AbstractJob (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.workflowV2.model.AbstractJob

All Implemented Interfaces:

Job

Direct Known Subclasses:

BashJob, JavaJob, JavaSeqwareModuleJob, JobBatch, PerlJob
```
public class AbstractJob
extends Object
implements Job
```

Field Summary

Fields
Modifier and Type Field and Description

protected boolean hasMetadataWriteback

Fields
Modifier and Type	Field and Description
`protected boolean`	`hasMetadataWriteback`

Constructor Summary

Constructors
Constructor and Description

AbstractJob(String algo)
for bash Job

AbstractJob(String algo, String cp, String mainclass)
for Java/Perl/JavaModule job

Constructors
Constructor and Description
`AbstractJob(String algo)` for bash Job
`AbstractJob(String algo, String cp, String mainclass)` for Java/Perl/JavaModule job

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addFile(SqwFile file)` This adds a file specifically to a job for provisioning.
`void`	`addParent(AbstractJob parent)` add a parent
`Job`	`addParent(Job parent)` add job's parent
`Job`	`addRequirement(Requirement requirement)`
`String`	`getAlgo()` get the job algorithm
`Map<String,String>`	`getAnnotations()` Set arbitrary key-value annotations on jobs.
`String`	`getClassPath()`
`Command`	`getCommand()`
`Collection<SqwFile>`	`getFiles()` This should only be called from the back-end and should not be called by workflow developers.
`String`	`getMainClass()` return the main class for a Java job, or the script.pl for a perl Job
`String`	`getMaxMemory()`
`Collection<String>`	`getParentAccessions()`
`Collection<Job>`	`getParents()` add all parent jobs
`String`	`getQsubOptions()`
`String`	`getQueue()`
`Collection<Requirement>`	`getRequirements()` get job requirements
`int`	`getThreads()`
`boolean`	`hasMetadataWriteback()` job specific metadata is not supported yet
`boolean`	`isLocal()` Whether this job should run locally instead of out on a cluster.
`void`	`setAlgo(String algo)` set the job algorithm
`Command`	`setCommand(String cmd)` set the job command
`void`	`setHasMetadataWriteback(boolean metadata)` job specific metadata is not supported yet
`void`	`setLocal()` Sets this job to run locally.
`void`	`setLocal(boolean runLocal)` Sets whether this job should run locally.
`AbstractJob`	`setMaxMemory(String mem)` set max memory
`void`	`setParentAccessions(Collection<String> parentAccessions)` set parent accessiosns for the job
`void`	`setParents(Collection<Job> parents)` set parent jobs
`void`	`setQsubOptions(String qsubOptions)` Allows specifying options to qsub.
`Job`	`setQueue(String queue)` set the queue
`void`	`setRequirements(Collection<Requirement> requirements)`
`AbstractJob`	`setThreads(int count)` set the max thread number

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - hasMetadataWriteback
```
protected boolean hasMetadataWriteback
```
- Constructor Detail
  - AbstractJob
```
public AbstractJob(String algo)
```
    for bash Job
    
    Parameters:
    algo -
  - AbstractJob
```
public AbstractJob(String algo,
           String cp,
           String mainclass)
```
    for Java/Perl/JavaModule job
    
    Parameters:
    algo -
    mainclass -
    cp -
- Method Detail
  - getCommand
```
public Command getCommand()
```
    Specified by:
    
    getCommand in interface Job
    
    Returns:
    a job command object
  - getFiles
```
public Collection<SqwFile> getFiles()
```
    This should only be called from the back-end and should not be called by workflow developers.
    
    Returns:
    all the files for this job
  - addFile
```
public void addFile(SqwFile file)
```
    This adds a file specifically to a job for provisioning.
    
    Specified by:
    
    addFile in interface Job
  - getParents
```
public Collection<Job> getParents()
```
    add all parent jobs
    
    Specified by:
    
    getParents in interface Job
    
    Returns:
  - setParents
```
public void setParents(Collection<Job> parents)
```
    set parent jobs
    
    Parameters:
    parents -
  - addParent
```
public void addParent(AbstractJob parent)
```
    add a parent
    
    Parameters:
    parent -
  - getAlgo
```
public String getAlgo()
```
    get the job algorithm
    
    Returns:
  - setAlgo
```
public void setAlgo(String algo)
```
    set the job algorithm
    
    Parameters:
    algo -
  - getRequirements
```
public Collection<Requirement> getRequirements()
```
    get job requirements
    
    Returns:
  - setRequirements
```
public void setRequirements(Collection<Requirement> requirements)
```
  - getThreads
```
public int getThreads()
```
    Specified by:
    
    getThreads in interface Job
    
    Returns:
    the max thread number
  - setThreads
```
public AbstractJob setThreads(int count)
```
    Description copied from interface: Job
    
    set the max thread number
    
    Specified by:
    
    setThreads in interface Job
    
    Returns:
  - getMaxMemory
```
public String getMaxMemory()
```
    Specified by:
    
    getMaxMemory in interface Job
    
    Returns:
    the max memory
  - setMaxMemory
```
public AbstractJob setMaxMemory(String mem)
```
    Description copied from interface: Job
    
    set max memory
    
    Specified by:
    
    setMaxMemory in interface Job
    
    Returns:
  - getClassPath
```
public String getClassPath()
```
  - getMainClass
```
public String getMainClass()
```
    return the main class for a Java job, or the script.pl for a perl Job
    
    Returns:
  - setCommand
```
public Command setCommand(String cmd)
```
    Description copied from interface: Job
    
    set the job command
    
    Specified by:
    
    setCommand in interface Job
    
    Returns:
  - addParent
```
public Job addParent(Job parent)
```
    Description copied from interface: Job
    
    add job's parent
    
    Specified by:
    
    addParent in interface Job
    
    Returns:
  - addRequirement
```
public Job addRequirement(Requirement requirement)
```
  - setQueue
```
public Job setQueue(String queue)
```
    Description copied from interface: Job
    
    set the queue
    
    Specified by:
    
    setQueue in interface Job
    
    Returns:
  - getQueue
```
public String getQueue()
```
    Specified by:
    
    getQueue in interface Job
    
    Returns:
    queue
  - setHasMetadataWriteback
```
public void setHasMetadataWriteback(boolean metadata)
```
    Description copied from interface: Job
    
    job specific metadata is not supported yet
    
    Specified by:
    
    setHasMetadataWriteback in interface Job
  - hasMetadataWriteback
```
public boolean hasMetadataWriteback()
```
    Description copied from interface: Job
    
    job specific metadata is not supported yet
    
    Specified by:
    
    hasMetadataWriteback in interface Job
    
    Returns:
  - setParentAccessions
```
public void setParentAccessions(Collection<String> parentAccessions)
```
    Description copied from interface: Job
    
    set parent accessiosns for the job
    
    Specified by:
    
    setParentAccessions in interface Job
  - getParentAccessions
```
public Collection<String> getParentAccessions()
```
  - isLocal
```
public boolean isLocal()
```
    Description copied from interface: Job
    
    Whether this job should run locally instead of out on a cluster.
    
    Specified by:
    
    isLocal in interface Job
    
    Returns:
    true if it will run locally
  - setLocal
```
public void setLocal()
```
    Description copied from interface: Job
    
    Sets this job to run locally.
    
    Specified by:
    
    setLocal in interface Job
  - setLocal
```
public void setLocal(boolean runLocal)
```
    Description copied from interface: Job
    
    Sets whether this job should run locally.
    
    Specified by:
    
    setLocal in interface Job
    
    Parameters:
    runLocal - true to run locally, false otherwise
  - getQsubOptions
```
public String getQsubOptions()
```
  - setQsubOptions
```
public void setQsubOptions(String qsubOptions)
```
    Allows specifying options to qsub. When provided, options using queue, maxMem, and threads will not be generated.
    
    Parameters:
    qsubOptions -
  - getAnnotations
```
public Map<String,String> getAnnotations()
```
    Description copied from interface: Job
    
    Set arbitrary key-value annotations on jobs.
    
    Specified by:
    
    getAnnotations in interface Job
    
    Returns:
    the annotations

Class AbstractJob

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

hasMetadataWriteback

Constructor Detail

AbstractJob

AbstractJob

Method Detail

getCommand

getFiles

addFile

getParents

setParents

addParent

getAlgo

setAlgo

getRequirements

setRequirements

getThreads

setThreads

getMaxMemory

setMaxMemory

getClassPath

getMainClass

setCommand

addParent

addRequirement

setQueue

getQueue

setHasMetadataWriteback

hasMetadataWriteback

setParentAccessions

getParentAccessions

isLocal

setLocal

setLocal

getQsubOptions

setQsubOptions

getAnnotations