Class ExpressionExperimentWriteServiceImpl

java.lang.Object

ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentWriteServiceImpl

All Implemented Interfaces:

ExpressionExperimentWriteService

@Service("expressionExperimentWriteService")
public class ExpressionExperimentWriteServiceImpl
extends Object
implements ExpressionExperimentWriteService

Implementation of ExpressionExperimentWriteService.

All public methods are @Transactional (write). ACL enforcement is the responsibility of the facade ExpressionExperimentService interface -- this class is unsecured at the AOP boundary on purpose, so that intra-gemma-core callers that hold an authenticated session can bypass duplicate ACL checks.

For lifecycle removal, the heavy orchestration is preserved verbatim from the original monolith: subset removal, DEA / sample-coex / PCA cleanup, then removal from EE sets, then delegation to the DAO. The subset lookup goes directly through the DAO (expressionExperimentDao.getSubSets(ee)) so this service has no back-edge into ExpressionExperimentReadService and therefore introduces no new construction cycle.

See Also:

• ExpressionExperimentService

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentWriteServiceImpl(ExpressionExperimentDao expressionExperimentDao)

Method Summary

Modifier and Type	Method	Description
void	addCharacteristic(ExpressionExperiment ee, Characteristic vc)	Will add the characteristic to the expression experiment and persist the changes.
ExperimentalFactor	addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
FactorValue	addFactorValue(ExpressionExperiment ee, FactorValue fv)
void	addFactorValues(ExpressionExperiment ee, Map<BioMaterial, FactorValue> fvs)
static Class<? extends PreferredDataChangedEvent>	getPreferredDataChangedEventForVectorType(Class<? extends DataVector> vectorType)	Resolve the concrete PreferredDataChangedEvent subclass that matches a data-vector type, or null if no event is emitted for that vector type (currently: processed data — multiple processed sets are not allowed so a "preference change" has no meaning).
void	remove(Collection<ExpressionExperiment> entities)
void	remove(ExpressionExperiment ee)	Deletes an experiment and all of its associated objects, including coexpression links.
void	removeCharacteristics(ExpressionExperiment ee, Collection<Characteristic> characteristicsToRemove)
MeanVarianceRelation	updateMeanVarianceRelation(ExpressionExperiment ee, MeanVarianceRelation mvr)
void	updateQuantitationType(ExpressionExperiment ee, QuantitationType qt, QuantitationType previousPreferredQt)

Methods inherited from class Object

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

Constructor Details

ExpressionExperimentWriteServiceImpl

@Autowired
public ExpressionExperimentWriteServiceImpl(ExpressionExperimentDao expressionExperimentDao)

Method Details

addFactor

@Transactional
public ExperimentalFactor addFactor(ExpressionExperiment ee,
 ExperimentalFactor factor)

Specified by:

addFactor in interface ExpressionExperimentWriteService

addFactorValue

@Transactional
public FactorValue addFactorValue(ExpressionExperiment ee,
 FactorValue fv)

Specified by:

addFactorValue in interface ExpressionExperimentWriteService

addFactorValues

@Transactional
public void addFactorValues(ExpressionExperiment ee,
 Map<BioMaterial, FactorValue> fvs)

Specified by:

addFactorValues in interface ExpressionExperimentWriteService

addCharacteristic

@Transactional
public void addCharacteristic(ExpressionExperiment ee,
 Characteristic vc)

Will add the characteristic to the expression experiment and persist the changes.

Specified by:

addCharacteristic in interface ExpressionExperimentWriteService

Parameters:

ee - the experiment to add the characteristics to.

vc - If the evidence code is null, it will be filled in with IC. A category and value must be provided.

removeCharacteristics

@Transactional
public void removeCharacteristics(ExpressionExperiment ee,
 Collection<Characteristic> characteristicsToRemove)

Specified by:

removeCharacteristics in interface ExpressionExperimentWriteService

updateQuantitationType

@Transactional
public void updateQuantitationType(ExpressionExperiment ee,
 QuantitationType qt,
 @Nullable
 QuantitationType previousPreferredQt)

Specified by:

updateQuantitationType in interface ExpressionExperimentWriteService

getPreferredDataChangedEventForVectorType

@Nullable
public static Class<? extends PreferredDataChangedEvent> getPreferredDataChangedEventForVectorType(Class<? extends DataVector> vectorType)

Resolve the concrete PreferredDataChangedEvent subclass that matches a data-vector type, or null if no event is emitted for that vector type (currently: processed data — multiple processed sets are not allowed so a "preference change" has no meaning).

public static so the Audited.valueSpel() SpEL expressions in ExpressionExperimentWriteAuditServiceImpl can reach it via T(...).getPreferredDataChangedEventForVectorType(#vectorType).

updateMeanVarianceRelation

@Transactional
public MeanVarianceRelation updateMeanVarianceRelation(ExpressionExperiment ee,
 MeanVarianceRelation mvr)

Specified by:

updateMeanVarianceRelation in interface ExpressionExperimentWriteService

remove

@Transactional
public void remove(ExpressionExperiment ee)

Deletes an experiment and all of its associated objects, including coexpression links. Some types of associated objects may need to be deleted before this can be run (example: analyses involving multiple experiments; these will not be deleted automatically).

Specified by:

remove in interface ExpressionExperimentWriteService

remove

@Transactional
public void remove(Collection<ExpressionExperiment> entities)

Specified by:

remove in interface ExpressionExperimentWriteService