OozieJob (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.workflowV2.engine.oozie.object.OozieJob

All Implemented Interfaces:

Comparable<OozieJob>

Direct Known Subclasses:

BatchedOozieBashJob, BatchedOozieProvisionFileJob, OozieBashJob, OozieProvisionFileJob
```
public abstract class OozieJob
extends Object
implements Comparable<OozieJob>
```

Field Summary

Fields
Modifier and Type	Field and Description
`protected List<OozieJob>`	`children`
`protected AbstractJob`	`jobObj`
`protected String`	`maxMemorySgeParamFormat`
`protected boolean`	`metadataWriteback`
`protected String`	`okTo`
`protected String`	`oozie_working_dir`
`protected List<String>`	`parentAccessionFiles`
`protected Collection<String>`	`parentAccessions`
`protected List<OozieJob>`	`parents`
`static String`	`SCRIPTS_SUBDIR` The sub-directory (of the working directory) in which generated script files will be placed.
`protected File`	`scriptsDir`
`protected File`	`seqwareJar`
`protected String`	`seqwareJarPath`
`static String`	`SGE_MAX_MEMORY_PARAM_VARIABLE` Variable identifier to be used within the qsub max-memory parameter to specify the value.
`static String`	`SGE_THREADS_PARAM_VARIABLE` Variable identifier to be used within the qsub threads parameter to specify the value.
`static org.jdom.Namespace`	`SGE_XMLNS` Namespace of the Oozie SGE action xml node.
`protected String`	`threadsSgeParamFormat`
`protected boolean`	`useSge`
`static org.jdom.Namespace`	`WF_XMLNS` Namespace of the Oozie workflow xml nodes.
`protected String`	`wfrAccession`
`protected boolean`	`wfrAncesstor`

Constructor Summary

Constructors
Constructor and Description
`OozieJob(AbstractJob job, String longName, String oozie_working_dir, boolean useSge, File seqwareJar, String threadsSgeParamFormat, String maxMemorySgeParamFormat, StringTruncator truncator)`

Method Summary

Methods
Modifier and Type	Method and Description
`protected static org.jdom.Element`	`add(org.jdom.Element parent, String tag)`
`protected static org.jdom.Element`	`add(org.jdom.Element parent, String tag, String text)`
`void`	`addParent(OozieJob parent)`
`boolean`	`addParentAccessionFile(String... pafs)` Return true only when an accession file is added successfully
`protected static org.jdom.Element`	`addProp(org.jdom.Element config, String name, String value)`
`static String`	`annotationFileName(String jobName)`
`int`	`compareTo(OozieJob that)`
`static String`	`concat(String delim, List<String> args)`
`protected abstract org.jdom.Element`	`createJavaElement()`
`protected String`	`createPathToJava()`
`protected abstract org.jdom.Element`	`createSgeElement()`
`protected File`	`emitAnnotations(Map<String,String> annotations)`
`protected File`	`emitOptionsFile()`
`boolean`	`equals(Object obj)`
`protected static File`	`file(File dir, String filename, boolean exec)`
`List<String>`	`getAccessionFile()`
`Collection<OozieJob>`	`getChildren()`
`AbstractJob`	`getJobObject()`
`String`	`getLongName()`
`String`	`getOkTo()`
`String`	`getOozieWorkingDir()`
`Collection<OozieJob>`	`getParents()`
`File`	`getScriptsDir()`
`String`	`getShortName()`
`String`	`getWorkflowRunAccession()`
`boolean`	`hasFork()`
`int`	`hashCode()`
`boolean`	`hasJoin()`
`boolean`	`hasMetadataWriteback()`
`boolean`	`isUseCheckFile()`
`boolean`	`isWorkflowRunAncesstor()`
`static String`	`optsFileName(String jobName)`
`static String`	`runnerFileName(String jobName)`
`protected ArrayList<String>`	`runnerMetaDataArgs()` Returns the metadata arg list for the Runner.
`static File`	`scriptsDir(String oozieWorkingDir)`
`org.jdom.Element`	`serializeXML()`
`void`	`setLongName(String longName)`
`void`	`setMetadataWriteback(boolean metadataWriteback)`
`void`	`setOkTo(String okTo)`
`void`	`setParentAccessions(Collection<String> parentAccessions)`
`void`	`setUseCheckFile(boolean useCheckFile)`
`void`	`setWorkflowRunAccession(String wfrAccession)`
`void`	`setWorkflowRunAncesstor(boolean wfrAncesstor)`
`String`	`toString()`
`protected static void`	`write(String contents, File file)`
`protected void`	`writeScript(String contents, File file)`

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

Field Detail

SGE_THREADS_PARAM_VARIABLE
```
public static final String SGE_THREADS_PARAM_VARIABLE
```
Variable identifier to be used within the qsub threads parameter to specify the value.

See Also:
Constant Field Values

SGE_MAX_MEMORY_PARAM_VARIABLE
```
public static final String SGE_MAX_MEMORY_PARAM_VARIABLE
```
Variable identifier to be used within the qsub max-memory parameter to specify the value.

See Also:
Constant Field Values

SCRIPTS_SUBDIR
```
public static final String SCRIPTS_SUBDIR
```
The sub-directory (of the working directory) in which generated script files will be placed.

See Also:
Constant Field Values

WF_XMLNS
```
public static final org.jdom.Namespace WF_XMLNS
```
Namespace of the Oozie workflow xml nodes.

SGE_XMLNS
```
public static final org.jdom.Namespace SGE_XMLNS
```
Namespace of the Oozie SGE action xml node.

okTo
```
protected String okTo
```

parentAccessions

protected Collection<String> parentAccessions

wfrAccession
```
protected String wfrAccession
```

wfrAncesstor
```
protected boolean wfrAncesstor
```

jobObj
```
protected AbstractJob jobObj
```

metadataWriteback
```
protected boolean metadataWriteback
```

parents
```
protected List<OozieJob> parents
```

children
```
protected List<OozieJob> children
```

oozie_working_dir
```
protected String oozie_working_dir
```

parentAccessionFiles

protected List<String> parentAccessionFiles

useSge
```
protected boolean useSge
```

seqwareJarPath
```
protected String seqwareJarPath
```

threadsSgeParamFormat

protected final String threadsSgeParamFormat

maxMemorySgeParamFormat

protected final String maxMemorySgeParamFormat

scriptsDir
```
protected final File scriptsDir
```

seqwareJar
```
protected final File seqwareJar
```

Constructor Detail

OozieJob

public OozieJob(AbstractJob job,
        String longName,
        String oozie_working_dir,
        boolean useSge,
        File seqwareJar,
        String threadsSgeParamFormat,
        String maxMemorySgeParamFormat,
        StringTruncator truncator)

Method Detail

serializeXML

public final org.jdom.Element serializeXML()

createSgeElement

protected abstract org.jdom.Element createSgeElement()

createJavaElement

protected abstract org.jdom.Element createJavaElement()

runnerMetaDataArgs
```
protected ArrayList<String> runnerMetaDataArgs()
```
Returns the metadata arg list for the Runner.

Returns:
Runner args

scriptsDir

public static File scriptsDir(String oozieWorkingDir)

runnerFileName

public static String runnerFileName(String jobName)

optsFileName

public static String optsFileName(String jobName)

emitOptionsFile
```
protected File emitOptionsFile()
```

add

protected static org.jdom.Element add(org.jdom.Element parent,
                   String tag)

add

protected static org.jdom.Element add(org.jdom.Element parent,
                   String tag,
                   String text)

addProp

protected static org.jdom.Element addProp(org.jdom.Element config,
                       String name,
                       String value)

file

protected static File file(File dir,
        String filename,
        boolean exec)

write

protected static void write(String contents,
         File file)

writeScript

protected void writeScript(String contents,
               File file)

concat

public static String concat(String delim,
            List<String> args)

setLongName

public void setLongName(String longName)

getLongName
```
public String getLongName()
```

getOozieWorkingDir
```
public String getOozieWorkingDir()
```

setParentAccessions

public void setParentAccessions(Collection<String> parentAccessions)

hasMetadataWriteback
```
public boolean hasMetadataWriteback()
```

setMetadataWriteback

public void setMetadataWriteback(boolean metadataWriteback)

getWorkflowRunAccession

public String getWorkflowRunAccession()

setWorkflowRunAccession

public void setWorkflowRunAccession(String wfrAccession)

isWorkflowRunAncesstor

public boolean isWorkflowRunAncesstor()

setWorkflowRunAncesstor

public void setWorkflowRunAncesstor(boolean wfrAncesstor)

addParent

public void addParent(OozieJob parent)

getParents

public Collection<OozieJob> getParents()

getChildren

public Collection<OozieJob> getChildren()

setOkTo
```
public void setOkTo(String okTo)
```

getOkTo
```
public String getOkTo()
```

hasFork
```
public boolean hasFork()
```

hasJoin
```
public boolean hasJoin()
```

getJobObject
```
public AbstractJob getJobObject()
```

equals
```
public boolean equals(Object obj)
```
Overrides:

equals in class Object

hashCode
```
public int hashCode()
```
Overrides:

hashCode in class Object

toString
```
public String toString()
```
Overrides:

toString in class Object

addParentAccessionFile
```
public boolean addParentAccessionFile(String... pafs)
```
Return true only when an accession file is added successfully

Parameters:
pafs -

Returns:

getAccessionFile

public List<String> getAccessionFile()

isUseCheckFile
```
public boolean isUseCheckFile()
```
Returns:
the useCheckFile

setUseCheckFile
```
public void setUseCheckFile(boolean useCheckFile)
```
Parameters:
useCheckFile - the useCheckFile to set

createPathToJava
```
protected String createPathToJava()
```

getScriptsDir
```
public File getScriptsDir()
```
Returns:
the scriptsDir

annotationFileName

public static String annotationFileName(String jobName)

emitAnnotations

protected File emitAnnotations(Map<String,String> annotations)

getShortName
```
public String getShortName()
```
Returns:
the shortName

compareTo
```
public int compareTo(OozieJob that)
```
Specified by:

compareTo in interface Comparable<OozieJob>

Class OozieJob

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SGE_THREADS_PARAM_VARIABLE

SGE_MAX_MEMORY_PARAM_VARIABLE

SCRIPTS_SUBDIR

WF_XMLNS

SGE_XMLNS

okTo

parentAccessions

wfrAccession

wfrAncesstor

jobObj

metadataWriteback

parents

children

oozie_working_dir

parentAccessionFiles

useSge

seqwareJarPath

threadsSgeParamFormat

maxMemorySgeParamFormat

scriptsDir

seqwareJar

Constructor Detail

OozieJob

Method Detail

serializeXML

createSgeElement

createJavaElement

runnerMetaDataArgs

scriptsDir

runnerFileName

optsFileName

emitOptionsFile

add

add

addProp

file

write

writeScript

concat

setLongName

getLongName

getOozieWorkingDir

setParentAccessions

hasMetadataWriteback

setMetadataWriteback

getWorkflowRunAccession

setWorkflowRunAccession

isWorkflowRunAncesstor

setWorkflowRunAncesstor

addParent

getParents

getChildren

setOkTo

getOkTo

hasFork

hasJoin

getJobObject

equals

hashCode

toString

addParentAccessionFile

getAccessionFile

isUseCheckFile

setUseCheckFile

createPathToJava

getScriptsDir

annotationFileName

emitAnnotations

getShortName

compareTo