Class AnnotationSetTriageServiceImpl

java.lang.Object

ubic.gemma.persistence.service.common.auditAndSecurity.curation.AnnotationSetTriageServiceImpl

All Implemented Interfaces:

AnnotationSetTriageService

@Service
public class AnnotationSetTriageServiceImpl
extends Object
implements AnnotationSetTriageService

Default AnnotationSetTriageService.

Deliberately emits no audit event. Any audit event sets curationDetails.lastUpdated, and that field is the optimistic-concurrency token the curation commit checks — so triaging a dataset would 409 every draft in flight on it. Same reasoning as bebe778980 for snapshots. The triage row carries its own judgedBy / judgedAt, so it is its own record.

Constructor Summary

Constructors

Constructor	Description
AnnotationSetTriageServiceImpl(AnnotationSetTriageDao annotationSetTriageDao)

Method Summary

Modifier and Type	Method	Description
Map<TriageVerdict, Long>	countByVerdict()	Corpus-wide tally by verdict.
Optional<AnnotationSetTriage>	effectiveFor(AnnotationSet annotationSet)	The ruling that counts — the most recent — or empty when nobody has ruled.
Map<Long, AnnotationSetTriage>	effectiveForIds(Collection<Long> annotationSetIds)	Batched AnnotationSetTriageService.effectiveFor(AnnotationSet).
Map<Long, AnnotationSetTriage>	effectiveForInvestigationIds(Collection<Long> investigationIds)	The effective ruling for each of several datasets, keyed by dataset id — newest ruling across every annotation set the dataset owns.
List<AnnotationSetTriage>	findByInvestigation(Investigation investigation)	Every ruling on any set of one investigation, most recent first.
List<AnnotationSetTriage>	findBySet(AnnotationSet annotationSet)	Every ruling on one set, most recent first.
AnnotationSetTriage	judge(AnnotationSet annotationSet, TriageVerdict verdict, String judgedBy, TriageJudgeKind judgeKind, String note)	Record or replace judgedBy's ruling on annotationSet.
boolean	reviewedByHuman(AnnotationSet annotationSet)	Whether a person — not only a machine — has ruled on this set.
boolean	withdraw(AnnotationSet annotationSet, String judgedBy)	Withdraw judgedBy's ruling, returning the set to un-triaged if it was the only one.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

AnnotationSetTriageServiceImpl

@Autowired
public AnnotationSetTriageServiceImpl(AnnotationSetTriageDao annotationSetTriageDao)

Method Details

judge

@Transactional
public AnnotationSetTriage judge(AnnotationSet annotationSet,
 TriageVerdict verdict,
 String judgedBy,
 TriageJudgeKind judgeKind,
 @Nullable
 String note)

Description copied from interface: AnnotationSetTriageService

Record or replace judgedBy's ruling on annotationSet. Idempotent per judge: a second call from the same judge updates the standing row rather than adding one.

Specified by:

judge in interface AnnotationSetTriageService

Parameters:

judgedBy - the ruling identity — a username for a person, a run id for an agent. Never the transport's principal.

judgeKind - stored rather than inferred from judgedBy, so "has a person ruled on this" does not depend on knowing every agent run id.

note - why; the only place a TriageVerdict.WontFix says what it is declining to fix. Optional.

withdraw

@Transactional
public boolean withdraw(AnnotationSet annotationSet,
 String judgedBy)

Description copied from interface: AnnotationSetTriageService

Withdraw judgedBy's ruling, returning the set to un-triaged if it was the only one.

Specified by:

withdraw in interface AnnotationSetTriageService

Returns:

whether a row was removed

findBySet

@Transactional(readOnly=true)
public List<AnnotationSetTriage> findBySet(AnnotationSet annotationSet)

Description copied from interface: AnnotationSetTriageService

Every ruling on one set, most recent first.

Specified by:

findBySet in interface AnnotationSetTriageService

effectiveFor

@Transactional(readOnly=true)
public Optional<AnnotationSetTriage> effectiveFor(AnnotationSet annotationSet)

Description copied from interface: AnnotationSetTriageService

The ruling that counts — the most recent — or empty when nobody has ruled.

Specified by:

effectiveFor in interface AnnotationSetTriageService

effectiveForIds

@Transactional(readOnly=true)
public Map<Long, AnnotationSetTriage> effectiveForIds(Collection<Long> annotationSetIds)

Description copied from interface: AnnotationSetTriageService

Batched AnnotationSetTriageService.effectiveFor(AnnotationSet). Sets with no ruling are absent from the map rather than mapped to null.

Specified by:

effectiveForIds in interface AnnotationSetTriageService

effectiveForInvestigationIds

@Transactional(readOnly=true)
public Map<Long, AnnotationSetTriage> effectiveForInvestigationIds(Collection<Long> investigationIds)

Description copied from interface: AnnotationSetTriageService

The effective ruling for each of several datasets, keyed by dataset id — newest ruling across every annotation set the dataset owns. One round-trip for a whole page.

Specified by:

effectiveForInvestigationIds in interface AnnotationSetTriageService

findByInvestigation

@Transactional(readOnly=true)
public List<AnnotationSetTriage> findByInvestigation(Investigation investigation)

Description copied from interface: AnnotationSetTriageService

Every ruling on any set of one investigation, most recent first.

Specified by:

findByInvestigation in interface AnnotationSetTriageService

reviewedByHuman

@Transactional(readOnly=true)
public boolean reviewedByHuman(AnnotationSet annotationSet)

Description copied from interface: AnnotationSetTriageService

Whether a person — not only a machine — has ruled on this set.

Specified by:

reviewedByHuman in interface AnnotationSetTriageService

countByVerdict

@Transactional(readOnly=true)
public Map<TriageVerdict, Long> countByVerdict()

Description copied from interface: AnnotationSetTriageService

Corpus-wide tally by verdict.

Specified by:

countByVerdict in interface AnnotationSetTriageService