Package ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl

Class SISTRSampleUpdater

java.lang.Object

ca.corefacility.bioinformatics.irida.pipeline.results.updater.impl.SISTRSampleUpdater

All Implemented Interfaces:

AnalysisSampleUpdater

@Component
public class SISTRSampleUpdater
extends java.lang.Object
implements AnalysisSampleUpdater

AnalysisSampleUpdater that adds a number of results from a SISTR run to the metadata of a Sample

Constructor Summary

Constructors

Constructor	Description
SISTRSampleUpdater(MetadataTemplateService metadataTemplateService, SampleService sampleService, IridaWorkflowsService iridaWorkflowsService)

Method Summary

Modifier and Type	Method	Description
AnalysisType	getAnalysisType()	Gets the AnalysisType this updater service handles.
void	update(java.util.Collection<Sample> samples, AnalysisSubmission analysis)	Add SISTR results to the metadata of the given Samples

Methods inherited from class java.lang.Object

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

Constructor Detail

SISTRSampleUpdater

@Autowired
public SISTRSampleUpdater(MetadataTemplateService metadataTemplateService,
                          SampleService sampleService,
                          IridaWorkflowsService iridaWorkflowsService)

Method Detail

update

public void update(java.util.Collection<Sample> samples,
                   AnalysisSubmission analysis)
            throws PostProcessingException

Add SISTR results to the metadata of the given Samples

Specified by:

update in interface AnalysisSampleUpdater

Parameters:

samples - The samples to update.

analysis - the AnalysisSubmission to apply to the samples

Throws:

PostProcessingException - if the method cannot read the "sistr-predictions" output file

getAnalysisType

public AnalysisType getAnalysisType()

Description copied from interface: AnalysisSampleUpdater

Gets the AnalysisType this updater service handles.

Specified by:

getAnalysisType in interface AnalysisSampleUpdater

Returns:

The AnalysisType.