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

Class GzipFileProcessor

java.lang.Object

ca.corefacility.bioinformatics.irida.processing.impl.GzipFileProcessor

All Implemented Interfaces:

FileProcessor

@Component
public class GzipFileProcessor
extends java.lang.Object
implements FileProcessor

Handle gzip-ed files (if necessary). This class partially assumes that gzip compressed files have the extension ".gz" (not for determining whether or not the file is compressed, but rather for naming the decompressed file). If the compressed file does not end with ".gz", then it will be renamed as such so that the decompressed file name will not conflict with the compressed file name.

Constructor Summary

Constructors

Constructor	Description
GzipFileProcessor(SequenceFileRepository sequenceFileRepository)
GzipFileProcessor(SequenceFileRepository sequenceFileRepository, java.lang.Boolean removeCompressedFiles)

Method Summary

Modifier and Type	Method	Description
java.lang.Boolean	modifiesFile()	If the FileProcessor throws a FileProcessorException, the FileProcessor should inform the caller whether or not proceeding with the remaining FileProcessor instances in the chain is safe.
void	process(SequencingObject sequencingObject)	Process the provided SequenceFile, then (optionally) proceed to the next processor in the chain.
void	processSingleFile(SequenceFile sequenceFile)	Process a single SequenceFile
void	setDisableFileProcessor(boolean disableFileProcessor)	Disables this file processor from processing files.
void	setRemoveCompressedFiles(boolean removeCompressedFile)	Decide whether or not to delete the original compressed files that are uploaded once they're unzipped.
boolean	shouldProcessFile(SequencingObject sequencingObject)	This method asks the file processor whether it should act on this file.

Methods inherited from class java.lang.Object

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

Constructor Detail

GzipFileProcessor

@Autowired
public GzipFileProcessor(SequenceFileRepository sequenceFileRepository)

GzipFileProcessor

public GzipFileProcessor(SequenceFileRepository sequenceFileRepository,
                         java.lang.Boolean removeCompressedFiles)

Method Detail

setRemoveCompressedFiles

public void setRemoveCompressedFiles(boolean removeCompressedFile)

Decide whether or not to delete the original compressed files that are uploaded once they're unzipped. If false they will be kept in their revision directories.

Parameters:

removeCompressedFile - Whether or not to delete original compressed files.

setDisableFileProcessor

public void setDisableFileProcessor(boolean disableFileProcessor)

Disables this file processor from processing files.

Parameters:

disableFileProcessor - True if this processor should be disabled, false otherwise.

process

@Transactional
public void process(SequencingObject sequencingObject)

Process the provided SequenceFile, then (optionally) proceed to the next processor in the chain. Any modifications to the SequenceFile made by the FileProcessor should be persisted by the FileProcessor itself -- the FileProcessingChain *does not* handle persistence.

Specified by:

process in interface FileProcessor

Parameters:

sequencingObject - the SequencingObject to process

processSingleFile

public void processSingleFile(SequenceFile sequenceFile)
                       throws FileProcessorException

Process a single SequenceFile

Parameters:

sequenceFile - file to process

Throws:

FileProcessorException - if an error occurs while processing

modifiesFile

public java.lang.Boolean modifiesFile()

If the FileProcessor throws a FileProcessorException, the FileProcessor should inform the caller whether or not proceeding with the remaining FileProcessor instances in the chain is safe. If the FileProcessor modifies the file, then proceeding with the remaining FileProcessor in the chain is not safe.

Specified by:

modifiesFile in interface FileProcessor

Returns:

whether or not the FileProcessor modifies the SequenceFile.

shouldProcessFile

public boolean shouldProcessFile(SequencingObject sequencingObject)

Description copied from interface: FileProcessor

This method asks the file processor whether it should act on this file. The processor may have some settings that would not run on certain files.

Specified by:

shouldProcessFile in interface FileProcessor

Parameters:

sequencingObject - the SequencingObject to check

Returns:

true if the processor should act on the file