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/* Copyright (c) 2009 Peter Troshin
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
*
* This library is free software; you can redistribute it and/or modify it under the terms of the
* Apache License version 2 as published by the Apache Software Foundation
*
* This library 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 Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* must include this copyright and license notice.
*/
package compbio.engine.cluster.drmaa;
import java.io.IOException;
import java.text.NumberFormat;
import org.apache.log4j.Logger;
import org.ggf.drmaa.DrmaaException;
import org.ggf.drmaa.JobInfo;
import org.ggf.drmaa.Session;
import compbio.engine.Configurator;
import compbio.engine.client.Util;
import compbio.metadata.JobExecutionException;
import compbio.metadata.JobStatus;
public class ClusterUtil {
private static final Logger log = Logger.getLogger(ClusterUtil.class);
public static final NumberFormat CLUSTER_STAT_IN_SEC = NumberFormat
.getInstance();
static {
CLUSTER_STAT_IN_SEC.setMinimumFractionDigits(4);
}
public static final boolean cancelJob(final String jobId,
ClusterSession csession) {
assert Util.isValidJobId(jobId);
boolean cancelled = true;
Session session = csession.getSession();
try {
log.info("Job " + jobId + " is successfully cancelled");
compbio.engine.client.Util.writeMarker(Configurator.getWorkDirectory(jobId),
JobStatus.CANCELLED);
session.control(ClusterSession.getClusterJobId(jobId).getJobId(),
Session.TERMINATE);
} catch (DrmaaException e) {
// Log silently
log.error("Job " + jobId + " cancellation failed!");
log.error("Cause: " + e.getLocalizedMessage(), e.getCause());
cancelled = false;
} catch (IOException e) {
log.error(
"Could not read JOBID file to determine cluster jobid for taskid: "
+ jobId + " Message: " + e.getLocalizedMessage(), e
.getCause());
} finally {
log
.trace("Job "
+ jobId
+ " has been successfully removed from the cluster engine job list");
csession.removeJob(jobId);
}
return cancelled;
}
public static final JobInfo waitForResult(ClusterSession csession,
String jobId) throws JobExecutionException {
JobInfo jinfo = null;
assert Util.isValidJobId(jobId);
try {
jinfo = csession.waitForJob(jobId);
} catch (DrmaaException e) {
log.error(e.getLocalizedMessage(), e.getCause());
throw new JobExecutionException(e);
} catch (IOException e) {
log.error("Could not read JOBID file for job " + jobId
+ " Message " + e.getMessage(), e.getCause());
throw new JobExecutionException(e);
} finally {
// at this point the job has finished
csession.removeJob(jobId);
}
return jinfo;
}
}
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