class.tx_nG6_db.php 74.2 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!
***************************************************************/

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 {
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	/*
	 * Global functions
	*------------------------------------------------------------*/
	
	/**
	* Update the specified field of the table
	 *
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	* @param	string  $table the entity to change
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	* @param	string  $id     the element id to update
	* @param	string  $field  the field to change
	* @param	string  $value  the new value
	*/
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	function update_field($table, $id, $field, $value) {
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		if( $field == 'uid' ) {
			throw new Exception ("The function 'update_field' cannot change an id.") ;
		}	
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		$GLOBALS['TYPO3_DB']-> exec_UPDATEquery ($table, 'uid='.$id, array($field => $value));
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	}
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	/**
     * 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
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		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'];
					}
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				}
			}
		}

		$cumulated_size = 0;
    	while($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;
    		$current_size = 0;
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			if ($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;
			}
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    		// get all runs the usergroup can access to
    		$queryParts = array(
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    			'SELECT' 	=> 'tx_nG6_run.uid as run_id',
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    			'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 ',
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    			'WHERE' 	=> $where,
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    			'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'], $data_folder, $get_analyzes);
			}
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			// get all project analysis the usergroup can access to
			if ($get_analyzes) {
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				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;
				}
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	    		$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'], $data_folder);
				}
			}
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    		$cumulated_size += $current_size;
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    		if(!$cumul_values){
    	    	$res_tab[] = array($date_cursore*1000, $current_size);
    	    }else{
    	    	$res_tab[] = array($date_cursore*1000, $cumulated_size);
    	    }
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    		$date_cursors = $date_cursore + 1;
    	}
    	return $res_tab;	
    }
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	/*
	 * Project functions
	 *------------------------------------------------------------*/

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

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	/**
	* 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;
	}

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	/**
	 * 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);
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		$vals = $GLOBALS['TYPO3_DB']->sql_fetch_assoc($res);
		return array('id'			=> $vals['uid'],				
					 'name'			=> $vals['name'],
					 'hidden'		=> $vals['hidden'],
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					 'date'			=> $vals['crdate'],
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					 'public'		=> $vals['public'],
					 'description'	=> $vals['description']);
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	}

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

	
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		// 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)) {
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			$run_id = $row['run_id'];				
			if (!isset($results['run_'.$run_id])) {				
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				$results['run_'.$run_id] = array( 
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					'id'			=> $run_id,
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					'directory'		=> $row['run_directory'], 
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					'name' 			=> $row['run_name'],
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					'project_name' 	=> $row['project_name'],
					'hidden'		=> $row['run_hidden'],
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					'species' 		=> $row['run_species'],
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					'nb_sequences' 	=> $row['run_nb_sequences'],
					'full_seq_size' => $row['run_full_seq_size'],
					'project_id' 	=> $row['project_id'],
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					'date'			=> $row['run_date'],
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					'data_nature'	=> $row['run_data_nature'],
					'sequencer'		=> $row['run_sequencer'],
					'type'			=> $row['run_type'],
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					'description' 	=> $row['run_description']
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				);
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			}						
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		}
		return $results;
    }

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    /**
     * 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;
    }

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

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    /**
    * 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, '.
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    						'tx_nG6_analyze.is_editable AS analyze_is_editable, '.
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    						'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'],
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    					'is_editable' 	=> $row['analyze_is_editable'],
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    					'parent_id'		=> $row['analyze_parent_uid']	
    			);
    		}
    	}
    	return $results;
    }

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

		// Then all project analysis
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    	$project_analysis = tx_nG6_db::get_project_analysis($p_id);
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		foreach($project_analysis as $analysis_id => $analysis_values) {  
			tx_nG6_db::hide_analysis($analysis_values['id']);
		}
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		tx_nG6_db::unpublish_project($p_id);
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		// 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	$p_id	the project id to hide
     */
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	function unhide_project($p_id) {
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		// First change all project runs
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		$project_runs = tx_nG6_db::get_project_runs($p_id);
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		foreach($project_runs as $run_id => $run_values) {
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			tx_nG6_db::unhide_run($run_values['id']);
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		}

		// Then all project analysis
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    	$project_analysis = tx_nG6_db::get_project_analysis($p_id);
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		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	$p_id	the project id to publish
     */
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	function publish_project($p_id) {
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		// First unhide the project
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		tx_nG6_db::unhide_project($p_id);
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		// 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 $data_folder	the data folder
     */
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	function delete_project($p_id, $user_login, $user_pwd, $data_folder) {
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		$res = 0;
		// All runs
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		$project_runs = tx_nG6_db::get_project_runs($p_id);
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		foreach($project_runs as $run_id => $run_values) {
			if ($run_values['id'] != 'undefined' && $run_values['id'] != '') {
				//delete the run sublevels
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				$res = tx_nG6_db::delete_run($run_values['id'], $user_login, $user_pwd, $data_folder);
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				if ($res != 0) { break; }				
			}
		}
		
		// All project_analysis
		if ($res == 0) {
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			$project_analysis = tx_nG6_db::get_project_analysis($p_id);
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			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;}
		}
		
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		// 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;}
		}
		
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		return $res;
	}

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

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	/*
	 * Run functions
	 *------------------------------------------------------------*/
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	/**
	 * Select all run for the specified user
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	 * 
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	 * @param	string	$user_id	the user id
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	 * @return	table with all projects
	 */
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	function select_all_user_runs($user_id, $orderby='', $limit='') {
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		// If the user is not logged on display demonstration project
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		if ($user_id == null) { $where = 'tx_nG6_project.public=0'; } 
		else { $where = 'fe_rights.fe_user_id='.$user_id; }
		
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     	// Execute the request
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		$queryParts = Array( 
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			'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, '.
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						'tx_nG6_run.data_nature AS run_data_nature, '. 
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						'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, '.
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						'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 ',
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			'WHERE' => $where,
			'GROUPBY' => '',
			'ORDERBY' => $orderby,
			'LIMIT' 	=> $limit
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		); 
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		// 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)) {
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			$run_id = $row['run_id'];	
			if (!isset($results['run_'.$run_id])) {				
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				$results['run_'.$run_id] = array(
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					'id'			=> $run_id,  
					'directory'		=> $row['run_directory'], 
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					'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'],
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					'description' 	=> $row['run_description']				
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				);
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			}						
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		}
		return $results;

	}

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

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

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    /**
    * 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.
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    						' AND ((fe_rights.right_id<>2 AND tx_nG6_analyze.hidden=0) OR fe_rights.right_id=2)' ;
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    	}
    	
    	// 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, '.
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    						'tx_nG6_analyze.is_editable AS analyze_is_editable, '.
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    						'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'],
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    					'is_editable' 	=> $row['analyze_is_editable'],
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    					'parent_id'		=> $row['analyze_parent_uid']
    			);
    		}
    	}
    	return $results;
    }

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	/**
	 * 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 $data_folder	the data folder
	 */
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	function delete_run($r_id, $user_login, $user_pwd, $data_folder) {		
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		$res = 0;		
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		$run_analysis = tx_nG6_db::get_run_analysis($r_id);
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		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);