* 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(\TYPO3\CMS\Core\Utility\ExtensionManagementUtility::extPath('saltedpasswords').'/classes/salts/class.tx_saltedpasswords_salts_factory.php');
class tx_nG6_utils {
/**
* Describe all links between analyzes (and their ancestor) and build a tree. The main Array is the root.
* Example of result : Array( [a] => Array( ["data"] => Array(), ["child"] => Array( ... ) ) )
*
* @param Array $analyzes_map analyze array (for example, result of tx_nG6_db::get_project_analysis(...))
* @return a tree describing the links children-parents of all analyzes
*/
static function trace_hierarchy($analyzes_map) {
$base_tree = array();
foreach(array_values($analyzes_map) as $id => $analyze) {
$base_tree[$analyze['id']] = $analyze['parent_id'];
//$tree_analyze[$analyze['id']] = $analyze;
$tree_analyze[$analyze['id']] = array("data" => $analyze, "child" => array());
}
// Create relationships
$h_analysis = array();
foreach($tree_analyze as $analyze_id => $analyze_infos) {
if ($analyze_infos["data"]["parent_id"] == 0) {
$h_analysis[$analyze_id] = &$tree_analyze[$analyze_id];
} else {
$tree_analyze[$analyze_infos["data"]["parent_id"]]["child"][$analyze_id] = &$tree_analyze[$analyze_id];
}
}
return $h_analysis;
}
/**
* Test if the substring ends the string
*
* @param $str : the string to test
* @param $sub : the substring that may ends $str
* @return boolean
*/
static function ends_with($str, $sub) {
return ( substr( $str, strlen( $str ) - strlen( $sub ) ) == $sub );
}
/**
* Returns a string generated randomly
*
* @param $size : the random key size
* @return string
*/
static function create_random_key($size) {
$keyset = "abcdefghijklmABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789";
$randkey = "";
for ($i=0; $i<$size; $i++)
$randkey .= substr($keyset, rand(0, strlen($keyset)-1), 1);
return $randkey;
}
/**
* Delete directories
*
* @param string $user_login
* @param string $user_pwd
* @param string $directory
* @return 0=>everything ok, 1=>user right problem, 2=>wrong authentification, 3=>connection error
*/
static function delete_directory($user_login, $user_pwd, $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, $user_pwd)) return 2;
if ($directory != 'undefined' && $directory != '') {
// And process the directories structure
//TODO BUG NE RETOURNE PAS D'ERREUR si pas supprimer
$stream = ssh2_exec($connection, 'rm -rf '.$directory."/");
$errorStream = ssh2_fetch_stream($stream, SSH2_STREAM_STDERR);
// Enable blocking for both streams
stream_set_blocking($errorStream, true);
stream_set_blocking($stream, true);
// Whichever of the two below commands is listed first will receive its appropriate output. The second command receives nothing
if(stream_get_contents($errorStream)) {
// Close the streams
fclose($errorStream);
fclose($stream);
return 1;
}else{
// Close the streams
fclose($errorStream);
fclose($stream);
return 0;
}
}
return 0;
}
/**
* Purge directories
*
* @param string $user_login
* @param string $user_pwd
* @param string $directory
* @return 0=>everything ok, 1=>user right problem, 2=>wrong authentification, 3=>connection error
*/
static function purge_directory($user_login, $user_pwd, $directory) {
if ($directory != 'undefined' && $directory != '') {
// And process the directories structure, remove all files except .html ans .png
$connection = ssh2_connect('127.0.0.1', 22);
if (!$connection) {
return 3;
}
if (!ssh2_auth_password($connection, $user_login,$user_pwd )){
return 2;
}
$stream = ssh2_exec($connection, 'ls -d '.$directory.'/' );
$errorStream = ssh2_fetch_stream($stream, SSH2_STREAM_STDERR);
// Enable blocking for both streams
stream_set_blocking($errorStream, true);
stream_set_blocking($stream, true);
//if error is raised, $directory does not exist>no problem (in case of an analysis which do not have associated files
if(stream_get_contents($errorStream)) {
// Close the streams
fclose($errorStream);
fclose($stream);
return 0;
}
$stream = ssh2_exec($connection, 'find '.$directory.' -maxdepth 1 -not -name "*.html" -not -name "*.png" -type f -exec rm -f {} \;');
$errorStream = ssh2_fetch_stream($stream, SSH2_STREAM_STDERR);
// Enable blocking for both streams
stream_set_blocking($errorStream, true);
stream_set_blocking($stream, true);
//if error is raised, connected user does not have the right to delete the files
if(stream_get_contents($errorStream)) {
// Close the streams
fclose($errorStream);
fclose($stream);
return 1;
}else{
// Close the streams
fclose($errorStream);
fclose($stream);
return 0;
}
}
}
/**
* Return the string representation of a byte
*
* @param string $size
*/
static function get_octet_string_representation($size) {
$octets_link = array("Bytes", "kB", "MB", "GB", "TB", "PB", "EB", "ZB");
$p = (int)(ceil((float)(strlen(strval($size)))/(float)(3) - (float)(1)));
$pow_needed = $p * 10;
$pow_needed = pow(2, $pow_needed);
$value = (float)($size)/(float)($pow_needed);
$tmp = explode(".", $value);
$value = $tmp[0].".".substr($tmp[1], 0, 2);
$value = $value." ".$octets_link[$p];
return $value;
}
static function get_purge_mail($project_name, $project_id, $nb_run_purgeable,$nb_analyse_purgeable, $demand_id,
$purgeable_size, $project_size, $purge_delay, $url_price, $min_extention_duration,
$min_extention_size, $emails, $runs_list, $analyse_list) {
$template_mail= '
Data Purge on nG6
Dear user,
The two years data storage period of part or whole ###PROJECT_NAME### project (###nb_run### run(s) and ###nb_analyse### analyse(s)) is ended.
This purge alert No ###DEMAND_ID### corresponds to ###SIZE_STR### see list of impacted files below.
In ###PURGE_DELAY### days, your data will be deleted. Keep us informed if you wish to extend the storage period,
please have a look at our storage fees (###URL_PRICE###) and reply to this email with the following information:
----------------------------------------------
- Demand number: ###DEMAND_ID###
- Request for extension term: XXX (minimal unit: ###EXTENSION_DURATION###)
- Request for extension size: XXX (mininal unit: ###EXTENSION_SIZE###)
- Laboratory name/Institution:
----------------------------------------------
###EMAILS###We would appreciate if you could group your demands by laboratory.
Yours sincerely
nG6 team (for GeT-Genotoul and Bioinfo-Genotoul facilities)
Files impacted of:
- Runs : ###RUNS_LIST###
- Analyzes : ###ANALYSES_LIST###
';
$size_str = $purgeable_size . " purgeable data on ". $project_size ." of whole project";
if ($purgeable_size == $project_size) {
$size_str = "whole project (".$purgeable_size . ")";
}
$search=array("###nb_run###","###nb_analyse###","###PROJECT_NAME###","###PROJET_ID###","###DEMAND_ID###",
"###EMAILS###","###RUNS_LIST###","###ANALYSES_LIST###","###SIZE_STR###",
"###EXTENSION_DURATION###","###EXTENSION_SIZE###","###URL_PRICE###","###PURGE_DELAY###");
$replace=array($nb_run_purgeable,$nb_analyse_purgeable,$project_name,$project_id, $demand_id ,
$emails, $runs_list, $analyse_list, $size_str,
$min_extention_duration, $min_extention_size, $url_price, $purge_delay);
$mail=str_replace($search, $replace, $template_mail);
return $mail;
}
/**
* hash password (using default encryption method)
* @param string $password
* @return hashed password
*/
static function hash_password($password){
if (\TYPO3\CMS\Saltedpasswords\Utility\SaltedPasswordsUtility::isUsageEnabled('FE')) {
$objSalt = \TYPO3\CMS\Saltedpasswords\Salt\SaltFactory::getSaltingInstance(NULL);
if (is_object($objSalt)) {
$saltedPassword = $objSalt->getHashedPassword($password);
}
}
return $saltedPassword;
}
static function get_ssh_connection($user_login, $user_pwd){
$connection = ssh2_connect('127.0.0.1', 22);
if (!$connection) return NULL;
if (!ssh2_auth_password($connection, $user_login, $user_pwd)) return NULL;
return $connection ;
}
static function get_config_content(){
$config_file_path = __DIR__."/../../../application.properties";
$config_file_content = file_get_contents($config_file_path);
return($config_file_content);
}
static function get_retention_policy_from_space_id($space_id = "default"){
$config_file_content = tx_nG6_utils::get_config_content();
//To explode the file content by line, we use PHP_EOL
$array_config_content = explode(PHP_EOL, $config_file_content);
$space_id_retention_config = array();
$pattern_to_find = "[space_".$space_id."]";
$is_space_id_found = FALSE;
//We want to return the space id config as an array
foreach($array_config_content as $line_id => $line_content){
//if we found the right section
if($line_content == $pattern_to_find){
$is_space_id_found = TRUE;
}
//If we enter a new section, we stop the line copying
if($is_space_id_found && $line_content != $pattern_to_find && strpos($line_content,'[')===0 ){
$is_space_id_found = FALSE;
}
if($is_space_id_found){
$space_id_retention_config[] = $line_content;
}
}
return($space_id_retention_config);
}
static function get_project_retention_policy( $project_id ){
$space_id = tx_nG6_db::get_project_space_id($project_id);
$retention_policy = tx_nG6_utils::get_retention_policy_from_space_id($space_id);
$retention_line = "";
$policy = "";
$retention_value = "";
$return_text = "";
foreach($retention_policy as $line => $line_content){
if( strpos($line_content,"retention") === 0 ){
$retention_line = $line_content;
}
}
if( is_numeric(strpos($retention_line,"date"))){
$policy = "date";
}elseif( is_numeric(strpos($retention_line,"period"))){
$policy = "period";
}
$split_retention_line = explode('=',$retention_line);
$retention_value = $split_retention_line[1];
if($policy == "date"){
$date = date_create_from_format("d/m/Y", $retention_value);
$nice_date = date_format($date, 'l jS \of F Y');
$return_text = " until ".$nice_date;
}elseif($policy == "period"){
$return_text = " for ".$retention_value." months";
}
return($return_text);
}
//Return a php array with array[space_name]=space_name, containing all available space_ids
static function get_available_space_ids (){
$config_file_content = tx_nG6_utils::get_config_content();
//To explode the file content by line, we use PHP_EOL
$array_config_content = explode(PHP_EOL, $config_file_content);
$ret = array();
foreach($array_config_content as $line => $line_content){
//If the current line starts with "[space_"
if( strpos($line_content,'[space_') === 0 ){
$space_id = str_replace('[space_','',$line_content);
$space_id = str_replace(']','',$space_id);
$space_id = trim($space_id);
$ret[$space_id]=$space_id;
}
}
return($ret);
}
static function convert_epoch_timestamp_to_nice_date( $epoch_date ){
//return(gmdate('D, d M Y', $epoch_date));
return(gmdate('l jS \of F Y', $epoch_date));
}
}
if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_utils.php']) {
include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_utils.php']);
}
if (defined('TYPO3_MODE') && $TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_db.php']) {
include_once($TYPO3_CONF_VARS[TYPO3_MODE]['XCLASS']['ext/nG6/class.tx_nG6_db.php']);
}
?>