class.tx_nG6_eid.php 14.8 KB
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<?php
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/***************************************************************
*  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!
***************************************************************/
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require_once(PATH_t3lib.'class.t3lib_befunc.php');
require_once(PATH_t3lib.'stddb/tables.php');
require_once(t3lib_extMgm::extPath('cms','ext_tables.php'));
require_once(PATH_t3lib.'class.t3lib_db.php');
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require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_db.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_utils.php');
require_once(t3lib_extMgm::extPath('nG6').'/lib/class.tx_nG6_process.php');
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/**
 * Class 'tx_nG6_eid' for the 'nG6' extension.
 * This class is in charge of all communication between the client and the server using AJAX
 *
 * @author	PF bioinformatique de Toulouse <>
 */
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class tx_nG6_eid {

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    /**
     * The main function of the tx_nG6_eid, this function is the one called when using ajax
     */
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    function main() {

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    	// Connect to the databse
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    	tslib_eidtools::connectDB();
    	$type = trim(t3lib_div::_GP('type'));
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    	$user_group = trim(t3lib_div::_GP('user_group'));
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    	// If the type of data requested is project
    	if ($type == 'project') {
    		$project_id = trim(t3lib_div::_GP('id'));
	    	// Select all runs linked to the project
	    	$project_runs = tx_nG6_db::get_project_runs($user_group, $project_id);
	    	// for each run
	    	$html_tree = '';
			foreach($project_runs as $run_id => $run_values) {
				$html_tree .= '<li class="jstree-closed" name=\''.str_replace(array('###SPAN_NAME###', '###SPAN_DATE###'), array($run_values["name"], strftime('%d-%m-%y',$run_values["date"])), trim(t3lib_div::_GP('run_short_description'))).'\' id=\''.$run_id.'\'> <a href=\'#\'>'.str_replace(array('###SPAN_NAME###', '###SPAN_DATE###', '###SPAN_NB_SEQ###', '###SPAN_SPECIES###'), array($run_values["name"], strftime('%d-%m-%y',$run_values["date"]), $run_values["nb_sequences"], $run_values["species"]), trim(t3lib_div::_GP('run_description'))).'</a></li>';
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			}
	    	// Then all project analysis
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	    	$project_analysis = tx_nG6_db::get_project_analysis($user_group, $project_id);
			foreach($project_analysis as $analyse_id => $analyse_values) {  
				$html_tree .= '<li name=\''.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'\' id=\''.$analyse_id.'\'> <a href=\'#\'>'.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'</a></li>';
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			}
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			// Return the html_tree
	    	print $html_tree;
	    
	    // If the type of data requested is run
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    	} else if ($type == 'run'){
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			$run_id = trim(t3lib_div::_GP('id'));
			// Select all analysis linked to the run and the run information
			$run_analysis = tx_nG6_db::get_run_analysis($user_group, $run_id);
			$run_info = tx_nG6_db::get_run($run_id);
	    	// for each analysis
	    	$html_tree = '';
			$html_tree .= '<li name=\'run_'.$run_id.'_'.trim(t3lib_div::_GP("raw_data_description")).'\'  id=\'data_'.$run_id.'\'> <a href=\'#\'>'.trim(t3lib_div::_GP("raw_data_description")).'</a></li>';
			foreach($run_analysis as $analyse_id => $analyse_values) {   
				$html_tree .= '<li name=\'run_'.$run_id.'_'.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'\' id=\''.$analyse_id.'\'> <a href=\'#\'>'.str_replace(array('###SPAN_NAME###'), array($analyse_values["name"]), trim(t3lib_div::_GP('analyse_description'))).'</a></li>';
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			}
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			// Return the html_tree
	    	print $html_tree;
	    	
	    // If downloading data is requested
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    	} else if ($type == 'download') {
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    		$format = trim(t3lib_div::_GP('format'));
    		// If link in home directory
    		if ($format == 'home_link') {
				$ids = trim(t3lib_div::_GP('ids'));
				$data_folder = trim(t3lib_div::_GP('data_folder'));
				$user_login = trim(t3lib_div::_GP('user_login'));
				$user_pwd = trim(t3lib_div::_GP('user_pwd'));
				$user_directory = trim(t3lib_div::_GP('user_directory'));
				$retcode = $this->create_symbolic_links($user_group, $user_login, $user_pwd, $ids, $data_folder, $user_directory);
				print $retcode;
				
			// If a .tar.gz file
    		} else {
				$ids = trim(t3lib_div::_GP('ids'));
				$data_folder = trim(t3lib_div::_GP('data_folder'));
				$tmp_folder = trim(t3lib_div::_GP('tmp_folder'));
				$user_email = trim(t3lib_div::_GP('user_email'));
				$title_email = trim(t3lib_div::_GP('title_email'));
				$msg_email = trim(t3lib_div::_GP('msg_email'));
				$archive_info = $this->create_archive_script($user_group, $ids, $data_folder, $tmp_folder, "tar.gz", $user_email, $title_email, $msg_email); 
				$process = new Process("tcsh ".$archive_info[0]);
			    print "pid=".$process->getPid()."&archive_path=".$archive_info[1];
    		}
    		
    	// If asked to check a job status
    	} else if($type == 'check_status') {
    		$pid = trim(t3lib_div::_GP('pid'));
    		$archive_path = trim(t3lib_div::_GP('archive_path'));
    		$process = new Process();
    		$process->setPid($pid);
    		// If the job is done
    		if ($process->status()) {
    			print "pid=0&archive_path=".$archive_path;
    		// If the job is still runing
    		} else {
    			print "pid=".$process->getPid()."&archive_path=".$archive_path;
    		}
    	
    	// If file information is requested
    	} else if ($type == 'get_file_size') {
            $ids = trim(t3lib_div::_GP('ids'));
            $data_folder = trim(t3lib_div::_GP('data_folder'));
            print $this->get_file_size($user_group, $ids, $data_folder);
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        } 
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    } 

	/**
	 * Creates an archiving script to archive data from ids
	 *
	 * @param	string	$user_group		the user group 
	 * @param	array	$ids			list of ids to download 
	 * @param	string	$data_folder	the data folder where are stored the data
	 * @param	string	$tmp_folder		the output directory
	 * @param	string	$format			the archiving format (tar.gz)
	 * @param	string	$user_email		the user email
	 * @param	string	$title_email		the email title to send
	 * @param	string	$msg_email		the email message to send
	 * @return	array (the path to the script, the url path to the final archive)
	 */
	private function create_archive_script($user_group, $ids, $data_folder, $tmp_folder, $format, $user_email, $title_email, $msg_email) {
		// First get the archive name where will be stored the data
		$random_key = tx_nG6_utils::create_random_key(10);
		$archive_path = $tmp_folder."/ng6_".$random_key;
		while( file_exists($archive_path) )
			$archive_path = $tmp_folder."/ng6_".$random_key;
		
		// Then get the directories structure
		$directories = $this->get_directories_structure_and_content($user_group, $ids, $data_folder, $archive_path);
		$archive_script_path = $tmp_folder."/ng6_".$random_key.".sh";
		
		// And write down the script in charge to create the archive
		$fp = fopen($archive_script_path, 'w');
		foreach($directories[0] as $index => $src_directory) {
			if (!file_exists( $directories[1][$index])) {
				fwrite($fp, "mkdir -p ".$directories[1][$index]."\n");
			}
			// For each files in the source directory
			foreach(scandir($src_directory) as $file) {
				if (is_file($src_directory."/".$file) and $file != "analyse.xml" and $file != "index.html" and $file != "run.cfg") {
					fwrite($fp, "cp ".$src_directory."/".$file." ".$directories[1][$index]."\n");
				}
			}
		}
		fwrite($fp, "cd ".$tmp_folder."\n");
		fwrite($fp, "tar -czf ng6_".$random_key.".tar.gz ng6_".$random_key."\n");
		fwrite($fp, "rm -rf ".$archive_path."\n");
		fwrite($fp, 'echo "'.str_replace(array('SPAN_ARCHIVE_NAME'), array("ng6_".$random_key.".tar.gz"), $msg_email).'" | mail -s "'.$title_email.'" '.$user_email."\n");
		fclose($fp);
		return array($archive_script_path, "ng6_".$random_key.".tar.gz");
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    }
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	/**
	 * Creates symbolic links between ids from data_folder into user_directory
	 *
	 * @param	string	$user_group		the user group 
	 * @param	string	$user_login		the user login to make ssh
	 * @param	string	$user_pwd		the user pwd to make ssh
	 * @param	array	$ids			list of ids to download 
	 * @param	string	$data_folder	the data folder where are stored the data
	 * @param	string	$user_directory	the output directory
	 * @return	0=>everything ok, 1=>user rigth problem, 2=>wrong authentification, 3=>connection error
	 */
	private function create_symbolic_links($user_group, $user_login, $user_pwd, $ids, $data_folder, $user_directory) {
		// First try to connect the specified user using ssh
		$connection = ssh2_connect('127.0.0.1', 22);
		if (!$connection) return 3;
		if (!ssh2_auth_password($connection, $user_login, $user_pwd)) return 2;
		
		// Then get the directories structure
		$directories = $this->get_directories_structure_and_content($user_group, $ids, $data_folder, $user_directory);
		// And process the directories structure
		$creation = true;
		foreach($directories[0] as $index => $src_directory) {
			if (!file_exists("ssh2.sftp://".$connection.$directories[1][$index])) {
				if (!mkdir("ssh2.sftp://".$connection.$directories[1][$index], 0755, true)) {
					$creation = false;
					break;
				}
				// For each files in the source directory
				foreach(scandir("ssh2.sftp://".$connection.$src_directory) as $file) {
					if (is_file("ssh2.sftp://".$connection.$src_directory."/".$file) and $file != "analyse.xml" and $file != "index.html" and $file != "run.cfg") {
						if (!ssh2_exec($connection, 'ln -s '.$src_directory.'/'.$file.' '.$directories[1][$index].'/'.$file)) {
							$creation = false;
							break;
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						}
					}
				}
			}
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		}
		if (!$creation) return 1;
		return 0;
    }

    /**
     * for each $id, get the total size of all files in the corresponding folder
     * 
	 * @param	string	$user_group		the user group 
     * @param	string	$ids			names of run or analysis for which we want to get the sizes of the contained files
     * @param	string	$data_folder	root directory where the folders of the runs and analysis can be found
	 * @return	integer total size of the files
     */
	function get_file_size($user_group, $ids, $data_folder) {
		// First get the directories structure
		$directories = $this->get_directories_structure_and_content($user_group, $ids, $data_folder, "/");
		$full_size = 0;
		foreach($directories[0] as $index => $src_directory) {
			// For each files in the source directory
			foreach(scandir($src_directory) as $file) {
				if (is_file($src_directory."/".$file) and $file != "analyse.xml" and $file != "index.html" and $file != "run.cfg") {
					$full_size += filesize($src_directory."/".$file);
				}
			}
		}
		return $full_size;
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    }
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	/**
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	 * Returns a table with the right directories structure considering ids
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	 *
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	 * @param	string	$user_group	the user group
	 * @param	array	$ids			List of ids to download 
	 * @param	string	$data_folder	The data folder where are stored the data
	 * @param	string	$output_folder	The output directory
	 * @return	array	[0] => source_directories, [1] => dest_directories
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	 */
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	private function get_directories_structure_and_content($user_group, $ids, $data_folder, $output_folder) {
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		$src_directories = array();
		$dest_directories = array();
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		$vals = preg_split("/;/", $ids);
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		// Characters to be replaced in the names of the run, the analyses ...
		$char_to_replace = array(' ','/');
		
		// For each project/run/analysis
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		foreach($vals as $val) {
			if ($val != "undefined" && $val != "") {
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				$id = preg_split("/_/", $val);
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				if ($id[0] == "data") {
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					$run = tx_nG6_db::get_run($id[1]);
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					if (!in_array($data_folder.$run["directory"], $src_directories)) {
						$src_directories[] = $data_folder.$run["directory"];
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						$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]);
						$ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]).".".$id[1]."/RawData";
						$dest_directories[] = $ddest;
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					}
				} else if ($id[0] == "run") {
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					$run = tx_nG6_db::get_run($id[1]);
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					if (!in_array($data_folder.$run["directory"], $src_directories)) {
						$src_directories[] = $data_folder.$run["directory"];
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						$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]);
						$ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]).".".$id[1]."/RawData";
						$dest_directories[] = $ddest;
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					}
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					foreach(tx_nG6_db::get_run_analysis($user_group, $id[1]) as $analyse_id => $analyse_values) {
						$aid = preg_split("/_/", $analyse_id);
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						if (!in_array($data_folder.$analyse_values["directory"], $src_directories)) {
							$src_directories[] = $data_folder.$analyse_values["directory"];
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							$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $run["project_name"]);
							$ddest .= '.'.$run["project_id"]."/Run_".str_replace($char_to_replace, '_', $run["name"]);
							$ddest .= ".".$id[1]."/Analyse_".str_replace($char_to_replace, '_', $analyse_values["name"]).".".$aid[1];
							$dest_directories[] = $ddest;
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						}
					}
				} else if ($id[0] == "analyse") {
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					$analyse = tx_nG6_db::get_analyse($id[1]);
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					if (!in_array($data_folder.$analyse["directory"], $src_directories)) {
						$src_directories[] = $data_folder.$analyse["directory"];
						// If it's a project analyse
						if ($analyse["run_id"] == 'None') {
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							$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $analyse["project_name"]);
							$ddest .= ".".$analyse["project_id"]."/Project_analyses/".str_replace($char_to_replace, '_', $analyse["name"]).".".$id[1];
							$dest_directories[] = $ddest;
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						} else {
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							$ddest = $output_folder."/Project_".str_replace($char_to_replace, '_', $analyse["project_name"]);
							$ddest .= ".".$analyse["project_id"]."/Run_".str_replace($char_to_replace, '_', $analyse["run_name"]);
							$ddest .= ".".$analyse["run_id"]."/Analyse_".str_replace($char_to_replace, '_', $analyse["name"]).".".$id[1];
							$dest_directories[] = $ddest;
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						}
					}
				}
			}
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		}
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		return array($src_directories, $dest_directories);
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    }
    
}

if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_eid.php']) {
    include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_eid.php']);
}

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// Instanciation
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$SOBE = t3lib_div::makeInstance('tx_nG6_eid');
$SOBE->main();

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?>