Uses of Class
ubic.gemma.model.analysis.Investigation

Packages that use Investigation

Package	Description
ubic.gemma.model.common.auditAndSecurity.curation
ubic.gemma.model.common.description
ubic.gemma.model.expression.experiment
ubic.gemma.persistence.service.common.auditAndSecurity.curation
ubic.gemma.persistence.service.common.description
ubic.gemma.persistence.service.expression.experiment

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

Methods in ubic.gemma.model.common.auditAndSecurity.curation that return Investigation

Modifier and Type	Method	Description
Investigation	AnnotationSet.getInvestigation()
Investigation	CurationDecision.getInvestigation()
Investigation	CurationLock.getInvestigation()

Methods in ubic.gemma.model.common.auditAndSecurity.curation with parameters of type Investigation

Modifier and Type	Method	Description
void	AnnotationSet.setInvestigation(Investigation investigation)
void	CurationDecision.setInvestigation(Investigation investigation)
void	CurationLock.setInvestigation(Investigation investigation)

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

Methods in ubic.gemma.model.common.description that return Investigation

Modifier and Type	Method	Description
Investigation	PublicationAssociation.getInvestigation()

Methods in ubic.gemma.model.common.description with parameters of type Investigation

Modifier and Type	Method	Description
void	PublicationAssociation.setInvestigation(Investigation investigation)

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

Subclasses of Investigation in ubic.gemma.model.expression.experiment

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 Investigation in ubic.gemma.persistence.service.common.auditAndSecurity.curation

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

Modifier and Type	Method	Description
CurationLock	CurationLockService.acquire(Investigation ee, String lockedBy, boolean steal, int ttlMinutes)	Take or refresh the lock.
CurationLock	CurationLockService.acquire(Investigation ee, String lockedBy, boolean steal, int ttlMinutes, String runId, String agentName)	As CurationLockService.acquire(Investigation, String, boolean, int), recording WHAT is taking the lock as well as who it is for.
CurationLock	CurationLockServiceImpl.acquire(Investigation ee, String lockedBy, boolean steal, int ttlMinutes)
CurationLock	CurationLockServiceImpl.acquire(Investigation ee, String lockedBy, boolean steal, int ttlMinutes, String runId, String agentName)
AnnotationSetService.AttachedAnnotationSet	AnnotationSetService.attach(Investigation investigation, AnnotationSetRole role, AnnotationSetSource source, AgentCurationKind kind, String runId, String createdBy, String agentVersion, String model, Date ranAt, String payloadJson, AnnotationSet parent)	Attach (or return existing) an annotation set to the given investigation.
AnnotationSetService.AttachedAnnotationSet	AnnotationSetService.attach(Investigation investigation, AnnotationSetRole role, AnnotationSetSource source, AgentCurationKind kind, String runId, String createdBy, AnnotationSetService.RunProvenance runProvenance, String payloadJson, AnnotationSet parent)	As AnnotationSetService.attach(Investigation, AnnotationSetRole, AnnotationSetSource, AgentCurationKind, String, String, String, String, Date, String, AnnotationSet), but carrying the full run provenance rather than the agentVersion / model / ranAt triple.
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)
long	AnnotationSetDao.countByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)	Count rows attached to the given investigation matching the role filter (or all roles if null).
long	AnnotationSetDaoImpl.countByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)
long	AnnotationSetService.countByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)
long	AnnotationSetServiceImpl.countByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)
Optional<CurationLock>	CurationLockService.current(Investigation ee)	The current holder, or empty when the dataset is free.
Optional<CurationLock>	CurationLockServiceImpl.current(Investigation ee)
CurationDecision	CurationDecisionService.decide(Investigation investigation, CurationDecisionType decision, CurationDecisionScope scope, String decisionKey, AnnotationSet annotationSet, String reason, String decidedBy, TriageJudgeKind judgeKind)	Record a decision.
CurationDecision	CurationDecisionServiceImpl.decide(Investigation investigation, CurationDecisionType decision, CurationDecisionScope scope, String decisionKey, AnnotationSet annotationSet, String reason, String decidedBy, TriageJudgeKind judgeKind)
List<AnnotationSet>	AnnotationSetDao.findByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)	All sets attached to the given investigation, newest first.
List<AnnotationSet>	AnnotationSetDaoImpl.findByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)
List<AnnotationSet>	AnnotationSetService.findByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)
List<AnnotationSet>	AnnotationSetServiceImpl.findByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)
List<AnnotationSetTriage>	AnnotationSetTriageDao.findByInvestigation(Investigation investigation)	Every judgement on any set attached to one investigation, most recent first — the per-dataset triage view, without loading the sets.
List<AnnotationSetTriage>	AnnotationSetTriageDaoImpl.findByInvestigation(Investigation investigation)
List<AnnotationSetTriage>	AnnotationSetTriageService.findByInvestigation(Investigation investigation)	Every ruling on any set of one investigation, most recent first.
List<AnnotationSetTriage>	AnnotationSetTriageServiceImpl.findByInvestigation(Investigation investigation)
List<CurationDecision>	CurationDecisionDao.findByInvestigation(Investigation investigation)	Every decision on one experiment, most recent first -- the full log, decisions since reversed included.
List<CurationDecision>	CurationDecisionDaoImpl.findByInvestigation(Investigation investigation)
List<CurationDecision>	CurationDecisionService.findByInvestigation(Investigation investigation)	Every decision on one experiment, most recent first -- the full log.
List<CurationDecision>	CurationDecisionServiceImpl.findByInvestigation(Investigation investigation)
List<CurationDecision>	CurationDecisionDao.findByInvestigationAndKey(Investigation investigation, String decisionKey)	Every decision on one key, most recent first.
List<CurationDecision>	CurationDecisionDaoImpl.findByInvestigationAndKey(Investigation investigation, String decisionKey)
AnnotationSet	AnnotationSetDao.findByInvestigationAndRoleAndRunId(Investigation investigation, AnnotationSetRole role, String runId)	Find an existing row for the (investigation, role, runId) triple, or null.
AnnotationSet	AnnotationSetDaoImpl.findByInvestigationAndRoleAndRunId(Investigation investigation, AnnotationSetRole role, String runId)
AnnotationSet	AnnotationSetService.findByInvestigationAndRoleAndRunId(Investigation investigation, AnnotationSetRole role, String runId)
AnnotationSet	AnnotationSetServiceImpl.findByInvestigationAndRoleAndRunId(Investigation investigation, AnnotationSetRole role, String runId)
AnnotationSet	AnnotationSetDao.findLatestByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)	The most recent set attached to the given investigation matching the role filter (or all roles if null), or null.
AnnotationSet	AnnotationSetDaoImpl.findLatestByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)
AnnotationSet	AnnotationSetService.findLatestByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)
AnnotationSet	AnnotationSetServiceImpl.findLatestByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)
List<CurationDecision>	CurationDecisionDao.findStandingByInvestigation(Investigation investigation)	The standing decision under each key for one experiment.
List<CurationDecision>	CurationDecisionDaoImpl.findStandingByInvestigation(Investigation investigation)
List<AnnotationSetSummaryValueObject>	AnnotationSetDao.findSummariesByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)	Thin metadata projection of sets attached to the given investigation, newest first.
List<AnnotationSetSummaryValueObject>	AnnotationSetDaoImpl.findSummariesByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)
List<AnnotationSetSummaryValueObject>	AnnotationSetService.findSummariesByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)	Thin metadata projection.
List<AnnotationSetSummaryValueObject>	AnnotationSetServiceImpl.findSummariesByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)
boolean	CurationLockService.forceRelease(Investigation ee)	Release whoever holds it.
boolean	CurationLockServiceImpl.forceRelease(Investigation ee)
List<CurationDecision>	CurationDecisionService.historyForKey(Investigation investigation, String decisionKey)	Every decision on one key, most recent first.
List<CurationDecision>	CurationDecisionServiceImpl.historyForKey(Investigation investigation, String decisionKey)
boolean	CurationLockService.isHeldBy(Investigation ee, String username)	Whether username holds an unexpired lock.
boolean	CurationLockServiceImpl.isHeldBy(Investigation ee, String username)
int	AnnotationSetDao.rebindInvestigation(Investigation from, Investigation to)	Rebind every row currently attached to from so it points at to.
int	AnnotationSetDaoImpl.rebindInvestigation(Investigation from, Investigation to)
int	AnnotationSetService.rebindInvestigation(Investigation from, Investigation to)
int	AnnotationSetServiceImpl.rebindInvestigation(Investigation from, Investigation to)
Optional<CurationLock>	CurationLockService.refresh(Investigation ee, String heldBy, int ttlMinutes)	Extend the caller's existing lease without taking one they do not hold.
Optional<CurationLock>	CurationLockServiceImpl.refresh(Investigation ee, String heldBy, int ttlMinutes)
boolean	CurationLockService.release(Investigation ee, String heldBy)	Release the lock if heldBy holds it.
boolean	CurationLockServiceImpl.release(Investigation ee, String heldBy)
List<CurationDecision>	CurationDecisionService.standingFor(Investigation investigation)	The standing decision under each key.
List<CurationDecision>	CurationDecisionServiceImpl.standingFor(Investigation investigation)
AnnotationSet	AnnotationSetService.upsertDraft(Investigation investigation, String createdBy, String payloadJson, String parkedElements, AnnotationSet parent)	Convenience overload for the common DRAFT-upsert path used by the curation-UI: ensures one DRAFT per (investigation, curator) by deriving runId as "draft-{createdBy}".
AnnotationSet	AnnotationSetServiceImpl.upsertDraft(Investigation investigation, String createdBy, String payloadJson, String parkedElements, AnnotationSet parent)

Uses of Investigation in ubic.gemma.persistence.service.common.description

Methods in ubic.gemma.persistence.service.common.description with parameters of type Investigation

Modifier and Type	Method	Description
PublicationAssociation	PublicationAssociationService.assertAccepted(Investigation investigation, PublicationAssertion assertion, PublicationAssociationRole role)	Record a single acceptance without disturbing the investigation's other assertions.
PublicationAssociation	PublicationAssociationServiceImpl.assertAccepted(Investigation investigation, PublicationAssertion assertion, PublicationAssociationRole role)
PublicationAssociation	PublicationAssociationService.assertRejected(Investigation investigation, PublicationAssertion assertion)	Record that a publication has been ruled out for an investigation, without disturbing its other assertions.
PublicationAssociation	PublicationAssociationServiceImpl.assertRejected(Investigation investigation, PublicationAssertion assertion)
PublicationAssociation	PublicationAssociationService.find(Investigation investigation, BibliographicReference publication)	The assertion held for this exact pair, or null if the pair has never been ruled on.
PublicationAssociation	PublicationAssociationServiceImpl.find(Investigation investigation, BibliographicReference publication)
PublicationAssociation	PublicationAssociationService.findBlockingRejection(Investigation investigation, BibliographicReference publication, PublicationAssociationSource source)	The standing rejection that would refuse an attempt by source to accept publication for investigation, or null if the write is allowed.
PublicationAssociation	PublicationAssociationServiceImpl.findBlockingRejection(Investigation investigation, BibliographicReference publication, PublicationAssociationSource source)
List<PublicationAssociation>	PublicationAssociationDao.findByInvestigation(Investigation investigation, PublicationAssociationStatus statusFilter)	Every assertion attached to the investigation, accepted before rejected and stable thereafter by id.
List<PublicationAssociation>	PublicationAssociationDaoImpl.findByInvestigation(Investigation investigation, PublicationAssociationStatus statusFilter)
List<PublicationAssociation>	PublicationAssociationService.findByInvestigation(Investigation investigation, PublicationAssociationStatus statusFilter)	Every assertion attached to the investigation, accepted before rejected.
List<PublicationAssociation>	PublicationAssociationServiceImpl.findByInvestigation(Investigation investigation, PublicationAssociationStatus statusFilter)
PublicationAssociation	PublicationAssociationDao.findByInvestigationAndPublication(Investigation investigation, BibliographicReference publication)	The assertion held for this exact pair, or null if none.
PublicationAssociation	PublicationAssociationDaoImpl.findByInvestigationAndPublication(Investigation investigation, BibliographicReference publication)
List<PublicationAssociation>	PublicationAssociationDao.findByInvestigationAndPublications(Investigation investigation, Collection<BibliographicReference> publications)	Assertions for the investigation whose publication is one of publications, in one query.
List<PublicationAssociation>	PublicationAssociationDaoImpl.findByInvestigationAndPublications(Investigation investigation, Collection<BibliographicReference> publications)
Map<Long, PublicationAssociation>	PublicationAssociationService.findByPublications(Investigation investigation, Collection<BibliographicReference> publications)	Assertions for the investigation covering publications, in one query, keyed by publication id — the read path's way to decorate a dataset's publication list without a query per row.
Map<Long, PublicationAssociation>	PublicationAssociationServiceImpl.findByPublications(Investigation investigation, Collection<BibliographicReference> publications)
List<PublicationAssociation>	PublicationAssociationService.reconcile(Investigation investigation, PublicationAssertion primary, Collection<PublicationAssertion> otherRelevant, Collection<PublicationAssertion> rejected)	Bring the assertions for investigation into line with a set-replace of its publications, and record any explicit rejections.
List<PublicationAssociation>	PublicationAssociationServiceImpl.reconcile(Investigation investigation, PublicationAssertion primary, Collection<PublicationAssertion> otherRelevant, Collection<PublicationAssertion> rejected)

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

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type Investigation

Modifier and Type	Method	Description
WorkflowTransition	WorkflowService.advance(Investigation dataset, WorkflowState targetState, String reason, Long ticketId)	Advance the given dataset to targetState.
WorkflowTransition	WorkflowServiceImpl.advance(Investigation dataset, WorkflowState targetState, String reason, Long ticketId)
WorkflowState	WorkflowService.getCurrentState(Investigation investigation)
WorkflowState	WorkflowServiceImpl.getCurrentState(Investigation investigation)
List<AuditEvent>	WorkflowService.getHistory(Investigation investigation)	Retrieve the full chronological history of workflow transitions for a dataset, derived from the AUDIT_EVENT stream filtered to WorkflowStateChangedEvent rows.
List<AuditEvent>	WorkflowServiceImpl.getHistory(Investigation investigation)