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workspace.php
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workspace.php
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<?php
/*
*
*/
require __DIR__."/../../config/bootstrap.php";
redirectOutside();
//
// Check operation and input files
if (!isset($_REQUEST['op'])) {
header("location:../workspace/");
}
if (!isset($_REQUEST['fn']) && !isset($_REQUEST['fnPath']) && !preg_match('/cancelJob/',$_REQUEST['op']) ) {
$_SESSION['errorData']['Error'][] = "Selected operation ('".$_REQUEST['op']."') requires at least one file. Any file name received.";
header("location:../workspace/");
}
if (is_array($_REQUEST['fn']) && $_REQUEST['op'] != 'moveFiles')
$_REQUEST['fn']=$_REQUEST['fn'][0];
$fileData = $GLOBALS['filesCol']->findOne(array('_id' => $_REQUEST['fn'], 'owner' => $_SESSION['User']['id']));
$fileMeta = $GLOBALS['filesMetaCol']->findOne(array('_id' => $_REQUEST['fn']));
$filePath = getAttr_fromGSFileId($_REQUEST['fn'],'path');
$rfn = $GLOBALS['dataDir']."/$filePath";
// user project directory
$userPath = getAttr_fromGSFileId($_SESSION['User']['dataDir'],"path");
//
// Process operation
if (isset($_REQUEST['op'])){
switch ($_REQUEST['op']) {
case 'newFolder':
$r = createGSDirBNS($GLOBALS['filesCol'],$_REQUEST['fn']);
if ($r == 0){
mkdir ($rfn,0777);
chmod($rfn, 0777);
}
break;
case 'downloadFile' :
set_time_limit(0);
ini_set('memory_limit', '512M');
if(empty($rfn) || !file_exists($rfn) ){
$_SESSION['errorData']['Error'][] = "File ".$_REQUEST['fn']." not found in disk anymore or empty <a href=\"javascript:location.reload();\">[ OK ]</a>";
break;
}
downloadFile($rfn);
exit(0);
break;
case 'downloadAll':
$newName= "files.tar.gz";
$tmpZip = $GLOBALS['dataDir']."/".$userPath."/".$GLOBALS['tmpUser_dir']."/".basename($newName);
$fls = "";
foreach( $_GET['fn'] as $v ) {
if($v !== 'undefined'){
$filePath2 = getAttr_fromGSFileId($v,'path');
$relpath = implode("/", array_slice(split('/',$filePath2), 0, -1));
$filnam = end(split('/',$filePath2));
$rfn2 = $GLOBALS['dataDir']."/$relpath";
$fls .= "-C $rfn2 $filnam ";
}
}
$cmd = "/bin/tar czf $tmpZip $fls 2>&1";
exec($cmd,$output);
if ( !is_file($tmpZip) ){
$_SESSION['errorData']['Error'][] = "Uncompressed file not created.";
if ($output)
$_SESSION['errorData']['Error'][] = implode(" ", $output)."</br> <a href=\"javascript:location.reload();\">[ OK ]</a>";
break;
}
downloadFile($tmpZip);
unlink($tmpZip);
exit(0);
break;
case 'downloadtgz' :
if (filetype($rfn) != 'dir') {
$_SESSION['errorData']['Error'][] = "Cannot tar ".$_REQUEST['fn']." File is not a directory";
break;
}
$newName= $_REQUEST['fn'].".tar.gz";
$tmpZip = $GLOBALS['dataDir']."/".$userPath."/".$GLOBALS['tmpUser_dir']."/".basename($newName);
$cmd = "/bin/tar -czf $tmpZip -C $rfn . 2>&1";
exec($cmd,$output);
if ( !is_file($tmpZip) ){
$_SESSION['errorData']['Error'][] = "Uncompressed file not created.";
if ($output)
$_SESSION['errorData']['Error'][] = implode(" ", $output)."</br> <a href=\"javascript:location.reload();\">[ OK ]</a>";
break;
}
downloadFile($tmpZip);
unlink($tmpZip);
exit(0);
break;
case 'openPlainFileEdit':
// read the textfile
$text = file_get_contents($rfn);
?>
<form action="" method="post">
<textarea style="border:2px solid #92b854; background-color: #fefbfa;" cols=150 rows=37 name="text"><?php echo htmlspecialchars($text) ?></textarea>
</br>
<input type="submit" value="Save edited file"/>
<input type="reset" />
</form>
<?php
exit;
break;
case 'openPlainFile':
$fileInfo = pathinfo($rfn);
$contentType = "text/plain";
$fileExtension = $fileInfo['extension'];
$content_types_list = mimeTypes();
if (array_key_exists($fileExtension, $content_types_list))
$contentType = $content_types_list[$fileExtension];
if (!$fileData && !preg_match('/\.log/',$rfn) ){
break;
}
if (!is_file($rfn) || !filesize($rfn)){
$_SESSION['errorData']['error'][]= "'".basename($rfn). "' does not exist anymore or is empty. <a href=\"javascript:deleteMesg('".urlencode($_REQUEST['fn'])."')\">[ Delete ]</a> <a href=\"workspace/workspace.php\">[ OK ]</a>";
break;
}
header('Content-Type: ' . $contentType);
header("Accept-Ranges: bytes");
header("Access-Control-Allow-Methods:GET, HEAD, DNT");
header("Content-Disposition: inline; filename=".basename($rfn));
header("Content-Length: ".filesize($rfn));
print passthru("/bin/cat \"$rfn\"");
exit(0);
break;
case 'openPlainFileFromPath':
if (!$_REQUEST['fnPath']){
$_SESSION['errorData']['Error'][]="Cannot open file. Variable 'fnPath' not received. Please, try it latter or mail <a href=\"mailto:helpdesk@multiscalegenomics.eu\">helpdesk@multiscalegenomics.eu</a>";
break;
}
if (preg_match('/^\//',$_REQUEST['fnPath']))
$rfn = $_REQUEST['fnPath'];
else
$rfn = $GLOBALS['dataDir']."/".$_REQUEST['fnPath'];
$fileInfo = pathinfo($rfn);
$contentType = "text/plain";
$fileExtension = $fileInfo['extension'];
$content_types_list = mimeTypes();
if (array_key_exists($fileExtension, $content_types_list))
$contentType = $content_types_list[$fileExtension];
//if (!$fileData && !preg_match('/\.log/',$rfn) ){
// break;
//}
if (!is_file($rfn) || !filesize($rfn)){
$_SESSION['errorData']['error'][]= "'".basename($rfn). "' does not exist anymore or is empty. <a href=\"javascript:deleteMesg('".urlencode($_REQUEST['fn'])."')\">[ Delete ]</a> <a href=\"workspace/workspace.php\">[ OK ]</a>";
break;
}
header('Content-Type: ' . $contentType);
header("Accept-Ranges: bytes");
header("Access-Control-Allow-Methods:GET, HEAD, DNT");
header("Content-Disposition: inline; filename=".basename($rfn));
header("Content-Length: ".filesize($rfn));
print passthru("/bin/cat \"$rfn\"");
exit;
case 'deleteAll':
case 'deleteSure':
$r = deleteFiles($_REQUEST['fn']);
break;
case 'deleteDirOk':
if (basename($filePath) == "uploads" || basename($filePath) == "repository" ){
$_SESSION['errorData']['error'][]="Cannot delete structural directory '$filePath'.";
break;
}
$r = deleteGSDirBNS($_REQUEST['fn']);
if ($r == 0){
$_SESSION['errorData']['error'][]="Cannot delete directory '$filePath' file from repository";
break;
}
exec ("rm -r \"$rfn\" 2>&1",$output);
if (error_get_last()){
$_SESSION['errorData']['error'][]=implode(" ",$output);
}
break;
case 'cancelJobPids':
$r = delJob($_REQUEST['pids']);
break;
case 'cancelJobDir':
$jobList=Array();
$jobData = getUserJobs($_SESSION['userId']);
if (count($jobData)){
foreach ($jobData as $data){
$filesId = (!is_array($data['out'])? Array($data['out']):$data['out']);
foreach ($filesId as $fileId){
if (isset($fileId) && preg_match('/^'.preg_quote($_REQUEST['fn'],'/').'/',$fileId) ){
array_push($jobList,$fileId);
continue;
}
}
}
}
if (count($jobList)==0 ){
$_SESSION['errorData']['error'][]= "Cannot cancel tasks from ".$_REQUEST['fn'].". Not submited jobs found. Have they just finished? <a href=\"".$GLOBALS['managerDir']."/workspace.php\">[ OK ]</a>";
}else{
$dirFiles = "<li>- ". implode('</li><li>- ', array_map('basename', $jobList))."</li>";
$_SESSION['errorData']['error'][] = "Are you sure you want to cancel all jobs from project '".basename($_REQUEST['fn'])."'? <a href=\"".$GLOBALS['managerDir']."/workspace.php?op=cancelJobDirSure&fn=" . urlencode($_REQUEST['fn']). "\">[ Yes, I'm sure ]</a> <a href=\"".$GLOBALS['managerDir']."/workspace.php\">[ Cancel ]</a> <ul>$dirFiles</ul>";
}
break;
case 'cancelJob':
$_SESSION['errorData']['error'][] = "Are you sure you want to cancel job for file '" . basename($_REQUEST['fn']) . "'? ";
$pid = $_REQUEST['pid'];
//$pid = getPidFromOutfile($_REQUEST['fn']);
$jobInfo= getRunningJobInfo($pid);
$SGE_updated = getUserJobs($_SESSION['userId']);
$succList = "";
if (isset($jobInfo['jid_successor_list'])){
foreach (explode(",",trim($jobInfo['jid_successor_list'])) as $pidSucc ){
if (isset($SGE_updated[$pidSucc])){
if (!is_array($SGE_updated[$pidSucc]['out']))
$outSucc = $SGE_updated[$pidSucc]['out'];
else
$outSucc = $SGE_updated[$pidSucc]['out'][0];
$succList .= "<li>- ".basename($outSucc)."</li>";
}
}
}
if ($succList){
$_SESSION['errorData']['error'][] .= "The following execution dependencies will also be cancelled:<ul>$succList<ul/>";
}
$_SESSION['errorData']['error'][].= "<a href=\"".$GLOBALS['managerDir']."/workspace.php?op=cancelJobSure&fn=" . $_REQUEST['fn'] . "\">[ Yes, I'm sure ]</a> <a href=\"".$GLOBALS['managerDir']."/workspace.php\">[ Cancel ]</a>";
break;
case 'cancelJobSure':
$r = delJob($_REQUEST['pid']);
if (!$r){
$_SESSION['errorData']['Error'][]= "Cannot cancel task. Unsuccessfully exit of 'deljob' for job $pid.";
}
//$r = delJobFromOutfiles($_REQUEST['fn']);
break;
case 'cancelJobDirSure':
$jobList=Array();
$jobData = getUserJobs($_SESSION['User']['_id']);
$delJobs_ok = 1;
if (count($jobData)){
foreach ($jobData as $jobId =>$data){
if ($data['output_dir'] == $rfn){
$r = delJob($jobId);
if (!$r){
$_SESSION['errorData']['Error'][]= "Cannot cancel '".$jobData["execution"]."' task. Unsuccessfully exit of 'deljob' for job $pid.";
$delJobs_ok=0;
continue;
}
}
}
}
if ($delJobs_ok && count($fileData['files'])==0 && !isset($_SESSION['errorData']['SGE'])){
$r = deleteGSDirBNS($_REQUEST['fn']);
if ($r == 0)
break;
exec ("rm -r \"$rfn\" 2>&1",$output);
$_SESSION['errorData']['Error'][]=implode(" ",$output);
}
break;
case 'close':
session_destroy();
redirect($GLOBALS['homeURL']);
break;
case 'unzip':
case 'untar':
$ext = pathinfo($filePath, PATHINFO_EXTENSION);
$extClean = preg_replace('/_\d+$/',"",$ext);
$fn_Tmp = str_replace(".$ext","",$filePath);
$proj_dir = dirname($rfn);
$rfn_Tmp = "$proj_dir/".basename($fn_Tmp);
$cmd = "";
switch ($extClean) {
case 'dsrc':
$cmd ="";
case 'tar':
#touch option force tar to update uncompressed files atime - required by the expiration time
$cmd = "tar --touch -xf \"" . $rfn . "\" 2>&1";
break;
case 'zip':
list($files_compressed,$zip_output) = indexFiles_zip($rfn);
//check zip content
if (count($files_compressed) == 0){
$_SESSION['errorData']['Error'][]="No files found in given ZIP file '".basename($rfn)."'";
$_SESSION['errorData']['Error'][].= implode("</br>", $zip_output)."</br>";
break;
// do not accept more than 1 file
}elseif (count($files_compressed) > 1){
$_SESSION['errorData']['Error'][]="File '".basename($rfn)."' contains more than one file. Extraction not supported.";
$zip_output = str_replace(" ","  ",$zip_output);
$_SESSION['errorData']['Error'][].= implode("</br>", $zip_output)."</br>";
break;
// do not accept subfolders
}else{
$err=0;
foreach ($files_compressed as $name => $info){
if (preg_match('/\//',$name)){
$_SESSION['errorData']['Error'][]="File '".basename($rfn)."' contains subfolders. Only ZIPs without directory structures are supported.";
$zip_output = str_replace(" ","  ",$zip_output);
$_SESSION['errorData']['Error'][].= implode("</br>", $zip_output)."</br>";
$err=1;
break;
}
}
if ($err){break;}
}
$cmd = "unzip -o \"" . $rfn . "\" -d $proj_dir 2>&1";
/* // unzip certain file from zip
$file_compressed_names = array_keys($files_compressed);
$cmd = "unzip -j \"$rfn\" \"".$file_compressed_names[0]."\" -d \"$proj_dir\" 2>&1";
*/
break;
case 'bz2':
$cmd = "bzip2 -d \"" . $rfn . "\" 2>&1";
break;
case 'gz':
$cmd = "gunzip -S .$ext -f \"" . $rfn . "\" 2>&1";
break;
case 'tgz':
/*
//warning compressed subfolders will be merged
if (!isset($_REQUEST['sure'])){
exec("tar -tf \"$rfn\"", $output);
var_dump($output);
$subfolders = preg_grep('/\/$/',$output);
if (count($subfolders)> 1 || count($output)> 10 ){
$msg ="File '".basename($filePath)."' contains '".count($output)."' elements:</br>";
for ($i=0; $i<count($output); $i++){
$out = $output[$i];
$lev = preg_match_all('/\//i', $out, $m);
for ($n=0; $n<=$lev;$n++){ $msg .= "   ";}
$msg .= " $out</br>";
if ($i>19){
$msg .= " (...)</br>";
break;
}
}
$msg .= "All files will be directly extracted into '".basename($proj_dir)."' folder, without considering the tree file structure of the TAR file. Are you sure you want to uncompress '".basename($filePath)."'? <br/> ";
$msg .= "<a href=\"".$_SERVER[REQUEST_URI]."&sure=1\">[ Sure ]</a>  ";
$msg .= "<a href=\"workspace/\">[ Cancel ]</a>  ";
$_SESSION['errorData']['Warning'][] = $msg;
break;
}
}
*/
$cmd = "tar --touch -xzf \"$rfn\" -C \"$proj_dir\" 2>&1";
break;
default:
$_SESSION['errorData']['error'][] = "Cannot uncompress $extClean file. Method not supported";
}
if ($cmd){
exec($cmd, $output);
//$_SESSION['errorData']['Error'][] = "CMD = $cmd";
if (is_file($rfn_Tmp)){
$insertData = array(
'_id' => $_REQUEST['fn'],
'owner' => $_SESSION['User']['id'],
'size' => filesize($rfn_Tmp),
'mtime' => new MongoDB\BSON\UTCDateTime(filemtime($rfn_Tmp)*1000),
'path' => $fn_Tmp
);
$insertMeta = $fileMeta;
$insertMeta['compress'] = 0;
$r = uploadGSFileBNS($fn_Tmp,$rfn_Tmp,$insertData,$insertMeta,FALSE);
if ($r == 0)
break;
if (is_file($rfn)){
unlink($rfn);
}
}elseif (is_dir($rfn_Tmp) ){
/*
exec("find $rfn_Tmp -type f 2>&1",$rfn_Tmp_files);
foreach ($rfn_Tmp_files as $f){
$f_new = "$proj_dir/".basename($f);
exec("mv $f $proj_dir 2>&1",$output);
if (!is_file($f_new)){
$_SESSION['errorData']['error'][]=" Error inflating ".basename($filePath).". File '$f' contained inside '".basename($filePath)."' cannot be moved to $f_new. Cannot uncompress directory</br>";
unlink($rfn_Tmp);
break;
}
//TODO register each of the files individually. Which metadata?
}
*/
$_SESSION['errorData']['Error'][]=" Error inflating ".basename($filePath).". Directories cannot be uncompressed </br>";
unlink($rfn_Tmp);
}else{
$_SESSION['errorData']['Error'][]= "Error wile uncompressing ".basename($filePath).". Outfile not created.<br/>";
if ($output)
$_SESSION['errorData']['Error'][].= implode("</br>", $output)."</br>";
}
}
unset($_REQUEST['op']);
break;
case 'zip':
$rfn_TmpZip = dirname($rfn)."/".basename($rfn).".gz";
$fn_TmpZip = dirname($filePath)."/".basename($filePath).".gz";
$cmd = "gzip -f \"$rfn\" 2>&1";
exec($cmd, $output);
if (file_exists($rfn_TmpZip)){
$insertData=array(
'_id' => $_REQUEST['fn'],
'owner' => $_SESSION['User']['id'],
'size' => filesize($rfn_TmpZip),
'path' => $fn_TmpZip,
'mtime' => new MongoDB\BSON\UTCDateTime(filemtime($rfn_TmpZip)*1000)
);
$insertMeta = $fileMeta;
$insertMeta['compressed'] = "zip";
$r = uploadGSFileBNS($fn_TmpZip,$rfn_TmpZip,$insertData,$insertMeta,FALSE);
if ($r == 0)
break;
// $r = deleteGSFileBNS($_REQUEST['fn']);
// if ($r == 0)
// break;
}else{
$_SESSION['errorData']['error'][] = "Compressed ZIP file not created.";
if ($output)
$_SESSION['errorData']['error'][] .= implode(" ", $output)."</br> <a href=\"javascript:history.go(-1)\">[ OK ]</a>";
}
unset($_REQUEST['op']);
break;
case 'tar':
// $cmd = "tar --touch -cf \"" . $_REQUEST['fn'] . ".tar\" \"" . $_REQUEST['fn'] . "\" 2>&1";
// chdir($_SESSION['curDir']);
// exec($cmd, $output);
// $_SESSION['errorData']['error'][] = implode(" ", $output);
// chdir($_SESSION['User']->dataDir);
break;
case 'moveFiles':
case 'moveFile':
if (!isset($_REQUEST['target'])){
print('{"error":true, "msg": "Error while moving file. Target path not given."}');die();
break;
}
// Move file/s
$r = moveFiles($_REQUEST['fn'],$_REQUEST['target']);
if ($r === FALSE){
$msg = printErrorData();
print('{"error":true, "msg": "'.$msg.'"}');die();
}else{
$_SESSION['errorData']['Info'][]="File/s successfully moved!!";
print('{"error":false, "msg": "File/s successfully moved!"}');die();
}
break;
case 'moveDir':
if (!isset($_REQUEST['target'])){
$_SESSION['errorData']['Error'][]="Error while moving directory. Target path not given.";
print('{"error":true, "msg": "Error while moving directory. Target path not given."}');die();
break;
}
$rfn_target = $GLOBALS['dataDir']."/".$_REQUEST['target'];
// Move file in mongo
$r = moveGSDirBNS($filePath,$_REQUEST['target']);
if ($r == "0"){
$_SESSION['errorData']['Error'][]="Error while moving directory";
print('{"error":true, "msg": "Error while moving directory"}');die();
break;
}
// Move dir in disk
rename($rfn,$rfn_target);
if (!is_dir($rfn_target)){
$_SESSION['errorData']['Error'][]="Error while writting moved directory";
break;
}
$_SESSION['errorData']['Info'][]="Directory successfully moved!";
print('{"error":false, "msg": "Directory successfully moved!"}');die();
break;
case 'moveDirAll':
break;
}
}
header("location:../workspace/");
//redirect($GLOBALS['BASEURL']."/workspace/");
//scan disk to upload Mongo
// TODO move function upper, for syncronizing before showing the table but after processingPendingJobs
//syncWorkDir2Mongo($GLOBALS['dataDir']."/".$_SESSION['curDir']);
?>