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launchTool.php
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launchTool.php
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<?php
require __DIR__."/../../config/bootstrap.php";
redirectOutside();
$debug=0;
$SGE_updated = getUserJobs($_SESSION['User']['id']);
if ($debug){
print "</br>REQUEST FILES ARE [FN]:</br>";
var_dump($_REQUEST['fn']);
print "<br/>";
print "</br>RAW ARGUMENTS ARE<br/>";
var_dump($_REQUEST['arguments']);
print "<br/>";
print "</br>RAW INPUT_FILES ARE<br/>";
var_dump($_REQUEST['input_files']);
print "<br/>";
print "</br>RAW INPUT_FILES PUBLIC ARE<br/>";
var_dump($_REQUEST['input_files_public_dir']);
print "<br/>";
foreach ($_REQUEST as $k=>$v){
if ($k!="arguments" && $k!="input_files" && $k!="input_files_public_dir" && $k!="fn"){
print "<br/><br/>REQUEST[$k]</br>";
var_dump($v);
}
}
}
//
// Get tool.
$tool = getTool_fromId($_REQUEST['tool'],1);
if (empty($tool)){
$_SESSION['errorData']['Error'][]="Tool not specified or not registered. Please, register '".$_REQUEST['tool']."'";
redirect($GLOBALS['BASEURL']."workspace/");
}
//
// Set Tooljob
/*
if (!isset($_REQUEST['execution']) ){ ## TODO: TEMPORAL HACK TO ENSURE WE HAVE EXECUTION VAR. WAIT UNTIL GENIS MODERNIZE ALL FORMS
$_REQUEST['execution'] = $_REQUEST['project'];
$_REQUEST['project'] = "99";
}
*/
if (!isset($_REQUEST['execution']) || !isset($_REQUEST['project'])){
$_SESSION['errorData']['Internal'][]="Error launching tool. 'execution' or 'project' are not received";
redirect($GLOBALS['BASEURL']."workspace/");
}
$jobMeta = new Tooljob($tool,$_REQUEST['execution'],$_REQUEST['project'],$_REQUEST['description']);
if ($debug){
print "<br/>NEW TOOLJOB SET:</br>";
var_dump($jobMeta);
}
//
// Check input file requirements
if (!isset($_REQUEST['input_files'])){
$_SESSION['errorData']['Error'][]="Tool is not receiving input files. Please, select them from your workspace table.";
redirect($GLOBALS['BASEURL']."workspace/");
}
//
// Get input_files medatada (with associated_files)
$files = Array(); // distinct file Objs to stage in
$filesId = Array();
foreach($_REQUEST['input_files'] as $input_file){
if (is_array($input_file)){
$filesId = array_merge($filesId,$input_file);
}else{
if ($input_file)
array_push($filesId,$input_file);
}
}
$filesId=array_unique($filesId);
foreach ($filesId as $fnId){
$file = getGSFile_fromId($fnId);
if (!$file){
$_SESSION['errorData']['Error'][]="Input file $fnId does not belong to current user or has been not properly registered. Stopping execution";
redirect($GLOBALS['BASEURL']."workspace/");
}
$files[$file['_id']]=$file;
$associated_files = getAssociatedFiles_fromId($fnId);
foreach ($associated_files as $assocId){
$assocFile = getGSFile_fromId($assocId);
if (!$assocFile){
$_SESSION['errorData']['Error'][]="File associated to ".basename($file['path'])." ($assocId) does not belong to current user or has been not properly registered. Stopping execution";
redirect($GLOBALS['BASEURL']."workspace/");
}
$files[$assocFile['_id']]=$assocFile;
}
}
if ($debug){
print "<br/></br>TOTAL number of FILES given as params : ".count($filesId);
print "<br/></br>TOTAL number of FILES (including associated) : ".count(array_keys($files))."</br>";
}
//
// Set Arguments
if (!$_REQUEST['arguments']){
$_REQUEST['arguments']=array();
}
$jobMeta->setArguments($_REQUEST['arguments'],$tool);
//
// Set InputFiles
$r = $jobMeta->setInput_files($_REQUEST['input_files'],$tool,$files);
if ($debug){
print "<br/>TOOL Input_files are:</br>";
var_dump($jobMeta->input_files);
}
if ($r == "0"){
redirect($_SERVER['HTTP_REFERER']);
}
//
// Checking input_files locally
foreach ($files as $fnId => $file) {
$fn = getAttr_fromGSFileId($fnId,'path');
$rfn = $GLOBALS['dataDir']."/$fn";
if (! is_file($rfn)){
$_SESSION['errorData']['Error'][]="File '".basename($fn)."' is not found or has size zero. Stopping execution";
?><script type="text/javascript">//window.history.go(-1);</script><?php
//exit(0);
redirect($_SERVER['HTTP_REFERER']);
}
}
//
// Set InputFilesPublic from public directory
$files_pub = array();
if ($_REQUEST['input_files_public_dir']){
//Get input_file public data medatadata
$files_pub = $jobMeta->createMetadata_from_Input_files_public($_REQUEST['input_files_public_dir'],$tool);
if ($debug){
print "<br/>TOOL METADATA for Input_files_public are:</br>";
var_dump($files_pub);
}
if (!count($files_pub)){
redirect($_SERVER['HTTP_REFERER']);
}
// Set InputFiles public dir
$r = $jobMeta->setInput_files_public($_REQUEST['input_files_public_dir'],$tool,$files_pub);
if ($debug){
print "<br/>TOOL Input_files public are:</br>";
var_dump($jobMeta->input_files_pub);
}
if ($r == "0"){
redirect($_SERVER['HTTP_REFERER']);
}
}
// Stage in (fake) TODO
//
// Create working_dir
$jobId = $jobMeta->createWorking_dir();
if ($debug)
echo "<br/></br>WD CREATED SCCESSFULLY AT: $jobMeta->working_dir<br/>";
if (!$jobId){
redirect($_SERVER['HTTP_REFERER']);
}
//
// Setting Command line. Adding parameters
$r = $jobMeta->prepareExecution($tool,$files,$files_pub);
if ($debug)
echo "<br/></br>PREPARE EXECUTION RETURNS ($r). <br/>";
if($r == 0){
redirect($_SERVER['HTTP_REFERER']);
}
//
// Launching Tooljob
$pid = $jobMeta->submit($tool);
if ($debug)
echo "<br/></br>JOB SUBMITTED. PID = $pid<br/>";
if(!$pid)
redirect($GLOBALS['BASEURL']."workspace/");
if ($debug){
print "<br/>ERROR_DATA<br/>";
var_dump($_SESSION['errorData']);
unset($_SESSION['errorData']);
print "</br><br/>JOB_META END<br/>";
var_dump((array)$jobMeta);
}
if ($debug)
echo "<br/>Saving JOB MEDATA USER <br/>";
addUserJob($_SESSION['User']['_id'],(array)$jobMeta,$jobMeta->pid);
if ($debug)
exit(0);
if (!isset($_SESSION['errorData']['Error'])){
$proj = getProject($jobMeta->project);
$_SESSION['errorData']['Info'][]="Job successfully sent! Monitor it at <b>".$proj['name']." › ".$jobMeta->execution." › ".$jobMeta->title."</b>.";
if ($_SESSION['User']['activeProject'] != $jobMeta->project){
$projWS = getProject($_SESSION['User']['activeProject']);
$_SESSION['errorData']['Info'][]="Notice that your current workspace belongs to project '".$projWS['name']."'. Move to '".$proj['name']."' to check out your job.";
}
}
redirect($GLOBALS['BASEURL']."workspace/");
?>