Uses of Annotation Interface
ubic.gemma.core.security.audit.AuditedConditional

Packages that use AuditedConditional

Package	Description
ubic.gemma.core.analysis.preprocess	This package contains classes for preprocessing expression data.
ubic.gemma.core.analysis.report
ubic.gemma.core.loader.expression.geo.service
ubic.gemma.core.security.audit
ubic.gemma.persistence.service.common.auditAndSecurity.curation
ubic.gemma.persistence.service.expression.biomaterial
ubic.gemma.persistence.service.expression.experiment

Uses of AuditedConditional in ubic.gemma.core.analysis.preprocess

Methods in ubic.gemma.core.analysis.preprocess with annotations of type AuditedConditional

Modifier and Type	Method	Description
Integer	PreprocessorHelperServiceImpl.batchCorrect(ExpressionExperiment ee)	If possible, batch correct the processed data vectors.
Collection<RawExpressionDataVector>	TwoChannelMissingValuesImpl.computeMissingValues(ExpressionExperiment ee)
Collection<RawExpressionDataVector>	TwoChannelMissingValuesImpl.computeMissingValues(ExpressionExperiment ee, double signalToNoiseThreshold, Collection<Double> extraMissingValueIndicators)
int	VectorMergingServiceImpl.mergeVectors(ExpressionExperiment ee)

Uses of AuditedConditional in ubic.gemma.core.analysis.report

Methods in ubic.gemma.core.analysis.report with annotations of type AuditedConditional

Modifier and Type	Method	Description
String	ExpressionExperimentReportServiceImpl.recalculateExperimentBatchConfound(ExpressionExperiment ee)
String	ExpressionExperimentReportServiceImpl.recalculateExperimentBatchEffect(ExpressionExperiment ee)

Uses of AuditedConditional in ubic.gemma.core.loader.expression.geo.service

Methods in ubic.gemma.core.loader.expression.geo.service with annotations of type AuditedConditional

Modifier and Type	Method	Description
void	GeoUpdateAuditServiceImpl.recordGeoUpdate(ExpressionExperiment ee, int numNewCharacteristics, boolean pubUpdate)

Uses of AuditedConditional in ubic.gemma.core.security.audit

Methods in ubic.gemma.core.security.audit with parameters of type AuditedConditional

Modifier and Type	Method	Description
void	AuditedAspect.afterAuditedConditionalMethod(org.aspectj.lang.JoinPoint joinPoint, AuditedConditional auditedConditional, Object result)	Phase C: AuditedConditional fires only when its SpEL AuditedConditional.when() predicate evaluates to true against the post-invocation context.

Uses of AuditedConditional in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Methods in ubic.gemma.persistence.service.common.auditAndSecurity.curation with annotations of type AuditedConditional

Modifier and Type	Method	Description
AnnotationSetService.AttachedAnnotationSet	AnnotationSetServiceImpl.attach(Investigation investigation, AnnotationSetRole role, AnnotationSetSource source, AgentCurationKind kind, String runId, String createdBy, String agentVersion, String model, Date ranAt, String payloadJson, AnnotationSet parent)
AnnotationSetService.AttachedAnnotationSet	AnnotationSetServiceImpl.attach(Investigation investigation, AnnotationSetRole role, AnnotationSetSource source, AgentCurationKind kind, String runId, String createdBy, AnnotationSetService.RunProvenance runProvenance, String payloadJson, AnnotationSet parent)

Uses of AuditedConditional in ubic.gemma.persistence.service.expression.biomaterial

Methods in ubic.gemma.persistence.service.expression.biomaterial with annotations of type AuditedConditional

Modifier and Type	Method	Description
Characteristic	BioMaterialServiceImpl.removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId)
Characteristic	BioMaterialServiceImpl.removeAnnotation(ExpressionExperiment owner, BioMaterial bm, Long annotationId, String reason)	Reason-carrying overload; see BioMaterialServiceImpl.addAnnotation(ExpressionExperiment, BioMaterial, Characteristic, String).
int	BioMaterialServiceImpl.updateAnnotations(ExpressionExperiment owner, BioMaterial bm, Collection<Characteristic> desired)

Uses of AuditedConditional in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment with annotations of type AuditedConditional

Modifier and Type	Method	Description
WorkflowTransition	WorkflowServiceImpl.advance(Investigation dataset, WorkflowState targetState, String reason, Long ticketId)
DesignApplyOutcome	ExpressionExperimentServiceImpl.applyDesignChange(ExpressionExperiment ee, ExperimentalDesignValueObject proposed)
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome	SingleCellExpressionExperimentServiceImpl.changePreferredCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension dimension, CellTypeAssignment newPreferredCta, boolean recreateCellTypeFactorIfNecessary, boolean ignoreCompatibleFactor)
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome	SingleCellExpressionExperimentServiceImpl.clearPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType quantitationType)
SingleCellExpressionExperimentService.PreferredCellTypeAssignmentChangeOutcome	SingleCellExpressionExperimentServiceImpl.clearPreferredCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension dimension)
Characteristic	ExpressionExperimentServiceImpl.removeAnnotation(ExpressionExperiment ee, Long annotationId)	Per-tag REST-write counterpart to ExpressionExperimentServiceImpl.removeCharacteristics(ExpressionExperiment, Collection).
Characteristic	ExpressionExperimentServiceImpl.removeAnnotation(ExpressionExperiment ee, Long annotationId, String reason)	Reason-carrying overload; see ExpressionExperimentServiceImpl.addAnnotation(ExpressionExperiment, Characteristic, String).
int	SingleCellExpressionExperimentServiceImpl.removeSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType)
int	ExpressionExperimentServiceImpl.updateAnnotations(ExpressionExperiment ee, Collection<Characteristic> desired)	Idempotent set-replace for an EE's direct characteristic set.