security bugfix of neurocloud related with owncloud

ajax/checkrunnable.php

@@ -13,7 +13,7 @@
 $study=$_POST["study"];
 
 
-#error_log(print_r($_SESSION["nc_sync_paths"],true));
+//#error_log(print_r($_SESSION["nc_sync_paths"],true));
 
 if (OC_Neurocloud::is_study_runnable($study)) {
     echo "1";

ajax/getoutput.php

@@ -17,7 +17,7 @@
 /*
  * max size of output file, to avoid reading a very big output and clogging the network
  */
-$MAX_SIZE = 1024 * 512; # "512k of memory should be enough for everyone"
+$MAX_SIZE = 1024 * 512; //# "512k of memory should be enough for everyone"
 $content = "";
 if (OC_Filesystem::is_file($filename) && OC_Filesystem::is_readable($filename)) {
     if (OC_Filesystem::filesize($filename) > $MAX_SIZE) {

ajax/inplace_update.php

@@ -27,11 +27,11 @@
     $prefix = "/tmp/owncloud";
 }
 
-# backup current installation
+//# backup current installation
 echo "Backup of current version in $datadir\n";
 exec("tar czf " . $datadir . "/owncloud_bkp$(date +%Y%m%d).tar.gz $root");
 
-# download latest version
+//# download latest version
 echo "Downloading last version\n";
 $curl = curl_init($url);
 $fp = fopen("/tmp/owncloud-latest.tar.bz2", "w");
@@ -42,7 +42,7 @@
 curl_close($curl);
 fclose($fp);
 
-# TODO: check version MD5
+//# TODO: check version MD5
 $md5_try = file_get_contents($url . ".md5");
 if (strlen($md5_try) > 32) {
     $md5_try = substr($md5_try, 0, 32);
@@ -56,7 +56,7 @@
 }
 
 
-# unpack latest version
+//# unpack latest version
 echo "Unpacking last version\n";
 exec("mkdir $datadir/owncloud_latest; tar -C $datadir/owncloud_latest -xjf /tmp/owncloud-latest.tar.bz2");
 

ajax/job_info_row.php

@@ -20,7 +20,7 @@
 $rowid = $_GET['rowid'];
 
 
-# check if we have to print the <tr> elements (we do not print them if this file is called from a AJAX call
+//# check if we have to print the <tr> elements (we do not print them if this file is called from a AJAX call
 if (isset($_GET["print_tr"])) {
     $print_tr = $_GET["print_tr"];
 } else {
@@ -80,7 +80,7 @@
 $killjs = OC_Helper::linkTo("neurocloud", "ajax/kill_job.php", array("study" => $file, "jobid" => $job, "redirect" => 1));
 $refreshstatusjs = "javascript:refresh_job_status('" . $rowid . "','" . $file . "','" . $job . "','" . $outputid . "')";
 $showjobinfojs = "javascript:show_output('" . $outputid . "','". get_job_info_file($file, $job) . "', true)";
-#$queueinfojs = "javascript:show_queue_info('" . $outputid . "','". $jobinfo['qsub_jobname'] . "', true)";
+//#$queueinfojs = "javascript:show_queue_info('" . $outputid . "','". $jobinfo['qsub_jobname'] . "', true)";
 $deletejs = "javascript:delete_results('" . $rowid . "','" . $file . "','" . $job . "')";
 
 $script = isset($jobinfo["script"]) ? basename($jobinfo["script"]) : false;
@@ -171,4 +171,4 @@
 </tr>
 <?php
 }
-?>
+?>

ajax/updateCache.php

@@ -9,10 +9,10 @@
  */
 
 
-# first, clear the "fast" cache, to make sure that missing DB items are inserted/updated
+//# first, clear the "fast" cache, to make sure that missing DB items are inserted/updated
 OC_Cache::clear();
 
-# then scan the filesystem
+//# then scan the filesystem
 OC_FileCache::scan("");
 
 echo 'true';

appinfo/app.php

@@ -13,7 +13,7 @@
     'order' => 74, 
     'href' => OC_Helper::linkTo('neurocloud', 'index.php'), 
     'icon' => OC_Helper::imagePath('neurocloud', 'neurocloud.png'), 
-    'name' => 'Neurocloud'));
+    'name' => 'NeuroBox'));
 
 /**
  * register the classpath
@@ -60,4 +60,4 @@
 
 OC_FileProxy::register(new NC_FileProxy());
 
-?>
+?>

appinfo/info.xml

@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
 <info>
 	<id>neurocloud</id>
-	<name>Neurocloud</name>
-	<description>Neurocloud app description here</description>
+	<name>NeuroBox</name>
+	<description>Neurobox app description here</description>
 	<version>1.0.0</version>
 	<licence></licence>
-	<author>Neurocloud developers</author>
+	<author>Neurobox developers</author>
 	<require>4.5</require>
     <types>
         <filesystem />

execute.php

@@ -11,8 +11,8 @@
 require_once 'lib/common.php';
 
 
-# TODO: SUBSTITUTE WITH REAL CONFIG VALUE !!!
-#OC_Config::setValue("nc_exec_env_root" ,"/tmp/neurocloud");
+//# TODO: SUBSTITUTE WITH REAL CONFIG VALUE !!!
+//#OC_Config::setValue("nc_exec_env_root" ,"/tmp/neurocloud");
 
 
 function create_job_id($study_name, $script_name) {
@@ -57,20 +57,20 @@ function create_execution_env($study_name, $script_name) {
 
     OC_Filesystem::mkdir("$study_name/results/$jobid");
 
-    # le dir /data e /results sono link simbolici alle vere directory del caso di studio
+    //# le dir /data e /results sono link simbolici alle vere directory del caso di studio
     mkdir($job_dir . "/pipeline");
     symlink($datadir, $job_dir . "/data");
     symlink($resultsdir, $job_dir . "/results");
 
-    # creo il file in cui verrà rediretto lo standard output
+    //# creo il file in cui verrà rediretto lo standard output
     $date = date("Y-m-d H:i:s");
     OC_Filesystem::file_put_contents(get_job_output_file($study_name, $jobid), "Standard output for job $jobid, run at $date\n");
 
     $jobinfo = array("jobid" => $jobid, "study" => $study_name);
 
     save_job_info($study_name, $jobid, $jobinfo);
 
-    # copia gli script del caso di studio nella pipeline
+    //# copia gli script del caso di studio nella pipeline
     copy_dir($pipelinedir, $job_dir . "/pipeline");
 
     return $jobid;
@@ -87,7 +87,7 @@ function execute_script_local($workdir, $cmd, $study, $jobid) {
 
     if (chdir($workdir)) {
         $outfile = get_absolute_path(get_job_output_file($study, $jobid));
-        # things that are needed to proc_open, see http://it2.php.net/manual/en/function.proc-open.php
+        //# things that are needed to proc_open, see http://it2.php.net/manual/en/function.proc-open.php
         $pipes = 0;
         $descriptors = array(
             0 => array('pipe', 'r'),
@@ -98,7 +98,7 @@ function execute_script_local($workdir, $cmd, $study, $jobid) {
 
         $env["HOME"] = get_local_exec_dir(OC_User::getUser());
         $env["PATH"] = $_SERVER["PATH"];
-        # use a UNIX command to get the current user name
+        //# use a UNIX command to get the current user name
         $env["USER"] = exec("whoami"); 
 
         chmod($cmd, 0755);
@@ -155,7 +155,7 @@ function execute_script_remote($study, $jobid, $workdir, $rerun, $cmd, $args = "
     $jobid_qsub = 'j' . str_replace(".","_", $jobid);
     $orig_cmd = $cmd;
 
-    # check if the command is a python script
+    //# check if the command is a python script
     if (is_python_script($cmd) !== false) {
         // prepend the python script with our command
 
@@ -177,7 +177,7 @@ function execute_script_remote($study, $jobid, $workdir, $rerun, $cmd, $args = "
 
         $cmd = $NC_CONFIG["python-bin"] . " " . $cmd;
     } elseif (strpos($cmd, ".sh") !== false) {
-        #$cmd = "qsub -cwd -l mf=1.4G -N $jobid_qsub -sync y -o results/nc_stdout.log -e results/nc_stdout.log " . $cmd;
+        //#$cmd = "qsub -cwd -l mf=1.4G -N $jobid_qsub -sync y -o results/nc_stdout.log -e results/nc_stdout.log " . $cmd;
         $cmd = "/bin/bash " . $cmd;
         $args = $jobid_qsub;
     }
@@ -218,7 +218,7 @@ function execute_script_remote($study, $jobid, $workdir, $rerun, $cmd, $args = "
 
     $space = get_used_space_remote();
     if (is_array($space) && (int)$space['percent'] > (int)$NC_CONFIG['minimum_exec_space']) {
-        # Redirect to neurocloud app index , showing an error message
+        //# Redirect to neurocloud app index , showing an error message
         $link = OC_Helper::linkTo("neurocloud", "index.php", array("error" => "Cannot execute script, low free space in remote server.<br>Contact administration or delete old jobs"));
         header("Location: " . $link);
         exit();
@@ -248,15 +248,15 @@ function execute_script_remote($study, $jobid, $workdir, $rerun, $cmd, $args = "
             $exec_dir = get_job_exec_dir($job_id);
             $pid = execute_script_local($exec_dir, "pipeline" . DIRECTORY_SEPARATOR . $script, $study, $job_id);
         }
-        # Redirect to neurocloud app index , showing an info (or error) message
+        //# Redirect to neurocloud app index , showing an info (or error) message
         if ($pid) {
             $link = OC_Helper::linkTo("neurocloud", "index.php", array("jobid" => $job_id, "pid" => $pid, "action" => "launch"));
         } else {
             $link = OC_Helper::linkTo("neurocloud", "index.php", array("error" => "Cannot launch job, see log for details"));
         }
         header("Location: " . $link);
     } else {
-        # Redirect to neurocloud app index , showing an error message
+        //# Redirect to neurocloud app index , showing an error message
         $link = OC_Helper::linkTo("neurocloud", "index.php", array("error" => "Sync is in progress, cannot execute script"));
         header("Location: " . $link);
     }

index.php

@@ -12,7 +12,7 @@
 OC_Util::addStyle('neurocloud', "nc");
 
 OC_App::setActiveNavigationEntry( 'neurocloud_index');
-$tmpl = new OC_Template( 'neurocloud', 'main', 'user');
+$tmpl = new OC_Template('neurocloud', 'main', 'user');
 
 $message = "";
 $action = "launch";

lib/common.php

@@ -77,8 +77,8 @@ function create_ssh_command() {
     $host = $NC_CONFIG["remote_host"];
     $key = get_private_key_file($user);
 
-    # The option BatchMode=yes is used to not asking for password
-    # StrictHostKeyChecking=no is used to not ask to include the host in .ssh/known_hosts file
+    //# The option BatchMode=yes is used to not asking for password
+    //# StrictHostKeyChecking=no is used to not ask to include the host in .ssh/known_hosts file
     return "ssh -n -i $key -o BatchMode=yes -o StrictHostKeyChecking=no $user@$host ";
 }
 
@@ -156,8 +156,8 @@ function get_used_space_remote() {
     include "neurocloud/config.inc.php";
     $cmd = create_ssh_command() . " df -h " . $NC_CONFIG['remote_mount'];
     $lastrow = exec($cmd);
-    # example of lastrow : 
-    # korempba:/nilab0      2.0T   28G  1.9T   2% /nilab0
+    //# example of lastrow : 
+    //# korempba:/nilab0      2.0T   28G  1.9T   2% /nilab0
 
     if (is_string($lastrow)) {
         $spl = preg_split("/\s+/", $lastrow);
@@ -166,7 +166,7 @@ function get_used_space_remote() {
             $ret["total"] = $spl[1];
             $ret["used"] = $spl[2];
             $ret["free"] = $spl[3];
-            $ret["percent"] = substr($spl[4],0,-1); # omit the % character
+            $ret["percent"] = substr($spl[4],0,-1); //# omit the % character
 
             return $ret;
         }
@@ -181,7 +181,7 @@ function get_used_space_remote() {
  */
 function get_user_jobs($user) {
     include "neurocloud/config.inc.php";
-    $basedir = sprintf($NC_CONFIG["local_exec_dir"],$user);
+    $basedir = sprintf($NC_CONFIG["local_exec_dir"], $user);
     $jobs = array();
     if (is_dir($basedir)) {
         $dh = opendir($basedir);
@@ -410,25 +410,25 @@ function get_queue_info($qsub_jobname) {
          */
 
         if ($xml->queue_info->job_list->count() == 0 && $xml->job_info->job_list->count() == 0) {
-            #$return_string = "No running SGE jobs in queue for job_id " . $qsub_jobname;
+            //#$return_string = "No running SGE jobs in queue for job_id " . $qsub_jobname;
             return $return_string;
         } else {
-            #$return_string = "Running SGE jobs:\n";
+            //#$return_string = "Running SGE jobs:\n";
 
             foreach ($xml->queue_info->job_list as $job) {
                 // check if the SGE job name contains the generated job id for this neurocloud job
                 if (strpos($job->JB_name, $qsub_jobname)) {
-                    #$return_string = $return_string . $job->JB_name . "\n";
+                    //#$return_string = $return_string . $job->JB_name . "\n";
                     $return_string[1] = $return_string[1] + 1;
                 }
             }
 
-            #$return_string = $return_string . "\nQueued SGE jobs:\n";
+            //#$return_string = $return_string . "\nQueued SGE jobs:\n";
 
             foreach ($xml->job_info->job_list as $job) {
                 // check if the SGE job name contains the generated job id for this neurocloud job
                 if (strpos($job->JB_name, $qsub_jobname)) {
-                    #$return_string = $return_string . $job->JB_name . "\n";
+                    //#$return_string = $return_string . $job->JB_name . "\n";
                     $return_string[0] = $return_string[0] + 1;
                 }
             }

lib/hooks.php

@@ -242,7 +242,7 @@ public static function is_study_runnable($study) {
         $array = PersistentMap::get_paths();
         foreach(array_keys($array) as $key) {
             if (strpos($key, $study) > 0) {
-                #$syncing = self::$SYNC_STATUS[$key];
+                //#$syncing = self::$SYNC_STATUS[$key];
                 $syncing = $array[$key];
                 if ($syncing) {
                     return false;

settings.php

@@ -5,7 +5,7 @@
 OC_Util::addStyle('neurocloud', "nc");
 OC_Util::addScript("neurocloud", "admin");
 
-$tmpl = new OC_Template( 'neurocloud', 'settings');
+$tmpl = new OC_Template('neurocloud', 'settings');
 
 return $tmpl->fetchPage();
 

templates/main.php

@@ -72,7 +72,7 @@
             <tr>
 
             <?php
-            # TODO: gli script con gli spazi nel nome non sono permessi, perché lanciandoli via SSH vengono parsati come due comandi
+            //# TODO: gli script con gli spazi nel nome non sono permessi, perché lanciandoli via SSH vengono parsati come due comandi
             if (strpos($s, " ") !== false) {
             ?>
 
@@ -90,7 +90,7 @@
             </td>
             <td>
                 <?php 
-                if (is_file(get_private_key_file(OC_User::getUser())) || $NC_CONFIG['default_exec_type'] === 'local') { # checking if the user can run scripts
+                if (is_file(get_private_key_file(OC_User::getUser())) || $NC_CONFIG['default_exec_type'] === 'local') { //# checking if the user can run scripts
                 ?>
                 <span ><a href="<?php echo $exec_link ?>" title="Click to execute this script">Run</a></span>
                 &nbsp;

templates/settings.php

@@ -22,9 +22,9 @@ function get_public_key() {
 </script>
 
 <div class="personalblock">
-    <strong>Neurocloud users public keys</strong>
+    <strong>NeuroBox users public keys</strong>
 <?php
-/*
+/**
 $datadir = OC_Config::getValue("datadirectory");
 $files = array();
 $dh = opendir($datadir);