Package ca.corefacility.bioinformatics.irida.processing

Interface FileProcessingChain

All Known Implementing Classes:

DefaultFileProcessingChain

public interface FileProcessingChain

A collection of FileProcessor that are executed, in order, on a specific SequencingObject.

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.

Method Detail

launchChain

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

Launch the chain of FileProcessor on the specific SequencingObject.

Parameters:

sequencingObjectId - the id of the SequencingObject to process.

Returns:

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

Throws:

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

getFileProcessors

java.util.List<FileProcessor> getFileProcessors()

Get the collection of FileProcessor that this FileProcessingChain manages.

Returns:

the FileProcessor collection managed by this FileProcessingChain.

setFastFail

void setFastFail(java.lang.Boolean fastFail)

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

Parameters:

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

setTimeout

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.

Parameters:

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

setSleepDuration

void setSleepDuration(java.lang.Integer sleepDuration)

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

Parameters:

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