Class PreprocessorHelperServiceImpl

java.lang.Object

ubic.gemma.core.analysis.preprocess.PreprocessorHelperServiceImpl

All Implemented Interfaces:

PreprocessorHelperService

@Service
@Transactional(propagation=NEVER)
public class PreprocessorHelperServiceImpl
extends Object
implements PreprocessorHelperService

Implementation of PreprocessorHelperService: a thin co-bean that exists so each processFor* method is invoked through a Spring proxy and the AuditedOnError aspect can intercept its catch path.

The methods previously lived as private members of PreprocessorServiceImpl and were self-invoked via this. -- Spring AOP cannot intercept either case, so their imperative auditTrailService.addUpdateEvent( ee, FailedXEvent.class, ..., e ) blocks could not be migrated to AuditedOnError during bucket 2e. Hoisting them onto this separately-injected bean lets the aspect see them.

Propagation.NEVER matches PreprocessorServiceImpl -- these diagnostic steps each manage their own transactions internally.

Constructor Summary

Constructors

Constructor	Description
PreprocessorHelperServiceImpl()

Method Summary

Modifier and Type	Method	Description
Integer	batchCorrect(ExpressionExperiment ee)	If possible, batch correct the processed data vectors.
void	processForMeanVarianceRelation(ExpressionExperiment ee)	Create the scatter plot to evaluate heteroscedasticity.
void	processForPca(ExpressionExperiment ee)	Run SVD / PCA for diagnostics.
void	processForSampleCorrelation(ExpressionExperiment ee)	Create the heatmaps used to judge similarity among samples.

Methods inherited from class Object

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

Constructor Details

PreprocessorHelperServiceImpl

public PreprocessorHelperServiceImpl()

Method Details

batchCorrect

@AuditedConditional(value=BatchCorrectionEvent.class,
                    when="#result != null",
                    messageSpel="'ComBat batch correction, vectors were replaced with ' + #result + ' batch-corrected ones.'")
public Integer batchCorrect(ExpressionExperiment ee)
                     throws PreprocessingException

If possible, batch correct the processed data vectors. Returns the number of vectors that were replaced — used by the @Audited aspect's messageSpel to render the audit note. Returns null when the experiment is not batch-correctable; the @AuditedConditional predicate then skips emission.

Specified by:

batchCorrect in interface PreprocessorHelperService

Returns:

the number of processed vectors that were replaced by the batch-corrected matrix, or null when the experiment is not batch-correctable (no audit event written in that case). The return value drives the @Audited note via messageSpel; callers may ignore it.

Throws:

PreprocessingException

processForMeanVarianceRelation

@AuditedOnError(FailedMeanVarianceUpdateEvent.class)
public void processForMeanVarianceRelation(ExpressionExperiment ee)
                                    throws PreprocessingException

Create the scatter plot to evaluate heteroscedasticity.

Specified by:

processForMeanVarianceRelation in interface PreprocessorHelperService

Throws:

PreprocessingException

processForPca

@AuditedOnError(FailedPCAAnalysisEvent.class)
public void processForPca(ExpressionExperiment ee)
                   throws SVDRelatedPreprocessingException

Description copied from interface: PreprocessorHelperService

Run SVD / PCA for diagnostics. A failure emits a FailedPCAAnalysisEvent via the audit aspect.

Specified by:

processForPca in interface PreprocessorHelperService

Throws:

SVDRelatedPreprocessingException

processForSampleCorrelation

@AuditedOnError(FailedSampleCorrelationAnalysisEvent.class)
public void processForSampleCorrelation(ExpressionExperiment ee)
                                 throws SampleCoexpressionRelatedPreprocessingException

Create the heatmaps used to judge similarity among samples.

Specified by:

processForSampleCorrelation in interface PreprocessorHelperService

Throws:

SampleCoexpressionRelatedPreprocessingException