Class ExpressionExperimentDataVectorServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDataVectorServiceImpl

All Implemented Interfaces:

ExpressionExperimentDataVectorService

@Service("expressionExperimentDataVectorService")
public class ExpressionExperimentDataVectorServiceImpl
extends Object
implements ExpressionExperimentDataVectorService

Implementation of ExpressionExperimentDataVectorService.

Read methods are @Transactional(readOnly = true); write methods are @Transactional. ACL enforcement is the responsibility of the facade ExpressionExperimentService interface — this class is unsecured at the AOP boundary on purpose, so intra-gemma-core callers can bypass duplicate ACL checks once authenticated.

See Also:

• ExpressionExperimentService

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentDataVectorServiceImpl(ExpressionExperimentDao expressionExperimentDao, BioAssayDimensionService bioAssayDimensionService, QuantitationTypeService quantitationTypeService)

Method Summary

Modifier and Type	Method	Description
int	addRawDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<RawExpressionDataVector> newVectors)	Add raw data vectors for a quantitation type.
int	createProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
Map<QuantitationType, Collection<RawExpressionDataVector>>	getMissingValuesVectors(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)
Optional<Collection<ProcessedExpressionDataVector>>	getProcessedDataVectors(ExpressionExperiment ee)
Optional<Collection<ProcessedExpressionDataVector>>	getProcessedDataVectors(ExpressionExperiment ee, List<BioAssay> assays)
Collection<RawExpressionDataVector>	getRawDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType qt)
Collection<RawExpressionDataVector>	getRawDataVectors(ExpressionExperiment ee, QuantitationType qt)
int	removeAllRawDataVectors(ExpressionExperiment ee)
int	removeProcessedDataVectors(ExpressionExperiment ee)
int	removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt)	Equivalent to removeRawDataVectors(ee, qt, false).
int	removeRawDataVectors(ExpressionExperiment ee, QuantitationType qt, boolean keepDimension)
int	replaceAllRawDataVectors(ExpressionExperiment ee, Collection<RawExpressionDataVector> newVectors)	Replace all raw vectors on an experiment, grouping the input by QT and routing each group to either ExpressionExperimentDataVectorService.replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) or ExpressionExperimentDataVectorService.addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) depending on whether the QT already exists; any QT in the experiment that is no longer represented in the input is removed.
int	replaceProcessedDataVectors(ExpressionExperiment ee, Collection<ProcessedExpressionDataVector> vectors)
int	replaceRawDataVectors(ExpressionExperiment ee, QuantitationType qt, Collection<RawExpressionDataVector> vectors)

Methods inherited from class Object

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

Constructor Details

ExpressionExperimentDataVectorServiceImpl

@Autowired
public ExpressionExperimentDataVectorServiceImpl(ExpressionExperimentDao expressionExperimentDao,
 BioAssayDimensionService bioAssayDimensionService,
 QuantitationTypeService quantitationTypeService)

Method Details

getRawDataVectors

@Transactional(readOnly=true)
public Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt)

Specified by:

getRawDataVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.getRawDataVectors(ExpressionExperiment, QuantitationType)

getRawDataVectors

@Transactional(readOnly=true)
public Collection<RawExpressionDataVector> getRawDataVectors(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType qt)

Specified by:

getRawDataVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.getRawDataVectors(ExpressionExperiment, List, QuantitationType)

getPreferredRawDataVectors

@Transactional(readOnly=true)
public Collection<RawExpressionDataVector> getPreferredRawDataVectors(ExpressionExperiment expressionExperiment)

Specified by:

getPreferredRawDataVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.getPreferredRawDataVectors(ExpressionExperiment)

getMissingValuesVectors

@Transactional(readOnly=true)
public Map<QuantitationType, Collection<RawExpressionDataVector>> getMissingValuesVectors(ExpressionExperiment ee)

Specified by:

getMissingValuesVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.getMissingValuesVectors(ExpressionExperiment)

addRawDataVectors

@Transactional
public int addRawDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 Collection<RawExpressionDataVector> newVectors)

Description copied from interface: ExpressionExperimentDataVectorService

Add raw data vectors for a quantitation type. The dimension and QT are created on-demand if they are still transient.

Specified by:

addRawDataVectors in interface ExpressionExperimentDataVectorService

replaceRawDataVectors

@Transactional
public int replaceRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt,
 Collection<RawExpressionDataVector> vectors)

Specified by:

replaceRawDataVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection)

replaceAllRawDataVectors

@Transactional
public int replaceAllRawDataVectors(ExpressionExperiment ee,
 Collection<RawExpressionDataVector> newVectors)

Description copied from interface: ExpressionExperimentDataVectorService

Replace all raw vectors on an experiment, grouping the input by QT and routing each group to either ExpressionExperimentDataVectorService.replaceRawDataVectors(ExpressionExperiment, QuantitationType, Collection) or ExpressionExperimentDataVectorService.addRawDataVectors(ExpressionExperiment, QuantitationType, Collection) depending on whether the QT already exists; any QT in the experiment that is no longer represented in the input is removed.

Specified by:

replaceAllRawDataVectors in interface ExpressionExperimentDataVectorService

removeAllRawDataVectors

@Transactional
public int removeAllRawDataVectors(ExpressionExperiment ee)

Specified by:

removeAllRawDataVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.removeAllRawDataVectors(ExpressionExperiment)

removeRawDataVectors

@Transactional
public int removeRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt)

Description copied from interface: ExpressionExperimentDataVectorService

Equivalent to removeRawDataVectors(ee, qt, false).

Specified by:

removeRawDataVectors in interface ExpressionExperimentDataVectorService

removeRawDataVectors

@Transactional
public int removeRawDataVectors(ExpressionExperiment ee,
 QuantitationType qt,
 boolean keepDimension)

Specified by:

removeRawDataVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.removeRawDataVectors(ExpressionExperiment, QuantitationType, boolean)

getProcessedDataVectors

@Transactional(readOnly=true)
public Optional<Collection<ProcessedExpressionDataVector>> getProcessedDataVectors(ExpressionExperiment ee)

Specified by:

getProcessedDataVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.getProcessedDataVectors(ExpressionExperiment)

getProcessedDataVectors

@Transactional(readOnly=true)
public Optional<Collection<ProcessedExpressionDataVector>> getProcessedDataVectors(ExpressionExperiment ee,
 List<BioAssay> assays)

Specified by:

getProcessedDataVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.getProcessedDataVectors(ExpressionExperiment, List)

createProcessedDataVectors

@Transactional
public int createProcessedDataVectors(ExpressionExperiment ee,
 Collection<ProcessedExpressionDataVector> vectors)

Specified by:

createProcessedDataVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.createProcessedDataVectors(ExpressionExperiment, Collection)

removeProcessedDataVectors

@Transactional
public int removeProcessedDataVectors(ExpressionExperiment ee)

Specified by:

removeProcessedDataVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.removeProcessedDataVectors(ExpressionExperiment)

replaceProcessedDataVectors

@Transactional
public int replaceProcessedDataVectors(ExpressionExperiment ee,
 Collection<ProcessedExpressionDataVector> vectors)

Specified by:

replaceProcessedDataVectors in interface ExpressionExperimentDataVectorService

See Also:

• ExpressionExperimentDao.replaceProcessedDataVectors(ExpressionExperiment, Collection)