Class BatchInfoPopulationHelperServiceImpl

java.lang.Object

ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationHelperServiceImpl

All Implemented Interfaces:

BatchInfoPopulationHelperService

@Service
public class BatchInfoPopulationHelperServiceImpl
extends Object
implements BatchInfoPopulationHelperService

Author:

paul

Field Summary

Fields

Modifier and Type	Field	Description
static final String	BATCH_FACTOR_NAME_PREFIX	Prefix to use when generating batch factor names.

Constructor Summary

Constructors

Constructor	Description
BatchInfoPopulationHelperServiceImpl()

Method Summary

Modifier and Type	Method	Description
ExperimentalFactor	createBatchFactor(ExpressionExperiment ee, Map<BioMaterial, Date> dates)
ExperimentalFactor	createRnaSeqBatchFactor(ExpressionExperiment ee, Map<BioMaterial, String> headers)	For RNA-seq, we based the batching on the available device/run/flowcell/lane information
void	recordBatchInformationFetched(ExpressionExperiment ee, String note)	Record a BatchInformationFetchingEvent on ee.
void	recordSingleBatchDetermination(ExpressionExperiment ee, String note)	Record a SingleBatchDeterminationEvent on ee.

Methods inherited from class Object

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

Field Details

BATCH_FACTOR_NAME_PREFIX

public static final String BATCH_FACTOR_NAME_PREFIX

Prefix to use when generating batch factor names.

See Also:

• Constant Field Values

Constructor Details

BatchInfoPopulationHelperServiceImpl

public BatchInfoPopulationHelperServiceImpl()

Method Details

createRnaSeqBatchFactor

@Transactional(noRollbackFor={FASTQHeadersPresentButNotUsableException.class,SingletonBatchesException.class})
@AuditedOnError(value=UninformativeFASTQHeadersForBatchingEvent.class,exception=FASTQHeadersPresentButNotUsableException.class,message="Batches unable to be determined") @AuditedOnError(value=SingletonBatchInvalidEvent.class,exception=SingletonBatchesException.class,message="At least one singleton batch")
public ExperimentalFactor createRnaSeqBatchFactor(ExpressionExperiment ee,
 Map<BioMaterial, String> headers)

For RNA-seq, we based the batching on the available device/run/flowcell/lane information

Two failure modes are surfaced as exceptions so the AuditedOnError aspect (which runs @AfterThrowing on the proxy boundary) can write the matching audit row before the caller in BatchInfoPopulationServiceImpl catches them and converts them to a null return:

• FASTQHeadersPresentButNotUsableException → UninformativeFASTQHeadersForBatchingEvent
• SingletonBatchesException → SingletonBatchInvalidEvent

The aspect picks the most-specific exception match, so the two declarations dispatch deterministically. The 4-arg addUpdateEvent detail string (the verbose "RNA-seq experiment, FASTQ headers ..." text) is dropped on migration pending the AuditEventPayload Phase A landing.

Specified by:

createRnaSeqBatchFactor in interface BatchInfoPopulationHelperService

Parameters:

ee - experiment

headers - map of biomaterial to a string. If there was no usable FASTQ header, we just use the GPL ID

Returns:

factor

createBatchFactor

@Transactional
public ExperimentalFactor createBatchFactor(ExpressionExperiment ee,
 Map<BioMaterial, Date> dates)

Specified by:

createBatchFactor in interface BatchInfoPopulationHelperService

recordSingleBatchDetermination

@Transactional
@Audited(value=SingleBatchDeterminationEvent.class,
         messageSpel="#note")
public void recordSingleBatchDetermination(ExpressionExperiment ee,
 String note)

Record a SingleBatchDeterminationEvent on ee. Exists so the branch in BatchInfoPopulationServiceImpl that chooses between a single-batch and a multi-batch event can dispatch through a Spring proxy carrying a single, deterministic Audited annotation -- the @Audited aspect requires one event class per method, so the original multi-branch private method had to be split.

The Audited annotation drives emission through the AuditedAspect; this method body is intentionally a logging-only marker so the proxy-intercepted return triggers exactly one SingleBatchDeterminationEvent.

Specified by:

recordSingleBatchDetermination in interface BatchInfoPopulationHelperService

Parameters:

ee - experiment

note - short summary stored in AUDIT_EVENT.NOTE

recordBatchInformationFetched

@Transactional
@Audited(value=BatchInformationFetchingEvent.class,
         messageSpel="#note")
public void recordBatchInformationFetched(ExpressionExperiment ee,
 String note)

Record a BatchInformationFetchingEvent on ee. Companion to BatchInfoPopulationHelperService.recordSingleBatchDetermination(ExpressionExperiment, String) for the multi-batch branch; see that method's javadoc for rationale.

Companion to recordSingleBatchDetermination(ExpressionExperiment, String); see that method for the dispatch rationale.

Specified by:

recordBatchInformationFetched in interface BatchInfoPopulationHelperService

Parameters:

ee - experiment

note - short summary stored in AUDIT_EVENT.NOTE