Class AnnotationSetTriageDaoImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<AnnotationSetTriage>

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

All Implemented Interfaces:

BaseDao<AnnotationSetTriage>, AnnotationSetTriageDao

@Repository
public class AnnotationSetTriageDaoImpl
extends AbstractDao<AnnotationSetTriage>
implements AnnotationSetTriageDao

Hibernate implementation of AnnotationSetTriageDao.

Field Summary

Fields inherited from class AbstractDao

log

Constructor Summary

Constructors

Constructor	Description
AnnotationSetTriageDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
Map<TriageVerdict, Long>	countByVerdict()	Corpus-wide tally by verdict, for the triage queue's counts.
List<AnnotationSetTriage>	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>	findBySet(AnnotationSet annotationSet)	Every judgement on one set, most recent first.
AnnotationSetTriage	findBySetAndJudge(AnnotationSet annotationSet, String judgedBy)	The judgement judgedBy has standing on this set, or null.
Map<Long, AnnotationSetTriage>	findEffectiveByInvestigationIds(Collection<Long> investigationIds)	The effective ruling for each of several INVESTIGATIONS, keyed by investigation id.
Map<Long, AnnotationSetTriage>	findEffectiveBySetIds(Collection<Long> annotationSetIds)	The effective (most recent) judgement for each of annotationSetIds.

Methods inherited from class AbstractDao

countAll, create, create, find, findByProperty, findByPropertyIn, findIdByProperty, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getEntityName, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, streamQuery, update, update

Methods inherited from class Object

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

Methods inherited from interface BaseDao

countAll, create, create, find, findOrCreate, getElementClass, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, save, save, streamAll, streamAll, update, update

Constructor Details

AnnotationSetTriageDaoImpl

@Autowired
public AnnotationSetTriageDaoImpl(SessionFactory sessionFactory)

Method Details

findBySetAndJudge

@Nullable
public AnnotationSetTriage findBySetAndJudge(AnnotationSet annotationSet,
 String judgedBy)

Description copied from interface: AnnotationSetTriageDao

The judgement judgedBy has standing on this set, or null. This is the uniqueness key, so there is at most one.

Specified by:

findBySetAndJudge in interface AnnotationSetTriageDao

findBySet

public List<AnnotationSetTriage> findBySet(AnnotationSet annotationSet)

Description copied from interface: AnnotationSetTriageDao

Every judgement on one set, most recent first. The first element is the effective verdict.

Specified by:

findBySet in interface AnnotationSetTriageDao

findByInvestigation

public List<AnnotationSetTriage> findByInvestigation(Investigation investigation)

Description copied from interface: AnnotationSetTriageDao

Every judgement on any set attached to one investigation, most recent first — the per-dataset triage view, without loading the sets.

Specified by:

findByInvestigation in interface AnnotationSetTriageDao

findEffectiveBySetIds

public Map<Long, AnnotationSetTriage> findEffectiveBySetIds(Collection<Long> annotationSetIds)

Description copied from interface: AnnotationSetTriageDao

The effective (most recent) judgement for each of annotationSetIds.

Batched deliberately: the effective verdict is a per-set "latest row" lookup, and doing it one set at a time turns a list query into N+1 round trips. Sets with no judgement are absent from the map rather than mapped to null, so containsKey answers "has anyone ruled".

Specified by:

findEffectiveBySetIds in interface AnnotationSetTriageDao

findEffectiveByInvestigationIds

public Map<Long, AnnotationSetTriage> findEffectiveByInvestigationIds(Collection<Long> investigationIds)

Description copied from interface: AnnotationSetTriageDao

The effective ruling for each of several INVESTIGATIONS, keyed by investigation id.

Same rule as AnnotationSetTriageDao.findEffectiveBySetIds(Collection) — newest ruling wins — applied across every annotation set the investigation owns rather than one set. Exists so a list view can ask about a page of datasets in one round-trip instead of one query per row.

Specified by:

findEffectiveByInvestigationIds in interface AnnotationSetTriageDao

Returns:

investigation id -> effective ruling; ids with no ruling are absent

countByVerdict

public Map<TriageVerdict, Long> countByVerdict()

Description copied from interface: AnnotationSetTriageDao

Corpus-wide tally by verdict, for the triage queue's counts.

Specified by:

countByVerdict in interface AnnotationSetTriageDao