Class AnnotationSetDispositionServiceImpl

java.lang.Object

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

All Implemented Interfaces:

AnnotationSetDispositionService

@Service
public class AnnotationSetDispositionServiceImpl
extends Object
implements AnnotationSetDispositionService

Default AnnotationSetDispositionService.

Deliberately emits no audit event, for the reason AnnotationSetTriageServiceImpl gives: any audit event sets curationDetails.lastUpdated, which is the optimistic-concurrency token the curation commit checks — so ruling on a finding would 409 every draft in flight on that dataset. The row carries its own decidedBy / decidedAt, so it is its own record.

Constructor Summary

Constructors

Constructor	Description
AnnotationSetDispositionServiceImpl(AnnotationSetDispositionDao annotationSetDispositionDao)

Method Summary

Modifier and Type	Method	Description
int	clearDispositions(AnnotationSet annotationSet)	Erase every ruling on one set, so it can be dispositioned again from scratch.
List<AnnotationSetDisposition>	findBySet(AnnotationSet annotationSet)	Every ruling on one set, most recent first — the full log, superseded rulings included.
List<AnnotationSetDisposition>	historyFor(AnnotationSet annotationSet, String targetId)	Every ruling on one finding, most recent first.
AnnotationSetDisposition	rule(AnnotationSet annotationSet, String targetId, String findingId, FindingDisposition disposition, String decidedBy, TriageJudgeKind judgeKind, String reason)	Record a ruling on one finding.
List<AnnotationSetDisposition>	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.
Map<Long, List<AnnotationSetDisposition>>	standingForIds(Collection<Long> annotationSetIds)	Batched AnnotationSetDispositionService.standingFor(AnnotationSet), keyed by annotation set id.

Methods inherited from class Object

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

Constructor Details

AnnotationSetDispositionServiceImpl

@Autowired
public AnnotationSetDispositionServiceImpl(AnnotationSetDispositionDao annotationSetDispositionDao)

Method Details

rule

@Transactional
public AnnotationSetDisposition rule(AnnotationSet annotationSet,
 String targetId,
 @Nullable
 String findingId,
 FindingDisposition disposition,
 String decidedBy,
 TriageJudgeKind judgeKind,
 @Nullable
 String reason)

Description copied from interface: AnnotationSetDispositionService

Record a ruling on one finding. Always a new row: a curator changing their mind adds to the history rather than overwriting it.

Specified by:

rule in interface AnnotationSetDispositionService

Parameters:

targetId - the target, in the producer's own numbering. Opaque — the payload is never parsed here, so an id naming no finding is accepted and only the producer can tell.

findingId - which finding, when the producer supplies one. Opaque, like targetId. A target does NOT name a finding — one target routinely carries several, and two of them can be actionable — so a ruling keyed on the target alone cannot say what it ruled on. Null keeps the row target-keyed, which is what pre-existing rows and producers not emitting ids get.

decidedBy - 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 decidedBy, so "has a person ruled on this" does not depend on knowing every agent run id.

reason - why; what the agent needs in order to stop emitting a finding it got wrong. Optional on FindingDisposition.ACCEPTED and FindingDisposition.DISMISSED, REQUIRED on FindingDisposition.NEEDS_MORE_INFO — see below. Free text either way; there is no vocabulary.

findBySet

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

Description copied from interface: AnnotationSetDispositionService

Every ruling on one set, most recent first — the full log, superseded rulings included.

Specified by:

findBySet in interface AnnotationSetDispositionService

historyFor

@Transactional(readOnly=true)
public List<AnnotationSetDisposition> historyFor(AnnotationSet annotationSet,
 String targetId)

Description copied from interface: AnnotationSetDispositionService

Every ruling on one finding, most recent first. The head is the standing ruling.

Specified by:

historyFor in interface AnnotationSetDispositionService

standingFor

@Transactional(readOnly=true)
public List<AnnotationSetDisposition> standingFor(AnnotationSet annotationSet)

Description copied from interface: AnnotationSetDispositionService

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. The two are separate buckets: a ruling on a finding never supersedes a ruling on a target, or the reverse.

Specified by:

standingFor in interface AnnotationSetDispositionService

standingForIds

@Transactional(readOnly=true)
public Map<Long, List<AnnotationSetDisposition>> standingForIds(Collection<Long> annotationSetIds)

Description copied from interface: AnnotationSetDispositionService

Batched AnnotationSetDispositionService.standingFor(AnnotationSet), keyed by annotation set id. One round-trip for a whole page rather than one query per set.

Specified by:

standingForIds in interface AnnotationSetDispositionService

clearDispositions

@Transactional
public int clearDispositions(AnnotationSet annotationSet)

Description copied from interface: AnnotationSetDispositionService

Erase every ruling on one set, so it can be dispositioned again from scratch. Returns how many rows went.

🛑 A do-over after a FAULT, not a curator changing their mind. The rulings on a rebuilt calibration package, or ones taken through a wire-schema bug, record a mistake rather than a decision; superseding them one by one would preserve exactly the noise the caller is trying to be rid of. A curator who has reconsidered calls AnnotationSetDispositionService.rule(AnnotationSet, String, String, FindingDisposition, String, TriageJudgeKind, String) again and the append-only history keeps both.

This does NOT undo design edits a curator made in response to those rulings. Those live in the draft, and discarding the draft is a separate act.

Specified by:

clearDispositions in interface AnnotationSetDispositionService

Returns:

how many rulings were deleted; 0 when there were none