Package net.sf.basedb.opengrid

Class JobDefinition

java.lang.Object

net.sf.basedb.opengrid.JobDefinition

public class JobDefinition
extends Object

Define a job that should be submitted to the cluster. The definition consists of four parts: The command/bash script that should be executed Options for the job (eg. parameters to the 'qsub'/'sbatch' command) Files that must be transmitted to the cluster before the job can be executed A BASE job item that acts as a proxy for the job. This is optional but without it the job will not be managed by this extension.

Since:

1.0

Author:

nicklas

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	JobDefinition.UploadSourceWithPermission	Class for storing a file and a permission as one entity.

Field Summary

Fields

Modifier and Type	Field	Description
private Job	baseJob
private BatchConfig	batchConfig
private String	cmd
private JobConfig	config
private static AtomicInteger	COUNTER
private boolean	debug
private static DateFormatter	DF
private List<JobDefinition.UploadSourceWithPermission>	filesToUpload
private String	name

Constructor Summary

Constructors

Constructor	Description
JobDefinition(String namePrefix, JobConfig config)	Create a new job definition that is not connected to a BASE job item.
JobDefinition(String namePrefix, JobConfig config, Job baseJob)	Create a new job definition that is connected to a BASE job.
JobDefinition(String namePrefix, JobConfig config, BatchConfig batchConfig, Job baseJob)	Create a job definition with a batch configuration that overrides the default job configuration.

Method Summary

Modifier and Type	Method	Description
void	addFile(UploadSource file)
void	addFile(UploadSource file, FilePermission permission)	Register a file that should be uploaded to the cluster as part of this job.
String	asJobScript(String workFolder, String tmpFolder)	Deprecated. In 1.4, use OpenGridEngine.createQsubScript(JobDefinition, String, String) instead
Job	getBaseJob()	Get the BASE job that this job definition is connected with.
BatchConfig	getBatchConfig()	Get the batch configuration settings.
String	getCmd()
JobConfig	getConfig()	Get the configuration settings for this job.
boolean	getDebug()
List<JobDefinition.UploadSourceWithPermission>	getFiles()	Get all files that should be uploaded to the cluster as part of this job.
String	getName()	Get the name of this job definition.
void	setCmd(String cmd)	Set the command/bash script to execute as part of this job.
void	setDebug(boolean debug)	Set the debug flag.

Methods inherited from class java.lang.Object

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

Field Details

DF

private static final DateFormatter DF

COUNTER

private static final AtomicInteger COUNTER

name

private final String name

config

private final JobConfig config

batchConfig

private final BatchConfig batchConfig

baseJob

private final Job baseJob

cmd

private String cmd

debug

private boolean debug

filesToUpload

private final List<JobDefinition.UploadSourceWithPermission> filesToUpload

Constructor Details

JobDefinition

public JobDefinition(String namePrefix,
JobConfig config)

Create a new job definition that is not connected to a BASE job item. The given prefix is combined with a random UUID to create a unique name for the job.

Parameters:

namePrefix - A prefix for the job name. Checked with OpenGrid.checkValidFilename(String)

JobDefinition

public JobDefinition(String namePrefix,
JobConfig config,
Job baseJob)

Create a new job definition that is connected to a BASE job. The given prefix is combined with a random UUID to create a unique name for the job.

Parameters:

namePrefix - A prefix for the job name. Checked with OpenGrid.checkValidFilename(String)

config - Configuration settings for the job, or null to use JobConfig.DEFAULT

baseJob - Optional BASE Job item that is a representation of the job on the cluster

JobDefinition

public JobDefinition(String namePrefix,
JobConfig config,
BatchConfig batchConfig,
Job baseJob)

Create a job definition with a batch configuration that overrides the default job configuration.

Parameters:

batchConfig - A batch configuration, if null the JobConfig.getBatchConfig() is used

Since:

1.5

Method Details

getName

public String getName()

Get the name of this job definition.

getConfig

public JobConfig getConfig()

Get the configuration settings for this job.

getBatchConfig

public BatchConfig getBatchConfig()

Get the batch configuration settings.

Since:

1.5

getBaseJob

public Job getBaseJob()

Get the BASE job that this job definition is connected with.

Returns:

A BASE Job item or null if not connected to a a job

setCmd

public void setCmd(String cmd)

Set the command/bash script to execute as part of this job.

getCmd

public String getCmd()

setDebug

public void setDebug(boolean debug)

Set the debug flag. This affectes which temporary working folder to use and if it should automatically be deleted after a job has been completed or not.

See Also:

ClusterConfig.getTmpFolder(boolean)

getDebug

public boolean getDebug()

addFile

public void addFile(UploadSource file)

See Also:

addFile(UploadSource, FilePermission)

addFile

public void addFile(UploadSource file,
FilePermission permission)

Register a file that should be uploaded to the cluster as part of this job. The file will be stored in the working directory of the job under the name UploadSource.getName(). The actual upload of the file is done as part of registering the job with an Open Grid cluster. See OpenGridSession.qsub(DbControl, List).

Parameters:

file - The file to upload

permission - The permission to give to the file (FilePermission.USER_RW is used as default)

getFiles

public List<JobDefinition.UploadSourceWithPermission> getFiles()

Get all files that should be uploaded to the cluster as part of this job.

asJobScript

@Deprecated
public String asJobScript(String workFolder,
String tmpFolder)

Deprecated.

In 1.4, use OpenGridEngine.createQsubScript(JobDefinition, String, String) instead

Generate a script for this job that fits what 'qsub' expects.