Uses of Class
ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSet

Packages that use AnnotationSet

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

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

Subclasses with type arguments of type AnnotationSet in ubic.gemma.model.common.auditAndSecurity.curation

Modifier and Type	Class	Description
class	AnnotationSetSummaryValueObject	Thin metadata projection of an AnnotationSet row, served by the REST surface when ?shape=meta is requested.

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

Modifier and Type	Method	Description
AnnotationSet	AnnotationSetDisposition.getAnnotationSet()
AnnotationSet	AnnotationSetTriage.getAnnotationSet()
AnnotationSet	CurationDecision.getAnnotationSet()
AnnotationSet	AnnotationSet.getParent()

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

Modifier and Type	Method	Description
static Map<String, CurationDraftDispositions.Disposition>	CurationDraftDispositions.derive(AnnotationSet draft)	Derive dispositions for a draft, reading the proposal payload through the draft's parent.
void	AnnotationSetDisposition.setAnnotationSet(AnnotationSet annotationSet)
void	AnnotationSetTriage.setAnnotationSet(AnnotationSet annotationSet)
void	CurationDecision.setAnnotationSet(AnnotationSet annotationSet)
void	AnnotationSet.setParent(AnnotationSet parent)

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

Subclasses with type arguments of type AnnotationSet in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Modifier and Type	Class	Description
class	AnnotationSetDaoImpl	Hibernate implementation of AnnotationSetDao.

Subinterfaces with type arguments of type AnnotationSet in ubic.gemma.persistence.service.common.auditAndSecurity.curation

Modifier and Type	Interface	Description
interface	AnnotationSetDao	DAO for AnnotationSet rows.

Methods in ubic.gemma.persistence.service.common.auditAndSecurity.curation that return AnnotationSet

Modifier and Type	Method	Description
AnnotationSet	AnnotationSetService.finalizeSet(Long id, String finalizedBy, String notes)	Stamp finalizedAt + finalizedBy on the row, marking a DRAFT as "done editing" or a SNAPSHOT as the polished canonical view.
AnnotationSet	AnnotationSetServiceImpl.finalizeSet(Long id, String finalizedBy, String notes)
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)
AnnotationSet	AnnotationSetService.AttachedAnnotationSet.getAnnotationSet()
AnnotationSet	AnnotationSetService.load(Long id)
AnnotationSet	AnnotationSetServiceImpl.load(Long id)
AnnotationSet	AnnotationSetService.reopenSet(Long id)	Clear finalizedAt + finalizedBy + finalizedNotes on the row, reopening a finalized DRAFT or unblessing a polished SNAPSHOT.
AnnotationSet	AnnotationSetServiceImpl.reopenSet(Long id)
AnnotationSet	AnnotationSetService.updateProvenance(Long id, AnnotationSetService.RunProvenance provenance)	Correct the run-provenance envelope on an existing row in place, so a mis-stamped agentVersion / model / agentName / runSha / ranAt is fixed without the delete-and-recreate that mints a new id.
AnnotationSet	AnnotationSetServiceImpl.updateProvenance(Long id, AnnotationSetService.RunProvenance provenance)
AnnotationSet	AnnotationSetService.updateStatus(AnnotationSet annotationSet, String status)	Record where a proposal stands with its reviewer, and return the updated set.
AnnotationSet	AnnotationSetServiceImpl.updateStatus(AnnotationSet annotationSet, String status)
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)

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

Modifier and Type	Method	Description
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)

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

Modifier and Type	Method	Description
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)
int	AnnotationSetDispositionService.clearDispositions(AnnotationSet annotationSet)	Erase every ruling on one set, so it can be dispositioned again from scratch.
int	AnnotationSetDispositionServiceImpl.clearDispositions(AnnotationSet annotationSet)
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)
int	AnnotationSetDispositionDao.deleteBySet(AnnotationSet annotationSet)	Delete every ruling on one set and report how many rows went.
int	AnnotationSetDispositionDaoImpl.deleteBySet(AnnotationSet annotationSet)
Optional<AnnotationSetTriage>	AnnotationSetTriageService.effectiveFor(AnnotationSet annotationSet)	The ruling that counts — the most recent — or empty when nobody has ruled.
Optional<AnnotationSetTriage>	AnnotationSetTriageServiceImpl.effectiveFor(AnnotationSet annotationSet)
List<AnnotationSetDisposition>	AnnotationSetDispositionDao.findBySet(AnnotationSet annotationSet)	Every ruling on one set, most recent first — the full log, including rulings that have since been superseded.
List<AnnotationSetDisposition>	AnnotationSetDispositionDaoImpl.findBySet(AnnotationSet annotationSet)
List<AnnotationSetDisposition>	AnnotationSetDispositionService.findBySet(AnnotationSet annotationSet)	Every ruling on one set, most recent first — the full log, superseded rulings included.
List<AnnotationSetDisposition>	AnnotationSetDispositionServiceImpl.findBySet(AnnotationSet annotationSet)
List<AnnotationSetTriage>	AnnotationSetTriageDao.findBySet(AnnotationSet annotationSet)	Every judgement on one set, most recent first.
List<AnnotationSetTriage>	AnnotationSetTriageDaoImpl.findBySet(AnnotationSet annotationSet)
List<AnnotationSetTriage>	AnnotationSetTriageService.findBySet(AnnotationSet annotationSet)	Every ruling on one set, most recent first.
List<AnnotationSetTriage>	AnnotationSetTriageServiceImpl.findBySet(AnnotationSet annotationSet)
AnnotationSetTriage	AnnotationSetTriageDao.findBySetAndJudge(AnnotationSet annotationSet, String judgedBy)	The judgement judgedBy has standing on this set, or null.
AnnotationSetTriage	AnnotationSetTriageDaoImpl.findBySetAndJudge(AnnotationSet annotationSet, String judgedBy)
List<AnnotationSetDisposition>	AnnotationSetDispositionDao.findBySetAndTarget(AnnotationSet annotationSet, String targetId)	Every ruling on one finding, most recent first.
List<AnnotationSetDisposition>	AnnotationSetDispositionDaoImpl.findBySetAndTarget(AnnotationSet annotationSet, String targetId)
List<AnnotationSetDisposition>	AnnotationSetDispositionDao.findStandingBySet(AnnotationSet annotationSet)	The standing ruling for each finding in one set — the most recent row per finding id, or per target id for rows carrying no finding id.
List<AnnotationSetDisposition>	AnnotationSetDispositionDaoImpl.findStandingBySet(AnnotationSet annotationSet)
List<AnnotationSetDisposition>	AnnotationSetDispositionService.historyFor(AnnotationSet annotationSet, String targetId)	Every ruling on one finding, most recent first.
List<AnnotationSetDisposition>	AnnotationSetDispositionServiceImpl.historyFor(AnnotationSet annotationSet, String targetId)
AnnotationSetTriage	AnnotationSetTriageService.judge(AnnotationSet annotationSet, TriageVerdict verdict, String judgedBy, TriageJudgeKind judgeKind, String note)	Record or replace judgedBy's ruling on annotationSet.
AnnotationSetTriage	AnnotationSetTriageServiceImpl.judge(AnnotationSet annotationSet, TriageVerdict verdict, String judgedBy, TriageJudgeKind judgeKind, String note)
boolean	AnnotationSetTriageService.reviewedByHuman(AnnotationSet annotationSet)	Whether a person — not only a machine — has ruled on this set.
boolean	AnnotationSetTriageServiceImpl.reviewedByHuman(AnnotationSet annotationSet)
AnnotationSetDisposition	AnnotationSetDispositionService.rule(AnnotationSet annotationSet, String targetId, String findingId, FindingDisposition disposition, String decidedBy, TriageJudgeKind judgeKind, String reason)	Record a ruling on one finding.
AnnotationSetDisposition	AnnotationSetDispositionServiceImpl.rule(AnnotationSet annotationSet, String targetId, String findingId, FindingDisposition disposition, String decidedBy, TriageJudgeKind judgeKind, String reason)
List<AnnotationSetDisposition>	AnnotationSetDispositionService.standingFor(AnnotationSet annotationSet)	The standing ruling for each finding in one set — the most recent per finding id, or per target id for rows carrying no finding id.
List<AnnotationSetDisposition>	AnnotationSetDispositionServiceImpl.standingFor(AnnotationSet annotationSet)
AnnotationSet	AnnotationSetService.updateStatus(AnnotationSet annotationSet, String status)	Record where a proposal stands with its reviewer, and return the updated set.
AnnotationSet	AnnotationSetServiceImpl.updateStatus(AnnotationSet annotationSet, String status)
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)
boolean	AnnotationSetTriageService.withdraw(AnnotationSet annotationSet, String judgedBy)	Withdraw judgedBy's ruling, returning the set to un-triaged if it was the only one.
boolean	AnnotationSetTriageServiceImpl.withdraw(AnnotationSet annotationSet, String judgedBy)

Constructors in ubic.gemma.persistence.service.common.auditAndSecurity.curation with parameters of type AnnotationSet

Modifier	Constructor	Description
	AttachedAnnotationSet(AnnotationSet annotationSet, boolean created)

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

Methods in ubic.gemma.persistence.service.expression.experiment that return AnnotationSet

Modifier and Type	Method	Description
AnnotationSet	CurationCommitRequest.getRunParentProposal()	The PROPOSAL annotation set this commit applies, if it applies one.

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

Modifier and Type	Method	Description
void	CurationCommitRequest.setRunParentProposal(AnnotationSet runParentProposal)