class.tx_nG6_pi6.php

<?php
/***************************************************************
*  Copyright notice
*
*  (c) 2009 PF bioinformatique de Toulouse <>
*  All rights reserved
*
*  This script is part of the TYPO3 project. The TYPO3 project is
*  free software; you can redistribute it and/or modify
*  it under the terms of the GNU General Public License as published by
*  the Free Software Foundation; either version 2 of the License, or
*  (at your option) any later version.
*
*  The GNU General Public License can be found at
*  http://www.gnu.org/copyleft/gpl.html.
*
*  This script is distributed in the hope that it will be useful,
*  but WITHOUT ANY WARRANTY; without even the implied warranty of
*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
*  GNU General Public License for more details.
*
*  This copyright notice MUST APPEAR in all copies of the script!
***************************************************************/
/**
 * Plugin 'nG6' for the 'nG6' extension.
 *
 * @author	PF bioinformatique de Toulouse <>
 */

require_once(PATH_tslib.'class.tslib_pibase.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_utils.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_db.php');
require_once(t3lib_extMgm::extPath('nG6').'/res/smarty/libs/Smarty.class.php'); 

class tx_nG6_pi6 extends tslib_pibase {
	var $prefixId = 'tx_nG6_pi6';		// Same as class name
	var $scriptRelPath = 'pi6/class.tx_nG6_pi6.php';	// Path to this script relative to the extension dir.
	var $extKey = 'nG6';	// The extension key.
	//var $pi_checkCHash = TRUE;

	/**
	 * Main method of your PlugIn
	 *
	 * @param	string		$content: The content of the PlugIn
	 * @param	array		$conf: The PlugIn Configuration
	 * @return	The content that should be displayed on the website
	 */
	function main($content,$conf)	{
			
		if (strstr($this->cObj->currentRecord,'tt_content'))	{
			$conf['pidList'] = $this->cObj->data['pages'];
			$conf['recursive'] = $this->cObj->data['recursive'];
		}

		$this->pi_loadLL();
		$this->conf=$conf;
		$this->pi_setPiVarDefaults();
		$this->pi_USER_INT_obj=1;
                
		// Add the jquery libs + the tree plugins and its css
		$GLOBALS['TSFE']->additionalHeaderData[$this->prefixId] = '
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/highstock.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.highcharts.exporting.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jquery.dataTables.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/bootstrap.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/dataTables.bootstrap.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/typeahead.bundle.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/jflow.min.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_utils.js"></script>
			<script type="text/javascript" src="'.t3lib_extMgm::siteRelPath($this->extKey).'res/js/tx_nG6_pi6.js"></script>
					
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/bootstrap-theme.min.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/dataTables.bootstrap.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/typeaheadjs.css"/>	
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/font-awesome.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/jflow.min.css"/>
			<link type="text/css" rel="stylesheet" media="screen" href="'.t3lib_extMgm::siteRelPath($this->extKey).'res/css/tx_nG6.css"/>';

		$smarty = new Smarty();
		$smarty->setTemplateDir(t3lib_extMgm::extPath('nG6').'/pi6');
		$smarty->setCompileDir(t3lib_extMgm::extPath('nG6').'/res/smarty/templates_c');
		$smarty->setCacheDir(t3lib_extMgm::extPath('nG6').'/res/smarty/cache');
		$smarty->setConfigDir(t3lib_extMgm::extPath('nG6').'/res/smarty/configs');
		$smarty->security = true;
		$smarty->security_settings['MODIFIER_FUNCS'] = array('count');

		$group_list = tx_nG6_db::get_group_list();		
		$smarty->assign('login_user', $GLOBALS['TSFE']->loginUser);
		$smarty->assign('user_id', $GLOBALS['TSFE']->fe_user->user['uid']);
		$smarty->assign('group_list', $group_list);
		$smarty->assign('data_folder', $this->conf["data"]);
		$smarty->assign('server_url', $this->conf['server_url']);
                
		$distribution = tx_nG6_db::select_projects_repartition('create_user', 'title');
		$smarty->assign('distribution', $distribution);
		$smarty->assign('ng6_admin_users', tx_nG6_db::get_ng6_admin_users() );
               
		$smarty->assign('ng6_purge_delay',$GLOBALS['TYPO3_CONF_VARS']['EXT']['extConf']['ng6']['delay_purge']);
		$txNG6Utils = new tx_nG6_utils;
		$smarty->assign_by_ref('tx_nG6_utils', $txNG6Utils);
		return $smarty->fetch('administration_view.tpl');
	}
        
        function send_purge_demand_mail($user_id,$project_ids)	{
                 $template_mail=  'Dear user,
                 
The data storage time limit of ###nb_run### run(s) and ###nb_analyse### analyse(s) of ###PROJECT_NAME### project (###PROJET_ID###) is coming to end. 

This purge alert number ###DEMAND_ID### corresponds to the files (size :  ###STORAGE_SIZE###) linked to the following 
* runs names: 	###RUNS_LIST###
* analyses ids:	###ANALYSES_LIST###

In ###PURGE_DELAY### days, your data will be delete. Until then, you can save them by your own, or ask for extention period with number ###DEMAND_ID###. 

###EMAILS###Keep us informed if you wish to extend the storage so that we do not delete the data by error, by answering to this email with following this informations :

Demand number :  ###DEMAND_ID### 
Extension term (min ###EXTENSION_DURATION###) : 
Extension size (min ###EXTENSION_SIZE###) : 
Price for ###EXTENSION_SIZE### during ###EXTENSION_DURATION### is about ###EXTENSION_PRICE###.

Yours sincerely
nG6 team';
                $project_name="";
                $txNG6Utils = new tx_nG6_utils;
                foreach(explode(",", $project_ids) as $project_id){
                        #retrieve project data
                        $p=tx_nG6_db::select_a_project_retention_data_info($project_id);
                
                        #build email list of managers
                        $managers_email=Array();
                        $managers_name=Array();
                        $admin_email = Array();
                        $admin_name = Array();
                        foreach ( $p[$project_id]["users"] as  $u ){
                             if ( $u["right_level_label"] == "manager" ){
                                      $managers_email[]=$u["email"];
                                      $managers_name[]=$u["user_name"];
                             }elseif( $u["right_level_label"] == "administrator"){
                                     $admin_email[] = $u["email"];
                                     $admin_name[] = $u["user_name"];
                             }
                        }      
                        
                        #Warn if mail is sent to several manager
                        $email_warn="" ;
                        $purge_email_to="";
                        if ( count($managers_email) > 1 ) {
                                $email_warn="This project is associated to several managers (all recieved this email), please send only one answer per purge alert number.(".join(',', $managers_email).")\n";
                                $purge_email_to=join(',', $managers_email);
                        }elseif ( count($managers_email ==0)) {
                                $email_warn="As this project do not have managers, administrators recieved this alert (".join(',', $admin_email).")\n";
                                $purge_email_to=join(',', $admin_email);
                        }
                        //Retrieve purgeable information for email
                        $run_info=""; 
                        
                        $all_purgeable_runs=array_merge($p[$project_id]["state"]["stored"]["run_ids"],$p[$project_id]["state"]["extended"]["run_ids"]);
                        $all_purgeable_analysis=array_merge($p[$project_id]["state"]["stored"]["analysis_ids"],$p[$project_id]["state"]["extended"]["analysis_ids"]);
                        $nb_run_purgeable = $p[$project_id]["state"]["stored"]["nb_run"]+ $p[$project_id]["state"]["extended"]["nb_run"];
                        $nb_analyse_purgeable = $p[$project_id]["state"]["stored"]["nb_analyze"]+ $p[$project_id]["state"]["extended"]["nb_analyze"];
                        //Retrieve run name
                        foreach($all_purgeable_runs as $run_id ){
                                $run = tx_nG6_db::select_run($run_id);
                                $run_name = $run["name"];    
                                $run_info .= $run["name"]." ($run_id), ";
                        }
                        
                        #Add purge demand to get id
                        $purge_demand_id = tx_nG6_db::add_purge_demand($user_id,$project_id,$p[$project_id]["total_purgeable_size"],$all_purgeable_runs,$all_purgeable_analysis,$managers_name);
                        
                        #Build corresponding string array                        
                        $search=array("###nb_run###","###nb_analyse###","###PROJECT_NAME###","###PROJET_ID###","###DEMAND_ID###",
                                                "###EMAILS###","###RUNS_LIST###","###ANALYSES_LIST###","###STORAGE_SIZE###", 
                                                "###EXTENSION_DURATION###","###EXTENSION_SIZE###","###EXTENSION_PRICE###","###PURGE_DELAY###");
                        $replace=array($nb_run_purgeable,$nb_analyse_purgeable,$p[$project_id]["project_name"],$project_id, $purge_demand_id ,
                                                $email_warn, $run_info , $analysis_list, tx_nG6_utils::get_octet_string_representation($p[$project_id]["total_purgeable_size"] ),
                                                $GLOBALS['TYPO3_CONF_VARS']['EXT']['extConf']['ng6']['min_extension_duration'],$GLOBALS['TYPO3_CONF_VARS']['EXT']['extConf']['ng6']['min_extension_size'],
                                                $GLOBALS['TYPO3_CONF_VARS']['EXT']['extConf']['ng6']['min_extension_price'],$GLOBALS['TYPO3_CONF_VARS']['EXT']['extConf']['ng6']['delay_purge']);
                        
                        $mail=str_replace($search, $replace, $template_mail);
                        
                        $to      =  $purge_email_to;
                        $subject = '[nG6 purge] No '.$purge_demand_id.' - Project '.$p[$project_id]["project_name"];
                        $headers[] = 'From: '.$GLOBALS['TYPO3_CONF_VARS']['EXT']['extConf']['ng6']['email_from'];
                        #$headers[] = 'Cc: '.$GLOBALS['TYPO3_CONF_VARS']['EXT']['extConf']['ng6']['email_from'];
                        $headers[] = 'Reply-To: '.$GLOBALS['TYPO3_CONF_VARS']['EXT']['extConf']['ng6']['email_from'];
                        $headers[] = 'X-Mailer: PHP/' . phpversion();
                        #TODO Uncomment
                        #mail($to, $subject, $mail, implode("\r\n", $headers));
                        //return    $headers  ;
			}	
                return $mail;
        }
 
        function set_purge_demand_processed($demand_ids,$process, $value,$user,$pwd){
                $all_demands=tx_nG6_db::get_purge_demand_from_id($demand_ids);
                $all_runs=array();
                $all_analyses=array();
                foreach($all_demands as $res){
                        if ($res["state"] != "deleted")
                        {
                                $all_analyses=array_merge($all_analyses,explode(',',$res["analyze_ids"]));
                                $all_runs=array_merge($all_runs,explode(',',$res["run_ids"]));
                        }
                }
                //extend
                if ($process == "extend"){
                        $date=$value;
                        tx_nG6_db::update_field('tx_nG6_run', $all_runs, 
                                array("retention_date","data_state", "mail_sent_date","purge_demand_id"),
                                array($date,"extended","","NULL"),
                                array("purge_demand_id"));
                        tx_nG6_db::update_field('tx_nG6_analyze',$all_analyses,
                                array("retention_date","data_state", "mail_sent_date","purge_demand_id"),
                                array($date,"extended","","NULL"),
                                array("purge_demand_id"));
                        tx_nG6_db::update_field('tx_nG6_purge_demand',$demand_ids,
                                array("processed_date","demand_state"),
                                array($date,"extended"));
                        return("Done extend");
                }else{ //delete
                        $data_folder=$value;
                        $date= time();
                        $all_runs_purged=array();
                        $all_analyses_purged=array();
                        $connexion=tx_nG6_utils::get_ssh_connection($user,$pwd);
                        if ( $connexion ) 
                        {
                                foreach ($all_runs as $run_id){
                                        $r = tx_nG6_db::select_run($run_id);
                                        if ($r["directory"] != "" ) {
                                                $res = tx_nG6_utils::purge_files($connexion, $data_folder.$r["directory"]);
                                                if ($res == 0){
                                                        $all_runs_purged[]=$run_id;
                                                }else{
                                                        error_log("Error ".$res." while purging run id >".$run_id."< directory : >".$data_folder.$r["directory"]."< \n");
                                                }
                                        }
                                }
                                foreach ($all_analyses as $analyse_id){
                                        $a = tx_nG6_db::select_analyse($analyse_id);
                                        if ($a["directory"] != "" ) {
                                                $res = tx_nG6_utils::purge_files($connexion, $data_folder.$a["directory"]);
                                                if ($res == 0){
                                                        $all_analyses_purged[]=$analyse_id;
                                                }else{
                                                        error_log("Error ".$res." while purging analyse id >".$analyse_id."< directory : >".$data_folder.$a["directory"]."< \n");
                                                }
                                        }
                                }
                                
                                //purged_size = storage_size !!!
                                tx_nG6_db::update_field('tx_nG6_run', $all_runs_purged,  array("purged_size","data_state", "purged_date", "storage_size"),
                                                array("storage_size","purged",$date, 0),
                                                array("purged_size"));
                                
                                tx_nG6_db::update_field('tx_nG6_analyze',$all_analyses_purged, array("purged_size","data_state", "purged_date", "storage_size"),
                                                array("storage_size","purged",$date, 0),
                                                array("purged_size"));
                                
                                if (count($all_runs_purged)==count($all_runs) and count($all_analyses_purged)==count($all_analyses)){
                                        tx_nG6_db::update_field('tx_nG6_purge_demand',$demand_ids,
                                                array("processed_date","demand_state"),
                                                array($date,"deleted"));
                                                return("Done delete, res : ".$res);
                                }else{
                                              return("Error: not all runs or analyses were purged , please check unix permission (see apache logs).");
                                }
                        }else{
                                return("Error while ssh login.");
                        }

                }
             }
}

if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/pi6/class.tx_nG6_pi6.php'])	{
	include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/pi6/class.tx_nG6_pi6.php']);
}

?>