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

Packages that use Auditable

Package	Description
ubic.gemma.cli.util
ubic.gemma.core.analysis.report
ubic.gemma.core.security.audit
ubic.gemma.model.analysis
ubic.gemma.model.analysis.expression
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.model.pipeline
ubic.gemma.persistence.service.common.auditAndSecurity

Uses of Auditable in ubic.gemma.cli.util

Classes in ubic.gemma.cli.util with type parameters of type Auditable

Modifier and Type	Class	Description
class	AbstractAutoSeekingCLI<T extends Auditable>	Provide auto-seeking capabilities to a CLI.

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.security.audit

Methods in ubic.gemma.core.security.audit that return Auditable

Modifier and Type	Method	Description
Auditable	AuditedEvent.getTarget()

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.

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

Modifier	Constructor	Description
	AuditedEvent(Object source, Auditable target, AuditEventType eventType, AuditEventPayload payload, AuditEvent auditEvent)

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.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.

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

Modifier and Type	Class	Description
class	Ticket	A curation ticket targeting one or more entities (initially TicketTargetType.EXPRESSION_EXPERIMENT and TicketTargetType.ARRAY_DESIGN).

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	Hibernate Search 7 indexed root.
class	ExpressionExperimentSubSet	A subset of assays (or derived assays) from an ExpressionExperiment.
class	PreboardedExperiment	Subclass of Investigation representing a proposed-but-not-yet-loaded dataset.

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.model.pipeline

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

Modifier and Type	Class	Description
class	PipelineJobBatch	One curator-initiated submission of a pipeline against a set of experiments.

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

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

Modifier and Type	Method	Description
<T extends Auditable> Map<T, AuditEvent>	AuditEventDao.getCreateEvents(Collection<T> auditables)	Obtain the creation events for the given auditables.
<T extends Auditable> Map<T, AuditEvent>	AuditEventDaoImpl.getCreateEvents(Collection<T> auditables)
<T extends Auditable> Map<T, AuditEvent>	AuditEventService.getCreateEvents(Collection<T> auditable)
<T extends Auditable> Map<T, AuditEvent>	AuditEventServiceImpl.getCreateEvents(Collection<T> auditables)
<T extends Auditable> Set<Long>	AuditEventDao.getIdsHavingEvent(Class<T> auditableClass, Collection<Class<? extends AuditEventType>> types)	Obtain the ids of every auditable of a class whose trail carries at least one event of any of the given types.
<T extends Auditable> Set<Long>	AuditEventDaoImpl.getIdsHavingEvent(Class<T> auditableClass, Collection<Class<? extends AuditEventType>> types)
<T extends Auditable> Set<Long>	AuditEventService.getIdsHavingEvent(Class<T> auditableClass, Collection<Class<? extends AuditEventType>> types)	Obtain the ids of every auditable of a class whose trail carries at least one event of any of the given types.
<T extends Auditable> Set<Long>	AuditEventServiceImpl.getIdsHavingEvent(Class<T> auditableClass, Collection<Class<? extends AuditEventType>> types)
<T extends Auditable> Map<T, AuditEvent>	AuditEventDao.getLastEvents(Class<T> auditableClass, Class<? extends AuditEventType> type)	Obtain the latest events of a specified type for all auditable of a given type.
<T extends Auditable> Map<T, AuditEvent>	AuditEventDao.getLastEvents(Collection<T> auditables)	Obtain the latest event of any type for all given auditables — the batch counterpart of AuditEventDao.getLastEvent(Auditable).
<T extends Auditable> Map<T, AuditEvent>	AuditEventDao.getLastEvents(Collection<T> auditables, Class<? extends AuditEventType> type)	Obtain the latest events of a specified type for all given auditables.
<T extends Auditable> Map<T, AuditEvent>	AuditEventDaoImpl.getLastEvents(Class<T> auditableClass, Class<? extends AuditEventType> type)
<T extends Auditable> Map<T, AuditEvent>	AuditEventDaoImpl.getLastEvents(Collection<T> auditables)
<T extends Auditable> Map<T, AuditEvent>	AuditEventDaoImpl.getLastEvents(Collection<T> auditables, Class<? extends AuditEventType> type)
<T extends Auditable> Map<T, AuditEvent>	AuditEventService.getLastEvents(Class<T> auditableClass, Class<? extends AuditEventType> type)
<T extends Auditable> Map<T, AuditEvent>	AuditEventService.getLastEvents(Collection<T> auditables)	Obtain the latest typed event for each of the given auditables, whatever its type.
<T extends Auditable> Map<Class<? extends AuditEventType>, Map<T, AuditEvent>>	AuditEventService.getLastEvents(Collection<T> auditables, Collection<Class<? extends AuditEventType>> types)	Fast method to retrieve auditEventTypes of multiple classes.
<T extends Auditable> Map<T, AuditEvent>	AuditEventServiceImpl.getLastEvents(Class<T> auditableClass, Class<? extends AuditEventType> type)
<T extends Auditable> Map<T, AuditEvent>	AuditEventServiceImpl.getLastEvents(Collection<T> auditables)
<T extends Auditable> Map<Class<? extends AuditEventType>, Map<T, AuditEvent>>	AuditEventServiceImpl.getLastEvents(Collection<T> auditables, Collection<Class<? extends AuditEventType>> types)
<T extends Auditable> Collection<T>	AuditEventDao.getNewSinceDate(Class<T> auditableClass, Date date)	Get auditables that have been created since the given date.
<T extends Auditable> Collection<T>	AuditEventDaoImpl.getNewSinceDate(Class<T> auditableClass, Date date)
<T extends Auditable> Collection<T>	AuditEventService.getNewSinceDate(Class<T> auditableClass, Date date)
<T extends Auditable> Collection<T>	AuditEventServiceImpl.getNewSinceDate(Class<T> auditableClass, Date date)
<T extends Auditable> Collection<T>	AuditEventDao.getUpdatedSinceDate(Class<T> auditableClass, Date date)	Get auditables that have been updated since the given date.
<T extends Auditable> Collection<T>	AuditEventDaoImpl.getUpdatedSinceDate(Class<T> auditableClass, Date date)
<T extends Auditable> Collection<T>	AuditEventService.getUpdatedSinceDate(Class<T> auditableClass, Date date)
<T extends Auditable> Collection<T>	AuditEventServiceImpl.getUpdatedSinceDate(Class<T> auditableClass, 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)
AuditEvent	AuditTrailService.addUpdateEventWithPayload(Auditable auditable, Class<? extends AuditEventType> type, String note, String payloadJson)	Add an update audit event of a specific type, attaching a JSON payload string.
AuditEvent	AuditTrailServiceImpl.addUpdateEventWithPayload(Auditable auditable, Class<? extends AuditEventType> type, String note, String payloadJson)
List<AuditEvent>	AuditEventDao.getEvents(Auditable auditable)	Obtain the audit events associated to a given auditable.
List<AuditEvent>	AuditEventDaoImpl.getEvents(Auditable auditable)
List<AuditEvent>	AuditEventService.getEvents(Auditable auditable)
List<AuditEvent>	AuditEventServiceImpl.getEvents(Auditable auditable)
CursorPage<AuditEvent>	AuditEventDao.getEventsByCursor(Auditable auditable, Cursor cursor, int limit)	Keyset-pagination counterpart to AuditEventDao.getEvents(Auditable) — cursor mode for GET /datasets/{dataset}/auditEvents (step 1q of CURSOR_PAGINATION_STEP1_PLAN.md).
CursorPage<AuditEvent>	AuditEventDaoImpl.getEventsByCursor(Auditable auditable, Cursor cursor, int limit)
CursorPage<AuditEvent>	AuditEventService.getEventsByCursor(Auditable auditable, Cursor cursor, int limit)	Keyset-pagination counterpart to AuditEventService.getEvents(Auditable) for the GET /datasets/{dataset}/auditEvents endpoint — see CURSOR_PAGINATION_STEP1_PLAN.md step 1q.
CursorPage<AuditEvent>	AuditEventServiceImpl.getEventsByCursor(Auditable auditable, Cursor cursor, int limit)
List<AuditEvent>	AuditEventDao.getEventsWithType(Auditable auditable)	Obtain all events with a non-null event type for a given auditable.
List<AuditEvent>	AuditEventDaoImpl.getEventsWithType(Auditable auditable)
List<AuditEvent>	AuditEventService.getEventsWithType(Auditable auditable)	Retrieve all events with an event type.
List<AuditEvent>	AuditEventServiceImpl.getEventsWithType(Auditable auditable)
AuditEvent	AuditEventDao.getLastEvent(Auditable auditable)	Obtain the latest event for a given auditable.
AuditEvent	AuditEventDao.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type)	Obtain the latest event of a given type for a given auditable.
AuditEvent	AuditEventDao.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)	Obtain the latest event of a given type, excluding a certain number of types.
AuditEvent	AuditEventDaoImpl.getLastEvent(Auditable auditable)
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)
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)
AuditEvent	AuditEventServiceImpl.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type)
AuditEvent	AuditEventServiceImpl.getLastEvent(Auditable auditable, Class<? extends AuditEventType> type, Collection<Class<? extends AuditEventType>> excludedTypes)
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
void	AuditEventService.retainHavingEvent(Collection<? extends Auditable> a, Class<? extends AuditEventType> type)
void	AuditEventServiceImpl.retainHavingEvent(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)