Uses of Interface
ubic.gemma.model.common.auditAndSecurity.Auditable

Packages that use Auditable

Package	Description
ubic.gemma.core.analysis.report
ubic.gemma.core.apps
ubic.gemma.core.security.audit
ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression
ubic.gemma.model.association.phenotype
ubic.gemma.model.common.auditAndSecurity
ubic.gemma.model.common.auditAndSecurity.curation
ubic.gemma.model.common.description
ubic.gemma.model.expression.arrayDesign
ubic.gemma.model.expression.experiment
ubic.gemma.model.genome.gene
ubic.gemma.persistence.service.common.auditAndSecurity
ubic.gemma.web.remote

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

Methods in ubic.gemma.core.analysis.report that return types with arguments of type Auditable

Modifier and Type	Method	Description
Collection<Auditable>	WhatsNew.getNewObjects()
Collection<Auditable>	WhatsNew.getUpdatedObjects()

Methods in ubic.gemma.core.analysis.report with parameters of type Auditable

Modifier and Type	Method	Description
void	WhatsNew.addNewObjects(Auditable newObject)	adds a single auditable to the new object list
void	WhatsNew.addUpdatedObjects(Auditable updatedObject)	adds a single auditable to the updated object list

Method parameters in ubic.gemma.core.analysis.report with type arguments of type Auditable

Modifier and Type	Method	Description
void	WhatsNew.addNewObjects(Collection<? extends Auditable> objs)	adds a collection of auditables to the new object list
void	WhatsNew.addUpdatedObjects(Collection<? extends Auditable> objs)	adds a collection of auditables to the updated object list
void	WhatsNew.setNewObjects(Collection<Auditable> newObjects)
void	WhatsNew.setUpdatedObjects(Collection<Auditable> updatedObjects)

Uses of Auditable in ubic.gemma.core.apps

Methods in ubic.gemma.core.apps with parameters of type Auditable

Modifier and Type	Method	Description
protected boolean	ExpressionExperimentManipulatingCLI.noNeedToRun(Auditable auditable, Class<? extends AuditEventType> eventClass)

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

Methods in ubic.gemma.core.security.audit that return types with arguments of type Auditable

Modifier and Type	Method	Description
static Collection<Auditable>	AuditAdvice.extractAuditables(Object object)	Efficiently extract all auditable of a given type in an object's tree.

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

Modifier and Type	Method	Description
void	AuditLogger.log(Auditable auditable, AuditEvent event)	Log a given audit event.

Uses of Auditable in ubic.gemma.model.analysis

Classes in ubic.gemma.model.analysis that implement Auditable

Modifier and Type	Class	Description
class	Investigation	An abstract concept of a scientific study

Uses of Auditable in ubic.gemma.model.analysis.expression

Classes in ubic.gemma.model.analysis.expression that implement Auditable

Modifier and Type	Class	Description
class	ExpressionExperimentSet	A grouping of expression studies.

Uses of Auditable in ubic.gemma.model.association.phenotype

Classes in ubic.gemma.model.association.phenotype that implement Auditable

Modifier and Type	Class	Description
class	DataAnalysisEvidence	Deprecated.
class	DifferentialExpressionEvidence	Deprecated.
class	ExperimentalEvidence	Deprecated.
class	GenericEvidence	Deprecated.
class	GenericExperiment	Deprecated.
class	LiteratureEvidence	Deprecated.
class	PhenotypeAssociation	Deprecated.

Uses of Auditable in ubic.gemma.model.common.auditAndSecurity

Classes in ubic.gemma.model.common.auditAndSecurity that implement Auditable

Modifier and Type	Class	Description
class	AbstractAuditable	An entity which can have an audit trail attached to it.
class	UserGroup	An organized group of researchers with an identifiable leader and group members.

Uses of Auditable in ubic.gemma.model.common.auditAndSecurity.curation

Subinterfaces of Auditable in ubic.gemma.model.common.auditAndSecurity.curation

Modifier and Type	Interface	Description
interface	Curatable	Created by tesarst on 06/03/17.

Uses of Auditable in ubic.gemma.model.common.description

Classes in ubic.gemma.model.common.description that implement Auditable

Modifier and Type	Class	Description
class	ExternalDatabase

Uses of Auditable in ubic.gemma.model.expression.arrayDesign

Classes in ubic.gemma.model.expression.arrayDesign that implement Auditable

Modifier and Type	Class	Description
class	ArrayDesign	Represents an assembly of design elements that are assayed all at once.

Uses of Auditable in ubic.gemma.model.expression.experiment

Classes in ubic.gemma.model.expression.experiment that implement Auditable

Modifier and Type	Class	Description
class	BioAssaySet	Represents a set of BioAssays.
class	ExpressionExperiment
class	ExpressionExperimentSubSet	A subset of samples from an ExpressionExperiment

Uses of Auditable in ubic.gemma.model.genome.gene

Classes in ubic.gemma.model.genome.gene that implement Auditable

Modifier and Type	Class	Description
class	GeneSet	A grouping of genes that share a common relationship

Uses of Auditable in ubic.gemma.persistence.service.common.auditAndSecurity

Methods in ubic.gemma.persistence.service.common.auditAndSecurity that return types with arguments of type Auditable

Modifier and Type	Method	Description
Map<Auditable,AuditEvent>	AuditEventDao.getCreateEvents(Collection<? extends Auditable> auditables)
Map<Auditable,AuditEvent>	AuditEventDaoImpl.getCreateEvents(Collection<? extends Auditable> auditables)
Map<Auditable,AuditEvent>	AuditEventService.getCreateEvents(Collection<? extends Auditable> auditable)
Map<Auditable,AuditEvent>	AuditEventServiceImpl.getCreateEvents(Collection<? extends Auditable> auditables)
Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>	AuditEventService.getLastEvents(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)	Fast method to retrieve auditEventTypes of multiple classes.
Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>	AuditEventServiceImpl.getLastEvents(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)
Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>	AuditEventDao.getLastEventsByType(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)
Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>	AuditEventDaoImpl.getLastEventsByType(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)
Collection<Auditable>	AuditEventDao.getNewSinceDate(Date date)	Get auditables that have been Created since the given date
Collection<Auditable>	AuditEventDaoImpl.getNewSinceDate(Date date)	Note that this only returns selected classes of auditables.
Collection<Auditable>	AuditEventService.getNewSinceDate(Date date)
Collection<Auditable>	AuditEventServiceImpl.getNewSinceDate(Date date)
Collection<Auditable>	AuditEventDao.getUpdatedSinceDate(Date date)	Get auditables that have been Updated since the given date
Collection<Auditable>	AuditEventDaoImpl.getUpdatedSinceDate(Date date)	Note that this only returns selected classes of auditables.
Collection<Auditable>	AuditEventService.getUpdatedSinceDate(Date date)
Collection<Auditable>	AuditEventServiceImpl.getUpdatedSinceDate(Date date)

Methods in ubic.gemma.persistence.service.common.auditAndSecurity with parameters of type Auditable

Modifier and Type	Method	Description
AuditEvent	AuditTrailService.addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note)
AuditEvent	AuditTrailService.addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, String detail)
AuditEvent	AuditTrailService.addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, String detail, Date performedDate)	Add an update audit event of a specific type to the passed auditable entity.
AuditEvent	AuditTrailService.addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, Throwable throwable)	Add an update audit event with an exception.
AuditEvent	AuditTrailService.addUpdateEvent(Auditable auditable, String note)	Add an update event defined by the given parameters, to the given auditable.
AuditEvent	AuditTrailServiceImpl.addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note)
AuditEvent	AuditTrailServiceImpl.addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, String detail)
AuditEvent	AuditTrailServiceImpl.addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, String detail, Date performedDate)
AuditEvent	AuditTrailServiceImpl.addUpdateEvent(Auditable auditable, Class<? extends AuditEventType> type, String note, Throwable throwable)	This is using the Propagation.REQUIRES_NEW so that if the throwable is raised, it will not roll back the audit trail event.
AuditEvent	AuditTrailServiceImpl.addUpdateEvent(Auditable auditable, String note)
List<AuditEvent>	AuditEventDao.getEvents(Auditable auditable)
List<AuditEvent>	AuditEventDaoImpl.getEvents(Auditable auditable)
List<AuditEvent>	AuditEventService.getEvents(Auditable auditable)
List<AuditEvent>	AuditEventServiceImpl.getEvents(Auditable auditable)
AuditEvent	AuditEventDao.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type)
AuditEvent	AuditEventDao.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)	Obtain the latest AuditEvent of a specified type, excluding a certain number of types.
AuditEvent	AuditEventDaoImpl.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type)
AuditEvent	AuditEventDaoImpl.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
AuditEvent	AuditEventService.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type)
AuditEvent	AuditEventService.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
AuditEvent	AuditEventServiceImpl.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type)
AuditEvent	AuditEventServiceImpl.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
boolean	AuditEventDao.hasEvent(Auditable a, Class<? extends AuditEventType> type)
boolean	AuditEventDaoImpl.hasEvent(Auditable a, Class<? extends AuditEventType> type)
boolean	AuditEventService.hasEvent(Auditable a, Class<? extends AuditEventType> type)
boolean	AuditEventServiceImpl.hasEvent(Auditable a, Class<? extends AuditEventType> type)

Method parameters in ubic.gemma.persistence.service.common.auditAndSecurity with type arguments of type Auditable

Modifier and Type	Method	Description
Map<Auditable,AuditEvent>	AuditEventDao.getCreateEvents(Collection<? extends Auditable> auditables)
Map<Auditable,AuditEvent>	AuditEventDaoImpl.getCreateEvents(Collection<? extends Auditable> auditables)
Map<Auditable,AuditEvent>	AuditEventService.getCreateEvents(Collection<? extends Auditable> auditable)
Map<Auditable,AuditEvent>	AuditEventServiceImpl.getCreateEvents(Collection<? extends Auditable> auditables)
Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>	AuditEventService.getLastEvents(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)	Fast method to retrieve auditEventTypes of multiple classes.
Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>	AuditEventServiceImpl.getLastEvents(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)
Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>	AuditEventDao.getLastEventsByType(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)
Map<Class<? extends AuditEventType>,Map<Auditable,AuditEvent>>	AuditEventDaoImpl.getLastEventsByType(Collection<? extends Auditable> auditables, Collection<Class<? extends AuditEventType>> types)
void	AuditEventDao.retainHavingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void	AuditEventDaoImpl.retainHavingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void	AuditEventService.retainHavingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void	AuditEventServiceImpl.retainHavingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void	AuditEventDao.retainLackingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void	AuditEventDaoImpl.retainLackingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void	AuditEventService.retainLackingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void	AuditEventServiceImpl.retainLackingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)

Uses of Auditable in ubic.gemma.web.remote

Method parameters in ubic.gemma.web.remote with type arguments of type Auditable

Modifier and Type	Method	Description
void	AuditController.addAuditEvent(EntityDelegator<? extends Auditable> e, String auditEventType, String comment, String detail)
Collection<AuditEventValueObject>	AuditController.getEvents(EntityDelegator<? extends Auditable> e)