compbio.engine.cluster.drmaa

Class ClusterSession

java.lang.Object

compbio.engine.cluster.drmaa.ClusterSession

public final class ClusterSession
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
private static ClusterSession	INSTANCE
static java.lang.String	JOBID
(package private) static java.util.List<Job>	jobs
private static org.apache.log4j.Logger	log
private static boolean	open
private static compbio.util.PropertyHelper	ph
private java.lang.String	sContact
private org.ggf.drmaa.Session	session

Constructor Summary

Constructors

Modifier	Constructor and Description
private	ClusterSession()

Method Summary

Modifier and Type	Method and Description
(package private) void	addJob(java.lang.String jobId, ConfiguredExecutable<?> executable)
void	close()
static ClusterJobId	getClusterJobId(java.lang.String taskId)
(package private) static ClusterSession	getInstance()
int	getJobStatus(ClusterJobId jobId) Apparently completed jobs cannot be found! If this happened most likely that the job is not running any more and Most likely it has been cancelled, finished or failed.
static java.lang.String	getJobStatus(int status) Deprecated.
ConfiguredExecutable<?>	getResults(java.lang.String taskId)
org.ggf.drmaa.Session	getSession()
static StatisticManager	getStatistics(org.ggf.drmaa.JobInfo status)
(package private) static void	logStatistics(org.ggf.drmaa.JobInfo status)
void	removeJob(java.lang.String taskId)
private static void	removeJobFromListbyTaskId(java.lang.String taskId)
org.ggf.drmaa.JobInfo	waitForJob(java.lang.String taskId)
org.ggf.drmaa.JobInfo	waitForJob(java.lang.String jobId, long waitingTime)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

log

private static final org.apache.log4j.Logger log

ph

private static final compbio.util.PropertyHelper ph

JOBID

public static final java.lang.String JOBID

See Also:

Constant Field Values

jobs

static final java.util.List<Job> jobs

open

private static boolean open

INSTANCE

private static final ClusterSession INSTANCE

session

private final org.ggf.drmaa.Session session

sContact

private final java.lang.String sContact

Constructor Detail

ClusterSession

private ClusterSession()

Method Detail

getInstance

static ClusterSession getInstance()

getSession

public org.ggf.drmaa.Session getSession()

close

public void close()

addJob

void addJob(java.lang.String jobId,
            ConfiguredExecutable<?> executable)

removeJob

public void removeJob(java.lang.String taskId)

waitForJob

public org.ggf.drmaa.JobInfo waitForJob(java.lang.String taskId)
                                 throws org.ggf.drmaa.DrmaaException,
                                        java.io.IOException

Throws:

org.ggf.drmaa.DrmaaException

java.io.IOException

getClusterJobId

public static ClusterJobId getClusterJobId(java.lang.String taskId)
                                    throws java.io.IOException

Throws:

java.io.IOException

waitForJob

public org.ggf.drmaa.JobInfo waitForJob(java.lang.String jobId,
                                        long waitingTime)
                                 throws org.ggf.drmaa.DrmaaException,
                                        java.io.IOException

Throws:

org.ggf.drmaa.DrmaaException

java.io.IOException

removeJobFromListbyTaskId

private static void removeJobFromListbyTaskId(java.lang.String taskId)

getResults

public ConfiguredExecutable<?> getResults(java.lang.String taskId)
                                   throws org.ggf.drmaa.DrmaaException,
                                          ResultNotAvailableException

Throws:

org.ggf.drmaa.DrmaaException

ResultNotAvailableException

getStatistics

public static StatisticManager getStatistics(org.ggf.drmaa.JobInfo status)
                                      throws org.ggf.drmaa.DrmaaException

Throws:

org.ggf.drmaa.DrmaaException

logStatistics

static void logStatistics(org.ggf.drmaa.JobInfo status)
                   throws org.ggf.drmaa.DrmaaException

Throws:

org.ggf.drmaa.DrmaaException

getJobStatus

public int getJobStatus(ClusterJobId jobId)
                 throws org.ggf.drmaa.DrmaaException,
                        org.ggf.drmaa.InvalidJobException

Apparently completed jobs cannot be found! If this happened most likely that the job is not running any more and Most likely it has been cancelled, finished or failed.

Throws:

org.ggf.drmaa.InvalidJobException - if the job is no longer in the queue or running. basically it will throw this exception for all finished or cancelled jobs

org.ggf.drmaa.DrmaaException

getJobStatus

@Deprecated
public static java.lang.String getJobStatus(int status)
                                                 throws org.ggf.drmaa.DrmaaException

Deprecated.

Method for getting jobs status by quering the cluster, It returns status in therms of a Sessions, not a JobStatus Should only be used for testing!

Parameters:

status -

Returns:

job status

Throws:

org.ggf.drmaa.DrmaaException