class.tx_nG6_eid.php 44.5 KB
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<?php
/***************************************************************
*  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!
***************************************************************/

require_once(PATH_t3lib.'class.t3lib_befunc.php');
require_once(PATH_t3lib.'stddb/tables.php');
require_once(t3lib_extMgm::extPath('cms','ext_tables.php'));
require_once(PATH_t3lib.'class.t3lib_db.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_db.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_utils.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_process.php');
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require_once(t3lib_extMgm::extPath('nG6').'/res/smarty/libs/Smarty.class.php');
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/**
 * Class 'tx_nG6_eid' for the 'nG6' extension.
 * This class is in charge of all communication between the client and the server using AJAX
 *
 * @author	PF bioinformatique de Toulouse <>
 */
class tx_nG6_eid {

    /**
     * The main function of the tx_nG6_eid, this function is the one called when using ajax
     */
    function main() {

    	// Connect to the databse
    	tslib_eidtools::connectDB();
    	$type = trim(t3lib_div::_GP('type'));
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    	$user_id = trim(t3lib_div::_GP('user_id'));
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    	// If the type of data requested is project
    	if ($type == 'project') {
    		$project_id = trim(t3lib_div::_GP('id'));
	    	// Select all runs linked to the project
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	    	$project_runs = tx_nG6_db::get_user_project_runs($user_id, $project_id, 'tx_nG6_run.date DESC');
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	    	// for each run
	    	$html_tree = '';
			foreach($project_runs as $run_id => $run_values) {
				$html_tree .= '<li class="jstree-closed" name=\''.str_replace(array('###SPAN_NAME###', '###SPAN_DATE###'), array($run_values['name'], strftime('%d-%m-%y',$run_values['date'])), trim(t3lib_div::_GP('run_short_description'))).'\' id=\''.$run_id.'\'> <a href=\'#\'>'.str_replace(array('###SPAN_NAME###', '###SPAN_DATE###', '###SPAN_NB_SEQ###', '###SPAN_SPECIES###'), array($run_values['name'], strftime('%d-%m-%y',$run_values['date']), $run_values['nb_sequences'], $run_values['species']), trim(t3lib_div::_GP('run_description'))).'</a></li>';
			}
	    	// Then all project analysis
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	    	$project_analysis = tx_nG6_db::get_user_project_analysis($user_id, $project_id, 'tx_nG6_analyze.name');
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			foreach($project_analysis as $analyse_id => $analyse_values) {  
				$html_tree .= '<li name=\''.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'\' id=\''.$analyse_id.'\'> <a href=\'#\'>'.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'</a></li>';
			}
			// Return the html_tree
	    	print $html_tree;
	    	
	    // If the type of data requested is run
    	} else if ($type == 'run'){
			$run_id = trim(t3lib_div::_GP('id'));
			// Select all analysis linked to the run and the run information
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			$run_analysis = tx_nG6_db::get_user_run_analysis($user_id, $run_id, 'tx_nG6_analyze.name');
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			$run_info = tx_nG6_db::select_run($run_id);
	    	// for each analysis
	    	$html_tree = '';
			$html_tree .= '<li name=\'run_'.$run_id.'_'.trim(t3lib_div::_GP("raw_data_description")).'\'  id=\'data_'.$run_id.'\'> <a href=\'#\'>'.trim(t3lib_div::_GP("raw_data_description")).'</a></li>';
			foreach($run_analysis as $analyse_id => $analyse_values) {   
				$html_tree .= '<li name=\'run_'.$run_id.'_'.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'\' id=\''.$analyse_id.'\'> <a href=\'#\'>'.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'</a></li>';
			}
			// Return the html_tree
			print $html_tree;
	    	
	    // If downloading data is requested
    	} else if ($type == 'download') {
    		$format = trim(t3lib_div::_GP('format'));
    		// If link in home directory
    		if ($format == 'home_link') {
				$ids = trim(t3lib_div::_GP('ids'));
				$data_folder = trim(t3lib_div::_GP('data_folder'));
				$user_login = trim(t3lib_div::_GP('user_login'));
				$user_pwd = trim(t3lib_div::_GP('user_pwd'));
				$user_directory = trim(t3lib_div::_GP('user_directory'));
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				$retcode = $this->create_symbolic_links($user_id, $user_login, $user_pwd, $ids, $data_folder, $user_directory);
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				print $retcode;
				
			// If a .tar.gz file
    		} else {
				$ids = trim(t3lib_div::_GP('ids'));
				$data_folder = trim(t3lib_div::_GP('data_folder'));
				$tmp_folder = trim(t3lib_div::_GP('tmp_folder'));
				$user_email = trim(t3lib_div::_GP('user_email'));
				$title_email = trim(t3lib_div::_GP('title_email'));
				$msg_email = trim(t3lib_div::_GP('msg_email'));
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				$archive_info = $this->create_archive_script($user_id, $ids, $data_folder, $tmp_folder, "tar.gz", $user_email, $title_email, $msg_email); 
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				$process = new Process("tcsh ".$archive_info[0]);
			    print "pid=".$process->getPid()."&archive_path=".$archive_info[1];
    		}
    		
    	// If asked to check a job status
    	} else if($type == 'check_status') {
    		$pid = trim(t3lib_div::_GP('pid'));
    		$archive_path = trim(t3lib_div::_GP('archive_path'));
    		$process = new Process();
    		$process->setPid($pid);
    		// If the job is done
    		if ($process->status()) {
    			print "pid=0&archive_path=".$archive_path;
    		// If the job is still runing
    		} else {
    			print "pid=".$process->getPid()."&archive_path=".$archive_path;
    		}
            
    	// If asked to hide a {project/run}
    	} else if ($type == 'hide') {
    		
    		$ids = trim(t3lib_div::_GP('ids'));
    		// {project/run}_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
    		$hide_level = trim(t3lib_div::_GP('hide_level'));
    		
    		if ($hide_level == 'project') {
	    		foreach($tab_ids as $id => $value) {
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		    		tx_nG6_db::hide_project($value);
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	    		}
    		} else if ($hide_level == 'run') {
	    		foreach($tab_ids as $id => $value) {
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		    		tx_nG6_db::hide_run($value, $user_id);
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	    		}
    		} else if ($hide_level == 'analysis') {
	    		foreach($tab_ids as $id => $value) {
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		    		tx_nG6_db::hide_analysis($value, $user_id);
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	    		}
    		}

        // If asked to unhide a {project/run}
    	} else if ($type == 'unhide') {
    		    		
    		$ids = trim(t3lib_div::_GP('ids'));
    		// {project/run}_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
    		$unhide_level = trim(t3lib_div::_GP('unhide_level'));

    		if ($unhide_level == 'project') {
	    		foreach($tab_ids as $id => $value) {
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		    		tx_nG6_db::unhide_project($value);
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	    		}
    		} else if ($unhide_level == 'run') {
	    		foreach($tab_ids as $id => $value) {
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		    		tx_nG6_db::unhide_run($value, true);
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	    		}
    		} else if ($unhide_level == 'analysis') {
	    		foreach($tab_ids as $id => $value) {
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		    		tx_nG6_db::unhide_analysis($value, true);
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	    		}
    		}
    		
    	// If asked to delete a {project/run/analyze}	
    	} else if ($type == 'delete') {

    		$ids = trim(t3lib_div::_GP('ids'));
    		// {project/run}_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
    		$delete_level = trim(t3lib_div::_GP('del_level'));
    		$data_folder = trim(t3lib_div::_GP('data_folder'));
			$user_login = trim(t3lib_div::_GP('user_login'));
			$user_pwd = trim(t3lib_div::_GP('user_pwd'));

    		$res = 0;
    		// check login and password
    		if (isset($user_login) && isset($user_pwd) && $user_login != 'undefined' && $user_pwd != 'undefined') {
    			$res = 0;
		    	$connection = ssh2_connect('127.0.0.1', 22);
				if (!$connection) { $res = 3; }
				if (!ssh2_auth_password($connection, $user_login, $user_pwd)) { $res=2;}
    		} else {
    			$res = 3;
    		}
			
			if ($res == 0) {
	    		if ($delete_level == 'project') {
		    		foreach($tab_ids as $id => $value) {
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			    		$res = tx_nG6_db::delete_project($value, $user_login, $user_pwd, $data_folder);
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			    		if ($res != 0) { break; }
		    		}
	    		} else if ($delete_level == 'run') {
		    		foreach($tab_ids as $id => $value) {
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			    		$res = tx_nG6_db::delete_run($value, $user_login, $user_pwd, $data_folder);
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			    		if ($res != 0) { break; }
		    		}
	    		} else if ($delete_level == 'analysis') {
		    		foreach($tab_ids as $id => $value) {
			    		$res = tx_nG6_db::delete_analysis($value, $user_login, $user_pwd, $data_folder);
			    		if ($res != 0) { break; }
		    		}
	    		}
			}
    		print $res;

        // If asked to publish a project
    	} else if ($type == 'publish') {
    		    		
    		$ids = trim(t3lib_div::_GP('ids'));
    		// project_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
    		foreach($tab_ids as $id => $value) {
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	    		tx_nG6_db::publish_project($value);
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    		}
    		
        // If asked to unpublish a project
    	} else if ($type == 'unpublish') {
    		    		
    		$ids = trim(t3lib_div::_GP('ids'));
    		// project_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
    		foreach($tab_ids as $id => $value) {
	    		tx_nG6_db::unpublish_project($value);
    		}
    		
        // If asked the size
    	} else if ($type == 'get_size') {
    		$ids = trim(t3lib_div::_GP('ids'));
    		$view = trim(t3lib_div::_GP('view'));
    		$tab_ids = explode(",",$ids);
    		$full_size = 0;
    		foreach($tab_ids as $id => $value) {
    			if ($view == "run") {
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    				$full_size += tx_nG6_db::get_run_size($value, true);
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    			} else if ($view == "project") {
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    				$full_size += tx_nG6_db::get_project_size($value, true);
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    			}
    		}
    		print tx_nG6_utils::get_octet_string_representation($full_size);
    	
    	// If update a field
    	} else if ($type == 'update_db_field') {
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    		//Retrieve infomation
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    		$table = trim(t3lib_div::_GP('table'));
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    		$id     = trim(t3lib_div::_GP('pk'));
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    		$field  = trim(t3lib_div::_GP('field'));
    		$value  = trim(t3lib_div::_GP('value'));
    	
    		//If change concernes a date
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    		if( $field == "date" || $field == "crdate" ) {
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    			//Change date format
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    			$date = explode('-', $value);
    			$timestamp = mktime (0, 0, 1, $date[1], $date[2], $date[0]);
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    			//Update the entity
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    			tx_nG6_db::update_field($table, $id, $field, $timestamp);
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    		}
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    		else {
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    			//Update the entity
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    			tx_nG6_db::update_field($table, $id, $field, $value);
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    		}
    		print $value;
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    	}
    	// add comment
    	else if ($type == 'add_comment') {	
    		$view 			= trim(t3lib_div::_GP('view'));
    		$view_id    	= trim(t3lib_div::_GP('view_id')); // project_id or run_id or analyze_id
    		$new_comment  	= trim(t3lib_div::_GP('new_comment'));
    		$cruser_id		= trim(t3lib_div::_GP('cruser_id'));
    		$res = 0 ;
    		
    		if ($new_comment){
	    			if($view == 'project'){
	    				$res = tx_nG6_db::add_project_comment($view_id, $cruser_id, $new_comment) ;
	    			}
	    			elseif ($view == 'run') {
	    				$res = tx_nG6_db::add_run_comment($view_id, $cruser_id, $new_comment) ;
	    			}
	    			elseif ($view == 'analyze') {
	    				$res = tx_nG6_db::add_analyze_comment($view_id, $cruser_id, $new_comment) ;
	    			}
    		}
    		
    		print $res;
    	}
    	//delete comment
    	else if ($type == 'delete_comment') {
    		$view 			= trim(t3lib_div::_GP('view'));
    		$view_id    	= trim(t3lib_div::_GP('view_id')); // project_id or run_id or analyze_id
    		$comment_id		= trim(t3lib_div::_GP('comment_id'));
    		$res = 0 ;
    		if($view == 'project'){
    			$res = tx_nG6_db::delete_project_comment($view_id, $comment_id);
    		}
    		elseif ($view == 'run') {
    			$res = tx_nG6_db::delete_run_comment($view_id, $comment_id);
    		}
    		elseif ($view == 'analyze') {
    			$res = tx_nG6_db::delete_analyze_comment($view_id, $comment_id);
    		}
    		print $res;
    	}
    	//update comment
    	else if ($type == 'update_comment') {
    		$comment_id		= trim(t3lib_div::_GP('comment_id'));
    		$new_comment  	= trim(t3lib_div::_GP('new_comment'));
    		$res = 0;
    		$new_comment = urldecode($new_comment);
   			$res = tx_nG6_db::update_comment($comment_id, $new_comment);
   			print $res;
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    	// If asked the krona page
    	} else if ($type == 'get_krona') {
    		
    		$data_folder = trim(t3lib_div::_GP('data_folder'));
    		$file_name = trim(t3lib_div::_GP('file_name'));
    		$sequence_name = trim(t3lib_div::_GP('sequence_name'));
    		
    		$doc = new DomDocument();
    		$data_root = $doc->createElement('data');
    		$doc->appendChild($data_root);
    		$attr_data_root = $doc->createAttribute("xml:id");
    		$data_root->appendChild($attr_data_root);
    		
    		$t_data_root = $doc->createTextNode('data_root');
    		$attr_data_root->appendChild($t_data_root);
    		$data_root->setIdAttribute("xml:id", true);
    		
    		$magnitude = $doc->createElement('magnitude');
    		$magnitude->setAttribute("attribute", "g");
    		$magnitude = $data_root->appendChild($magnitude);
    		$magnitudet = $doc->createTextNode('');
    		$magnitudet = $magnitude->appendChild($magnitudet); 
    		
    		$color = $doc->createElement('color');
    		$color = $data_root->appendChild($color);    		
    		$colort = $doc->createTextNode('');
    		$colort = $color->appendChild($colort); 
    		
    		$attributes = $doc->createElement('attributes');
    		$attributes->setAttribute("g", $sequence_name);
    		$attributes = $data_root->appendChild($attributes);  
    		$attributest = $doc->createTextNode('');
    		$attributest = $attributes->appendChild($attributest); 
    		
    		$datasets = $doc->createElement('datasets');
    		$datasets->setAttribute("names", $file_name);
    		$datasets = $data_root->appendChild($datasets); 
    		$datasetst = $doc->createTextNode('');
    		$datasetst = $datasets->appendChild($datasetst); 

			$file_path = trim(t3lib_div::_GP('file_path'));
			$file_path = $data_folder."/".$file_path;
			
			// If the file exists
			$total = 0;
			if (file_exists($file_path)) {
				$lines = file($file_path);
				// Loop through our array
				foreach ($lines as $line_num => $line) {
					if ($line != "") {
						$mparts = explode("\t", trim($line));
						if ($mparts[0] != "taxlevel" and $mparts[0] != "0") {
							// If this guy doesnt exist yet
							$id_searched = str_replace(".", "_", "node_".$mparts[1]);
							if (is_null($doc->getElementById($id_searched))) {
    	        				$parentl = implode("_", array_slice(explode(".", $mparts[1]), 0, -1));
        	        			// If no parent yet, this is the root
        	        			if (is_null($doc->getElementById("node_".$parentl))) {
        	        				$current_node = $doc->createElement('node');
        	        				$current_node->setAttribute("name", $mparts[2]);
        	        				$current_node->setAttribute("g", $mparts[4]);
        	        				$id = $doc->getElementById("data_root");
        	        				$id->appendChild($current_node);
        	        				$attr_current_node = $doc->createAttribute("xml:id");
									$current_node->appendChild($attr_current_node);	        	        				
        	        				$t_current_node = $doc->createTextNode("node_".str_replace(".", "_", $mparts[1]));
									$attr_current_node->appendChild($t_current_node);
									$current_node->setIdAttribute("xml:id", true);
						    		$current_nodet = $doc->createTextNode('');
						    		$current_nodet = $current_node->appendChild($current_nodet);
        	        			} else {
        	        				$current_node = $doc->createElement('node');
        	        				$current_node->setAttribute("name", $mparts[2]);
        	        				$current_node->setAttribute("g", $mparts[4]);
        	        				$id = $doc->getElementById("node_".$parentl);
        	        				$id->appendChild($current_node);
        	        				$attr_current_node = $doc->createAttribute("xml:id");
									$current_node->appendChild($attr_current_node);	        	        				
        	        				$t_current_node = $doc->createTextNode("node_".str_replace(".", "_", $mparts[1]));
									$attr_current_node->appendChild($t_current_node);
									$current_node->setIdAttribute("xml:id", true);
						    		$current_nodet = $doc->createTextNode('');
						    		$current_nodet = $current_node->appendChild($current_nodet); 
        	        			}
    	        			}
						}
						if ($mparts[0] == "1") {
							$total += (int)$mparts[4];
						}
					}
				}
			}    			
			
    		$color->setAttribute("attribute", "g");
    		$color->setAttribute("valueStart", "0");
    		$color->setAttribute("valueEnd", (string)$total);
    		$color->setAttribute("hueStart", "120");
    		$color->setAttribute("hueEnd", "360");
			
			$xml_string = $doc->saveXML();
			$xml_parts = explode("\n", $xml_string);
    		$val = '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">';
    		$val .= '<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="fr" lang="fr">';
    		$val .= '<head>';
    		$val .= '</head>';
    		$val .= '<body>';
    		$val .= '<div id="options" style="position:absolute;left:0;top:0"></div>';
    		$val .= '<div id="details" style="position:absolute;top:1%;right:2%;text-align:right;"></div>';
    		$val .= '<canvas id="canvas" width="100%" height="100%">This browser does not support HTML5</canvas><div>';
    		$val .= '<img id="hiddenImage" src="http://krona.sourceforge.net/img/hidden.png" visibility="hide"/>';
    		$val .= '<script name="tree" src="'.t3lib_extMgm::siteRelPath('nG6').'res/js/krona-1.1.js"></script>';
    		$val .= $xml_parts[1];
    		$val .= '</div>';
    		$val .= '</body>';
    		$val .= '</html>';
    		print $val;
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    	} else if ($type == 'delete_users') {
    		
    		$ids = trim(t3lib_div::_GP('ids'));
    		// users_id to array (1;2;3;...) -> [1;2;3;...]
    		$tab_ids = explode(";",$ids);
			$project_id = trim(t3lib_div::_GP('project_id'));
			
			// try to delete users in project ...
			if($project_id != "") {				
				$none_access = "";
				foreach($tab_ids as $id => $del_user_id) {
					tx_nG6_db::delete_access_to_project($del_user_id, $project_id);
					
					// find if user can't access to any project
					$users_access = tx_nG6_db::count_number_of_project_access($del_user_id);
					if($users_access == '0'){
						$none_access .= $del_user_id.";";
					}
				}
				
				if($none_access == ""){		// everybody has at least one access to a project
					$others_access = '0';	
				}else{						// list separate by coma of users who can't access to any project
					$others_access = substr($none_access, 0, -1);
				}
				
				print $others_access;
				
			// delete users of DB...
			}else{
				
				foreach($tab_ids as $k_id => $v_id){
					// delete group
					$gid = tx_nG6_db::get_user_usergroup($v_id);
					// delete user
					tx_nG6_db::delete_user($v_id);
					if(tx_nG6_db::count_users_in_group($gid) == 0){
						tx_nG6_db::delete_group($gid);
					}
				}
				
			}
			
		// to change users' right on project
    	} else if ($type == 'change_right') {
    		
			$project_id = trim(t3lib_div::_GP('project_id'));
			$c_user_id = trim(t3lib_div::_GP('c_user_id'));
			$right_id = trim(t3lib_div::_GP('right_id'));

			tx_nG6_db::change_access_to_project($c_user_id, $project_id, $right_id);
			
		// jquery autocomplete
    	} else if ($type == 'autocomplete') {
    		
    		$col = trim(t3lib_div::_GP('gender'));
    		$project_id = trim(t3lib_div::_GP('project_id'));
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    		$name_start = trim(t3lib_div::_GP('name_start'));
    		
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    		// user search
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    		if($col != 'title' && $col != 'location' && $col != 'organism'){
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    			$res = tx_nG6_db::get_all_names_starting_with($name_start, $col);
	    		foreach($res as $res_id => $res_val){
	    			// find right on project
	    			$res[$res_id]['right_id'] = tx_nG6_db::get_user_right_on_project($res_val['uid'], $project_id);
	    			
	    			// find creator username 
	    			$cruser_infos = tx_nG6_db::get_user_informations($res[$res_id]['cruser_id']);
	    			$res[$res_id]['cruser_username'] = $cruser_infos['username'];
	    		}
	    		
	    	// group search
    		}else{
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    			if ($col == "location" || $col == "organism") { $col = "tx_nG6_".$col; }
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    			$res = tx_nG6_db::get_all_starts_with_in_group($name_start, $col);
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    		}
    		$json_res = json_encode($res);
    		print $json_res;
    	
    	// add a new member on project
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    	} else if ($type == 'add_user') {
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    		$part 		= trim(t3lib_div::_GP('part'));
    		$user_name	= trim(t3lib_div::_GP('username'));
    		$project_id = trim(t3lib_div::_GP('project_id'));
    		$right_id	= trim(t3lib_div::_GP('right'));
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    		$group_name	= trim(t3lib_div::_GP('title'));
    		$location	= trim(t3lib_div::_GP('location'));
    		$organism	= trim(t3lib_div::_GP('organism'));
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    		$email = trim(t3lib_div::_GP('email'));
    		$first_name = trim(t3lib_div::_GP('first_name'));
    		$last_name = trim(t3lib_div::_GP('last_name'));
    		$password = trim(t3lib_div::_GP('password'));
			$cruser_id = trim(t3lib_div::_GP('creator'));
			$from_email = trim(t3lib_div::_GP('from_email'));
			$pid = trim(t3lib_div::_GP('pid'));
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			$project_url = trim(t3lib_div::_GP('project_url'));
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			$send_an_email = filter_var(trim(t3lib_div::_GP('send_an_email')), FILTER_VALIDATE_BOOLEAN);
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    		// if group not exists, create group
    		$group_id = tx_nG6_db::get_group_id($group_name);
    		if( !isset($group_id) ){
    			
    			$cruser_id = trim(t3lib_div::_GP('creator'));
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    			tx_nG6_db::create_new_group($cruser_id, $group_name, $organism, $location);
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    			$group_id = tx_nG6_db::get_group_id($group_name);
    			
    		}
    			
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    		$user = tx_nG6_db::select_user_by_username($user_name);
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    		// if user does not exists in DB
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    		if(!isset($user)){
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    			$create_user_email = trim(t3lib_div::_GP('create_user_email'));
    			$create_user_title = trim(t3lib_div::_GP('create_user_title'));
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    			$res_code = tx_nG6_db::add_user($user_name, $first_name, $last_name, $email, tx_nG6_utils::hash_password($password), $cruser_id, $group_id, $pid);
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    			if ($res_code == 0) {
	    			// find the new user id
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	    			$user = tx_nG6_db::select_user_by_username($user_name);
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	    			// authorize new access
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	    			tx_nG6_db::add_access_to_project($user["uid"], $project_id, $right_id);
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	    			if ($send_an_email) {
		    			// send an email to the new user
		    			$message = str_replace("###USER_FIRST_NAME###", $first_name, $create_user_email);
		    			$message = str_replace("###USER_LAST_NAME###", $last_name, $message);
		    			$message = str_replace("###USER_LOGIN###", $user_name, $message);
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		    			$message = str_replace("###USER_PASSWORD###", $password, $message);
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		    			$message = str_replace("###PROJECT_LINK###", $project_url, $message);
		    			$msg_table = explode('\n', $message);
		    			$message = implode("\n", $msg_table);
		    			mail($email, $create_user_title, $message, "From: <".$from_email.">");
		    		}
	    			print '2'; // ok
	    		} else if ($res_code == 1) {
	    			print '4'; // username exists
	    		} else if ($res_code == 2) {
	    			print '5'; // email exists
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	    		}
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    		// user exists in DB
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    		} else if ($user["username"] != $user_name || $user["email"] != $email || $user["first_name"] != $first_name || $user["last_name"] != $last_name) {
    			// there is difference between information provided and the user account
    			print '3';
    		} else {
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    			// can user access to the project ? 
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    			if(tx_nG6_db::get_user_right_on_project($user["uid"], $project_id) == -1){
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    				// authorize new access
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    				tx_nG6_db::add_access_to_project($user["uid"], $project_id, $right_id);
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	    			// send an email to the  user
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	    			if ($email != "" && $send_an_email) {
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		    			$add_user_email = trim(t3lib_div::_GP('add_user_email'));
		    			$add_user_title = trim(t3lib_div::_GP('add_user_title'));
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	    				$project = tx_nG6_db::select_project($project_id);
		    			$message = str_replace("###USER_FIRST_NAME###", $first_name, $add_user_email);
		    			$message = str_replace("###USER_LAST_NAME###", $last_name, $message);
		    			$message = str_replace("###PROJECT_NAME###", $project["name"], $message);
		    			$message = str_replace("###PROJECT_DESCRIPTION###", $project["description"], $message);
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		    			$message = str_replace("###PROJECT_LINK###", $project_url, $message);
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		    			$msg_table = explode('\n', $message);
		    			$message = implode("\n", $msg_table);
		    			mail($email, $add_user_title, $message, "From: <".$from_email.">");
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		    		}
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    				print '0';
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    			} else {
    				print '1';	// already access to the project
    			}
    		}
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    	}
    	
    	else if ( $type == 'add_to_ng6_admin'){
    		$userid = trim(t3lib_div::_GP('userid'));
    		tx_nG6_db::add_to_ng6_admin($userid);
    	}
    	else if ( $type == 'delete_from_ng6_admin'){
    		$userids = trim(t3lib_div::_GP('userids'));
    		$userids = explode(',', $userids);
    		tx_nG6_db::remove_from_ng6_admin($userids);
    	}
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    	else if($type == 'update_user'){
    		$email = trim(t3lib_div::_GP('email'));
    		$first_name = trim(t3lib_div::_GP('first_name'));
    		$last_name = trim(t3lib_div::_GP('last_name'));
    		$group_name	= trim(t3lib_div::_GP('title'));
    		$location	= trim(t3lib_div::_GP('location'));
    		$organism	= trim(t3lib_div::_GP('organism'));
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    		$user_id = trim(t3lib_div::_GP('id'));
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    		$password = trim(t3lib_div::_GP('password'));
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    		$cruser_id = trim(t3lib_div::_GP('creator'));
    		$send_an_email = filter_var(trim(t3lib_div::_GP('send_an_email')), FILTER_VALIDATE_BOOLEAN);
    		$from_email = trim(t3lib_div::_GP('from_email'));
    		
    		$updated = tx_nG6_db::update_user($user_id, $first_name, $last_name, $email, $group_name, $organism, $location, tx_nG6_utils::hash_password($password)) ;
    		
    		$nb_updated = count($updated);
    		
    		if ( $nb_updated > 0 && $send_an_email){
    			$user_infos = tx_nG6_db::get_user_informations($user_id);
    			$email = $user_infos['email'];
    			$first_name =  $user_infos['first_name'];
    			$last_name =  $user_infos['last_name'];
    			$mail_title = "[NG6]Your user informations have been updated.";
    			$mail_content = "Dear " . $first_name . " " . $last_name . ",\n\nSome of your personnal informations have been updated : \n\n";
    			if ($email != ''){
    				foreach($updated as $key => $value){
    					
    					if($key == 'password'){
    						$mail_content .= 'password' . "\t: " . $password . "\n" ;
    					}
    					elseif ($key == 'usergroup'){
    						$mail_content .= 'title' . "\t: " . $group_name . "\n" ;
    						$mail_content .= 'location' . "\t: " . $location . "\n" ;
    						$mail_content .= 'organism' . "\t: " . $organism . "\n" ;
    					}
    					else {
    						$mail_content .= ucwords(str_replace("_", " ", $key)) . "\t: " . $value . "\n" ;
    					}
    				}
    				$mail_content .= "\nThe NG6 team";
    				mail($email, $mail_title, $mail_content, "From: <".$from_email.">");
    			}
    		}
    		
    		print $nb_updated;
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    	}
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    	else if ($type == 'get_user_group'){
    		$id = trim(t3lib_div::_GP('id'));
    		print json_encode(tx_nG6_db::get_group_informations(tx_nG6_db::get_user_usergroup($id)));
    	}
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    	elseif($type == 'runs_table') {
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    		$smarty = new Smarty();
    		$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi1');
    		$smarty->setCompileDir(t3lib_extMgm::extPath('nG6').'/res/smarty/templates_c');
    		$smarty->setCacheDir(t3lib_extMgm::extPath('nG6').'/res/smarty/cache');
    		$smarty->setConfigDir(t3lib_extMgm::extPath('nG6').'/res/smarty/configs');
    		$smarty->security = true;
    		$smarty->security_settings['MODIFIER_FUNCS'] = array('count');
    		$project_id = intVal(trim(t3lib_div::_GP('project_id')));
    		$user_id = intVal(trim(t3lib_div::_GP('user_id')));
    		$login_user = intVal(trim(t3lib_div::_GP('login_user')));
    		$page_id = intVal(trim(t3lib_div::_GP('page_id')));
    		$project_runs = tx_nG6_db::get_project_runs($project_id);
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    		$is_project_admin = tx_nG6_db::is_administrator($user_id, 'project', $project_id);
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    		$is_at_least_admin_of_1_run = false;
    		foreach($project_runs as $run_id => $run_values) {
    			$is_admin = tx_nG6_db::is_administrator($user_id, 'run', $run_values['id']);
    			$project_runs[$run_id]['is_admin'] = $is_admin;
    			if ($is_admin) { $is_at_least_admin_of_1_run = true; }
    			$href = '<a href="index.php?id='.$page_id.'&tx_nG6_pi1[run_id]='.$run_values['id'].'&tx_nG6_pi1[project_id]='.$run_values['project_id'].'">'.$run_values['name'].'</a>';
    			$project_runs[$run_id]['href'] = $href;
    		}
    		$smarty->assign('runs', $project_runs);
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    		$smarty->assign('is_project_admin', $is_project_admin);
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    		$smarty->assign('is_at_least_admin_of_1_run', $is_at_least_admin_of_1_run);
    		$smarty->assign('login_user', $login_user);
    		print $smarty->fetch('run_table.tpl');
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    	} elseif($type == 'projects_table') {
    		$smarty = new Smarty();
    		$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi1');
    		$smarty->setCompileDir(t3lib_extMgm::extPath('nG6').'/res/smarty/templates_c');
    		$smarty->setCacheDir(t3lib_extMgm::extPath('nG6').'/res/smarty/cache');
    		$smarty->setConfigDir(t3lib_extMgm::extPath('nG6').'/res/smarty/configs');
    		$smarty->security = true;
    		$smarty->security_settings['MODIFIER_FUNCS'] = array('count');
    		$user_id = trim(t3lib_div::_GP('user_id'));
    		$login_user = intVal(trim(t3lib_div::_GP('login_user')));
    		$page_id = intVal(trim(t3lib_div::_GP('page_id')));
    		$projects = tx_nG6_db::select_all_user_projects($user_id, 'tx_nG6_project.name');
    		$is_at_least_admin_of_1_project = false;
    		foreach($projects as $project_id => $project_values) {
    			$is_admin = tx_nG6_db::is_project_administrator($user_id, $project_values['id']);
    			if ($is_admin) { $is_at_least_admin_of_1_project = true; }
    			$projects[$project_id]['is_admin'] = $is_admin;
    			$projects[$project_id]['is_manager'] = tx_nG6_db::is_project_manager($user_id, $project_values['id']);
    			$projects[$project_id]['is_member'] = tx_nG6_db::is_project_member($user_id, $project_values['id']);
    			$href = '<a href="index.php?id='.$page_id.'&tx_nG6_pi1[project_id]='.$project_values['id'].'">'.$project_values['name'].'</a>';
    			$projects[$project_id]['href'] = $href;
    		}
    		$smarty->assign('projects', $projects);
    		$smarty->assign('is_at_least_admin_of_1_project', $is_at_least_admin_of_1_project);
    		$smarty->assign('login_user', $login_user);
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    		$smarty->assign('is_ng6_admin', tx_nG6_db::is_ng6_administrator($user_id) ? true : false);
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    		print $smarty->fetch('project_table.tpl');
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    	} elseif($type == 'analyses_table') {    		
    		$smarty = new Smarty();
    		$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi1');
    		$smarty->setCompileDir(t3lib_extMgm::extPath('nG6').'/res/smarty/templates_c');
    		$smarty->setCacheDir(t3lib_extMgm::extPath('nG6').'/res/smarty/cache');
    		$smarty->setConfigDir(t3lib_extMgm::extPath('nG6').'/res/smarty/configs');
    		$smarty->security = true;
    		$smarty->security_settings['MODIFIER_FUNCS'] = array('count');
    		$user_id = trim(t3lib_div::_GP('user_id'));
    		$login_user = intVal(trim(t3lib_div::_GP('login_user')));
    		$page_id = intVal(trim(t3lib_div::_GP('page_id')));
    		$project_id = intVal(trim(t3lib_div::_GP('project_id')));
    		$run_id = intVal(trim(t3lib_div::_GP('run_id')));
    		if ($run_id != "") {
    			$analysis = tx_nG6_db::get_run_analysis($run_id);
    		} else {
    			$analysis = tx_nG6_db::get_project_analysis($project_id);
    		}
			// Add some information to the table
			foreach($analysis as $analysis_id => $analysis_values) {
				if (tx_nG6_db::is_administrator($user_id, 'analyze', $analysis_values['id'])) { $is_admin = true; }
				$analysis[$analysis_id]['is_admin'] = tx_nG6_db::is_administrator($user_id, 'analyze', $analysis_values['id']);
				if ($run_id != "") {
					$href = '<a href="index.php?id='.$page_id.'&tx_nG6_pi1[project_id]='.$project_id.'&tx_nG6_pi1[run_id]='.$run_id.'&tx_nG6_pi1[analyze_id]='.$analysis_values['id'].'">'.$analysis_values['name'].'</a>';
				} else {
					$href = '<a href="index.php?id='.$page_id.'&tx_nG6_pi1[project_id]='.$project_id.'&tx_nG6_pi1[analyze_id]='.$analysis_values['id'].'">'.$analysis_values['name'].'</a>';
				}
				$analysis[$analysis_id]['href'] = $href;
			}
			$smarty->assign('display_analysis_result', $is_admin);
			$smarty->assign('is_admin', $is_admin);
    		$smarty->assign('h_analysis', tx_nG6_utils::trace_hierarchy($analysis));
    		$smarty->assign('login_user', $login_user);
    		print $smarty->fetch('analysis_table.tpl');
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    	} elseif($type == 'install') {
    		$res = tx_nG6_db::select_user_by_username("admin_install");
    		if ($res != null){
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    			$res2 = tx_nG6_db::finalize_installation($res["uid"],
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    					trim(t3lib_div::_GP('username')),
    					trim(t3lib_div::_GP('first_name')),
    					trim(t3lib_div::_GP('last_name')),
    					trim(t3lib_div::_GP('email')),
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    					tx_nG6_utils::hash_password(trim(t3lib_div::_GP('password'))),
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    					trim(t3lib_div::_GP('pid')),
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    					"Demo project",
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    					"This project presents demonstration workflows",
    					trim(t3lib_div::_GP('title')),
    					trim(t3lib_div::_GP('organism')),
    					trim(t3lib_div::_GP('location'))
    					
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    			);
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    			// if there is a result, then log the user
    			if ($res2) {
    				$GLOBALS['TSFE'] = t3lib_div::makeInstance('tslib_fe', $GLOBALS['TYPO3_CONF_VARS'], t3lib_div::_GP('id'), '');
    				$GLOBALS['TSFE']->initFEuser();
    				$GLOBALS['TSFE']->fe_user->createUserSession(array('uid' =>$res["uid"]));
    			}
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    		}
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    		print $res;
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    	} elseif($type == 'project_data_repartition') {
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    		$role = trim(t3lib_div::_GP('role'));    		
    		$by = trim(t3lib_div::_GP('by'));
    		print json_encode(tx_nG6_db::select_projects_repartition($role, $by));
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    	} elseif($type == 'project_distribution') {
    		$values = split(",", trim(t3lib_div::_GP('values')));
    		$by = trim(t3lib_div::_GP('by'));
    		$role = trim(t3lib_div::_GP('role'));
    		print json_encode(tx_nG6_db::select_projects_distribution($values, $by, $role));
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    	} elseif($type == 'project_evolution') {
    		$values = split(",", trim(t3lib_div::_GP('values')));
    		$by = trim(t3lib_div::_GP('by'));
    		$role = trim(t3lib_div::_GP('role'));
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    	    $cumulate = false;
    		if(trim(t3lib_div::_GP('cumulate')) == '1'){
    			$cumulate = true;
    		}
    		print json_encode(tx_nG6_db::select_projects_evolution($values, $by, $role, $cumulate));
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    	} elseif($type == 'data_distribution'){
    		$values = split(",", trim(t3lib_div::_GP('values')));
    		$by = trim(t3lib_div::_GP('by'));
    		$role = trim(t3lib_div::_GP('role'));
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    		$get_analyzes = false;
    		if(trim(t3lib_div::_GP('get_analyzes')) == '1'){
    			$get_analyzes = true;
    		}
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    		$octet = true;
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    		if(trim(t3lib_div::_GP('bases')) == '1'){
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    			$octet = false;
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    		}
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    		print json_encode(tx_nG6_db::select_storage_distribution($values, $by, $role, $get_analyzes, $octet));
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		} elseif($type == 'data_evolution'){
    		$values = split(",", trim(t3lib_div::_GP('values')));
    		$by = trim(t3lib_div::_GP('by'));
    		$role = trim(t3lib_div::_GP('role'));
    		$get_analyzes = false;
    		if(trim(t3lib_div::_GP('get_analyzes')) == '1'){
    			$get_analyzes = true;
    		}
    		$octet = true;
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    		if(trim(t3lib_div::_GP('bases')) == '1'){
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    			$octet = false;
    		}
    		$cumulate = false;
    		if(trim(t3lib_div::_GP('cumulate')) == '1'){
    			$cumulate = true;
    		}
    		print json_encode(tx_nG6_db::select_storage_evolution($values, $by, $role, $get_analyzes, $octet, $cumulate));
    	}  	
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    }

	/**
	 * Creates an archiving script to archive data from ids
	 *
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	 * @param	string	$user_id		the user id 
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	 * @param	array	$ids			list of ids to download 
	 * @param	string	$data_folder	the data folder where are stored the data
	 * @param	string	$tmp_folder		the output directory
	 * @param	string	$format			the archiving format (tar.gz)
	 * @param	string	$user_email		the user email
	 * @param	string	$title_email		the email title to send
	 * @param	string	$msg_email		the email message to send
	 * @return	array (the path to the script, the url path to the final archive)
	 */
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	private function create_archive_script($user_id, $ids, $data_folder, $tmp_folder, $format, $user_email, $title_email, $msg_email) {
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		// First get the archive name where will be stored the data
		$random_key = tx_nG6_utils::create_random_key(10);
		$archive_path = $tmp_folder."/ng6_".$random_key;
		while( file_exists($archive_path) )
			$archive_path = $tmp_folder."/ng6_".$random_key;
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		// Then get the directories structure
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		$directories = $this->get_directories_structure_and_content($user_id, $ids, $data_folder, $archive_path);
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		$archive_script_path = $tmp_folder."/ng6_".$random_key.".sh";
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		// And write down the script in charge to create the archive
		$fp = fopen($archive_script_path, 'w');
		foreach($directories[0] as $index => $src_directory) {
			if (!file_exists( $directories[1][$index])) {
				fwrite($fp, "mkdir -p ".$directories[1][$index]."\n");
			}
			// For each files in the source directory
			foreach(scandir($src_directory) as $file) {
				if (is_file($src_directory."/".$file) and $file != "analyse.xml" and $file != "index.html" and $file != "run.cfg") {
					fwrite($fp, "cp ".$src_directory."/".$file." ".$directories[1][$index]."\n");
				}
			}
		}
		fwrite($fp, "cd ".$tmp_folder."\n");
		fwrite($fp, "tar -czf ng6_".$random_key.".tar.gz ng6_".$random_key."\n");
		fwrite($fp, "rm -rf ".$archive_path."\n");
		fwrite($fp, 'echo "'.str_replace(array('SPAN_ARCHIVE_NAME'), array("ng6_".$random_key.".tar.gz"), $msg_email).'" | mail -s "'.$title_email.'" '.$user_email."\n");
		fclose($fp);
		return array($archive_script_path, "ng6_".$random_key.".tar.gz");
    }

	/**
	 * Creates symbolic links between ids from data_folder into user_directory
	 *
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	 * @param	string	$user_id		the user id 
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	 * @param	string	$user_login		the user login to make ssh
	 * @param	string	$user_pwd		the user pwd to make ssh
	 * @param	array	$ids			list of ids to download 
	 * @param	string	$data_folder	the data folder where are stored the data
	 * @param	string	$user_directory	the output directory
	 * @return	0=>everything ok, 1=>user rigth problem, 2=>wrong authentification, 3=>connection error
	 */
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	private function create_symbolic_links($user_id, $user_login, $user_pwd, $ids, $data_folder, $user_directory) {
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		// First try to connect the specified user using ssh
		$connection = ssh2_connect('127.0.0.1', 22);
		if (!$connection) return 3;
		if (!ssh2_auth_password($connection, $user_login, $user_pwd)) return 2;
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		// Then get the directories structure
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		$directories = $this->get_directories_structure_and_content($user_id, $ids, $data_folder, $user_directory);
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		// And process the directories structure
		$creation = true;
		foreach($directories[0] as $index => $src_directory) {
			if (!file_exists("ssh2.sftp://".$connection.$directories[1][$index])) {
				if (!mkdir("ssh2.sftp://".$connection.$directories[1][$index], 0755, true)) {
					$creation = false;
					break;
				}
				// For each files in the source directory
				foreach(scandir($src_directory) as $file) {
					if (is_file($src_directory."/".$file) and $file != "analyse.xml" and $file != "index.html" and $file != "run.cfg") {
						if (!ssh2_exec($connection, 'ln -s '.$src_directory.'/'.$file.' '.$directories[1][$index].'/'.$file)) {
							$creation = false;
							break;
						}
					}
				}
			}
		}
		if (!$creation) return 1;
		return 0;
    }

	/**
	 * Returns a table with the right directories structure considering ids
	 *
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	 * @param	string	$user_id		The user id
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	 * @param	array	$ids			List of ids to download 
	 * @param	string	$data_folder	The data folder where are stored the data
	 * @param	string	$output_folder	The output directory
	 * @return	array	[0] => source_directories, [1] => dest_directories
	 */
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	private function get_directories_structure_and_content($user_id, $ids, $data_folder, $output_folder) {
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		$src_directories = array();
		$dest_directories = array();
		$vals = preg_split("/;/", $ids);
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		// Characters to be replaced in the names of the run, the analyses ...
		$char_to_replace = array(' ','/');
		
		// For each project/run/analysis
		foreach($vals as $val) {
			if ($val != "undefined" && $val != "") {
				$id = preg_split("/_/", $val);
				if ($id[0] == "data") {
					$run = tx_nG6_db::select_run($id[1]);
					if (!in_array($data_folder.$run["directory"], $src_directories)) {
						$src_directories[] = $data_folder.$run["directory"];
						$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]);
						$ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]).".".$id[1]."/RawData";
						$dest_directories[] = $ddest;
					}
				} else if ($id[0] == "run") {
					$run = tx_nG6_db::select_run($id[1]);
					if (!in_array($data_folder.$run["directory"], $src_directories)) {
						$src_directories[] = $data_folder.$run["directory"];
						$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]);
						$ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]).".".$id[1]."/RawData";
						$dest_directories[] = $ddest;
					}
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					foreach(tx_nG6_db::get_user_run_analysis($user_id, $id[1], 'tx_nG6_analyze.name') as $analyse_id => $analyse_values) {
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						$aid = preg_split("/_/", $analyse_id);
						if (!in_array($data_folder.$analyse_values["directory"], $src_directories)) {
							$src_directories[] = $data_folder.$analyse_values["directory"];
							$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]);
							$ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]);
							$ddest .= ".".$id[1]."/Analyse_".str_replace($char_to_replace, '_', $analyse_values["name"]).".".$aid[1];
							$dest_directories[] = $ddest;
						}
					}
				} else if ($id[0] == "analyse") {
					$analyse = tx_nG6_db::select_analyse($id[1]);
					if (!in_array($data_folder.$analyse["directory"], $src_directories)) {
						$src_directories[] = $data_folder.$analyse["directory"];
						// If it's a project analyse
						if ($analyse["run_id"] == 'None') {
							$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $analyse["project_name"]);
							$ddest .= ".".$analyse["project_id"]."/Project_analyses/".str_replace($char_to_replace, '_', $analyse["name"]).".".$id[1];
							$dest_directories[] = $ddest;
						} else {
							$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $analyse["project_name"]);
							$ddest .= ".".$analyse["project_id"]."/Run_".str_replace($char_to_replace, '_', $analyse["run_name"]);
							$ddest .= ".".$analyse["run_id"]."/Analyse_".str_replace($char_to_replace, '_', $analyse["name"]).".".$id[1];
							$dest_directories[] = $ddest;
						}
					}
				}
			}
		}
		return array($src_directories, $dest_directories);
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    }    
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}

if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_eid.php']) {
    include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_eid.php']);
}