class.tx_nG6_db.php

<?php
/***************************************************************
*  Copyright notice
*
*  (c) 2009 PF bioinformatique de Toulouse <>
*  All rights reserved
*
*  This script is part of the TYPO3 project. The TYPO3 project is
*  free software; you can redistribute it and/or modify
*  it under the terms of the GNU General Public License as published by
*  the Free Software Foundation; either version 2 of the License, or
*  (at your option) any later version.
*
*  The GNU General Public License can be found at
*  http://www.gnu.org/copyleft/gpl.html.
*
*  This script is distributed in the hope that it will be useful,
*  but WITHOUT ANY WARRANTY; without even the implied warranty of
*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
*  GNU General Public License for more details.
*
*  This copyright notice MUST APPEAR in all copies of the script!
***************************************************************/

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));
	}
	
	
	/*
	 * 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'];
			
			// Is the user allowed to see this project
			$user_allowed = false;
			if ($row['project_hidden'] == 0 || $row['project_public'] == 0) {
				$user_allowed = true;
			} 
			
			if (!isset ($projects['project_'.$project_id]) and $user_allowed) {		
				$projects['project_'.$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'];
			
			// Is the user allowed to see this run
			$user_allowed = false;
			if ($row['run_hidden'] == 0) {
				$user_allowed = true;
			} 
								
			if (!isset($results['run_'.$run_id]) and $user_allowed) {				
				$results['run_'.$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    	
    	$queryParts = array( 
			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
						'tx_nG6_analyze.name AS analyze_name, '.
						'tx_nG6_analyze.class AS analyze_class, '.
						'tx_nG6_analyze.date AS analyze_date, '.
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.version AS analyze_version, '.
						'tx_nG6_analyze.params AS analyze_params, '.
						'tx_nG6_analyze.description AS analyze_description, '.
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid, '.
						'tx_nG6_analyze.hidden AS analyze_hidden ',
			'FROM' => 'tx_nG6_project '.
						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_project.uid = tx_nG6_project_analyze.project_id '.
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id ',
			'WHERE' => 'tx_nG6_project.uid='.$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'];
			
			// Is the user allowed to see this analyse
			$user_allowed = false;
			if ($row['analyze_hidden'] == 0) {
				$user_allowed = true;
			}
			
			if (!isset ($results['analyse_'.$analyze_id]) and $user_allowed) {				
				$results['analyse_'.$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'],
					'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
     * @param	string	$user_id	the current user id
     */
	function hide_project($p_id, $user_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'], $user_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']);
		}
		
		// 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
     * @param	string	$user_id	the current user id
     */
	function unhide_project($p_id, $user_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'], $user_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
     * @param	int 	$user_id	the current user id
     */
	function publish_project($p_id, $user_id) {
		// First unhide the project
		tx_nG6_db::unhide_project($p_id, $user_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 $user_id		the user id
     * @param string $p_id			the project id
     * @param string $user_login	the user login
     * @param string $user_pwd		the user password
     * @param string $data_folder	the data folder
     */
	function delete_project($user_id, $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
				$res = tx_nG6_db::delete_run($user_id, $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;}
		}
		
		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	string	$user_id	the user id
     */
	function get_project_size($p_id, $data_folder, $user_id) {
		
		$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'], $data_folder, $user_id);
		}
		// 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);
		}
		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'];
			
			// Is the user allowed to see this run
			$user_allowed = false;
			if ($row['run_hidden'] == 0) {
				$user_allowed = true;
			}
					
			if (!isset($results['run_'.$run_id]) and $user_allowed) {				
				$results['run_'.$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
		$queryParts = Array( 
			'SELECT' => 'tx_nG6_project.uid AS project_id,'.
						'tx_nG6_project.name AS project_name,'.
						'tx_nG6_run.uid AS run_id,'.
					 	'tx_nG6_run.directory AS run_directory,'.
						'tx_nG6_run.description AS run_description, '.
						'tx_nG6_run.species AS run_species, '.
						'tx_nG6_run.name AS run_name, '.
						'tx_nG6_run.data_nature AS run_data_nature, '.
						'tx_nG6_run.sequencer AS run_sequencer, '.
						'tx_nG6_run.type AS run_type, '.
						'tx_nG6_run.full_seq_size, '.
						'tx_nG6_run.hidden AS run_hidden, '.
						'tx_nG6_run.nb_sequences, '.
						'tx_nG6_run.date AS run_date',
			'FROM' => 'fe_rights '.
						'INNER JOIN tx_nG6_project ON tx_nG6_project.uid=fe_rights.project_id '.
						'INNER JOIN tx_nG6_project_run ON tx_nG6_project.uid=tx_nG6_project_run.project_id '.
						'INNER JOIN tx_nG6_run ON tx_nG6_project_run.run_id=tx_nG6_run.uid ',
			'WHERE' => 'tx_nG6_run.uid='.$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'],
				'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	int	$user_id	the user id
	 * @param	string	$run_id	the run id
	 * @return	hash table with all analysis information
	 */
    function get_run_analysis($user_id, $run_id, $orderby='', $limit='') {
		// First select all analysis from the database
		$queryParts = array( 
			'SELECT' => 'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
						'tx_nG6_analyze.name AS analyze_name, '.
						'tx_nG6_analyze.params AS analyze_params, '.
						'tx_nG6_analyze.class AS analyze_class, '.
						'tx_nG6_analyze.date AS analyze_date, '.
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.version AS analyze_version, '.
						'tx_nG6_analyze.hidden AS analyze_hidden, '.
						'tx_nG6_analyze.description AS analyze_description, '.
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
			'FROM' => 'fe_rights '.
						'INNER JOIN tx_nG6_project ON tx_nG6_project.uid=fe_rights.project_id '.
						'INNER JOIN tx_nG6_project_run ON tx_nG6_project_run.project_id = tx_nG6_project.uid '.
						'INNER JOIN tx_nG6_run ON tx_nG6_run.uid = tx_nG6_project_run.run_id '.
						'INNER JOIN tx_nG6_run_analyze ON tx_nG6_run_analyze.run_id = tx_nG6_run.uid '.
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id ',
			'WHERE' => 'tx_nG6_run_analyze.run_id='.$run_id.' AND fe_rights.fe_user_id='.$user_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'];
			
			// Is the user allowed to see this analyse
			$user_allowed = false;
			if ($row['analyze_hidden'] == 0) {
				$user_allowed = true;
			} 
			
			if (!isset ($results['analyse_'.$analyze_id]) and $user_allowed) {				
				$results['analyse_'.$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'],
					'parent_id'		=> $row['analyze_parent_uid']
				);
			}						
		}
		return $results;
    }

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

		$res = 0;		
		$run_analysis = tx_nG6_db::get_run_analysis($user_id, $r_id);
		foreach($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	int	$user_id	the user id
     */
	function get_run_size($r_id, $data_folder, $user_id) {
		$full_size = 0;
		$run_analysis = tx_nG6_db::get_run_analysis($user_id, $r_id);
		foreach($run_analysis as $analyse_id => $analyze_values) {
			$full_size += tx_nG6_db::get_analysis_size($analyze_values['id'], $data_folder);
		}
		// Then select the run
		$my_run = tx_nG6_db::select_run($r_id);
		foreach(scandir($data_folder.$my_run['directory']) as $file) {
			if (is_file($data_folder.$my_run['directory']."/".$file)) {
				$full_size += filesize($data_folder.$my_run['directory']."/".$file);
			}
		}
		return $full_size;
	}

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

		// First select all run analysis
    	$run_analysis = tx_nG6_db::get_run_analysis($user_id, $r_id);
		foreach($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
     * @param	int	$user_id	the current user id
     */
	function unhide_run($r_id, $user_id) {

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

	/*
	 * 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
		$queryParts = array( 
			'SELECT' => 'tx_nG6_project.uid AS project_id,'. 
						'tx_nG6_project.name AS project_name,'. 
						'tx_nG6_analyze.uid AS analyze_id,'. 
						'tx_nG6_analyze.directory AS analyze_directory,'. 
						'tx_nG6_analyze.name AS analyze_name, '.
						'tx_nG6_analyze.params AS analyze_params, '.
						'tx_nG6_analyze.software AS analyze_software, '.
						'tx_nG6_analyze.class AS analyze_class, '.
						'tx_nG6_analyze.date AS analyze_date, '.
						'tx_nG6_analyze.description AS analyze_description, '.
						'tx_nG6_analyze.version AS analyze_version, '.
						'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
			'FROM' => 'tx_nG6_project '.
						'INNER JOIN tx_nG6_project_analyze ON tx_nG6_project.uid = tx_nG6_project_analyze.project_id '.
						'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid=tx_nG6_project_analyze.analyze_id ',
			'WHERE' => 'tx_nG6_analyze.uid='.$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'],
					'version'		=> $row['analyze_version']				
				);				
			}
			return $result;
		} else { // If it's a run analyse, add run information
			$queryParts = array( 
				'SELECT' => 'tx_nG6_project.name AS project_name,'.
							'tx_nG6_project.uid AS project_id,'.
							'tx_nG6_run.uid AS run_id,'. 
							'tx_nG6_run.name AS run_name,'.
							'tx_nG6_analyze.uid AS analyze_id,'. 
							'tx_nG6_analyze.directory AS analyze_directory,'. 
							'tx_nG6_analyze.name AS analyze_name, '.
							'tx_nG6_analyze.params AS analyze_params, '.
							'tx_nG6_analyze.class AS analyze_class, '.
							'tx_nG6_analyze.date AS analyze_date, '.
							'tx_nG6_analyze.software AS analyze_software, '.
							'tx_nG6_analyze.version AS analyze_version, '.
							'tx_nG6_analyze.description AS analyze_description,'.
							'tx_nG6_analyze.parent_uid AS analyze_parent_uid ',
				'FROM' => 'tx_nG6_project '.
							'INNER JOIN tx_nG6_project_run ON tx_nG6_project_run.project_id = pro.uid '.
							'INNER JOIN tx_nG6_run ON tx_nG6_run.uid = tx_nG6_project_run.run_id '.
							'INNER JOIN tx_nG6_run_analyze ON tx_nG6_run_analyze.run_id = tx_nG6_run.uid '.
							'INNER JOIN tx_nG6_analyze ON tx_nG6_analyze.uid = tx_nG6_run_analyze.analyze_id ',
				'WHERE' => 'tx_nG6_analyze.uid='.$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']			
				);				
			}
			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, $data_folder) {
		// First select the analyse
		$my_analysis = tx_nG6_db::select_analyse($a_id);
		$full_size = 0;
		foreach(scandir($data_folder.$my_analysis['directory']) as $file) {
			if (is_file($data_folder.$my_analysis['directory']."/".$file)) {
				$full_size += filesize($data_folder.$my_analysis['directory']."/".$file);
			}
		}
		return $full_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) {
		$queryParts = array(
			'SELECT'  => 'tx_nG6_project_analyze.uid',
			'FROM'    => 'tx_nG6_project_analyze',
			'WHERE'   => 'tx_nG6_project_analyze.analyze_id = '.$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 ?
		$queryParts = array(
			'SELECT' => 'public',
			'FROM' => 'tx_nG6_project',
			'WHERE' => 'uid='.$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);
		
		// 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.uid='.$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;
    }