ var sel = get_selected_ids(),
+ run_ids = sel[0],
+ data_ids = sel[1],
+ analysis_ids = sel[2];
+
+ var wfform_options = {
+ workflowClass: selected_download_option.wfName,
+ serverURL: $("#server_url").val(),
+ displayRunButton: false,
+ displayResetButton: false,
+ parameters : {
+ "admin_login" : $("#user_login").val(),
+ "run_id" : sel[0],
+ "data_id" : sel[1],
+ "analysis_id" : sel[2],
+ }
+ };
+
+ $('#wfform').on("loaded.wfform", function(event, workflow) {
+ $("#reset_workflow, #run_workflow").show();
+ $("#close").hide();
+ if(workflow){
+ modal.$label.html(workflow["name"]) ;
+ $('#wf-help').html(workflow["help"]);
+ }
+ else{
+ modal.$body.html('<div class="alert alert-warning"> <strong>Warning !</strong> The selected donwload type "' + selected_download_option.label + '" is not available</div>');
+ }
+ });
+
+ $("#reset_workflow").click(function(){
+ $('#wfform').wfform('reset');
+ });
+ $("#run_workflow").click(function(){
+ $('#wfform').wfform('run');
+ });
+ // remove plugin data
+ $('#wfform').removeData();
+ selected_download_option.run(wfform_options, modal);
+ });
+
});
\ No newline at end of file