Interface ExpressionExperimentWriteService

All Known Implementing Classes:

ExpressionExperimentWriteServiceImpl

public interface ExpressionExperimentWriteService

Thin write/mutation service for ExpressionExperiment.

Phase 2 of the ExpressionExperimentService decomposition (strangler fig). This service houses the design-mutation (bucket E) and lifecycle (bucket F) methods that were previously on ExpressionExperimentServiceImpl: factor / factor-value / characteristic add/remove, quantitation-type + mean-variance updates, and the heavy remove that cascades through subsets, DEA, sample-coex, PCA, and EE sets.

Callers should generally keep using ExpressionExperimentService as the facade -- the facade delegates to this service. Direct injection is appropriate where a class would otherwise create a Spring dependency cycle through the heavier facade.

ACL / @Secured annotations live on ExpressionExperimentService (the caller-facing facade interface); enforcement happens at the facade proxy boundary.

See Also:

• ExpressionExperimentService
• ExpressionExperimentReadService

Method Summary

Modifier and Type	Method	Description
void	addCharacteristic(ExpressionExperiment ee, Characteristic vc)
ExperimentalFactor	addFactor(ExpressionExperiment ee, ExperimentalFactor factor)
FactorValue	addFactorValue(ExpressionExperiment ee, FactorValue fv)
void	addFactorValues(ExpressionExperiment ee, Map<BioMaterial, FactorValue> fvs)
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)

Method Details

addFactor

ExperimentalFactor addFactor(ExpressionExperiment ee,
 ExperimentalFactor factor)

addFactorValue

FactorValue addFactorValue(ExpressionExperiment ee,
 FactorValue fv)

addFactorValues

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

addCharacteristic

void addCharacteristic(ExpressionExperiment ee,
 Characteristic vc)

removeCharacteristics

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

updateQuantitationType

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

updateMeanVarianceRelation

MeanVarianceRelation updateMeanVarianceRelation(ExpressionExperiment ee,
 MeanVarianceRelation mvr)

remove

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).

remove

void remove(Collection<ExpressionExperiment> entities)