Class BioAssayMetadataServiceImpl

java.lang.Object

ubic.gemma.core.analysis.service.BioAssayMetadataServiceImpl

All Implemented Interfaces:

BioAssayMetadataService

@Service
public class BioAssayMetadataServiceImpl
extends Object
implements BioAssayMetadataService

Constructor Summary

Constructors

Constructor	Description
BioAssayMetadataServiceImpl()

Method Summary

Modifier and Type	Method	Description
Set<String>	getValidLibraryStrategies()	What BioAssayMetadataService.setLibraryStrategy(ExpressionExperiment, Collection, String) will accept, for the 400 message and for callers that want to offer a menu.
Collection<BioAssay>	setExtractedMolecule(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)	Set extractedMolecule on the given samples.
Collection<BioAssay>	setLibrarySelection(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)	Set librarySelection on the given samples.
Collection<BioAssay>	setLibraryStrategy(ExpressionExperiment ee, Collection<BioAssay> bioAssays, String value)	Set libraryStrategy on the given samples.

Methods inherited from class Object

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

Constructor Details

BioAssayMetadataServiceImpl

public BioAssayMetadataServiceImpl()

Method Details

getValidLibraryStrategies

public Set<String> getValidLibraryStrategies()

Description copied from interface: BioAssayMetadataService

What BioAssayMetadataService.setLibraryStrategy(ExpressionExperiment, Collection, String) will accept, for the 400 message and for callers that want to offer a menu.

Specified by:

getValidLibraryStrategies in interface BioAssayMetadataService

setLibraryStrategy

@Transactional
public Collection<BioAssay> setLibraryStrategy(ExpressionExperiment ee,
 Collection<BioAssay> bioAssays,
 @Nullable
 String value)

Description copied from interface: BioAssayMetadataService

Set libraryStrategy on the given samples.

Specified by:

setLibraryStrategy in interface BioAssayMetadataService

Parameters:

ee - the experiment the samples belong to; every assay must be one of its samples

bioAssays - the samples to change

value - a GeoLibraryStrategy constant name, MICROARRAY_ONE_COLOR or MICROARRAY_TWO_COLOR, or null to clear the field

Returns:

the samples actually changed; empty when every sample already held value

setLibrarySelection

@Transactional
public Collection<BioAssay> setLibrarySelection(ExpressionExperiment ee,
 Collection<BioAssay> bioAssays,
 @Nullable
 String value)

Description copied from interface: BioAssayMetadataService

Set librarySelection on the given samples. Free text by design — see the class javadoc.

Specified by:

setLibrarySelection in interface BioAssayMetadataService

Parameters:

value - trimmed; null or blank clears the field

Returns:

the samples actually changed

setExtractedMolecule

@Transactional
public Collection<BioAssay> setExtractedMolecule(ExpressionExperiment ee,
 Collection<BioAssay> bioAssays,
 @Nullable
 String value)

Description copied from interface: BioAssayMetadataService

Set extractedMolecule on the given samples.

Specified by:

setExtractedMolecule in interface BioAssayMetadataService

Parameters:

value - an ExtractedMolecule constant name, or null to clear the field

Returns:

the samples actually changed