</td>
<td>
<span>
<?php
if (isset($jobinfo['usedspace'])) {
echo $jobinfo['usedspace'];
} else {
echo "--";
}
?>
</span>
</td> <!-- occupied space tmp -->
<td> <!-- commands -->
<?php
if ($status !== JobStatus::$RUNNING) {
if (is_dir(get_job_exec_dir($job))) {
?>
<a href="<?php
echo $rerun_link;
?>
">Rerun</a>
<?php
}
}
?>
<a href="<?php
echo $showjobinfojs;
?>
">Info</a>
/**
* Executes a script in a remote server via SSH
*
* @param type $study the case study
* @param type $jobid the job id
* @param type $workdir the working directory
* @param type $rerun if the execution is a re-run of an existing job
* @param type $script_path the script file, with path relative to the study_dir
*/
function execute_script_remote($study, $jobid, $workdir, $rerun, $cmd, $args = "")
{
include 'config.inc.php';
$jobid_qsub = 'j' . str_replace(".", "_", $jobid);
$orig_cmd = $cmd;
# check if the command is a python script
if (is_python_script($cmd) !== false) {
// prepend the python script with our command
$exec_dir_local = get_job_exec_dir($jobid);
if (!$rerun) {
// if the job is NOT a re-run, prepend the python script with the python-prepend.py file
$script_content = file_get_contents($exec_dir_local . "/" . $cmd);
$script_prepend = file_get_contents("lib/pipeline_prepend.py", true);
$script_content = $script_prepend . $script_content;
//error_log("Prepending python script at " . $exec_dir_local . "/" . $cmd);
file_put_contents($exec_dir_local . "/" . $cmd, $script_content);
// copying qsub_template.sh to workdir
$template = file_get_contents("lib/qsub_template.sh", true);
file_put_contents($exec_dir_local . "/qsub_template.sh", $template);
}
$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 = "/bin/bash " . $cmd;
$args = $jobid_qsub;
}
// http://unix.stackexchange.com/a/29495
// The jobs submitted by nipype using qsub are set with the name
// node_name.workflow_name.user_name
// the user_name is passed to nipype through the environment variable $LOGNAME
// we cannot customize easily this behavior, so we customize the variable $LOGNAME to
// job_id.user_name
// in this way, the final job name will be
// node_name.workflow_name.user_name.job_id
// and it will be easier for the Neurocloud webapp to know if there are still running/queued SGE jobs for this job id
$cmdline = create_ssh_command() . " 'cd {$workdir} && chmod +x {$orig_cmd} && { LOGNAME={$jobid_qsub}.\$LOGNAME nohup {$cmd} {$args} >>results/nc_stdout.log 2>&1 & } && echo \$!' ";
//error_log($cmdline);
$pid = exec($cmdline);
$jobinfo = array("study" => $study, "jobid" => $jobid, "qsub_jobname" => $jobid_qsub, "pid" => $pid, "start_date" => date("Y-m-d H:i:s"), "script" => $orig_cmd, "cmdline" => $cmdline, "exec_dir" => $workdir, "exec_type" => "remote");
save_job_info($study, $jobid, $jobinfo);
return $pid;
}
<?php
/*
* delete_results
* Created on: Jan 30, 2013 12:30:40 PM
*
* Copyright 2013 EnginSoft S.p.A.
* All rights reserved
*/
include_once 'neurocloud/lib/common.php';
$study = $_POST["study"];
$jobid = $_POST["jobid"];
$path = "{$study}/results/{$jobid}";
$jobinfo = get_job_info($study, $jobid);
$usedspace = isset($jobinfo["usedspace"]) ? $jobinfo["usedspace"] : "undefined";
insert_job_log($study, $jobid, "deleted results. Used disk space: {$usedspace}");
if (\OC\Files\Filesystem::is_dir($path)) {
//rmdirr($path);
\OC\Files\Filesystem::unlink($path);
// from Owncloud 5.0.0, this will recurse on subdirs (delTree)
}
$execdir = get_job_exec_dir($jobid);
if (is_dir($execdir)) {
rmdirr($execdir);
}
exit;
/**
*
* @param array $info the associative array of info for the file being processed
*/
public static function beforeFileRenameDelete($info)
{
$file = $info['path'];
if (!$file) {
$file = $info['oldpath'];
}
if (self::$DO_LOG) {
error_log("path === {$file}");
}
$pathsplit = explode("/", $file);
$len = count($pathsplit);
$lastelem = $pathsplit[$len - 1];
// the splitted path has always the first element empty, so $pathsplit[0] === ""
$firstelem = $pathsplit[1];
if (is_valid_casestudy("/" . $firstelem) === null) {
if (self::$DO_LOG) {
error_log("{$firstelem} is a valid case study");
}
if ($len > 3 && $pathsplit[2] === 'results' && \OC\Files\Filesystem::is_dir($file)) {
// case 1: trying to delete/rename one the results directories of a running job
if (is_job_running($firstelem, $lastelem)) {
// since the job is still running, do not allow to rename/delete the results directory
if (self::$DO_LOG) {
error_log("beforeFileRenameDelete : trying to rename/delete {$file} while the job is still running");
}
$info['run'] = false;
} else {
if (self::$DO_LOG) {
error_log("beforeFileRenameDelete : no job running for {$file}");
}
// the user is deleting a results directory: delete also the temp directory if existing
$tempdir = get_job_exec_dir($file);
if (is_dir($tempdir)) {
rmdirr($tempdir);
}
}
}
if ($lastelem === 'data' || $lastelem === 'pipeline' || $lastelem === 'results') {
// case 2: we are trying to rename/delete one of the directories data/pipeline/results of a case study
if (any_jobs_running($firstelem)) {
if (self::$DO_LOG) {
error_log("beforeFileRenameDelete : trying to rename/delete {$file} while jobs are running");
}
$info['run'] = false;
} else {
if (self::$DO_LOG) {
error_log("beforeFileRenameDelete : no jobs running for {$file}");
}
}
}
if ($len > 3 && $pathsplit[2] === 'data') {
// case 3: renaming/deleting a file inside the data directory, while a job is running. Do not always allow it
if (any_jobs_running($firstelem)) {
if (self::$DO_LOG) {
error_log("beforeFileRenameDelete : trying to rename/delete {$file} while jobs are running");
}
$info['run'] = false;
} else {
if (self::$DO_LOG) {
error_log("beforeFileRenameDelete : no jobs running for {$file}");
}
}
}
}
}
