class.tx_nG6_pi1.php 38.2 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!
***************************************************************/
/**
 * Plugin 'nG6' for the 'nG6' extension.
 *
 * @author	PF bioinformatique de Toulouse <>
 */

require_once(PATH_tslib.'class.tslib_pibase.php');

class tx_nG6_pi1 extends tslib_pibase {
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	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,$conf)	{
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		if (strstr($this->cObj->currentRecord,'tt_content'))	{
			$conf['pidList'] = $this->cObj->data['pages'];
		}
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		$this->conf=$conf;		// Setting the TypoScript passed to this function in $this->conf		
		$this->internal['results_at_a_time'] = $conf["results_at_a_time"];
		
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		$this->pi_setPiVarDefaults();
		$this->pi_USER_INT_obj=1;	// 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_loadLL();		// Loading the LOCAL_LANG values
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		$piFlexForm = $this->cObj->data['pi_flexform'];
		print_r($piFlexForm);
		
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		if ($this->userIsAuthorized()) {
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			switch((string)$this->conf['view'])	{
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				case 'project':
					if ($this->piVars['analyze_id']) {
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						return $this->pi_wrapInBaseClass($this->pi_analyze_view('analyze'));
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					} elseif ($this->piVars['project_id'] && $this->piVars['run_id']) {
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						return $this->pi_wrapInBaseClass($this->pi_run_view());
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					}elseif ($this->piVars['project_id'] && $this->piVars['summary']) {
						return $this->pi_wrapInBaseClass($this->pi_project_summary());
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					} else {
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						return $this->pi_wrapInBaseClass($this->pi_project_view());
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					}
					break;
				case 'run':
					if ($this->piVars['analyze_id']) {
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						return $this->pi_wrapInBaseClass($this->pi_analyze_view('analyze'));
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					} else {
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						return $this->pi_wrapInBaseClass($this->pi_run_view());
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					}
				break;
				default:
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					return $this->pi_wrapInBaseClass($this->pi_project_view());
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				break;
			}
		} else {
			return $this->pi_wrapInBaseClass($this->getFieldHeader('not_authorized'));
		}
	}
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	/**
	 * Shows the summary and statistics for a project
	 *
	 * @return	HTML list of table entries
	 */
	function pi_project_summary()	{

			$queryParts = array(
				'SELECT' => 'tx_nG6_run.uid AS run_id, tx_nG6_run.name AS name, tx_nG6_project.name AS project_name,' .
							'tx_nG6_run.date AS date, tx_nG6_run.species AS run_species, tx_nG6_run.data_nature AS run_data_nature,' .
							'tx_nG6_run.type AS run_type, tx_nG6_run.nb_sequences AS run_nb_sequences, tx_nG6_run.full_seq_size AS run_full_seq_size,' .
							'tx_nG6_run.description AS run_description, tx_nG6_run.sequencer AS run_sequencer,' .
							'tx_nG6_run.directory AS run_directory, tx_nG6_run.hidden AS run_hidden, tx_nG6_project.name AS project_name,' .
							'tx_nG6_project.fe_group AS project_fe_group',
				'FROM' => 'tx_nG6_run INNER JOIN (tx_nG6_project_run INNER JOIN tx_nG6_project ON tx_nG6_project_run.project_id=tx_nG6_project.uid)' .
						  'ON tx_nG6_run.uid=tx_nG6_project_run.run_id',
				'WHERE' => 'tx_nG6_project.uid = '.$this->piVars['project_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$content = "Le projet ".$this->piVars['project_id']." contient " . $GLOBALS['TYPO3_DB']->sql_num_rows($res) . " runs.";
			return $content;
	}
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	/**
	 * Shows a list of database entries
	 *
	 * @return	HTML list of table entries
	 */
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	function pi_project_view()	{

		if ($this->piVars['project_id'])	{ // If a single element should be displayed
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			$queryParts = array(
				'SELECT' => '*',
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'tx_nG6_project.uid = '.$this->piVars['project_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
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			return $this->pi_project_single_view();
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		} else {
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			if (isset($this->piVars['project_page']))	//project position 
			{
				$current_page = intval($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'] ; 		
		
		
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			// If the user is not logged on display demonstration project
			if (!$GLOBALS['TSFE']->loginUser) { 
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				$where = 'fe_group=0';
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			} else {
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				$where = 'fe_group IN ('.$this->getCurrentUserGroups().')';	
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			}
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			$queryParts = array(
				'SELECT' => '*',
				'FROM' => 'tx_nG6_project',
				'WHERE' => $where,
				'GROUPBY' => '',
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				'ORDERBY' => 'tx_nG6_project.name',
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				'LIMIT' => $limit
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			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
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			// If there is at least one result
			if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {
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				//request total in DB
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				$queryPartsc = array(
					'SELECT' => $queryParts['SELECT'],
					'FROM' => $queryParts['FROM'],
					'WHERE' => $queryParts['WHERE'],
					'GROUPBY' => '',
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					'ORDERBY' => $queryParts['ORDERBY'],
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					'LIMIT' => ''
				);
				$resc = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryPartsc);
	         	$total_count = $GLOBALS['TYPO3_DB']->sql_num_rows($resc);
		         //generate HTML   
	         	$project_list= $this->pi_project_list_view($res);
	         	$nav_links = 	$this->pi_navigation_link_view('project_page', $this->piVars['project_page'], $total_count);
         		return $project_list ."\n". $nav_links;			
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			} else { // If no results
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				return $this->getFieldHeader('no_raw');
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			}
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		}
	}

	/**
	 * Creates a list from a database query
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	 * 
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	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
	function pi_project_list_view($res)	{
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		$nb_project = 0;
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		$content = '<table'.$this->pi_classParam('listrow').'>
						<tr>
							<th>'.$this->getFieldHeader('project_name').'</th>
							<th>'.$this->getFieldHeader('description').'</th>
						</tr>';
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		while($this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
			if ($this->internal['currentRow']['hidden'] == 0) { // If it's not a hidden project
				$content .= '<tr>
					<td>'.$this->getFieldContent('name', array('project_id'=>$this->internal['currentRow']['uid'])).'</td>
					<td>'.$this->getFieldContent('description').'</td>
					</tr>';
				$nb_project++;
			} else {
				$user_groups = t3lib_div::intExplode(',',$this->getCurrentUserGroups());
				$user_allowed = false;
			    foreach($this->getSuperGroupsOf($this->internal['currentRow']['fe_group']) AS $valeur) {
					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
						$nb_project++;
					}
			    }
			    if ($user_allowed) {
					$content .= '<tr>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('name', array('project_id'=>$this->internal['currentRow']['uid'])).'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('description').'</td>
						</tr>';
			    }
			}
		}
		if ($nb_project > 0) {
			return $content .= '</table>';
		} else {
			return $this->getFieldHeader('no_raw');
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		}
	}

	/**
	 * Display a single item from the database
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	 * 
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	 * @return	HTML of a single database entry
	 */
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	function pi_project_single_view()	{
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		$content = '<div'.$this->pi_classParam('singleView').'>
			         <h2>Projet '.$this->internal['currentRow']['name'].' :</h2>
				     <p><strong>'.$this->getFieldContent('description').'</strong></p>
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		             </div>'.$this->pi_getEditPanel().$this->pi_run_view($content, $this->conf, $this->internal['currentRow']['uid']);
		$content .= $this->pi_analyze_view('project');
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		return $content;
	}
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	/**
	 * Shows a list of database entries
	 *
	 * @return	HTML list of table entries
	 */
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    function pi_run_view() {
		if ($this->piVars['run_id'])    {       // If a single element should be displayed:
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			$queryParts = array(
				'SELECT' => 'tx_nG6_run.uid AS run_id, tx_nG6_run.name AS name, tx_nG6_project.name AS project_name,' .
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							'tx_nG6_run.date AS date, tx_nG6_run.species AS run_species, tx_nG6_run.data_nature AS run_data_nature,' .
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							'tx_nG6_run.type AS run_type, tx_nG6_run.nb_sequences AS run_nb_sequences, tx_nG6_run.full_seq_size AS run_full_seq_size,' .
							'tx_nG6_run.description AS run_description, tx_nG6_run.sequencer AS run_sequencer,' .
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							'tx_nG6_run.directory AS run_directory, tx_nG6_run.hidden AS run_hidden, tx_nG6_project.name AS project_name,' .
							'tx_nG6_project.fe_group AS project_fe_group',
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				'FROM' => 'tx_nG6_run INNER JOIN (tx_nG6_project_run INNER JOIN tx_nG6_project ON tx_nG6_project_run.project_id=tx_nG6_project.uid)' .
						  'ON tx_nG6_run.uid=tx_nG6_project_run.run_id',
                'WHERE' => 'tx_nG6_run.uid='.$this->piVars['run_id'],
                'GROUPBY' => '',
                'ORDERBY' => '',
                'LIMIT' => ''
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            );             
         
         $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
         $this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
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			return $this->pi_run_single_view();
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		} else {        
		
			if (isset($this->piVars['run_page']))	//run position 
			{
				$current_page = intval($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'] ; 
		   
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			// First off, build the rigth sql request
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			if ($this->piVars['project_id']) {
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				$where = 'tx_nG6_project_run.project_id='.$this->piVars['project_id'];

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			} else {
				if (!$GLOBALS['TSFE']->loginUser) { // If the user is not logged on
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					$where = 'project_id IN ('.$GLOBALS['TYPO3_DB']->SELECTquery('uid', 'tx_nG6_project', 'fe_group=0').')';
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            } else {
            	$where = 'project_id IN ('.$GLOBALS['TYPO3_DB']->SELECTquery('uid', 'tx_nG6_project', 'fe_group IN('.$this->getCurrentUserGroups().')').')';
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            }
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         }
         // Then execute it
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			$queryParts = array(
				'SELECT' => 'tx_nG6_run.uid AS run_id, tx_nG6_run.name AS name, tx_nG6_project.name AS project_name,' .
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							'tx_nG6_run.date AS date, tx_nG6_run.species AS run_species, tx_nG6_run.data_nature AS run_data_nature,' .
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							'tx_nG6_run.type AS run_type, tx_nG6_run.nb_sequences AS run_nb_sequences, tx_nG6_run.full_seq_size AS run_full_seq_size,' .
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							'tx_nG6_run.description AS run_description, tx_nG6_run.sequencer AS run_sequencer, tx_nG6_run.hidden AS run_hidden,' .
							'tx_nG6_project.name AS project_name, tx_nG6_project.fe_group AS project_fe_group',
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				'FROM' => 'tx_nG6_run INNER JOIN (tx_nG6_project_run INNER JOIN tx_nG6_project ON tx_nG6_project_run.project_id=tx_nG6_project.uid)' .
						  'ON tx_nG6_run.uid=tx_nG6_project_run.run_id',
                'WHERE' => $where,
                'GROUPBY' => '',
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                'ORDERBY' => 'tx_nG6_run.date DESC, tx_nG6_run.name ASC',
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                'LIMIT' => $limit
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            );
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         $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);			
         
         if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) { // There is some results to display
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			//request total in DB
			$queryPartsc = array(
				'SELECT' => $queryParts['SELECT'],
				'FROM' => $queryParts['FROM'],
				'WHERE' => $queryParts['WHERE'],
                'GROUPBY' => '',
                'ORDERBY' => '',
                'LIMIT' => ''
            );
			$resc = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryPartsc);
         	$total_count = $GLOBALS['TYPO3_DB']->sql_num_rows($resc);
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	         //generate HTML   
         	$run_list= $this->pi_run_list_view($res);
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         	$nav_links = 	$this->pi_navigation_link_view('run_page', $this->piVars['run_page'], $total_count);
     		return $run_list ."\n". $nav_links;
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         } else { // no results
             return $this->getFieldHeader('no_raw');
         }
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       }
    }

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	/**
	 * Creates a list from a database query
	 *
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
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	function pi_run_list_view($res)	{		
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		$nb_run = 0;
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		if ($this->piVars['project_id']) {
			$content = '<br /> <h3> '.$this->getFieldHeader('runs_done').'</h3> <br />';
		}
		$content .= '<table'.$this->pi_classParam('listrow').'>
						<tr>
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							<th>'.$this->getFieldHeader('run_name').'</th>
							<th>'.$this->getFieldHeader('project_name').'</th>
							<th>'.$this->getFieldHeader('date').'</th>
							<th>'.$this->getFieldHeader('species').'</th>
							<th>'.$this->getFieldHeader('data_nature').'</th>
							<th>'.$this->getFieldHeader('type').'</th>
							<th>'.$this->getFieldHeader('nb_sequences').'</th>
							<th>'.$this->getFieldHeader('full_seq_size').'</th>
							<th>'.$this->getFieldHeader('description').'</th>
							<th>'.$this->getFieldHeader('sequencer').'</th>
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						</tr>';
		while($this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
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			if ($this->internal['currentRow']['run_hidden'] == 0) { // If it's not a hidden run
				$content .= '<tr>
					<td>'.$this->getFieldContent('name', array('run_id'=>$this->internal['currentRow']['run_id'], 'project_id'=>$this->piVars['project_id'])).'</td>
					<td>'.$this->getFieldContent('project_name').'</td>
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					<td>'.$this->getFieldContent('date').'</td>
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					<td>'.$this->getFieldContent('run_species').'</td>
					<td>'.$this->getFieldContent('run_data_nature').'</td>
					<td>'.$this->getFieldContent('run_type').'</td>
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					<td>'.number_format($this->getFieldContent('run_nb_sequences'), 0, ',', ' ').'</td>
					<td>'.number_format($this->getFieldContent('run_full_seq_size'), 0, ',', ' ').'</td>
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					<td>'.$this->getFieldContent('run_description').'</td>
					<td>'.$this->getFieldContent('run_sequencer').'</td>
					</tr>';
				$nb_run++;
			} else {
				$user_groups = t3lib_div::intExplode(',',$this->getCurrentUserGroups());
				$user_allowed = false;
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			   foreach($this->getSuperGroupsOf($this->internal['currentRow']['project_fe_group']) AS $valeur) {
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					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
						$nb_run++;
					}
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			   }
			   if ($user_allowed) {
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					$content .= '<tr>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('name', array('run_id'=>$this->internal['currentRow']['run_id'], 'project_id'=>$this->piVars['project_id'])).'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('project_name').'</td>
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						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('date').'</td>
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						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_species').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_data_nature').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_type').'</td>
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						<td '.$this->pi_classParam('hidden').' >'.number_format($this->getFieldContent('run_nb_sequences'), 0, ',', ' ').'</td>
						<td '.$this->pi_classParam('hidden').' >'.number_format($this->getFieldContent('run_full_seq_size'), 0, ',', ' ').'</td>
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						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_description').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('run_sequencer').'</td>
						</tr>';
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			   }
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			}
		}
		if ($nb_run > 0) {
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			$content .= "\n".'</table>' ; 		
			return $content;
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		} else {
			return '';
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		}
	}

	/**
	 * Display a single item from the database
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	 * 
	 * @param	ressource	$res: A database result ressource
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	 * @return	HTML of a single database entry
	 */
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	function pi_run_single_view() {		
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		$content = '<div'.$this->pi_classParam('singleView').'><h2>Run '.$this->internal['currentRow']['name'].' :</h2>';
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		$content .= '<p><strong>'.$this->getFieldContent('run_description').'</strong></p> </div>
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				<table'.$this->pi_classParam('listrow').'>
					<tr>
						<th align="left">'.$this->getFieldHeader('project_name').' :</th>
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						<td align="left">'.$this->getFieldContent('project_name').'</td>
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					</tr>	
					<tr>
						<th align="left">'.$this->getFieldHeader('date').' :</th>
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						<td align="left">'.$this->getFieldContent('date').'</td>
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					</tr>					
					<tr>
						<th align="left">'.$this->getFieldHeader('species').' :</th>
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						<td align="left">'.$this->getFieldContent('run_species').'</td>
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					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('type').' :</th>
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						<td align="left">'.$this->getFieldContent('run_type').'</td>
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					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('data_nature').' :</th>
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						<td align="left">'.$this->getFieldContent('run_data_nature').'</td>
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					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('nb_sequences').' :</th>
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						<td align="left">'.number_format($this->getFieldContent('run_nb_sequences'), 0, ',', ' ').'</td>
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					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('full_seq_size').' :</th>
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						<td align="left">'.number_format($this->getFieldContent('run_full_seq_size'), 0, ',', ' ').'</td>
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					</tr>						
					<tr>
						<th align="left">'.$this->getFieldHeader('sequencer').' :</th>
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						<td align="left">'.$this->getFieldContent('run_sequencer').'</td>
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					</tr>
					<tr>
						<th align="left">'.$this->getFieldHeader('downloads').' :</th>
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						<td align="left">'.$this->get_downloads_list().'</td>
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					</tr>
				</table>';
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		$content .= $this->pi_analyze_view('run');
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		return $content.$this->pi_getEditPanel();
	}
	
	/**
	 * Shows a list of database entries
	 *
	 * @param	string		$type: What kind of analyze is it : run or project
	 * 	 * @return	HTML list of table entries
	 */
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	function pi_analyze_view($type)	{
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		if ($type == 'analyze')	{	// If a single element should be displayed:
			$queryParts = array(
				'SELECT' => '*',
				'FROM' => 'tx_nG6_analyze',
				'WHERE' => 'tx_nG6_analyze.uid = '.$this->piVars['analyze_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
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			return $this->pi_analyze_single_view();
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		} else {
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			if (isset($this->piVars['analyze_page']))	//run position 
			{
				$current_page = intval($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'] ; 	
				
		
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			if ($type == 'run') {
				// Selects Analyzis done on this run
				$queryParts = array(
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					'SELECT' => 'tx_nG6_analyze.uid AS uid, tx_nG6_analyze.name AS name, tx_nG6_analyze.description AS description,' .
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								'tx_nG6_analyze.software AS software, tx_nG6_analyze.version AS version, tx_nG6_analyze.hidden AS hidden,' .
								'tx_nG6_project.fe_group AS project_fe_group',
					'FROM' => 'tx_nG6_analyze INNER JOIN (tx_nG6_run_analyze INNER JOIN ( tx_nG6_run INNER JOIN ( tx_nG6_project_run INNER JOIN tx_nG6_project ' .
							  'ON tx_nG6_project_run.project_id=tx_nG6_project.uid ) ' .
							  'ON tx_nG6_run.uid=tx_nG6_project_run.run_id ) ' .
							  'ON tx_nG6_run.uid=tx_nG6_run_analyze.run_id ) ' .
							  'ON tx_nG6_analyze.uid=tx_nG6_run_analyze.analyze_id ',
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					'WHERE' => 'tx_nG6_run_analyze.run_id = '.$this->piVars['run_id'],
					'GROUPBY' => '',
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					'ORDERBY' => 'tx_nG6_analyze.name',
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					'LIMIT' => $limit
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				);
			} elseif ($type == 'project') {
				// Selects Analyzis done on this project
				$queryParts = array(
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					'SELECT' => 'tx_nG6_analyze.uid AS uid, tx_nG6_analyze.name AS name, tx_nG6_analyze.description AS description,' .
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								'tx_nG6_analyze.software AS software, tx_nG6_analyze.version AS version, tx_nG6_analyze.hidden AS hidden,' .
								'tx_nG6_project.fe_group AS project_fe_group',
					'FROM' => 'tx_nG6_analyze INNER JOIN ( tx_nG6_project_analyze INNER JOIN tx_nG6_project ON tx_nG6_project.uid=tx_nG6_project_analyze.project_id ) ' .
							  'ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id',
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					'WHERE' => 'tx_nG6_project_analyze.project_id = '.$this->piVars['project_id'],
					'GROUPBY' => '',
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					'ORDERBY' => 'tx_nG6_analyze.name',
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					'LIMIT' => $limit
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				);
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			}	
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			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);		
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			$content='';
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			if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {	
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				//request total in DB
				$queryPartsc = array(
					'SELECT' => $queryParts['SELECT'],
					'FROM' => $queryParts['FROM'],
					'WHERE' => $queryParts['WHERE'],
	                'GROUPBY' => '',
	                'ORDERBY' => '',
	                'LIMIT' => ''
	            );
				$resc = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryPartsc);
	         	$total_count = $GLOBALS['TYPO3_DB']->sql_num_rows($resc);
		         //generate HTML   
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				$analyze_list=$this->pi_analyze_list_view($res , $total_count);
				$nav_links = $this->pi_navigation_link_view('analyze_page', $this->piVars['analyze_page'], $total_count);
				$content.= $analyze_list ."\n".$nav_links;
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			}
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			return $content;
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		}
	}

	/**
	 * Creates a list from a database query
	 *
	 * @param	ressource	$res: A database result ressource
	 * @return	A HTML list if result items
	 */
	function pi_analyze_list_view($res)	{
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		$nb_analyse = 0;
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		$content.='<br /> <h3> '.$this->getFieldHeader('analyzes_done').'</h3> <br />
				<table'.$this->pi_classParam('listrow').'>
					<tr>
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						<th>'.$this->getFieldHeader('name').'</th>
						<th>'.$this->getFieldHeader('description').'</th>
						<th>'.$this->getFieldHeader('software').'</th>
						<th>'.$this->getFieldHeader('version').'</th>
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					</tr>';
		while($this->internal['currentRow'] = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
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			if ($this->internal['currentRow']['hidden'] == 0) { // If it's not a hidden project
				$content .= '<tr>
					<td>'.$this->getFieldContent('name', array('analyze_id'=>$this->internal['currentRow']['uid'], 'run_id'=>$this->piVars['run_id'], 'project_id'=>$this->piVars['project_id'])).'</td>
					<td>'.$this->getFieldContent('description').'</td>
					<td>'.$this->getFieldContent('software').'</td>
					<td>'.$this->getFieldContent('version').'</td>
					</tr>';
				$nb_analyse++;
			} else {
				$user_groups = t3lib_div::intExplode(',',$this->getCurrentUserGroups());
				$user_allowed = false;
			    foreach($this->getSuperGroupsOf($this->internal['currentRow']['project_fe_group']) AS $valeur) {
					if (in_array($valeur, $user_groups)) {
						$user_allowed = true;
						$nb_analyse++;
					}
			    }
			    if ($user_allowed) {
					$content .= '<tr>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('name', array('analyze_id'=>$this->internal['currentRow']['uid'], 'run_id'=>$this->piVars['run_id'], 'project_id'=>$this->piVars['project_id'])).'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('description').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('software').'</td>
						<td '.$this->pi_classParam('hidden').' >'.$this->getFieldContent('version').'</td>
						</tr>';
			    }
			}
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		}
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		if ($nb_analyse > 0) {			
			$content .= "\n".'</table>' ;						
			return $content ;
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		} else {
			return '';
		}		
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	}

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	/**
	 * Display a single item from the database
	 *
	 * @return	HTML of a single database entry
	 */
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	function pi_analyze_single_view() {
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		// add the jquery libs + the tree plugins and its 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($this->extKey).'res/js/jquery.url.packed.js"></script>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($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"/>';

		// Sets the page content
		$content = '<script type="text/javascript" class="source">
						$(function () { 
						    $("#img_dialog").dialog({
							    autoOpen: false,
						        width: 850,
						        bgiframe: true,
						        resizable: false,
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						        position: "top",
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							    modal: true,
						        overlay: {
						            backgroundColor: "#000",
						            opacity: 0.5
						        }
						    });
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                            $(".tx-nG6-pi1-imglink").click(function() {
                               	jQuery.url.setUrl($(this).attr("href"));
                               	$("#img_dialog").dialog("option", "title", "nG6 - '.$this->internal['currentRow']['name'].'");
                               	if (jQuery.url.param("file")) {
                                       	$("#img_dialog").html(\'<img src="\'+jQuery.url.param("file")+\'"/>\').dialog("open");
                               	} else {
                                       	$("#img_dialog").html(\'<img src="\'+$(this).attr("href")+\'"/>\').dialog("open");
                               	}
                               	return false;
                            });
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						});
					</script>  ';


		$content .= '<div id="img_dialog" title=""></div>';

		$content .= '<div'.$this->pi_classParam('singleView').'><h2>Analyse '.$this->internal['currentRow']['name'].' : <span>'.$this->getFieldContent('description').'</span></h2></div>';
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		if (file_exists($this->conf['data'].$this->internal['currentRow']['directory'].'/analyse.xml' )) {
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			$xml = new DomDocument;
			$xml->load($this->conf['data'].$this->internal['currentRow']['directory'].'/analyse.xml');
			
			// Find out the analyse class
            $class = $xml->documentElement;
            $class_value = "";
			foreach ($class->childNodes AS $item) {
                if ($item->nodeName == "class") { $class_value = $item->nodeValue; } 
			}
			// If no class value : xml incorrect
			if ($class_value == "") { 
				$content .= $this->getFieldHeader('uncorrect_xml');
			} else {
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	            $xslt = new XSLTProcessor();
	            $xsl = new DOMDocument();
	            if (file_exists(PATH_typo3conf.ext.'/'.$this->extKey.'/res/xsl/'.$this->LLkey.'.'.$class_value.'.xsl')) {
	                    $xsl->load( 'typo3conf/ext/'.$this->extKey.'/res/xsl/'.$this->LLkey.'.'.$class_value.'.xsl', LIBXML_NOCDATA);
	                    $xslt->importStylesheet( $xsl );
	                    $content .= $xslt->transformToXML( $xml );
	            } else if (file_exists(PATH_typo3conf.ext.'/'.$this->extKey.'/res/xsl/default.'.$class_value.'.xsl')) {
	                    $xsl->load( 'typo3conf/ext/'.$this->extKey.'/res/xsl/default.'.$class_value.'.xsl', LIBXML_NOCDATA);
	                    $xslt->importStylesheet( $xsl );
	                    $content .= $xslt->transformToXML( $xml );
	            } else {
	                    $content .= $this->getFieldHeader('no_xsl_found');
	            }
			}
		} else if (file_exists($this->conf['data'].$this->internal['currentRow']['directory'].'/index.html' )) {
			$fp = fopen((string)$this->conf['data'].$this->internal['currentRow']['directory'].'/index.html',"r"); //lecture du fichier
			while (!feof($fp)) { //on parcourt toutes les lignes
				$content .= fgets($fp, 4096); // lecture du contenu de la ligne
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			}
		} else {
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			$content .= $this->getFieldHeader('not_synchro');
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		}
		return $content;
	}
	
	/**
	 * Returns the content of a given field
	 *
	 * @param	string		$fN: name of table field
	 * @return	Value of the field
	 */
	function getFieldContent($fN, $mergeArr=array())	{
		switch($fN) {
			case 'uid':
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				return $this->pi_list_linkSingle($this->internal['currentRow'][$fN],$this->internal['currentRow']['uid'],1, $mergeArr);	
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			break;
			case 'name':
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				return $this->pi_list_linkSingle($this->internal['currentRow'][$fN],$this->internal['currentRow']['uid'],1, $mergeArr);	
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			break;
			case 'date':
					// %A %e. %B %Y
				return strftime('%d-%m-%y',$this->internal['currentRow']['date']);
			break;			
			default:
				return $this->internal['currentRow'][$fN];
			break;
		}
	}
	/**
	 * Returns the label for a fieldname from local language array
	 *
	 * @param	[type]		$fN: ...
	 * @return	[type]		...
	 */
	function getFieldHeader($fN)	{
		switch($fN) {
			
			default:
				return $this->pi_getLL('listFieldHeader_'.$fN,'['.$fN.']');
			break;
		}
	}
	
	/**
	 * Returns a sorting link for a column header
	 *
	 * @param	string		$fN: Fieldname
	 * @return	The fieldlabel wrapped in link that contains sorting vars
	 */
	function getFieldHeader_sortLink($fN)	{
		return $this->pi_linkTP_keepPIvars($this->getFieldHeader($fN),array('sort'=>$fN.':'.($this->internal['descFlag']?0:1)));
	}
	
	/**
	 * 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 a list of downloadable file
	 *
	 * @return	HTML of a list of downlabale links
	 */
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	function get_downloads_list() {
		$directory = (string)$this->conf['data'].$this->internal['currentRow']['run_directory'];
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		try {
			if (!is_dir($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>';
			while($entry = @readdir($my_directory)) {
				if(!is_dir($directory.'/'.$entry)&& $entry != '.' && $entry != '..' && !$this->endsWith($entry, ".cfg")) {
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					$link = 'fileadmin/'.$this->internal['currentRow']['run_directory'].'/'.$entry;
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					$download .= '<li><a href="'.$link.'" target="_blank">'.$entry.'</a></li>';
				}
			}
			$download .= '</ul>';		
			closedir($my_directory);
			return $download;
		}
		catch (Exception $e) {
			return $this->getFieldHeader('not_synchro');
		}
	}
	
	// return true if $str ends with $sub
	function endsWith( $str, $sub ) {
		return ( substr( $str, strlen( $str ) - strlen( $sub ) ) == $sub );
	}
	
	function getCurrentUserGroups() {
		$tab_groups = array();
		$this->getSubGroups($GLOBALS['TSFE']->fe_user->user['usergroup'], '', $tab_groups);
		$groups = '';
		foreach($tab_groups as $valeur) { $groups .= $valeur.','; }
		return substr($groups, 0, -1);	
	}

	/**
	 * Fetches subgroups of groups. Function is called recursively for each subgroup.
	 * Function was previously copied from t3lib_userAuthGroup->fetchGroups and has been slightly modified.
	 *
	 * @param	string		Commalist of fe_groups uid numbers
	 * @param	string		List of already processed fe_groups-uids so the function will not fall into a eternal recursion.
	 * @return	array
	 * @access private
	 */
	function getSubGroups($grList, $idList='', &$groups)	{

			// Fetching records of the groups in $grList (which are not blocked by lockedToDomain either):
		$lockToDomain_SQL = ' AND (lockToDomain=\'\' OR lockToDomain IS NULL OR lockToDomain=\''.$this->authInfo['HTTP_HOST'].'\')';
		if (!$this->authInfo['showHiddenRecords'])	$hiddenP = 'AND hidden=0 ';
		$res = $GLOBALS['TYPO3_DB']->exec_SELECTquery('uid,subgroup', 'fe_groups', 'deleted=0 '.$hiddenP.' AND uid IN ('.$grList.')'.$lockToDomain_SQL);

		$groupRows = array();	// Internal group record storage

			// The groups array is filled
		while ($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
			if(!in_array($row['uid'], $groups))	{ $groups[] = $row['uid']; }
			$groupRows[$row['uid']] = $row;
		}

			// Traversing records in the correct order
		$include_staticArr = t3lib_div::intExplode(',', $grList);
		foreach($include_staticArr as $uid)	{	// traversing list

				// Get row:
			$row=$groupRows[$uid];
			if (is_array($row) && !t3lib_div::inList($idList,$uid))	{	// Must be an array and $uid should not be in the idList, because then it is somewhere previously in the grouplist

					// Include sub groups
				if (trim($row['subgroup']))	{
					$theList = implode(',',t3lib_div::intExplode(',',$row['subgroup']));	// Make integer list
					$this->getSubGroups($theList, $idList.','.$uid, $groups);		// Call recursively, pass along list of already processed groups so they are not recursed again.
				}
			}
		}
	}
	
	function userIsAuthorized () {
		if ($this->piVars['project_id']) {
			$queryParts = array(
				'SELECT' => 'fe_group',
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'uid='.$this->piVars['project_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
			$authorized_group = $val['fe_group'];
		} elseif ($this->piVars['run_id']) {
			$queryParts = array(
				'SELECT' => 'project_id',
				'FROM' => 'tx_nG6_project_run',
				'WHERE' => 'run_id='.$this->piVars['run_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res1 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res1);
			$queryParts = array(
				'SELECT' => 'fe_group',
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'uid='.$val['project_id'],
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res2 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res2);
			$authorized_group = $val['fe_group'];
		} else {
			return true;
		}
		if (!$GLOBALS['TSFE']->loginUser) { // If the user is not logged on
			return $authorized_group == 0;
		} else {
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			return in_array($authorized_group, preg_split("/,/", $this->getCurrentUserGroups()));
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		}
	}
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	function getSuperGroupsOf ($group) {
		// First get the super group of the given group
		$queryParts = array(
			'SELECT' => 'uid, subgroup',
			'FROM' => 'fe_groups',
			'WHERE' => '',
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		$reslist = array();
		$i = 0;
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res))	{
			if (in_array($group, t3lib_div::intExplode(',',$row['subgroup']))) {
				$reslist[$i] = $row['uid'];
				$i++;
			}
		}
		return $reslist;
	}
	
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	/**
	 * 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	$maxline	current total number of rows
	 *
	 * @return	HTML navigation links
	 */
	function pi_navigation_link_view($name, $start, $total_count) 
	{  
		$start = intval($start);		
		
		//max page number
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		$end = $total_count/$this->internal['results_at_a_time'] ;
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		$end = ceil($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;
		
		if( $end == '1' )	{			//do nothing
			return '' ;
		}		
		elseif($start == '1')	{		//don't display << nor <
			$go_back = '';
		}
		elseif($start == $end)	{	//don't display > nor >>
			$go_ahead = '';		
		}
		else 		{	//display both
		}		
		$content = '<div align="right">'.$go_back .' '. $current_pos .' '. $go_ahead .'</div>' ;
		return $content;
	}	
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}



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']);
}

?>