class.tx_nG6_pi1.php

<?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!
***************************************************************/
/**
 * Plugin 'nG6' for the 'nG6' extension.
 *
 * @author	PF bioinformatique de Toulouse <>
 */

require_once(PATH_tslib.'class.tslib_pibase.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').'/res/smarty/libs/Smarty.class.php'); 

class tx_nG6_pi1 extends tslib_pibase {
	
	var $prefixId = 'tx_nG6_pi1';		// Same as class name
	var $scriptRelPath = 'pi1/class.tx_nG6_pi1.php';	// Path to this script relative to the extension dir.
	var $extKey = 'nG6';	// The extension key.
	
	/**
	 * Main method of your PlugIn
	 *
	 * @param	string		$content: The content of the PlugIn
	 * @param	array		$conf: The PlugIn Configuration
	 * @return	The content that should be displayed on the website
	 */
	function main($content,$conf)	{
		
		if (strstr($this->cObj->currentRecord,'tt_content'))	{
			$conf['pidList'] = $this->cObj->data['pages'];
		}
		// Setting the TypoScript passed to this function in $this->conf
		$this->conf=$conf;
		$this->internal['results_at_a_time'] = $conf["results_at_a_time"];
		
		$this->pi_setPiVarDefaults();
		// Configuring so caching is not expected. This value means that no cHash params are ever set. We do this, because it's a USER_INT object!
		$this->pi_USER_INT_obj=1;
		// Loading the LOCAL_LANG values
		$this->pi_loadLL();

		// Add the ng6 plugins css
		$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] = '
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.core.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.dialog.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.draggable.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.resizable.min.js"></script> 
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.bgiframe.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.url.packed.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_pi1.js"></script>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/tx_nG6.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.core.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.theme.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.dialog.css"/>';

		$content .= '<div id="user_information_dialog" title=""></div>';
		$content .= '<div id="error_dialog" title=""></div>';
		
		$content .= '<input type="hidden" id="cancel_btn_label" value="'.$this->pi_getLL('cancel_btn_label', '[cancel_btn_label]').'" />';
		$content .= '<input type="hidden" id="ok_btn_label" value="'.$this->pi_getLL('ok_btn_label', '[ok_btn_label]').'" />';
		$content .= '<input type="hidden" id="yes_btn_label" value="'.$this->pi_getLL('yes_btn_label', '[yes_btn_label]').'" />';
		$content .= '<input type="hidden" id="no_btn_label" value="'.$this->pi_getLL('no_btn_label', '[no_btn_label]').'" />';
		$content .= '<input type="hidden" id="confirmation_dialog_title" value="'.$this->pi_getLL('confirmation_dialog_title', '[confirmation_dialog_title]').'" />';
		$content .= '<input type="hidden" id="information_error_title" value="'.$this->pi_getLL('information_error_title', '[information_error_title]').'" />';
		$content .= '<input type="hidden" id="hide_dialog_title" value="'.$this->pi_getLL('hide_dialog_title', '[hide_dialog_title]').'" />';
		$content .= '<input type="hidden" id="hide_confirmation_msg" value="'.$this->pi_getLL('hide_confirmation_msg', '[hide_confirmation_msg]').'" />';
		$content .= '<input type="hidden" id="unhide_dialog_title" value="'.$this->pi_getLL('unhide_dialog_title', '[unhide_dialog_title]').'" />';
		$content .= '<input type="hidden" id="unhide_confirmation_msg" value="'.$this->pi_getLL('unhide_confirmation_msg', '[unhide_confirmation_msg]').'" />';
		$content .= '<input type="hidden" id="information_error_msg" value="'.$this->pi_getLL('information_error_msg', '[information_error_msg]').'" />';
		
		$content .= '<input type="hidden" id="information_dialog_zero_check" value="'.$this->pi_getLL('information_dialog_zero_check', '[information_dialog_zero_check]').'" />';
		$content .= '<input type="hidden" id="delete_confirmation_msg" value="'.$this->pi_getLL('delete_confirmation_msg', '[delete_confirmation_msg]').'" />';
		$content .= '<input type="hidden" id="deleting_dialog_msg" value="'.$this->pi_getLL('deleting_dialog_msg', '[deleting_dialog_msg]').'" />';
		$content .= '<input type="hidden" id="delete_authentication_dialog_msg" value="'.str_replace(array('###SPAN_SERVER###'), array($this->conf["server_name"]), $this->pi_getLL('delete_authentication_dialog_msg', '[delete_authentication_dialog_msg]')).'" />';
		
		$content .= '<input type="hidden" id="user_login" value="'.$this->pi_getLL('user_login', '[user_login]').'" />';
		$content .= '<input type="hidden" id="user_pwd" value="'.$this->pi_getLL('user_pwd', '[user_pwd]').'" />';
		$content .= '<input type="hidden" id="user_group" value="'.$GLOBALS['TSFE']->fe_user->user['usergroup'].'" />';
		
		$content .= '<input type="hidden" id="deleting_dialog_title" value="'.$this->pi_getLL('deleting_dialog_title', '[deleting_dialog_title]').'" />';
		$content .= '<input type="hidden" id="delete_success_msg" value="'.$this->pi_getLL('delete_success_msg', '[delete_success_msg]').'" />';
		$content .= '<input type="hidden" id="delete_dialog_rigth_error" value="'.$this->pi_getLL('delete_dialog_rigth_error', '[delete_dialog_rigth_error]').'" />';
		$content .= '<input type="hidden" id="delete_dialog_authentification_error" value="'.$this->pi_getLL('delete_dialog_authentification_error', '[delete_dialog_authentification_error]').'" />';
		$content .= '<input type="hidden" id="delete_dialog_connection_error" value="'.$this->pi_getLL('delete_dialog_connection_error', '[delete_dialog_connection_error]').'" />';
	
		$content .= '<input type="hidden" id="publish_dialog_title" value="'.$this->pi_getLL('publish_dialog_title', '[publish_dialog_title]').'" />';
		$content .= '<input type="hidden" id="publish_confirmation_msg" value="'.$this->pi_getLL('publish_confirmation_msg', '[publish_confirmation_msg]').'" />';
		$content .= '<input type="hidden" id="unpublish_dialog_title" value="'.$this->pi_getLL('unpublish_dialog_title', '[unpublish_dialog_title]').'" />';
		$content .= '<input type="hidden" id="unpublish_confirmation_msg" value="'.$this->pi_getLL('unpublish_confirmation_msg', '[unpublish_confirmation_msg]').'" />';
		
		$content .= '<input type="hidden" id="data_folder" value="'.$this->conf["data"].'" />';	
		
		// If the user is authorized to access the specified project/run, display the page
		if (tx_nG6_db::user_is_authorized($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id'], $this->piVars['run_id'])) {
			switch((string)$this->conf['view'])	{
				// If the plugin is configured to display results by project
				case 'project':
					if ($this->piVars['analyze_id']) {
						$content .= $this->pi_analyze_view('analyze');
					} elseif ($this->piVars['project_id'] && $this->piVars['run_id']) {
						$content .= $this->pi_run_view();
					}elseif ($this->piVars['project_id'] && $this->piVars['summary']) {
						$content .= $this->pi_project_summary();
					} else {
						$content .= $this->pi_project_view();
					}
					break;
				// If the plugin is configured to display results by run
				case 'run':
					if ($this->piVars['analyze_id']) {
						$content .= $this->pi_analyze_view('analyze');
					} else {
						$content .= $this->pi_run_view();
					}
					break;
				// If the plugin is not configured, display by project is default
				default:
					$content .= $this->pi_project_view();
					break;
			}
		// If the user is not authorized
		} else {
			$content .= $this->pi_getLL('not_authorized','[not_authorized]');
		}
		return $this->pi_wrapInBaseClass($content);
	}
	
	/**
	 * Shows the summary and statistics for a project
	 * TODELETE
	 * @return	HTML list of table entries
	 */
	function pi_project_summary()	{
		$project_runs = tx_nG6_db::get_project_runs($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id']);
		$content = "Le projet ".$this->piVars['project_id']." contient ".count($project_runs)." runs.";
		return $content;
	}
	
	/**
	 * Shows a list of database entries
	 *
	 * @return	HTML list of table entries
	 */
	function pi_project_view()	{

		// If a single element should be displayed
		if ($this->piVars['project_id'])	{
			
			return $this->pi_project_single_view($this->piVars['project_id']);

		// If multiple projects
		} else {
			
			// If the user is on a specific page
			if (isset($this->piVars['project_page'])) {
				$current_page = intval($this->internal['results_at_a_time']) * (intval($this->piVars['project_page']) -1);
				$limit = "$current_page".",". $this->internal['results_at_a_time'] ;
			} else $limit = '0,'.$this->internal['results_at_a_time'] ; 
			
			// Select all user projects
			$projects = tx_nG6_db::select_all_user_projects($GLOBALS['TSFE']->fe_user->user['usergroup'], 'tx_nG6_project.name', $limit);
			$all_projects = tx_nG6_db::select_all_user_projects($GLOBALS['TSFE']->fe_user->user['usergroup']);
			
			// If there is at least one result
			if (count($projects) > 0) {

	         	$project_list = $this->pi_project_list_view($projects);
	         	$nav_links = $this->pi_navigation_link_view('project_page', $this->piVars['project_page'], count($all_projects));
         		return $project_list.$nav_links;
         		
         	// If there is no results to display		
			} else { 
				return $this->pi_getLL('no_raw','[no_raw]');
			}
		}
	}

	/**
	 * Creates a list from a database query
	 * 
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
	function pi_project_list_view($projects)	{

		// First add the table header
		$is_super_user = false;
		foreach($projects as $project_id => $project_values) {
			if ($GLOBALS['TSFE']->loginUser && tx_nG6_db::is_super_user($GLOBALS['TSFE']->fe_user->user['usergroup'], 'project', $project_values['id']) ) {
				$is_super_user = true;
			}
		}
		$content = '<table'.$this->pi_classParam('listrow').'><tr>';
		if ($is_super_user) {
			$content .= '<th><center><input type="checkbox" id="chk_all_project"></center></th>';
		}
		$content .= '<th>'.$this->pi_getLL('project_name','[project_name]').'</th>
					 <th>'.$this->pi_getLL('description','[description]').'</th>
					 </tr>';
						
		// Then the row for each project	
		foreach($projects as $project_id => $project_values) {
			
			// If it's not a hidden project
			$hidden = $this->pi_classParam('hidden');
			if ($project_values['hidden'] == 0) { $hidden = ''; }

			// If it's not a public project
			$public = '';
			if ($GLOBALS['TSFE']->loginUser && $project_values['public'] == 0) { $public = $this->pi_classParam('public'); }
			
			$content .= '<tr '.$public.'>';

			// projects updates possibility depends on projects rights (show checkboxes or not)
			if ( $GLOBALS['TSFE']->loginUser && tx_nG6_db::is_super_user($GLOBALS['TSFE']->fe_user->user['usergroup'], 'project', $project_values['id']) ) {
				$content .= '<td '.$hidden.'><center><input type="checkbox" id="chk_project_'.$project_values['id'].'" value="project_'.$project_values['id'].'"></center></td>';
			}
			$content .= '<td '.$hidden.' >'.$this->pi_list_linkSingle($project_values['name'],$project_values['id'],1, array('project_id'=>$project_values['id'])).'</td>
						<td '.$hidden.' >'.$project_values['description'].'</td>
						</tr>';

		}
		$content .= '</table>';
		
		// option toolbar
		if ($is_super_user) {
		$content .= '<div '.$this->pi_classParam('div-option-menu').'> '.$this->pi_getLL('toolbar_title','[toolbar_title]') .
					'<button id="hide_project" type="button" class="btn pill-l"><span><span>'.$this->pi_getLL('hide_btn','[hide_btn]').'</span></span></button>' .
					'<button id="unhide_project" type="button" class="btn pill-r"><span><span>'.$this->pi_getLL('unhide_btn','[unhide_btn]').'</span></span></button>' .
					'&nbsp;<button id="delete_project" type="button" class="btn"><span><span>'.$this->pi_getLL('delete_btn','[delete_btn]').'</span></span></button>&nbsp;' .
					'<button id="publish_project" type="button" class="btn pill-l"><span><span>'.$this->pi_getLL('publish_btn','[publish_btn]').'</span></span></button>' .
					'<button id="unpublish_project" type="button" class="btn pill-r"><span><span>'.$this->pi_getLL('unpublish_btn','[unpublish_btn]').'</span></span></button>' .		
					'</div>';
		}
		return $content;
	}

	/**
	 * Display a single project
	 * 
	 * @param	string	$project_id	the project id
	 * @return	HTML of a single project entry
	 */
	function pi_project_single_view($project_id)	{
		
		// First select the project values 
		$project = tx_nG6_db::select_project($project_id);
		
		// Add the project description
		$content = '<div'.$this->pi_classParam('singleView').'>
			        <h2>Projet '.$project['name'].' :</h2>
				    <p><strong>'.$project['description'].'</strong></p></div>';
		// The project runs view
		$content .= '<br /> <h3> '.$this->pi_getLL('runs_done','[runs_done]').'</h3> <br />';
		$content .= $this->pi_run_view();
		// And the analyses performed on the project
		$content .= $this->pi_analyze_view('project');
		return $content;
		
	}

	/**
	 * Shows a list of database entries
	 *
	 * @return	HTML list of table entries
	 */
    function pi_run_view() {
    	
    	// If a single element should be displayed
		if ($this->piVars['run_id'])    {       
		
			return $this->pi_run_single_view($this->piVars['run_id']);
		
		// If multiple runs
		} else {        
			
			// If the user is on a specific page
			if (isset($this->piVars['run_page'])) {
				$current_page = intval($this->internal['results_at_a_time']) * (intval($this->piVars['run_page']) -1);
				$limit = "$current_page".",". $this->internal['results_at_a_time'] ;
			} else $limit = '0,'.$this->internal['results_at_a_time'] ; 
		   
			// Select all runs from this project
			if ($this->piVars['project_id']) {
				$runs = tx_nG6_db::get_project_runs($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id'], 'tx_nG6_run.date DESC, tx_nG6_run.name ASC', $limit);
				$all_runs = tx_nG6_db::get_project_runs($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id']);
			// If no project defined, select all runs owned by the user
			} else {
            	$runs = tx_nG6_db::select_all_user_runs($GLOBALS['TSFE']->fe_user->user['usergroup'], 'tx_nG6_run.date DESC, tx_nG6_run.name ASC', $limit);
            	$all_runs = tx_nG6_db::select_all_user_runs($GLOBALS['TSFE']->fe_user->user['usergroup']);
         	}
	
         	// If there is some results to display
			if (count($runs) > 0) {

				$run_list = $this->pi_run_list_view($runs);
				$nav_links = $this->pi_navigation_link_view('run_page', $this->piVars['run_page'], count($all_runs));
				return $run_list ."\n". $nav_links;
 			
 			// If there is no results
 			} else { 
 				return $this->pi_getLL('no_raw','[no_raw]');
 			}
 			
		}
    }

	/**
	 * Creates a list from a database query
	 *
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
	function pi_run_list_view($runs) {
		
		// First add the table header
		$is_super_user = false;
		foreach($runs as $run_id => $run_values) {
			if ( $GLOBALS['TSFE']->loginUser && tx_nG6_db::is_super_user($GLOBALS['TSFE']->fe_user->user['usergroup'], 'run', $run_values['id']) ) {
				$is_super_user = true;
			}
		}
		$content = '<table'.$this->pi_classParam('listrow').'><tr>';
		if ($is_super_user) {
			$content .= '<th><center><input type="checkbox" id="chk_all_run"></center></th>';
		}
		$content .= '<th>'.$this->pi_getLL('run_name','[run_name]').'</th>
					 <th>'.$this->pi_getLL('project_name','[project_name]').'</th>
					 <th>'.$this->pi_getLL('date','[date]').'</th>
					 <th>'.$this->pi_getLL('species','[species]').'</th>
					 <th>'.$this->pi_getLL('data_nature','[data_nature]').'</th>
					 <th>'.$this->pi_getLL('type','[type]').'</th>
					 <th>'.$this->pi_getLL('nb_sequences','[nb_sequences]').'</th>
					 <th>'.$this->pi_getLL('full_seq_size','[full_seq_size]').'</th>
					 <th>'.$this->pi_getLL('description','[description]').'</th>
					 <th>'.$this->pi_getLL('sequencer','[sequencer]').'</th>
					 </tr>';
					 
		// Then the row for each run
		foreach($runs as $run_id => $run_values) {
			
			// If the run is hidden
			$hidden = $this->pi_classParam('hidden');
			if ($run_values['hidden'] == 0) { $hidden = ''; }

			// Add the row information
			$content .= '<tr>';
			// runs updates possibility depends on runs rights (show checkboxes or not)
			if ( $GLOBALS['TSFE']->loginUser && tx_nG6_db::is_super_user($GLOBALS['TSFE']->fe_user->user['usergroup'], 'run', $run_values['id']) ) {
				$content .= '<td '.$hidden.' ><center><input type="checkbox" id="chk_run_'.$run_values["id"].'" value="run_'.$run_values["id"].'"></center></td>';
			}
			$content .='<td '.$hidden.' >'.$this->pi_list_linkSingle($run_values['name'],$run_id,1, array('run_id'=>$run_values['id'], 'project_id'=>$run_values['project_id'])).'</td>
					<td '.$hidden.' >'.$run_values['project_name'].'</td>
					<td '.$hidden.' >'.strftime('%d-%m-%y',$run_values['date']).'</td>
					<td '.$hidden.' >'.$run_values['species'].'</td>
					<td '.$hidden.' >'.$run_values['data_nature'].'</td>
					<td '.$hidden.' >'.$run_values['type'].'</td>
					<td '.$hidden.' >'.number_format($run_values['nb_sequences'], 0, ',', ' ').'</td>
					<td '.$hidden.' >'.number_format($run_values['full_seq_size'], 0, ',', ' ').'</td>
					<td '.$hidden.' >'.$run_values['description'].'</td>
					<td '.$hidden.' >'.$run_values['sequencer'].'</td>
					</tr>';
		}
		// Return the html table
		$content .= '</table>' ;
		if ($is_super_user) {
		// option toolbar
		$content .= '<div '.$this->pi_classParam('div-option-menu').'> '.$this->pi_getLL('toolbar_title','[toolbar_title]') .
					'<button id="hide_run" type="button" class="btn pill-l"><span><span>'.$this->pi_getLL('hide_btn','[hide_btn]').'</span></span></button>' .
					'<button id="unhide_run" type="button" class="btn pill-r"><span><span>'.$this->pi_getLL('unhide_btn','[unhide_btn]').'</span></span></button>' .
					'&nbsp;<button id="delete_run" type="button" class="btn"><span><span>'.$this->pi_getLL('delete_btn','[delete_btn]').'</span></span></button>' .
					'</div>';
		}
		return $content;
	}

	/**
	 * Display a single item from the database
	 * 
	 * @param	ressource	$res: A database result ressource
	 * @return	HTML of a single database entry
	 */
	function pi_run_single_view($run_id) {	
		
		// First select the run
		$run = tx_nG6_db::select_run($run_id);
		
		// Add the run description to the page content
		$content = '<div'.$this->pi_classParam('singleView').'>';
		$content .= '<h2>Run '.$run['name'].' :</h2>';
		$content .= '<p><strong>'.$run['description'].'</strong></p> </div>
					 <table'.$this->pi_classParam('listrow').'>
					 <tr>
						<th align="left">'.$this->pi_getLL('project_name','[project_name]').' :</th>
						<td align="left">'.$run['project_name'].'</td>
					 </tr>	
					 <tr>
						<th align="left">'.$this->pi_getLL('date','[date]').' :</th>
						<td align="left">'.strftime('%d-%m-%y',$run['date']).'</td>
					 </tr>					
					 <tr>
						<th align="left">'.$this->pi_getLL('species','[species]').' :</th>
						<td align="left">'.$run['species'].'</td>
					 </tr>
					 <tr>
						<th align="left">'.$this->pi_getLL('type','[type]').' :</th>
						<td align="left">'.$run['type'].'</td>
					 </tr>
					 <tr>
						<th align="left">'.$this->pi_getLL('data_nature','[data_nature]').' :</th>
						<td align="left">'.$run['data_nature'].'</td>
					 </tr>
					 <tr>
						<th align="left">'.$this->pi_getLL('nb_sequences','[nb_sequences]').' :</th>
						<td align="left">'.number_format($run['nb_sequences'], 0, ',', ' ').'</td>
					 </tr>
					 <tr>
						<th align="left">'.$this->pi_getLL('full_seq_size','[full_seq_size]').' :</th>
						<td align="left">'.number_format($run['full_seq_size'], 0, ',', ' ').'</td>
					 </tr>						
					 <tr>
						<th align="left">'.$this->pi_getLL('sequencer','[sequencer]').' :</th>
						<td align="left">'.$run['sequencer'].'</td>
					 </tr>
					 <tr>
						<th align="left">'.$this->pi_getLL('downloads','[downloads]').' :</th>
						<td align="left">'.$this->get_downloads_list($run['directory']).'</td>
					 </tr>
					 </table>';
					 
		// Add the run analysis
		$content .= $this->pi_analyze_view('run');
		
		// Return the run HTML page
		return $content;
	}
	
	/**
	 * Display a list of downloadable file
	 *
	 * @return	HTML of a list of downlabale links
	 */
	function get_downloads_list($run_directory) {
		$directory = (string)$this->conf['data'].$run_directory;
		
		// Try to look at all files in the specified directory
		try {
			if (!is_dir($directory)) { throw new Exception('Error when attempting to open the data folder !'); }
			$my_directory = opendir($directory) or die('Error when attempting to open the data folder !');
			$download = '<p '.$this->pi_classParam('downloads').'><ul>';
			// For every files
			while($entry = @readdir($my_directory)) {
				if(!is_dir($directory.'/'.$entry)&& $entry != '.' && $entry != '..' && !tx_nG6_utils::ends_with($entry, ".cfg")) {
					$link = 'fileadmin/'.$run_directory.'/'.$entry;
					$download .= '<li><a href="'.$link.'" target="_blank">'.$entry.'</a></li>';
				}
			}
			$download .= '</ul>';		
			closedir($my_directory);
			return $download;
		}
		catch (Exception $e) {
			return $this->pi_getLL('not_synchro','[not_synchro]');
		}
	}	
	
	/**
	 * Shows a list of database entries
	 *
	 * @param	string		$type: What kind of analyze is it : run or project
	 * 	 * @return	HTML list of table entries
	 */
	function pi_analyze_view($type)	{
		
		// If a single element should be displayed:
		if ($type == 'analyze')	{
			
			return $this->pi_analyze_single_view($this->piVars['analyze_id']);
		
		// If multiple analyses
		} else {
			
			// If the user is on a specific page
			if (isset($this->piVars['analyze_page'])) {
				$current_page = intval($this->internal['results_at_a_time']) * (intval($this->piVars['analyze_page']) -1);
				$limit = "$current_page".",". $this->internal['results_at_a_time'] ;
			} else $limit = '0,'.$this->internal['results_at_a_time'] ; 
			
			// If we want run analyses
			if ($type == 'run') {
				// Selects Analyzis done on this run
				$analyses = tx_nG6_db::get_run_analysis($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['run_id'], 'tx_nG6_analyze.name', $limit);
				$all_analyses = tx_nG6_db::get_run_analysis($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['run_id']);
			} else {
				$analyses = tx_nG6_db::get_project_analysis($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id'], 'tx_nG6_analyze.name', $limit);
				$all_analyses = tx_nG6_db::get_project_analysis($GLOBALS['TSFE']->fe_user->user['usergroup'], $this->piVars['project_id']);
			}

			// Define an empty content
			$content='';
			
			// If there is some analyse
			if (count($analyses) > 0) {	
				$analyze_list = $this->pi_analyze_list_view($analyses);
				$nav_links = $this->pi_navigation_link_view('analyze_page', $this->piVars['analyze_page'], count($all_analyses));
				$content.= $analyze_list.$nav_links;
			}
			
			// Return the final HTML
			return $content;
		}
	}

	/**
	 * Creates a list from a database query
	 *
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
	function pi_analyze_list_view($analyses) {
		
		// First add the table header to the HTML
		// First add the table header
		$is_super_user = false;
		foreach($analyses as $analyse_id => $analyse_values) {
			if ( $GLOBALS['TSFE']->loginUser && tx_nG6_db::is_super_user($GLOBALS['TSFE']->fe_user->user['usergroup'], 'analyze', $analyse_values['id']) ) {
				$is_super_user = true;
			}
		}
		$content = '<br /> <h3> '.$this->pi_getLL('analyzes_done','[analyzes_done]').'</h3> <br />
				   <table'.$this->pi_classParam('listrow').'>';
		if ($is_super_user) {
			$content .= '<th><center><input type="checkbox" id="chk_all_analysis"></center></th>';
		}
		$content .= '<th>'.$this->pi_getLL('name','[name]').'</th>
					 <th>'.$this->pi_getLL('description','[description]').'</th>
					 <th>'.$this->pi_getLL('software','[software]').'</th>
					 <th>'.$this->pi_getLL('version','[version]').'</th>
				     </tr>';
				   
		// Then the row for each analyse
		foreach($analyses as $analyse_id => $analyse_values) {

			// If it's not a hidden analyse
			$hidden = $this->pi_classParam('hidden');
			if ($analyse_values['hidden'] == 0) { $hidden = ''; }

			$content .= '<tr>';
			// analyzes updates possibility depends on analyzes rights (show checkboxes or not)
			if ( $GLOBALS['TSFE']->loginUser && tx_nG6_db::is_super_user($GLOBALS['TSFE']->fe_user->user['usergroup'], 'analyze', $analyse_values['id']) ) {
				$content .= '<td '.$hidden.' ><center><input type="checkbox" id="chk_analysis_'.$analyse_values["id"].'" value="analysis_'.$analyse_values["id"].'"></center></td>';
			}
			$content .='<td '.$hidden.' >'.$this->pi_list_linkSingle($analyse_values['name'],$analyse_values['id'],1, array('analyze_id'=>$analyse_values['id'], 'project_id'=>$this->piVars['project_id'], 'run_id'=>$this->piVars['run_id'])).'</td>
						 <td '.$hidden.' >'.$analyse_values['description'].'</td>
						 <td '.$hidden.' >'.$analyse_values['software'].'</td>
						 <td '.$hidden.' >'.$analyse_values['version'].'</td>
						 </tr>';

		}
		$content.='</table>' ;
		if ($is_super_user) {
		// option toolbar
		$content .= '<div '.$this->pi_classParam('div-option-menu').'> '.$this->pi_getLL('toolbar_title','[toolbar_title]') .
					'<button id="hide_analysis" type="button" class="btn pill-l"><span><span>'.$this->pi_getLL('hide_btn','[hide_btn]').'</span></span></button>' .
					'<button id="unhide_analysis" type="button" class="btn pill-r"><span><span>'.$this->pi_getLL('unhide_btn','[unhide_btn]').'</span></span></button>' .
					'&nbsp;<button id="delete_analysis" type="button" class="btn"><span><span>'.$this->pi_getLL('delete_btn','[delete_btn]').'</span></span></button>' .
					'</div>';
		}
		return $content;
	}


	/**
	 * Display a single item from the database
	 *
	 * @return	HTML of a single database entry
	 */
	function pi_analyze_single_view($analyse_id) {
		
		// Add the jquery libs
		$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] = '
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.core.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.dialog.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.draggable.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.ui.resizable.min.js"></script> 
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.bgiframe.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.url.packed.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_pi1.js"></script>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/tx_nG6.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.core.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.theme.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jquery.ui.dialog.css"/>';

		// First select the analyse
		$analyse = tx_nG6_db::select_analyse($analyse_id);
		
		// Handle old fashion
		if (file_exists($this->conf['data'].$analyse['directory'].'/index.html' )) {
			// Add the analyse description
			$content = '<div id="img_dialog" title=""></div>';
			$content .= '<input type="hidden" id="analyse_name" value="'.$analyse['name'].'" />';
			$content .= '<div'.$this->pi_classParam('singleView').'>';
			$content .= '<h2>Analyse '.$analyse['name'].' : <span>'.$analyse['description'].'</span></h2></div>';
			$fp = fopen((string)$this->conf['data'].$analyse['directory'].'/index.html',"r");
			while (!feof($fp)) {
				$content .= fgets($fp, 4096);
			}
			
		// Else meaning using smarty
		} else {
			
			$smarty = new Smarty();
			$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi1/analyzes');
			$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');

			$smarty->assign('analyse', $analyse);
			
			// Then select analyse results
			$results = tx_nG6_db::select_analyse_results($analyse_id);		
			$smarty->assign('analyse_results', $results);
			
			// Select the run file description	
			if ($analyse['run_id'] != 'None') {
				$descriptions = tx_nG6_db::select_mid_descriptions($analyse['run_id']);
			} else {
				$descriptions = array();
			}
			$smarty->assign('descriptions', $descriptions);
			$smarty->assign('data_folder', $this->conf['data']);
			if (isset($this->LOCAL_LANG[$this->LLkey]) && count($this->LOCAL_LANG[$this->LLkey]) > 0) {
				$smarty->assign('llang', $this->LOCAL_LANG[$this->LLkey]);
			} else {
				$smarty->assign('llang', $this->LOCAL_LANG['default']);
			}			
			// Try to process the analyse template
			try { $content = $smarty->fetch($analyse['class'].'.tpl'); } 
			catch (Exception $e) { $content = str_replace(array('###ANALYSE_CLASS###'), array($analyse['class']), $this->pi_getLL('no_template_found','[no_template_found:###ANALYSE_CLASS###]')); }
		}
		
		// Return the analyse display
		return $content;
	}
	
	/**
	 * Overloading of the tslib_pibase->pi_list_linkSingle function so piVars[showUid] is not set.
	 * Uses pi_linkTP for the linking
	 *
	 * @param	string		The content string to wrap in <a> tags
	 * @param	integer		UID of the record for which to display details (basically this will become the value of [showUid]
	 * @param	boolean		See pi_linkTP_keepPIvars
	 * @param	array		Array of values to override in the current piVars. Same as $overrulePIvars in pi_linkTP_keepPIvars
	 * @param	boolean		If true, only the URL is returned, not a full link
	 * @param	integer		Alternative page ID for the link. (By default this function links to the SAME page!)
	 * @return	string		The input string wrapped in <a> tags
	 * @see pi_linkTP(), pi_linkTP_keepPIvars()
	 */
	function pi_list_linkSingle($str,$uid,$cache=FALSE,$mergeArr=array(),$urlOnly=FALSE,$altPageId=0)	{
		if ($this->prefixId)	{
			if ($cache)	{
				$overrulePIvars=(array)$mergeArr;
				$str = $this->pi_linkTP($str,Array($this->prefixId=>$overrulePIvars),$cache,$altPageId);
			} else {
				$overrulePIvars=(array)$mergeArr;
				$str = $this->pi_linkTP_keepPIvars($str,$overrulePIvars,$cache,0,$altPageId);
			}

				// If urlOnly flag, return only URL as it has recently be generated.
			if ($urlOnly)	{
				$str = $this->cObj->lastTypoLinkUrl;
			}
		}
		return $str;
	}
	
	/**
	 * Display links for navigation in run lists or analyse lists. Called only if $end>1
	 *
	 * @param	$name	name of the variable set in GET: run_page or analyze_page
	 * @param	$start	current page number
	 * @param	$total_count	current total number of rows
	 *
	 * @return	HTML navigation links
	 */
	function pi_navigation_link_view($name, $start, $total_count) 
	{  
		$start = intval($start);		
		
		//max page number
		$end = $total_count/$this->internal['results_at_a_time'] ;
		$end = ceil($end) ;
		//repair URL mistakes caused by the nasty user  		
		if ($start > $end)
			$start = $end;
		if (($start < 1) or (! $start))
			$start = 1; 
					
		$start=(string)$start ; $end=(string)$end ;
		//create navigation links
		
		$go_back = $this->pi_linkTP_keepPIvars ('<<', array ($name => 1))	.' '.		$this->pi_linkTP_keepPIvars ('<', array ($name => $start-1));
		$go_ahead= $this->pi_linkTP_keepPIvars ('>', array ($name => $start+1)).' '.$this->pi_linkTP_keepPIvars ('>>', array ($name => $end)); 
		$current_pos = 'page '.$start. '/'.$end;
		
		//do nothing
		if( $end == '1' ) { return '' ;
		//don't display << nor <
		} elseif($start == '1')	{ $go_back = '';
		//don't display > nor >>
		} elseif($start == $end) { $go_ahead = '';
		//display both		
		}		
		$content = '<div align="right">'.$go_back .' '. $current_pos .' '. $go_ahead .'</div>' ;
		return $content;
	}	
		
}

if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/pi1/class.tx_nG6_pi1.php'])	{
	include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/pi1/class.tx_nG6_pi1.php']);
}

?>