Package ca.corefacility.bioinformatics.irida.processing.impl

Class DefaultFileProcessingChain

java.lang.Object

ca.corefacility.bioinformatics.irida.processing.impl.DefaultFileProcessingChain

All Implemented Interfaces:

FileProcessingChain

public class DefaultFileProcessingChain
extends java.lang.Object
implements FileProcessingChain

Default implementation of FileProcessingChain. Simply iterates through a collection of FileProcessor.

Constructor Summary

Constructors

Constructor	Description
DefaultFileProcessingChain(SequencingObjectRepository sequencingObjectRepository, QCEntryRepository qcRepository, FileProcessor... fileProcessors)
DefaultFileProcessingChain(SequencingObjectRepository sequencingObjectRepository, QCEntryRepository qcRepository, java.util.List<FileProcessor> fileProcessors)

Method Summary

Modifier and Type	Method	Description
java.util.List<FileProcessor>	getFileProcessors()	Get the collection of FileProcessor that this FileProcessingChain manages.
java.util.List<java.lang.Exception>	launchChain(java.lang.Long sequencingObjectId)	Launch the chain of FileProcessor on the specific SequencingObject.
void	setFastFail(java.lang.Boolean fastFail)	Set whether or not the FileProcessingChain should fail on *all* exceptions.
void	setSleepDuration(java.lang.Integer sleepDuration)	Set the amount of time (in seconds) that the processor chain should sleep each time it sleeps.
void	setTimeout(java.lang.Integer timeout)	Set the total amount of time (in seconds) that the processor chain should wait for the SequencingObject to appear before failing.

Methods inherited from class java.lang.Object

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

Constructor Detail

DefaultFileProcessingChain

public DefaultFileProcessingChain(SequencingObjectRepository sequencingObjectRepository,
                                  QCEntryRepository qcRepository,
                                  FileProcessor... fileProcessors)

DefaultFileProcessingChain

public DefaultFileProcessingChain(SequencingObjectRepository sequencingObjectRepository,
                                  QCEntryRepository qcRepository,
                                  java.util.List<FileProcessor> fileProcessors)

Method Detail

launchChain

public java.util.List<java.lang.Exception> launchChain(java.lang.Long sequencingObjectId)
                                                throws FileProcessorTimeoutException

Launch the chain of FileProcessor on the specific SequencingObject.

Specified by:

launchChain in interface FileProcessingChain

Parameters:

sequencingObjectId - the id of the SequencingObject to process.

Returns:

any Exception thrown during chain processing (in the same order as FileProcessor returned by FileProcessingChain.getFileProcessors()).

Throws:

FileProcessorTimeoutException - when the processor chain waits too long for the specified SequencingObject to appear in the database.

getFileProcessors

public java.util.List<FileProcessor> getFileProcessors()

Get the collection of FileProcessor that this FileProcessingChain manages.

Specified by:

getFileProcessors in interface FileProcessingChain

Returns:

the FileProcessor collection managed by this FileProcessingChain.

setFastFail

public void setFastFail(java.lang.Boolean fastFail)

Description copied from interface: FileProcessingChain

Set whether or not the FileProcessingChain should fail on *all* exceptions.

Specified by:

setFastFail in interface FileProcessingChain

Parameters:

fastFail - whether or not the chain should fail on exceptions.

setTimeout

public void setTimeout(java.lang.Integer timeout)

Set the total amount of time (in seconds) that the processor chain should wait for the SequencingObject to appear before failing.

Specified by:

setTimeout in interface FileProcessingChain

Parameters:

timeout - the total amount of time in seconds that the processor chain should wait.

setSleepDuration

public void setSleepDuration(java.lang.Integer sleepDuration)

Set the amount of time (in seconds) that the processor chain should sleep each time it sleeps.

Specified by:

setSleepDuration in interface FileProcessingChain

Parameters:

sleepDuration - the amount of time in seconds that the processor chain should wait.