<?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(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_utils.php');

/**
 * Class_nG6_db' for the 'nG6' extension.
 * This class is in charge of all communication with the database
 *
 * @author	PF bioinformatique de Toulouse <>
 */
class tx_nG6_db {
	
	/*
	 * Global functions
	*------------------------------------------------------------*/
	
	/**
	* Update the specified field of the table
	 *
	* @param	string  $table the entity to change
	* @param	string  $id     the element id to update
	* @param	string  $field  the field to change
	* @param	string  $value  the new value
	*/
	function update_field($table, $id, $field, $value) {
		if( $field == 'uid' ) {
			throw new Exception ("The function 'update_field' cannot change an id.") ;
		}	
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ($table, 'uid='.$id, array($field => $value));
	}
	
	/**
     * Return the size used by ng6 datas from a starting date to a end date
     * 
     * @param int $usergroup		the usergroup
     * @param string $data_folder	the folder data
     * @param bool $get_analyzes	true if the admin wants to include analyzes
     * @param bool $cumul_values	true if the admin wants cumulatives values
     * @param int $step				the step (0 = one month, 1 = six months, 2 = one year)
     * @param int $date_start		the date start
     * @param int $date_end			the date end
     * @return array
     */
    function get_size($usergroup, $data_folder, $get_analyzes=false, $cumul_values=false, $step=2, $date_start=0, $date_end=0){
		
    	//const - tstamp is in seconds, nb of seconds in one day
    	$one_day_val = 24 * 3600;
    	
    	// init min max
    	if($date_start==0){ $date_start = intval(tx_nG6_db::get_run_min_date()); }
    	if($date_end==0){ $date_end = intval(tx_nG6_db::get_run_max_date()); }
  
    	$date_cursors = $date_start;
    	$res_tab = null;

		// get all users
		if ($usergroup != "0") {
			$users_in_group = tx_nG6_db::get_all_users_in_group($usergroup);
			$project_list_final = array();
			foreach($users_in_group as $list_current_user_id){
				// get all user projects
				$all_user_projects = tx_nG6_db::select_all_user_projects($list_current_user_id);
				foreach($all_user_projects as $p_val){
					if(!in_array($p_val['id'], $project_list_final)){
						$project_list_final[] = $p_val['id'];
					}
				}
			}
		}

		$cumulated_size = 0;
    	while($date_cursors < $date_end){
    		// increment step iterator
    		$total_day_count_tstamp = 0;
    		switch ($step) {
    			case 0:		// 1 month
    				$nb_days_in_month = date('t', $date_cursors);
    				$total_day_count_tstamp = $one_day_val * $nb_days_in_month;
    				break;
    			case 1:		// 6 months
    				$date_cursor_tmp = $date_cursors;
    				for($i = 0;$i < 6; $i++){
    					$nb_days_in_month = cal_days_in_month(CAL_GREGORIAN, date('n', $date_cursor_tmp), date('Y', $date_cursor_tmp));
    					$total_day_count_tstamp += $one_day_val * $nb_days_in_month;
    					// +1 month * 6
    					$date_cursor_tmp = strtotime('+1 month', $date_cursor_tmp);
    				}
    				break;
    			case 2:		// 1 year
    				$nb_days_in_year = date("z", mktime(0,0,0,12,31,date('Y', $date_cursors)));
    				$total_day_count_tstamp = $one_day_val * $nb_days_in_year;
    				break;
    		}
    		
    		$date_cursore = $date_cursors + $total_day_count_tstamp;
    		$current_size = 0;
    		
			if ($usergroup != "0") {
				$where = 'tx_nG6_project.uid IN ('.implode(",",$project_list_final).') AND tx_nG6_run.date BETWEEN '.$date_cursors.' AND '.$date_cursore;	
			} else {
				$where = 'tx_nG6_run.date BETWEEN '.$date_cursors.' AND '.$date_cursore;
			}
			
    		// get all runs the usergroup can access to
    		$queryParts = array(
    			'SELECT' 	=> 'tx_nG6_run.uid as run_id',
    			'FROM' 		=> 'tx_nG6_project '
    				.' INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id '
    				.' INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
    			'WHERE' 	=> $where,
    			'GROUPBY' 	=> '',
    			'ORDERBY' 	=> '',
    			'LIMIT' 	=> ''
    		);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
				$current_size += tx_nG6_db::get_run_size($res_row['run_id'], $get_analyzes);
			}
			
			// get all project analysis the usergroup can access to
			if ($get_analyzes) {
				if ($usergroup != "0") {
					$where = 'tx_nG6_project.uid IN ('.implode(",",$project_list_final).') AND tx_nG6_analyze.date BETWEEN '.$date_cursors.' AND '.$date_cursore;	
				} else {
					$where = 'tx_nG6_analyze.date BETWEEN '.$date_cursors.' AND '.$date_cursore;
				}
	    		$queryParts = array(
	    			'SELECT' 	=> 'tx_nG6_analyze.uid as analyze_id',
	    			'FROM' 		=> 'tx_nG6_project '
	    				.' INNER JOIN tx_nG6_project_analyze ON tx_nG6_project.uid=tx_nG6_project_analyze.project_id '
	    				.' INNER JOIN tx_nG6_analyze ON tx_nG6_project_analyze.analyze_id=tx_nG6_analyze.uid ',
	    			'WHERE' 	=> $where,
	    			'GROUPBY' 	=> '',
	    			'ORDERBY' 	=> '',
	    			'LIMIT' 	=> ''
	    		);
				$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
					$current_size += tx_nG6_db::get_analysis_size($res_row['analyze_id']);
				}
			}

    		$cumulated_size += $current_size;
    		if(!$cumul_values){
    	    	$res_tab[] = array($date_cursore*1000, $current_size);
    	    }else{
    	    	$res_tab[] = array($date_cursore*1000, $cumulated_size);
    	    }

    		$date_cursors = $date_cursore + 1;
    	}
    	return $res_tab;	
    }
	
    /**
     * Select all project for the current user
     *
     * @param	string	$by	by can group, organism, location
     * @param	string	$role	role can be create_user, manager
     * @return	table with all projects
     */
    function select_projects_repartition($role, $by='title') {
    	
    	if ($role == "create_user") {
    		$queryParts = array(
    				'SELECT' 	=> 'tx_nG6_project.uid as pid, fe_groups.title as title, fe_groups.tx_nG6_organism as organism, fe_groups.tx_nG6_location as location',
    				'FROM' 		=> 'tx_nG6_project '
    				.' INNER JOIN fe_users ON tx_nG6_project.cruser_id=fe_users.uid '
    				.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ',
    				'WHERE' 	=> "",
    				'GROUPBY' 	=> '',
    				'ORDERBY' 	=> '',
    				'LIMIT' 	=> ''
    		);
    		//$where = "tx_nG6_project.cruser_id="
    	} else if ($role == "manager") {
	    	$queryParts = array(
    				'SELECT' 	=> 'tx_nG6_project.uid as pid, fe_groups.title as title, fe_groups.tx_nG6_organism as organism, fe_groups.tx_nG6_location as location',
	    			'FROM' 		=> 'tx_nG6_project '
	    			.' INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '
	    			.' INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid '
	    			.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ',
	    			'WHERE' 	=> "fe_rights.right_id=1",
	    			'GROUPBY' 	=> '',
	    			'ORDERBY' 	=> '',
	    			'LIMIT' 	=> ''
	    	);
    	}
    	$by_title = array() ;
    	$by_organism = array();
    	$by_location = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		if (!isset ($by_title[$res_row['title']])) {
    			$by_title[$res_row['title']] = array(
    					'count'			=> 1,
    					'organism'		=> $res_row['organism'],
    					'location'		=> $res_row['location']);
    		} else {
    			$by_title[$res_row['title']]['count'] += 1;
    		}
    		
    		if (!isset ($by_organism[$res_row['organism']])) {
    			$by_organism[$res_row['organism']] = array(
    					'count'			=> 1);
    		} else {
    			$by_organism[$res_row['organism']]['count'] += 1;
    		}
    		
    		if (!isset ($by_location[$res_row['location']])) {
    			$by_location[$res_row['location']] = array(
    					'count'			=> 1);
    		} else {
    			$by_location[$res_row['location']]['count'] += 1;
    		}
    	}
    	if ($by=='title') {
    		return ($by_title);
    	} else if ($by=='organism') {
    		return ($by_organism);
    	} else if ($by=='location') {
    		return ($by_location);
    	}
    }

    function select_projects_evolution($values, $by, $role) {
		if ($by == "organism" || $by == "location") {
			$by = "tx_nG6_".$by;
		}
	
		$from = "" ;
		$where = "fe_groups.".$by." IN ('".implode("', '", $values)."')" ;
    	if ($role == "create_user") {
    		$from = 'tx_nG6_project '
	    			.' INNER JOIN fe_users ON tx_nG6_project.cruser_id=fe_users.uid '
	    			.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ' ;
    	} else if ($role == "manager") {
    		$from = 'tx_nG6_project '
    				.' INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '
    				.' INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid '
    				.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ';
    		$where .= " AND fe_rights.right_id=1" ;
    	}
    	$queryParts = array(
    			'SELECT' 	=> 'tx_nG6_project.crdate, count(tx_nG6_project.crdate) nb',
    			'FROM' 		=> $from,
    			'WHERE' 	=> $where,
    			'GROUPBY' 	=> 'tx_nG6_project.crdate',
    			'ORDERBY' 	=> 'tx_nG6_project.crdate',
    			'LIMIT' 	=> ''
    	);
    	$results = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$results[] = array($res_row["crdate"], $res_row["nb"]);
    	}

    	return $results;
    }

    function select_projects_distribution($values, $by, $role) {
		$from = "" ;
		$where = "" ;
		if ($by == "organism" || $by == "location") {
			$by = "tx_nG6_".$by;
		}
    	if ($role == "create_user") {
    		$from = 'tx_nG6_project '
	    			.' INNER JOIN fe_users ON tx_nG6_project.cruser_id=fe_users.uid '
	    			.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ' ;
    	} else if ($role == "manager") {
    		$from = 'tx_nG6_project '
    				.' INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '
    				.' INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid '
    				.' INNER JOIN fe_groups ON fe_groups.uid=fe_users.usergroup ';
    		$where = "fe_rights.right_id=1" ;
    	}
    	$queryParts = array(
    			'SELECT' 	=> 'fe_groups.'.$by.', count(fe_groups.'.$by.') nb',
    			'FROM' 		=> $from,
    			'WHERE' 	=> $where,
    			'GROUPBY' 	=> 'fe_groups.'.$by,
    			'ORDERBY' 	=> '',
    			'LIMIT' 	=> ''
    	);
    	$results = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$others = 0 ;
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		if( in_array($res_row[$by], $values) ) {
    			$results[] = array($res_row[$by], $res_row["nb"]);
    		} else {
    			$others += $res_row["nb"] ;
    		}
    	}
    	if ($others != 0) { 
    		$results[] = array("OTHERS", $others);
    	}
    	return $results;
    }
    
    
	/*
	 * Project functions
	 *------------------------------------------------------------*/

	/**
	 * Select all project for the current user
	 * 
	 * @param	string	$user_id	the user id
	 * @return	table with all projects
	 */
	function select_all_user_projects($user_id, $orderby='', $limit='') {		
		$projects = array();
		
		// If the user is not logged on display demonstration project
		if ($user_id == null) { $where = 'tx_nG6_project.public=0'; } 
		else { $where = 'fe_rights.fe_user_id='.$user_id; }
		
		//First, get the analyzis project-scale
		$queryParts = array(
			'SELECT' => 'tx_nG6_project.uid AS project_id, '.
						'tx_nG6_project.name AS project_name, '.
						'tx_nG6_project.description AS project_description, '.
						'tx_nG6_project.public AS project_public, '.
						'tx_nG6_project.crdate AS project_crdate, '.
						'tx_nG6_project.hidden AS project_hidden ',
			'FROM' => 'tx_nG6_project INNER JOIN fe_rights ON fe_rights.project_id=tx_nG6_project.uid',
			'WHERE' => $where,
			'GROUPBY' => '',
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
		);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);		
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$project_id = $row['project_id'];
			if (!isset ($projects['project_'.$project_id])) {		
				$projects['project_'.$project_id] = array(
					'id'			=> $project_id,				
					'name'			=> $row['project_name'],
					'hidden'		=> $row['project_hidden'],
					'date'			=> $row['project_crdate'],
					'public'		=> $row['project_public'],
					'description'	=> $row['project_description']);
			}
						
		}		
		return $projects;
	}

	/**
	* Select all project for the current user
	*
	* @param	string	$user_id	the user id
	* @return	table with all projects
	*/
	function get_user_projects($user_id, $orderby='', $limit='') {
		$projects = array();
	
		// If the user is not logged on display demonstration project
		if ($user_id == null) {
			$where = 'tx_nG6_project.public=0';
		}
		else { 
				$where = 'fe_rights.fe_user_id='.$user_id.' AND ((fe_rights.right_id<>2 AND tx_nG6_project.hidden=0) '
				.'OR fe_rights.right_id=2)' ;
		}
	
		//First, get the analyzis project-scale
		$queryParts = array(
				'SELECT' => 'tx_nG6_project.uid AS project_id, '.
							'tx_nG6_project.name AS project_name, '.
							'tx_nG6_project.description AS project_description, '.
							'tx_nG6_project.public AS project_public, '.
							'tx_nG6_project.crdate AS project_crdate, '.
							'tx_nG6_project.hidden AS project_hidden ',
				'FROM' => 'tx_nG6_project INNER JOIN fe_rights ON fe_rights.project_id=tx_nG6_project.uid',
				'WHERE' => $where,
				'GROUPBY' => '',
				'ORDERBY' => $orderby,
				'LIMIT' => $limit
		);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$project_id = $row['project_id'];
			if (!isset ($projects['project_'.$project_id])) {
				$projects['project_'.$project_id] = array(
						'id'			=> $project_id,				
						'name'			=> $row['project_name'],
						'hidden'		=> $row['project_hidden'],
						'date'			=> $row['project_crdate'],
						'public'		=> $row['project_public'],
						'description'	=> $row['project_description']);
			}
	
		}
		return $projects;
	}

	/**
	 * Select a run from the database
	 *
	 * @param	string	$project_id	the project id to return
	 * @return	hash table with all project information
	 */
	function select_project($project_id) {
		$queryParts = array(
			'SELECT' => '*',
			'FROM' => 'tx_nG6_project',
			'WHERE' => 'tx_nG6_project.uid = '.$project_id,
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		$vals = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
		return array('id'			=> $vals['uid'],				
					 'name'			=> $vals['name'],
					 'hidden'		=> $vals['hidden'],
					 'date'			=> $vals['crdate'],
					 'public'		=> $vals['public'],
					 'description'	=> $vals['description']);
	}

	/**
	 * Select all runs linked to the specified project
	 *
	 * @param	string	$project_id	the project id
	 * @return	hash table with all runs information
	 */
    function get_project_runs($project_id, $orderby='', $limit='') {
    	
		// First select all runs from the database
		$queryParts = Array( 
			'SELECT' => 'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
					 	'tx_nG6_run.species AS run_species,'.
						'tx_nG6_run.description AS run_description, '.
						'tx_nG6_run.data_nature AS run_data_nature, '.
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
						'tx_nG6_run.name AS run_name, '.
						'tx_nG6_run.nb_sequences AS run_nb_sequences, '.
						'tx_nG6_run.full_seq_size AS run_full_seq_size, '.
						'tx_nG6_run.date AS run_date, '.
						'tx_nG6_run.hidden AS run_hidden, '.
						'tx_nG6_project.uid AS project_id, '.
						'tx_nG6_project.name AS project_name ',
			'FROM' => 'tx_nG6_project '.
  						'INNER JOIN tx_nG6_project_run ON  tx_nG6_project.uid=tx_nG6_project_run.project_id '.
  						'INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
			'WHERE' => 'tx_nG6_project.uid='.$project_id,
			'GROUPBY' => '',
			'ORDERBY' => $orderby,
			'LIMIT' 	=> $limit
		);

	
		// Then create the result hash table
		$results = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$run_id = $row['run_id'];				
			if (!isset($results['run_'.$run_id])) {				
				$results['run_'.$run_id] = array( 
					'id'			=> $run_id,
					'directory'		=> $row['run_directory'], 
					'name' 			=> $row['run_name'],
					'project_name' 	=> $row['project_name'],
					'hidden'		=> $row['run_hidden'],
					'species' 		=> $row['run_species'],
					'nb_sequences' 	=> $row['run_nb_sequences'],
					'full_seq_size' => $row['run_full_seq_size'],
					'project_id' 	=> $row['project_id'],
					'date'			=> $row['run_date'],
					'data_nature'	=> $row['run_data_nature'],
					'sequencer'		=> $row['run_sequencer'],
					'type'			=> $row['run_type'],
					'description' 	=> $row['run_description']
				);
			}						
		}
		return $results;
    }

    /**
     * Select all runs linked to the specified project for the user
     *
     * @param	string	$user_id	the user id
     * @param	string	$project_id	the project id
     * @return	hash table with all runs information
     */
     function get_user_project_runs($user_id, $project_id, $orderby='', $limit='') {
    	// If the user is not logged on display demonstration project
	    if ($user_id == null) {
	    	$where = 'tx_nG6_project.uid='.$project_id.' AND tx_nG6_project.public=0 AND tx_nG6_run.hidden=0';
	    }
	    else {
	    	$where = 'fe_users.uid='.$user_id.' AND '.'tx_nG6_project.uid='.$project_id.
	    		' AND ((fe_rights.right_id<>2 AND tx_nG6_run.hidden=0) OR fe_rights.right_id=2)' ;
	    }
    	
	    // First select all runs from the database
	    $queryParts = Array(
		    'SELECT' => 'tx_nG6_run.uid AS run_id,'.
			    'tx_nG6_run.directory AS run_directory,'.
			    'tx_nG6_run.species AS run_species,'.
			    'tx_nG6_run.description AS run_description, '.
			    'tx_nG6_run.data_nature AS run_data_nature, '.
			    'tx_nG6_run.sequencer AS run_sequencer, '.
			    'tx_nG6_run.type AS run_type, '.
			    'tx_nG6_run.name AS run_name, '.
			    'tx_nG6_run.nb_sequences AS run_nb_sequences, '.
			    'tx_nG6_run.full_seq_size AS run_full_seq_size, '.
			    'tx_nG6_run.date AS run_date, '.
			    'tx_nG6_run.hidden AS run_hidden, '.
			    'tx_nG6_project.uid AS project_id, '.
			    'tx_nG6_project.name AS project_name ',
		    'FROM' => 'tx_nG6_run '.
			    'INNER JOIN tx_nG6_project_run ON tx_nG6_run.uid=tx_nG6_project_run.run_id '.
			    'INNER JOIN tx_nG6_project ON tx_nG6_project_run.project_id=tx_nG6_project.uid '.
			    'INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '.
			    'INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid ',
		    'WHERE' => $where,
		    'GROUPBY' => '',
		    'ORDERBY' => $orderby,
		    'LIMIT' 	=> $limit
	    );
    
	    // Then create the result hash table
	    $results = array();
	    $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
	    while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
	    	$run_id = $row['run_id'];
	    	if (!isset($results['run_'.$run_id])) {
			    $results['run_'.$run_id] = array(
			    'id'			=> $run_id,
			    'directory'		=> $row['run_directory'],
			    'name' 			=> $row['run_name'],
			    							'project_name' 	=> $row['project_name'],
			    'hidden'		=> $row['run_hidden'],
			    							'species' 		=> $row['run_species'],
			    'nb_sequences' 	=> $row['run_nb_sequences'],
			    							'full_seq_size' => $row['run_full_seq_size'],
			    							'project_id' 	=> $row['project_id'],
			    							'date'			=> $row['run_date'],
			    							'data_nature'	=> $row['run_data_nature'],
			    							'sequencer'		=> $row['run_sequencer'],
			    							'type'			=> $row['run_type'],
			    'description' 	=> $row['run_description']
			    				);
		    }
	    }
	    return $results;
    }

	/**
	 * Select all analysis linked to the specified project
	 *
	 * @param	string	$project_id	the project id
	 * @return	hash table with all analysis information
	 */
    function get_project_analysis($project_id, $orderby='', $limit='') {
    	
    	// First select all analysis from the database    	
    	$queryParts = array( 
			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
						'tx_nG6_analyze.name AS analyze_name, '.
						'tx_nG6_analyze.class AS analyze_class, '.
						'tx_nG6_analyze.date AS analyze_date, '.
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.version AS analyze_version, '.
						'tx_nG6_analyze.params AS analyze_params, '.
						'tx_nG6_analyze.description AS analyze_description, '.
    					'tx_nG6_analyze.is_editable AS analyze_is_editable, '.
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid, '.
						'tx_nG6_analyze.hidden AS analyze_hidden ',
			'FROM' => 'tx_nG6_project '.
						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_project.uid = tx_nG6_project_analyze.project_id '.
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id ',
			'WHERE' => 'tx_nG6_project.uid='.$project_id,
			'GROUPBY' => '',
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
		);
		// Then create the result hash table
		$results = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$analyze_id = $row['analyze_id'];
			if (!isset ($results['analyse_'.$analyze_id])) {				
				$results['analyse_'.$analyze_id] = array( 
					'directory'		=> $row['analyze_directory'], 
					'name' 			=> $row['analyze_name'],
					'class'			=> $row['analyze_class'],
					'id' 			=> $row['analyze_id'],
					'hidden' 		=> $row['analyze_hidden'],
					'params' 		=> $row['analyze_params'],
					'software' 		=> $row['analyze_software'],
					'version' 		=> $row['analyze_version'],
					'date'			=> $row['analyze_date'],
					'description' 	=> $row['analyze_description'],
					'is_editable' 	=> $row['analyze_is_editable'],
					'parent_id'		=> $row['analyze_parent_uid']	
				);
			}						
		}
		return $results;
    }

    /**
    * Select all analysis linked to the specified project for the user
    *
    * @param	string	$user_id	the user id
    * @param	string	$project_id	the project id
    * @return	hash table with all analysis information
    */
    function get_user_project_analysis($user_id, $project_id, $orderby='', $limit='') {
    	// If the user is not logged on display demonstration project
    	if ($user_id == null) {
    		$where = 'tx_nG6_project.uid='.$project_id.' AND tx_nG6_project.public=0 AND tx_nG6_run.hidden=0';
    	}
    	else {
    		$where = 'fe_users.uid='.$user_id.' AND tx_nG6_project.uid='.$project_id.
    					' AND ((fe_rights.right_id<>2 AND tx_nG6_analyze.hidden=0) OR fe_rights.right_id=2)' ;
    	}
    	
    	// First select all analysis from the database
    	$queryParts = array(
    			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
    						'tx_nG6_analyze.directory AS analyze_directory,'. 
    						'tx_nG6_analyze.name AS analyze_name, '.
    						'tx_nG6_analyze.class AS analyze_class, '.
    						'tx_nG6_analyze.date AS analyze_date, '.
    						'tx_nG6_analyze.software AS analyze_software, '.
    						'tx_nG6_analyze.version AS analyze_version, '.
    						'tx_nG6_analyze.params AS analyze_params, '.
    						'tx_nG6_analyze.description AS analyze_description, '.
    						'tx_nG6_analyze.is_editable AS analyze_is_editable, '.
    						'tx_nG6_analyze.parent_uid AS analyze_parent_uid, '.
    						'tx_nG6_analyze.hidden AS analyze_hidden ',
    			'FROM' => 'tx_nG6_analyze '.
    						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_analyze.uid = tx_nG6_project_analyze.analyze_id '.
    						'INNER JOIN tx_nG6_project ON tx_nG6_project_analyze.project_id=tx_nG6_project.uid '.
							'INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '.
					  		'INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid ',
    			'WHERE' => $where,
    			'GROUPBY' => '',
    			'ORDERBY' => $orderby,
    			'LIMIT' => $limit
    	);
    	// Then create the result hash table
    	$results = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$analyze_id = $row['analyze_id'];
    		if (!isset ($results['analyse_'.$analyze_id])) {
    			$results['analyse_'.$analyze_id] = array(
    					'directory'		=> $row['analyze_directory'], 
    					'name' 			=> $row['analyze_name'],
    					'class'			=> $row['analyze_class'],
    					'id' 			=> $row['analyze_id'],
    					'hidden' 		=> $row['analyze_hidden'],
    					'params' 		=> $row['analyze_params'],
    					'software' 		=> $row['analyze_software'],
    					'version' 		=> $row['analyze_version'],
    					'date'			=> $row['analyze_date'],
    					'description' 	=> $row['analyze_description'],
    					'is_editable' 	=> $row['analyze_is_editable'],
    					'parent_id'		=> $row['analyze_parent_uid']	
    			);
    		}
    	}
    	return $results;
    }

    /**
     * Hide a project and sublevels (runs & analyzes) datas from database project
     * 
     * @param	string	$p_id	the project id to hide
     */
	function hide_project($p_id) {
		
		// First change all project runs
		$project_runs = tx_nG6_db::get_project_runs($p_id);
		foreach($project_runs as $run_id => $run_values) {
			tx_nG6_db::hide_run($run_values['id']);
		}

		// Then all project analysis
    	$project_analysis = tx_nG6_db::get_project_analysis($p_id);
		foreach($project_analysis as $analysis_id => $analysis_values) {  
			tx_nG6_db::hide_analysis($analysis_values['id']);
		}
		tx_nG6_db::unpublish_project($p_id);
		// Finaly change the project itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_project', 'uid='.$p_id, array('hidden' => '1'));
	}

    /**
     * Unhide a project and sublevels (runs & analyzes) datas
     * 
     * @param	string	$p_id	the project id to hide
     */
	function unhide_project($p_id) {
		
		// First change all project runs
		$project_runs = tx_nG6_db::get_project_runs($p_id);
		foreach($project_runs as $run_id => $run_values) {
			tx_nG6_db::unhide_run($run_values['id']);
		}

		// Then all project analysis
    	$project_analysis = tx_nG6_db::get_project_analysis($p_id);
		foreach($project_analysis as $analysis_id => $analysis_values) {  
			tx_nG6_db::unhide_analysis($analysis_values['id']);
		}
		
		// Finaly change the project itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_project', 'uid='.$p_id, array('hidden' => '0'));
	}

    /**
     * Publish the project
     * 
     * @param	string	$p_id	the project id to publish
     */
	function publish_project($p_id) {
		// First unhide the project
		tx_nG6_db::unhide_project($p_id);
		// The set the project as visible
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_project', 'uid='.$p_id, array('public' => '0'));
	}

    /**
     * Unpublish the project
     * 
     * @param	string	$p_id	the project id to publish
     */
	function unpublish_project($p_id) {
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_project', 'uid='.$p_id, array('public' => '1'));
	}

    /**
     * Delete a project and sublevels (runs & analyzes) datas from database project
     * 
     * @param string $p_id			the project id
     * @param string $user_login	the user login
     * @param string $user_pwd		the user password
     * @param string $data_folder	the data folder
     */
	function delete_project($p_id, $user_login, $user_pwd, $data_folder) {
		
		$res = 0;
		// All runs
		$project_runs = tx_nG6_db::get_project_runs($p_id);
		foreach($project_runs as $run_id => $run_values) {
			if ($run_values['id'] != 'undefined' && $run_values['id'] != '') {
				//delete the run sublevels
				$res = tx_nG6_db::delete_run($run_values['id'], $user_login, $user_pwd, $data_folder);
				if ($res != 0) { break; }				
			}
		}
		
		// All project_analysis
		if ($res == 0) {
			$project_analysis = tx_nG6_db::get_project_analysis($p_id);
			foreach($project_analysis as $analyse_id => $analyze_values) {  
				if ($analyze_values['id'] != 'undefined' && $analyze_values['id'] != '') {
					// delete table 'analyze' entries
					$res = tx_nG6_db::delete_analysis($analyze_values['id'], $user_login, $user_pwd, $data_folder);
					if ($res != 0) { break; }
				}
			}
		}
		
		// Delete DB project entry
		if ($res == 0) {
			$table='tx_nG6_project';
			$where='tx_nG6_project.uid='.$p_id;
			$res1 = $GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
			if ($res1 != 1) {$res = 1;}
		}
		
		// Delete right associated to the project
		if ($res == 0) {
			$table='fe_rights';
			$where='fe_rights.project_id='.$p_id;
			$res1 = $GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
			if ($res1 != 1) {$res = 1;}
		}
		
		return $res;
	}

    /**
     * Return the size of the project
     * 
     * @param	string	$p_id	the project id to return the size
	 * @param	string	$data_folder	the data folder
	 * @param	boolean $get_analyzes	get analyzes size ? 
     */
	function get_project_size($p_id, $get_analyzes=false) {
		
		$full_size = 0;
		// All runs
		$project_runs = tx_nG6_db::get_project_runs($p_id);
		foreach($project_runs as $run_id => $run_values) {
			$full_size += tx_nG6_db::get_run_size($run_values['id'], $get_analyzes);
		}
		if ($get_analyzes) {
			// All analysis
			$project_analysis = tx_nG6_db::get_project_analysis($p_id);
			foreach($project_analysis as $analyse_id => $analyze_values) {  
				$full_size += tx_nG6_db::get_analysis_size($analyze_values['id']);
			}
		}
		return $full_size;
	}


	/*
	 * Run functions
	 *------------------------------------------------------------*/
	
	
	/**
	 * Select all run for the specified user
	 * 
	 * @param	string	$user_id	the user id
	 * @return	table with all projects
	 */
	function select_all_user_runs($user_id, $orderby='', $limit='') {

		// If the user is not logged on display demonstration project
		if ($user_id == null) { $where = 'tx_nG6_project.public=0'; } 
		else { $where = 'fe_rights.fe_user_id='.$user_id; }
		
     	// Execute the request
		$queryParts = Array( 
			'SELECT' => 'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
					 	'tx_nG6_run.species AS run_species,'.
						'tx_nG6_run.description AS run_description, '.
						'tx_nG6_run.data_nature AS run_data_nature, '. 
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
						'tx_nG6_run.name AS run_name, '.
						'tx_nG6_run.nb_sequences AS run_nb_sequences, '.
						'tx_nG6_run.full_seq_size AS run_full_seq_size, '.
						'tx_nG6_run.date AS run_date, '.
						'tx_nG6_run.hidden AS run_hidden, '.
						'tx_nG6_project.uid AS project_id, '.
						'tx_nG6_project.name AS project_name ',
			'FROM' => 'fe_rights '.
						'INNER JOIN tx_nG6_project ON tx_nG6_project.uid=fe_rights.project_id '.
						'INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id '.
						'INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
			'WHERE' => $where,
			'GROUPBY' => '',
			'ORDERBY' => $orderby,
			'LIMIT' 	=> $limit
		); 
		// Then create the result hash table
		$results = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$run_id = $row['run_id'];	
			if (!isset($results['run_'.$run_id])) {				
				$results['run_'.$run_id] = array(
					'id'			=> $run_id,  
					'directory'		=> $row['run_directory'], 
					'name' 			=> $row['run_name'],
					'project_name' 	=> $row['project_name'],
					'project_id' 	=> $row['project_id'],
					'hidden'		=> $row['run_hidden'],
					'species' 		=> $row['run_species'],
					'nb_sequences' 	=> $row['run_nb_sequences'],
					'full_seq_size' => $row['run_full_seq_size'],
					'date'			=> $row['run_date'],
					'data_nature'	=> $row['run_data_nature'],
					'sequencer'		=> $row['run_sequencer'],
					'type'			=> $row['run_type'],
					'description' 	=> $row['run_description']				
				);
			}						
		}
		return $results;

	}

	/**
	 * Select all information for the specified run
	 *
	 * @param	string	$run_id	the run id
	 * @return	hash table with all the run information
	 */
	function select_run($run_id) {
		
		// First select the run from the database
		$queryParts = Array( 
			'SELECT' => 'tx_nG6_project.uid AS project_id,'.
						'tx_nG6_project.name AS project_name,'.
						'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
						'tx_nG6_run.description AS run_description, '.
						'tx_nG6_run.species AS run_species, '.
						'tx_nG6_run.name AS run_name, '.
						'tx_nG6_run.data_nature AS run_data_nature, '.
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
						'tx_nG6_run.full_seq_size, '.
						'tx_nG6_run.hidden AS run_hidden, '.
						'tx_nG6_run.nb_sequences, '.
						'tx_nG6_run.storage_size, '.
						'tx_nG6_run.date AS run_date',
			'FROM' => 'fe_rights '.
						'INNER JOIN tx_nG6_project ON tx_nG6_project.uid=fe_rights.project_id '.
						'INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id '.
						'INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
			'WHERE' => 'tx_nG6_run.uid='.$run_id,
			'GROUPBY' => '',
			'ORDERBY' => 'tx_nG6_run.date DESC',
			'LIMIT' 	=> ''
		); 
		// Then create the result hash table
		$result = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {			
			$result = array( 
				'id'			=> $row['run_id'],  
				'project_id'	=> $row['project_id'], 
				'project_name'	=> $row['project_name'], 
				'directory'		=> $row['run_directory'], 
				'name' 			=> $row['run_name'],
				'hidden'		=> $row['run_hidden'],
				'species' 		=> $row['run_species'],
				'nb_sequences' 	=> $row['nb_sequences'],
				'storage_size' 	=> intval($row['storage_size']),
				'full_seq_size' => $row['full_seq_size'],
				'date'			=> $row['run_date'],
				'data_nature' 	=> $row['run_data_nature'],
				'sequencer' 	=> $row['run_sequencer'],
				'type' 			=> $row['run_type'],
				'description' 	=> $row['run_description']				
			);					
		}
		return $result;
    }

	/**
	 * Select all mids linked to the specified run
	 *
	 * @param	string	$run_id	the run id
	 * @return	hash table with all mids description
	 */
	function select_mid_descriptions($run_id) {
		
		// First select all analysis from the database
		$queryParts = array( 
			'SELECT' => 'mid, description ',
			'FROM' => 'tx_nG6_sample ',
			'WHERE' => 'run_id='.$run_id,
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
		
		$result = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$result[$row["mid"]] = $row["description"];
		}
		return $result;
		
	}	

	/**
	 * Select all analysis linked to the specified run
	 *
	 * @param	string	$run_id	the run id
	 * @return	hash table with all analysis information
	 */
    function get_run_analysis($run_id, $orderby='', $limit='') {
		// First select all analysis from the database
		$queryParts = array( 
			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
						'tx_nG6_analyze.name AS analyze_name, '.
						'tx_nG6_analyze.params AS analyze_params, '.
						'tx_nG6_analyze.class AS analyze_class, '.
						'tx_nG6_analyze.date AS analyze_date, '.
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.version AS analyze_version, '.
						'tx_nG6_analyze.hidden AS analyze_hidden, '.
						'tx_nG6_analyze.description AS analyze_description, '.
						'tx_nG6_analyze.is_editable AS analyze_is_editable, '.
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
			'FROM' => 'tx_nG6_run_analyze '.
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id ',
			'WHERE' => 'tx_nG6_run_analyze.run_id='.$run_id,
			'GROUPBY' => '',
			'ORDERBY' => $orderby,
			'LIMIT' => $limit
		);
		// Then create the result hash table
		$results = array();
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			$analyze_id = $row['analyze_id'];
			if (!isset ($results['analyse_'.$analyze_id])) {				
				$results['analyse_'.$analyze_id] = array( 
					'directory'		=> $row['analyze_directory'], 
					'name' 			=> $row['analyze_name'],
					'params' 		=> $row['analyze_params'],
					'class' 		=> $row['analyze_class'],
					'id' 			=> $row['analyze_id'],
					'hidden' 		=> $row['analyze_hidden'],
					'software' 		=> $row['analyze_software'],
					'version' 		=> $row['analyze_version'],
					'date'			=> $row['analyze_date'],
					'description' 	=> $row['analyze_description'],
					'is_editable' 	=> $row['analyze_is_editable'],
					'parent_id'		=> $row['analyze_parent_uid']
				);
			}						
		}
		return $results;
    }

    /**
    * Select all analysis linked to the specified run for the user
    *
    * @param	string	$user_id	the user id
    * @param	string	$run_id	the run id
    * @return	hash table with all analysis information
    */
    function get_user_run_analysis($user_id, $run_id, $orderby='', $limit='') {
    	// If the user is not logged on display demonstration project
    	if ($user_id == null) {
    		$where = 'tx_nG6_run_analyze.run_id='.$run_id.' AND tx_nG6_project.public=0 AND tx_nG6_analyze.hidden=0' ;
    	}
    	else {
    		$where = 'fe_users.uid='.$user_id.' AND '.'tx_nG6_run_analyze.run_id='.$run_id.
    						' AND ((fe_rights.right_id<>2 AND tx_nG6_analyze.hidden=0) OR fe_rights.right_id=2)' ;
    	}
    	
    	// First select all analysis from the database
    	$queryParts = array(
    			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
    						'tx_nG6_analyze.directory AS analyze_directory,'. 
    						'tx_nG6_analyze.name AS analyze_name, '.
    						'tx_nG6_analyze.params AS analyze_params, '.
    						'tx_nG6_analyze.class AS analyze_class, '.
    						'tx_nG6_analyze.date AS analyze_date, '.
    						'tx_nG6_analyze.software AS analyze_software, '.
    						'tx_nG6_analyze.version AS analyze_version, '.
    						'tx_nG6_analyze.hidden AS analyze_hidden, '.
    						'tx_nG6_analyze.description AS analyze_description, '.
    						'tx_nG6_analyze.is_editable AS analyze_is_editable, '.
    						'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
    			'FROM' => 'tx_nG6_analyze '.
							'INNER JOIN tx_nG6_run_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id '.
							'INNER JOIN tx_nG6_run ON tx_nG6_run_analyze.run_id = tx_nG6_run.uid '.
							'INNER JOIN tx_nG6_project_run ON tx_nG6_run.uid = tx_nG6_project_run.run_id '.
							'INNER JOIN tx_nG6_project ON tx_nG6_project_run.project_id = tx_nG6_project.uid '. 
							'INNER JOIN fe_rights ON tx_nG6_project.uid=fe_rights.project_id '.
							'INNER JOIN fe_users ON fe_rights.fe_user_id=fe_users.uid ',
    			'WHERE' => $where,
    			'GROUPBY' => '',
    			'ORDERBY' => $orderby,
    			'LIMIT' => $limit
    	);
    	// Then create the result hash table
    	$results = array();
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$analyze_id = $row['analyze_id'];
    		if (!isset ($results['analyse_'.$analyze_id])) {
    			$results['analyse_'.$analyze_id] = array(
    					'directory'		=> $row['analyze_directory'], 
    					'name' 			=> $row['analyze_name'],
    					'params' 		=> $row['analyze_params'],
    					'class' 		=> $row['analyze_class'],
    					'id' 			=> $row['analyze_id'],
    					'hidden' 		=> $row['analyze_hidden'],
    					'software' 		=> $row['analyze_software'],
    					'version' 		=> $row['analyze_version'],
    					'date'			=> $row['analyze_date'],
    					'description' 	=> $row['analyze_description'],
    					'is_editable' 	=> $row['analyze_is_editable'],
    					'parent_id'		=> $row['analyze_parent_uid']
    			);
    		}
    	}
    	return $results;
    }

	/**
	 * Delete a run, sample and sublevel (analyzes) datas from database project
	 * 
	 * @param string $r_id			the run id
	 * @param string $user_login	the user login
	 * @param string $user_pwd		the user password
	 * @param string $data_folder	the data folder
	 */
	function delete_run($r_id, $user_login, $user_pwd, $data_folder) {		

		$res = 0;		
		$run_analysis = tx_nG6_db::get_run_analysis($r_id);
		foreach($run_analysis as $analyse_id => $analyze_values) {
			if ($analyze_values['id'] != 'undefined' && $analyze_values['id'] != '') {				
				// delete table 'analyze' entries
				$res = tx_nG6_db::delete_analysis($analyze_values['id'], $user_login, $user_pwd, $data_folder);
				if ($res != 0) { break; }
			}
		}
		
		// First select the run
		$my_run = tx_nG6_db::select_run($r_id);
		
		// delete run
		if ($res == 0) {
			$table='tx_nG6_project_run';
			$where='run_id='.$r_id;
			$GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
			
			$table='tx_nG6_run';
			$where='tx_nG6_run.uid='.$r_id;
			$res1 = $GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
			if ($res1 != 1) {$res = 1;}
		}
			
		// delete run samples
		if ($res == 0) {
			$table='tx_nG6_sample';
			$where='tx_nG6_sample.run_id='.$r_id;
			$GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
		}
		
		if ($res == 0) {
			// Delete the run directory
			$res = tx_nG6_utils::delete_directory($user_login, $user_pwd, $data_folder.$my_run['directory']);
		}
		
		return $res;
	}

    /**
     * Return the size of the run
     * 
     * @param	string	$r_id	the run id to return the size
	 * @param	string	$data_folder	the data folder
	 * @param	boolean $get_analyzes	get analyzes size ? 
     */
	function get_run_size($r_id, $get_analyzes=false) {
		$full_size = 0;
		if($get_analyzes){
			$run_analysis = tx_nG6_db::get_run_analysis($r_id);
			foreach($run_analysis as $analyse_id => $analyze_values) {
				$full_size += tx_nG6_db::get_analysis_size($analyze_values['id']);
			}
		}
		// Then select the run
		$my_run = tx_nG6_db::select_run($r_id);
		$full_size += $my_run['storage_size'];
			
		return $full_size;
	}

    /**
     * Hide a run and sublevels (analysis)
     * 
     * @param	string	$r_id	the run id to hide
     */
	function hide_run($r_id) {

		// First select all run analysis
    	$run_analysis = tx_nG6_db::get_run_analysis($r_id);
		foreach($run_analysis as $analysis_id => $analysis_values) {  
			tx_nG6_db::hide_analysis($analysis_values['id']);
		}
		
		// Finaly change the project itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_run', 'uid='.$r_id, array('hidden' => '1'));
	}

    /**
     * Unhide a run and sublevels (analysis)
     * 
     * @param	string	$r_id	the run id to hide
     */
	function unhide_run($r_id, $unhide_up=false) {
	
		if ($unhide_up) {
			// Unhide the project
			$GLOBALS['TYPO3_DB']-> exec_UPDATEquery (
				'tx_nG6_project, tx_nG6_project_run',
				'tx_nG6_project.uid = tx_nG6_project_run.project_id AND tx_nG6_project_run.run_id = '.$r_id ,
				array('tx_nG6_project.hidden' => '0')
			);
		}

		// Then all run analysis
    	$run_analysis = tx_nG6_db::get_run_analysis($r_id);
		foreach($run_analysis as $analysis_id => $analysis_values) {  
			tx_nG6_db::unhide_analysis($analysis_values['id']);
		}
		
		// Finaly change the run itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_run', 'uid='.$r_id, array('hidden' => '0'));
	}

    /**
     * Get the run min date
     * 
     * @return int timestamp
     */
    function get_run_min_date(){
    	$queryParts = Array(
    		'SELECT' 	=> 'MIN(tx_nG6_run.date) as min_date ',
    		'FROM' 		=> 'tx_nG6_run',
    		'WHERE' 	=> 'tx_nG6_run.date!=0',
    		'GROUPBY' 	=> '',
    		'ORDERBY' 	=> '',
    		'LIMIT' 	=> ''
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
   		$min_date = 0;
    	if($GLOBALS['TYPO3_DB']->sql_num_rows($res) == 1) {
    		$tab = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
    		$min_date = intval($tab['min_date']);
    	}else{
    		$min_date = -1;
    	}
    	return $min_date;
    }
    
    /**
    * Get the run max date
    *
    * @return int timestamp
    */
    function get_run_max_date(){
    	$queryParts = Array(
        		'SELECT' 	=> 'MAX(tx_nG6_run.date) as max_date ',
        		'FROM' 		=> 'tx_nG6_run',
        		'WHERE' 	=> 'tx_nG6_run.date!=0',
        		'GROUPBY' 	=> '',
        		'ORDERBY' 	=> '',
        		'LIMIT' 	=> ''
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$max_date = 0;
    	if($GLOBALS['TYPO3_DB']->sql_num_rows($res) == 1) {
    		$tab = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
    		$max_date = intval($tab['max_date']);
    	}else{
    		$max_date = -1;
    	}
    	return $max_date;
    }
    
	/*
	 * Analysis functions
	 *------------------------------------------------------------*/
	 
	/**
	 * Select all information on an analyse
	 *
	 * @param	string	$analyse_id	the analyse id
	 * @return	hash table with all analyse information
	 */
    function select_analyse($analyse_id) {

		// First select all analyse information
		$queryParts = array( 
			'SELECT' => 'tx_nG6_project.uid AS project_id,'. 
						'tx_nG6_project.name AS project_name,'. 
						'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
						'tx_nG6_analyze.name AS analyze_name, '.
						'tx_nG6_analyze.params AS analyze_params, '.
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.class AS analyze_class, '.
						'tx_nG6_analyze.date AS analyze_date, '.
						'tx_nG6_analyze.description AS analyze_description, '.
						'tx_nG6_analyze.version AS analyze_version, '.
						'tx_nG6_analyze.is_editable AS analyze_is_editable, '.
						'tx_nG6_analyze.storage_size AS analyze_storage_size, '.
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
			'FROM' => 'tx_nG6_project '.
						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_project.uid = tx_nG6_project_analyze.project_id '.
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id ',
			'WHERE' => 'tx_nG6_analyze.uid='.$analyse_id,
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
		
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		
		// If it's a project analyse, add project information
		if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {
			$result = array();
			while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {	
				$result = array( 
					'project_name'	=> $row['project_name'], 
					'project_id'	=> $row['project_id'],
					'run_name'		=> 'None', 
					'run_id'		=> 'None',					 
					'directory'		=> $row['analyze_directory'], 
					'name' 			=> $row['analyze_name'],
					'class'			=> $row['analyze_class'],
					'params'		=> $row['analyze_params'],
					'date'			=> $row['analyze_date'],
					'description' 	=> $row['analyze_description'],
					'parent_id'		=> $row['analyze_parent_uid'],
					'software'		=> $row['analyze_software'],
					'storage_size'	=> intval($row['analyze_storage_size']),
					'version'		=> $row['analyze_version'],
					'is_editable'   => $row['analyze_is_editable']
				);				
			}
			return $result;
		} else { // If it's a run analyse, add run information
			$queryParts = array( 
				'SELECT' => 'tx_nG6_project.name AS project_name,'.
							'tx_nG6_project.uid AS project_id,'.
							'tx_nG6_run.uid AS run_id,'. 
							'tx_nG6_run.name AS run_name,'.
							'tx_nG6_analyze.uid AS analyze_id,'. 
							'tx_nG6_analyze.directory AS analyze_directory,'. 
							'tx_nG6_analyze.name AS analyze_name, '.
							'tx_nG6_analyze.params AS analyze_params, '.
							'tx_nG6_analyze.class AS analyze_class, '.
							'tx_nG6_analyze.date AS analyze_date, '.
							'tx_nG6_analyze.software AS analyze_software, '.
							'tx_nG6_analyze.version AS analyze_version, '.
							'tx_nG6_analyze.description AS analyze_description,'.
							'tx_nG6_analyze.is_editable AS analyze_is_editable,'.
							'tx_nG6_analyze.storage_size AS analyze_storage_size, '.
							'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
				'FROM' => 'tx_nG6_project '.
							'INNER JOIN tx_nG6_project_run ON tx_nG6_project_run.project_id = tx_nG6_project.uid '.
							'INNER JOIN tx_nG6_run ON tx_nG6_run.uid = tx_nG6_project_run.run_id '.
							'INNER JOIN tx_nG6_run_analyze ON tx_nG6_run_analyze.run_id = tx_nG6_run.uid '.
							'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id ',
				'WHERE' => 'tx_nG6_analyze.uid='.$analyse_id,
				'GROUPBY' => '',
				'ORDERBY' => 'tx_nG6_analyze.name',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$result = array();
			while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {	
				$result = array( 
					'project_name'	=> $row['project_name'], 
					'project_id'	=> $row['project_id'],
					'run_name'		=> $row['run_name'], 
					'run_id'		=> $row['run_id'], 			 
					'directory'		=> $row['analyze_directory'], 
					'name' 			=> $row['analyze_name'],
					'params'		=> $row['analyze_params'],
					'class' 		=> $row['analyze_class'],
					'date'			=> $row['analyze_date'],
					'description' 	=> $row['analyze_description'],
					'software'		=> $row['analyze_software'],
					'parent_id'		=> $row['analyze_parent_uid'],
					'version'		=> $row['analyze_version'], 
					'storage_size'	=> intval($row['analyze_storage_size']),
					'is_editable'	=> $row['analyze_is_editable']
				);				
			}
			return $result;
		}
    }

	/**
	 * Select all results of an analyse
	 *
	 * @param	string	$analyse_id	the analyse id
	 * @return	hash table with all analyse results
	 */
    function select_analyse_results($analyse_id) {

		// First select all analyse information
		$queryParts = array( 
			'SELECT' => 'uid,file,rkey,rvalue,rgroup ',
			'FROM' => 'tx_nG6_result ',
			'WHERE' => 'analyze_id='.$analyse_id,
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' => ''
		);
		
		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
		$result = array();
		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
			if (array_key_exists($row['file'], $result)) {
				if (array_key_exists($row['rgroup'], $result[$row['file']])) {
					$result[$row['file']][$row['rgroup']][$row['rkey']] = $row['rvalue'];
				} else {
					$result[$row['file']][$row['rgroup']] = array($row['rkey'] => $row['rvalue']);
				}
			} else {
				$result[$row['file']] = array($row['rgroup'] => array($row['rkey'] => $row['rvalue']));
			}			
		}
		return $result;
    }

    /**
     * Return the size of the analysis
     * 
     * @param	string	$a_id	the analysis id to return the size
	 * @param	string	$data_folder	the data folder
     */
	function get_analysis_size($a_id) {
		// First select the analyse
		$my_analysis = tx_nG6_db::select_analyse($a_id);
		return $my_analysis['storage_size'];
	}

    /**
     * Hide an analysis
     * 
     * @param	string	$a_id	the analysis id to hide
     */
	function hide_analysis($a_id) {
		// Change the analysis itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_analyze', 'uid='.$a_id, array('hidden' => '1'));
	}

    /**
     * Unhide an analysis
     * 
     * @param	string	$a_id	the analysis id to hide
     */
	function unhide_analysis($a_id, $unhide_up=false) {
	
		if ($unhide_up) {
			$queryParts = array(
				'SELECT'  => 'tx_nG6_project_analyze.uid',
				'FROM'    => 'tx_nG6_project_analyze',
				'WHERE'   => 'tx_nG6_project_analyze.analyze_id = '.$a_id,
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT'   => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts) ;
			$is_project_analyze = $GLOBALS['TYPO3_DB']->sql_num_rows( $res ) ;
			
			// If the analyse isn't link to run
			if( $is_project_analyze ) 
			{
				// unhide the project
				$GLOBALS['TYPO3_DB']-> exec_UPDATEquery (
					'tx_nG6_project, tx_nG6_project_analyze',
					'tx_nG6_project.uid = tx_nG6_project_analyze.project_id AND tx_nG6_project_analyze.analyze_id = '.$a_id ,
					array('tx_nG6_project.hidden' => '0')
				) ;
			}
			// If the analyse is link to run
			else
			{
				// unhide the project and the run
				$GLOBALS['TYPO3_DB']->exec_UPDATEquery (
					'tx_nG6_project, tx_nG6_project_run, tx_nG6_run, tx_nG6_run_analyze', 
					'tx_nG6_project.uid = tx_nG6_project_run.project_id '.
						'AND tx_nG6_project_run.run_id = tx_nG6_run.uid '.
						'AND tx_nG6_run.uid = tx_nG6_run_analyze.run_id '.
						'AND tx_nG6_run_analyze.analyze_id = '.$a_id ,
					array('tx_nG6_project.hidden' => '0', 'tx_nG6_run.hidden' => '0')
				) ;
			}
		}

		// Change the analysis itself
		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ('tx_nG6_analyze', 'uid='.$a_id, array('hidden' => '0'));
	}

	/**
	 * Delete an analyze and results from database project
	 * 
	 * @param string $a_id			the analyze id
	 * @param string $user_login	the user login
	 * @param string $user_pwd		the user password
	 * @param string $data_folder	the data folder
	 * @return	0=>everything ok, 1=>user right problem, 2=>wrong authentification, 3=>connection error
	 */
	function delete_analysis($a_id, $user_login, $user_pwd, $data_folder) {

		$res = 0;

		// First select the analyse
		$my_analysis = tx_nG6_db::select_analyse($a_id);
		
		// Delete the analysis results from the database
		$table='tx_nG6_result';
		$where='tx_nG6_result.analyze_id='.$a_id;
		$GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);

		// Intermediate tables
		$table='tx_nG6_project_analyze';
		$where='analyze_id='.$a_id;
		$GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
		$table='tx_nG6_run_analyze';
		$where='analyze_id='.$a_id;
		$GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
		
		// Finaly the analysis itself
		$table='tx_nG6_analyze';
		$where='tx_nG6_analyze.uid='.$a_id;
		$res1 = $GLOBALS['TYPO3_DB']-> exec_DELETEquery ($table, $where);
		if ($res1 != 1) { $res = 1; } 
		
		if ($res == 0) {
			// Delete the analyse directory
			$res = tx_nG6_utils::delete_directory($user_login, $user_pwd, $data_folder.$my_analysis['directory']);
		}

		return $res;
	}


	/*
	 * User functions
	 *------------------------------------------------------------*/
	
	/**
	 * Return if the user is authorized or not to access the specified project and run
	 *
	 * @param	int	$user_id	the user id
	 * @param	string	$project_id	the project id
	 * @param	string	$project_id	the run id
	 * @return	boolean
	 */
	function user_is_authorized ($user_id, $project_id, $run_id) {
		$authorized = false;
		
		// public project ?
		if ($project_id) {
			$queryParts = array(
				'SELECT' => 'public',
				'FROM' => 'tx_nG6_project',
				'WHERE' => 'uid='.$project_id,
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
			$authorized = ($val['public'] == 0);
		} elseif($run_id) {
			$queryParts = array(
				'SELECT' => 'public',
				'FROM' => 'tx_nG6_project INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id',
				'WHERE' => 'tx_nG6_project_run.run_id='.$run_id,
				'GROUPBY' => '',
				'ORDERBY' => '',
				'LIMIT' => ''
			);
			$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
			$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
			$authorized = ($val['public'] == 0);
		}
		
		// not a public project
		if(!$authorized){
		
			// authorized in project ?
			if ($project_id) {			
				$queryParts = array(
					'SELECT' => 'fe_rights.right_id ',
					'FROM' => 'fe_rights INNER JOIN tx_nG6_project ON tx_nG6_project.uid=fe_rights.project_id ',
					'WHERE' => 'fe_rights.fe_user_id='.$user_id.' AND tx_nG6_project.uid='.$project_id,
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$res1 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res1);
				
				if(isset($val['right_id'])){
					$authorized = true;
				}
				
			// authorized in run ?
			} elseif ($run_id) {
				$queryParts = array(
					'SELECT' => 'fe_rights.right_id ',
					'FROM' => 'fe_rights '.
							'INNER JOIN tx_nG6_project ON tx_nG6_project.uid=fe_rights.project_id '.
							'INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id ',
					'WHERE' => 'fe_rights.fe_user_id='.$user_id.' AND tx_nG6_project_run.run_id='.$run_id,
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$res1 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res1);
				
				if(isset($val['right_id'])){
					$authorized = true;
				}
				
			} 
		}
		return $authorized;
	}

	/**
	 * Return if the user is a superuser (administrator) for the specified project/run/analyse
	 *
	 * @param	string	$user_id		the user id
	 * @param	string	$type			can be project/run/analyse
	 * @param	string	$uid			the [project/run/analyse]'s uid
	 * @return	boolean {1 = ok, 0 = nok}
	 */
    function is_administrator($user_id, $type, $uid) {
    	
    	$is_admin = false;
    	
    	if(!$user_id == null){
    	
	    	// Project
	   		if ($type == 'project') {
				$is_admin = tx_nG6_db::is_project_administrator($user_id, $uid);
			
			// Run
			} elseif ($type == 'run') {
				$queryParts = array(
					'SELECT' => 'project_id',
					'FROM' => 'tx_nG6_project_run',
					'WHERE' => 'run_id='.$uid,
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$res1 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res1);
				$is_admin = tx_nG6_db::is_project_administrator($user_id, $val['project_id']);
			
			// Analyze
			} elseif ($type == 'analyze') {
				$queryParts = array(
					'SELECT' => 'run_id',
					'FROM' => 'tx_nG6_run_analyze',
					'WHERE' => 'analyze_id='.$uid,
					'GROUPBY' => '',
					'ORDERBY' => '',
					'LIMIT' => ''
				);
				$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
				
				// Run_analyze
				if ($GLOBALS['TYPO3_DB']->sql_num_rows($res) > 0) {
					$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
					$queryParts = array(
						'SELECT' => 'project_id',
						'FROM' => 'tx_nG6_project_run',
						'WHERE' => 'run_id='.$val['run_id'],
						'GROUPBY' => '',
						'ORDERBY' => '',
						'LIMIT' => ''
					);
					$res2 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
					$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res2);
					$is_admin = tx_nG6_db::is_project_administrator($user_id, $val['project_id']);
				
				// project_analyze
				} else {
					$queryParts = array(
						'SELECT' => 'project_id',
						'FROM' => 'tx_nG6_project_analyze',
						'WHERE' => 'analyze_id='.$uid,
						'GROUPBY' => '',
						'ORDERBY' => '',
						'LIMIT' => ''
					);
					$res2 = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
					$val = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res2);
					$is_admin = tx_nG6_db::is_project_administrator($user_id, $val['project_id']);
				}
				
			} 
    	}
		
		return $is_admin; 
    }

    /**
    * Get user's rights on project.
    *
    * @param int $project_id the project id
    * @param int $user_id the user id
    */
    function get_user_right_on_project($user_id, $project_id) {
    	$right_id = -1;
    	$queryParts = array(
    		'SELECT' => 'fe_rights.right_id AS right_id ',
    		'FROM' => 'fe_rights',
    		'WHERE' => 'fe_rights.fe_user_id='. $user_id .' AND fe_rights.project_id='.$project_id
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$right_id = $row['right_id'];
    	}    	
    	return $right_id;
    }
    
    /**
     * Return true if the user is a member on the project
     *
     * @param int $user_id the user id
     * @param int $project_id ths project id
     */
    function is_project_member($user_id, $project_id){
    	$is_member = false;
    	$right = tx_nG6_db::get_user_right_on_project($user_id, $project_id);
    	if ($right == 0) {
    		$is_member = true;
    	}
    	return $is_member;
    }
    
    /**
     * Return true if the user is a manager on the project
     *
     * @param int $user_id the user id
     * @param int $project_id ths project id
     */
    function is_project_manager($user_id, $project_id){
    	$is_manager = false;
    	$right = tx_nG6_db::get_user_right_on_project($user_id, $project_id);
    	if ($right == 1) {
    		$is_manager = true;
    	}
    	return $is_manager;
    }
    
    /**
     * Return true if the user is an administrator on the project
     *
     * @param int $user_id the user id
     * @param int $project_id ths project id
     */
    function is_project_administrator($user_id, $project_id){
    	$is_admin = false;
    	$right = tx_nG6_db::get_user_right_on_project($user_id, $project_id);
    	if ($right == 2) {
    		$is_admin = true;
    	}
    	return $is_admin;
    }

    
    /**
    * Get all users  with rights on the project.
    *
    * @param int $project_id the project id
    */
    function get_all_users_on_project($project_id){
    	$users = array();
    	$queryParts = Array(
    		'SELECT' => 'fe_users.uid, fe_users.username, fe_users.lastlogin, fe_users.first_name, '
			    	.' fe_users.last_name, fe_users.email, fe_rights.right_id, fe_users.cruser_id ',
			'FROM' => 'fe_users INNER JOIN fe_rights ON fe_users.uid=fe_rights.fe_user_id ',
    		'WHERE' => 'fe_rights.project_id='.$project_id,
    		'GROUPBY' => '',
    		'ORDERBY' => '',
    		'LIMIT' 	=> '',
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$res_tab = array();
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    
    		$user_id = $res_row['uid'];
    		$lastlogin = date("d-m-Y", $res_row['lastlogin']);
    
    		$cruser_infos = tx_nG6_db::get_user_informations($res_row['cruser_id']);
    		
    		if (!isset ($users['user_'.$user_id])){
    			$users['user_'.$user_id] = array(
    				'id' 			=>	$user_id,
    				'username' 		=>	$res_row['username'],
    				'lastlogin' 	=>	$lastlogin,
    				'first_name' 	=>	$res_row['first_name'],
    				'last_name' 	=>	$res_row['last_name'],
    				'email' 		=>	$res_row['email'],
    				'right_id' 		=>	$res_row['right_id'],
    				'cruser_id'		=>  $res_row['cruser_id'],
    				'cruser_name'	=>  $cruser_infos['username']
    			);
    		}
    
    	}
    	return $users;
    }
    

    /**
     * Delete acces from a project to a specific member
     * 
     * @param int $user_id	the user id
     * @param int $project_id	the project id
     */
    function delete_access_to_project($user_id, $project_id){
    	$GLOBALS['TYPO3_DB']->exec_DELETEquery('fe_rights', 'fe_rights.fe_user_id='.$user_id.' AND fe_rights.project_id='.$project_id);
    }
    
    
    /**
     * Change right on project for a member.
     * 
     * @param int $user_id		the user id
     * @param int $project_id	the project id
     * @param int $right		the right id (0=member, 1=manager, 2=admin)
     */
    function change_access_to_project($user_id, $project_id, $right){
    	$GLOBALS['TYPO3_DB']->exec_UPDATEquery ('fe_rights', 'fe_rights.fe_user_id='.$user_id.' AND fe_rights.project_id='.$project_id, array('fe_rights.right_id' => $right));
    }
    
    /**
     * Add a new member to the project.
     *
     * @param int $user_id		the user id
     * @param int $project_id	the project id
     * @param int $right			the right id (0=member, 1=manager, 2=admin)
     */
    function add_access_to_project($user_id, $project_id, $right_id){
    	
    	$member_tab = array(
    		'fe_user_id'	=>	$user_id,
    		'project_id'	=>	$project_id,
    		'right_id'	=>	$right_id
    	);
    	
    	$GLOBALS['TYPO3_DB']->exec_INSERTquery ('fe_rights', $member_tab);
    }
    
    
    /**
     * Get all usernames, firstnames and lastnames starting with a string.
     * 
     * @param string $name_start	the string part
     * @param string $user_col		the fe_users column to use
     * @return array
     */
    function get_all_names_starting_with($name_start, $user_col) {
    	$queryParts = Array(
    		'SELECT' => 'fe_users.uid, fe_users.username, fe_users.last_name, fe_users.first_name, fe_users.password, fe_users.email, fe_users.cruser_id, fe_groups.title, fe_groups.tx_nG6_organism, fe_groups.tx_nG6_location',
			'FROM' => 'fe_users INNER JOIN fe_groups ON fe_users.usergroup=fe_groups.uid',
			'WHERE' => 'fe_users.'.$user_col.' LIKE "'.$name_start.'%"',
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' 	=> '',
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$res_tab = array();
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$res_tab[] = array(
    			'uid'			=>	$res_row['uid'],
    			'username' 		=>	$res_row['username'],
    			'first_name' 	=>	$res_row['first_name'],
    			'last_name' 	=>	$res_row['last_name'],
    			'password' 		=>	$res_row['password'],
    			'email' 		=>	$res_row['email'],
    			'title' 		=>	$res_row['title'],
    			'cruser_id' 	=>	$res_row['cruser_id'],
    			'organism' 		=>	$res_row['tx_nG6_organism'],
    			'location' 		=>	$res_row['tx_nG6_location']
    				
    		);
    	}
    	return $res_tab;
    }
    
    
   /**
    * Get all groupnames starting with a string.
    * 
    * @param string $starts_with 	the string part
    * @param string $col 	        the colone name to seek in
    * @return array
    */
    function get_all_starts_with_in_group($starts_with, $col) {
    	$queryParts = Array(
        		'SELECT' => '*',
    			'FROM' => 'fe_groups',
    			'WHERE' => 'fe_groups.'.$col.' LIKE "'.$starts_with.'%"',
    			'GROUPBY' => '',
    			'ORDERBY' => '',
    			'LIMIT' 	=> '',
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$res_tab = array();
    	$distinct = array();
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		if( $col == 'title') {
	    		$res_tab[] = array(
	    			'uid'			=>	$res_row['uid'],
	        		'title'			=>	$res_row['title'],
	    			'organism'		=>	$res_row['tx_nG6_organism'],
	    			'location'		=>	$res_row['tx_nG6_location']
	    		);
    		} else {
    			if( !isset($distinct[$res_row[$col]]) ) {
	    			$res_tab[] = array(
	    				'uid'			=>	$res_row['uid'],
	    				substr($col, 7)		=>	$res_row[$col]
	    			);
	    			$distinct[$res_row[$col]] = True ;
    			}
    		}
    	}
    	return $res_tab;
    }
    
    
    /**
     * Get user informations.
     * 
     * @param int  $user_id the user id
     */
    function get_user_informations($user_id){
    	$queryParts = Array(
    		'SELECT' => 'fe_users.uid, fe_users.username, fe_users.last_name, fe_users.first_name, fe_users.password, fe_users.email, fe_users.cruser_id',
    		'FROM' => 'fe_users',
    		'WHERE' => 'fe_users.uid='.$user_id,
    		'GROUPBY' => '',
    		'ORDERBY' => '',
    		'LIMIT' 	=> '',
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$res_tab = null;
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$res_tab = array(
    			'uid'			=>	$res_row['uid'],
    			'username' 		=>	$res_row['username'],
    			'first_name' 	=>	$res_row['first_name'],
    			'last_name' 	=>	$res_row['last_name'],
    			'password' 		=>	$res_row['password'],
    			'email' 		=>	$res_row['email'],
    			'cruser_id' 	=>	$res_row['cruser_id']
    		);
    	}
    	return $res_tab;
    }
    
    function select_user_by_username($username){
    	$res_tab = null;
    	$queryParts = Array(
    		'SELECT' => 'fe_users.uid, fe_users.username, fe_users.first_name, fe_users.last_name, fe_users.email',
    		'FROM' => 'fe_users',
    		'WHERE' => 'fe_users.username LIKE "'.$username.'" ',
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' 	=> '',
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
	    	$res_tab = array(
    			'uid'			=>	$res_row['uid'],
    			'username' 		=>	$res_row['username'],
    			'first_name' 	=>	$res_row['first_name'],
    			'last_name' 	=>	$res_row['last_name'],
    			'email' 		=>	$res_row['email'],
    		);
    	}
    	return $res_tab;
    }
    
    function user_field_exist ($field, $value){
    	$queryParts = Array(
    		'SELECT' => 'fe_users.uid',
    		'FROM' => 'fe_users',
    		'WHERE' => 'fe_users.' . $field . ' LIKE "'.$value.'" ',
			'GROUPBY' => '',
			'ORDERBY' => '',
			'LIMIT' 	=> '',
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$uid = null;
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
	    	$uid = $res_row['uid'];
    	}
    	return isset($uid);
    }

    /**
     * Create a new user in the DB.
     * 
     * @param array $user_datas the user array
     * @return 0: ok, 1: username exists, 2: email exists
     */
    function add_user($user_name, $first_name, $last_name, $email, $password, $cruser_id, $group_id, $pid){
    	
    	// first check if username or email are unique
    	if (tx_nG6_db::user_field_exist("username", $user_name)) {
    		return 1;
    	} else if (tx_nG6_db::user_field_exist("email", $email)) {
    		return 2;
    	} else {
			// Create new user
			$user_datas = array(
				'username'		=>	$user_name,
				'pid'			=>	$pid,
				'first_name'	=>	$first_name,
				'last_name'		=>	$last_name,
				'email'			=>	$email,
				'password'		=>	$password,
				'cruser_id'		=>	$cruser_id,
				'usergroup'		=> 	$group_id,
				'tstamp'		=> 	time(),
				'crdate'		=> 	time()
			);
	    	$GLOBALS['TYPO3_DB']->exec_INSERTquery('fe_users', $user_datas);
	    	return 0;
	    }
    	
    }
    
    /**
     * Tell if the group name exists in the DB.
     * 
     * @param string $group_name the group name
     */
    function get_group_id($group_name) {
    	$exists = null;
    	$queryParts = Array(
    		'SELECT' => 'fe_groups.uid',
    		'FROM' => 'fe_groups',
    		'WHERE' => 'fe_groups.title="'.$group_name.'" ',
    		'GROUPBY' => '',
    		'ORDERBY' => '',
    		'LIMIT' 	=> '',
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		if(isset($res_row['uid'])){
    			$exists = $res_row['uid'];
    		}
    	}
    	return $exists;
    }
    
    
    /**
     * Found the usergroup of a user.
     * 
     * @param int $user_id user id
     * @return the user group, null error
     */
	function get_user_usergroup($user_id){
    	$usergroup = null;
    	$queryParts = Array(
    	    		'SELECT' => 'fe_users.usergroup',
    	    		'FROM' => 'fe_users',
    	    		'WHERE' => 'fe_users.uid='.$user_id,
    				'GROUPBY' => '',
    				'ORDERBY' => '',
    				'LIMIT' 	=> '',
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$usergroup = $res_row['usergroup'];
    	}
    	return $usergroup;
    }
    
    /**
     * Number of project the user can access to
     * 
     * @param int $user_id the user id
     * @return string the count
     */
    function count_number_of_project_access($user_id) {
    	$queryParts = array(
    			'SELECT' => 'COUNT(fe_rights.project_id) AS p_number ',
    			'FROM' => 'fe_rights',
    			'WHERE' => 'fe_rights.fe_user_id='.$user_id,
    			'GROUPBY' => '',
    			'ORDERBY' => '',
    			'LIMIT' => ''
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$number = $row['p_number'];
    	}
    	return $number;
    }
    
    /**
     * Delete a user from database
     * 
     * @param int $user_id the user id
     */
    function delete_user($user_id){
    	$GLOBALS['TYPO3_DB']->exec_DELETEquery('fe_users', 'fe_users.uid='.$user_id);
    }
    /**
     * finalize_installation : Update fe and be user from database
     *
     * @param string user_name the user id
     * @return bool true if ok false else
     */
    function finalize_installation($user_id, $user_name, $first_name, $last_name, $email, $password, $pid, $project, $descr){
    	
    	$fe_user_datas = array(
    			'username'		=>	$user_name,
    			'pid'			=>	$pid,
    			'first_name'	=>	$first_name,
    			'last_name'		=>	$last_name,
    			'email'			=>	$email,
    			'password'		=>	$password,
    			'tstamp'		=> 	time()
    	);
    	$be_user_datas = array(
    			'username'		=>	$user_name,
    			'realName'	=>	$first_name. " ".$last_name,
    			'email'			=>	$email,
    			'password'		=>	$password,
    			'tstamp'		=> 	time()
    	);

    	$project_datas = array(
    			'name'			=>	$project,
    			'description'	=>	$descr
    	);
    	 
    	$res = $GLOBALS['TYPO3_DB']->exec_UPDATEquery('fe_users', 'uid='.$user_id, $fe_user_datas );
    	if ($res == True){
    		$res2 = $GLOBALS['TYPO3_DB']->exec_UPDATEquery('be_users', 'uid='.$user_id, $be_user_datas );
    	}
    	if ($res == True){
    		$queryParts = array(
    				'SELECT' => 'uid',
    				'FROM' => 'tx_nG6_project',
    				'WHERE' => 'name = "project_install"',
    				'GROUPBY' => '',
    				'ORDERBY' => '',
    				'LIMIT' => ''
    		);
    		$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    		$project_id="";
    		while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    	    		$project_id = $row['uid'];
    		}
    		if ($project_id != "") {
    			$res = $GLOBALS['TYPO3_DB']->exec_UPDATEquery('tx_nG6_project', 'uid='.$project_id,$project_datas );
    		} else {
    			$res=False;
    		}
    	}
    	if ($res == True){
			$res = $GLOBALS['TYPO3_DB']->exec_UPDATEquery('pages', 'uid=2', array('hidden' => '0'));
			$res = $GLOBALS['TYPO3_DB']->exec_UPDATEquery('pages', 'uid=3', array('hidden' => '0', 'title' => 'Projects'));
			$res = $GLOBALS['TYPO3_DB']->exec_UPDATEquery('pages', 'uid=4', array('hidden' => '0'));
			$res = $GLOBALS['TYPO3_DB']->exec_UPDATEquery('pages', 'uid=6', array('hidden' => '0'));
    	}
    	return $res;
    }
    
    /**
     * Count user in a group
     * 
     * @param int $group_id the group id
     * @return string the count
     */
    function count_users_in_group($group_id){
    	$queryParts = array(
    		'SELECT' => 'COUNT(fe_users.usergroup) AS g_count ',
    		'FROM' => 'fe_users',
    		'WHERE' => 'fe_users.usergroup='.$group_id,
    		'GROUPBY' => '',
    		'ORDERBY' => '',
    		'LIMIT' => ''
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$number = $row['g_count'];
    	}
    	return $number;
    }
    
    /**
     * Delete a group from database
     * 
     * @param int $group_id the group id
     */
    function delete_group($group_id){
    	$GLOBALS['TYPO3_DB']->exec_DELETEquery('fe_groups', 'fe_groups.uid='.$group_id);
    }
    
    /**
    * Create a new group in the DB.
    *
    * @param array $group_datas the group array
    */
    function create_new_group($cruser_id, $group_name, $organism, $location) {
    
    	// Create new user
		$group_datas = array(
			'cruser_id'			=>	$cruser_id,
			'title'				=>	$group_name,
			'tx_nG6_organism'	=>	$organism,
			'tx_nG6_location'	=>	$location,
			'hidden'			=>	0,
			'deleted'			=>	0,
			'description'		=>	'',
			'subgroup'			=>	'',
			'tstamp'			=> 	time(),
			'crdate'			=> 	time()
		);
    
    	$GLOBALS['TYPO3_DB']->exec_INSERTquery('fe_groups', $group_datas);
    }
    
    /**
     * List all groups <uid,title>
     * 
     * @return array
     */
    function get_group_list(){
    	$queryParts = Array(
    		'SELECT' => 'fe_groups.uid, fe_groups.title',
    		'FROM' => 'fe_groups',
    		'WHERE' => '',
    		'GROUPBY' => '',
    		'ORDERBY' => 'fe_groups.uid',
    		'LIMIT' 	=> '',
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$res_tab = null;
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$res_tab[] = array(
    			'uid'	=>	$res_row['uid'],
    			'title' =>	$res_row['title']
    		);
    	}
    	return $res_tab;
    }
    
    /**
     * List all users in group
     * 
     * @param int $group_id	the grou pid
     * @return array
     */
    function get_all_users_in_group($group_id){
    	$users_in_group = null;
    	$queryParts = Array(
        		'SELECT' => 'fe_users.uid',
        		'FROM' => 'fe_users',
        		'WHERE' => 'fe_users.usergroup='.$group_id,
        		'GROUPBY' => '',
        		'ORDERBY' => '',
        		'LIMIT' 	=> '',
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$users_in_group[] = $res_row['uid'];
    	}
    	return $users_in_group;
    }
    
    /**
     * Get group informations.
     * 
     * @param int $group_id
     * @return array group information or null
     */
    function get_group_informations($group_id){
    	$queryParts = Array(
    		'SELECT' => 'fe_groups.uid, fe_groups.title, fe_groups.description, fe_groups.crdate, fe_groups.cruser_id ',
    		'FROM' => 'fe_groups',
    		'WHERE' => 'fe_groups.uid='.$group_id,
    		'GROUPBY' => '',
    		'ORDERBY' => '',
    		'LIMIT' 	=> '',
    	);
    	$res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
    	$res_tab = null;
    	while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
    		$res_tab = array(
    			'uid'			=>	$res_row['uid'],
    			'title' 		=>	$res_row['title'],
    			'description' 	=>	$res_row['description'],
    			'crdate' 		=>	$res_row['crdate'],
    			'cruser_id' 	=>	$res_row['cruser_id']
    		);
    	}
    	return $res_tab;
    }
    
    /*
     * DB integrity functions
     *------------------------------------------------------------*/
    
    /**
    * Check the integrity of 'fe_rights_levels' table.
    */
    function check_db_rights_level(){
	    $queryParts = Array(
		    'SELECT' 	=> 'fe_rights_levels.right_level_id, fe_rights_levels.right_level_label ',
		    'FROM' 		=> 'fe_rights_levels ',
		    'WHERE' 	=> '',
		    'GROUPBY' 	=> '',
		    'ORDERBY' 	=> '',
		    'LIMIT' 	=> '',
	    );
	    $res = $GLOBALS['TYPO3_DB']->exec_SELECT_queryArray($queryParts);
	     
	    $res_tab = array();
	    while($res_row = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res)) {
		    $res_tab = array(
			    'id' 	=>	$res_row['right_level_id'],
			    'label'	=>	$res_row['right_level_label']
		    );
	    }
	     
	    // insert
	    if( !in_array('member', array_values($res_tab)) ){
		    $insert_rows = Array(
			    'right_level_id' 	=> 0,
			    'right_level_label' => 'member'
		    );
		    $GLOBALS['TYPO3_DB']->exec_INSERTquery('fe_rights_levels', $insert_rows);
	    }
	     
	    if( !in_array('manager', array_values($res_tab)) ){
		    $insert_rows = Array(
		    	'right_level_id' 	=> 1,
		        'right_level_label' => 'manager'
		    );
		    $GLOBALS['TYPO3_DB']->exec_INSERTquery('fe_rights_levels', $insert_rows);
	    }
	    
	    if( !in_array('administrator', array_values($res_tab)) ){
		    $insert_rows = Array(
			    'right_level_id' 	=> 2,
			    'right_level_label' => 'administrator'
		    );
		    $GLOBALS['TYPO3_DB']->exec_INSERTquery('fe_rights_levels', $insert_rows);
	    }
    }
}

if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_db.php']) {
    include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_db.php']);
}

?>