Class AnnotationSetDaoImpl

java.lang.Object

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

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

All Implemented Interfaces:

BaseDao<AnnotationSet>, AnnotationSetDao

@Repository
public class AnnotationSetDaoImpl
extends AbstractDao<AnnotationSet>
implements AnnotationSetDao

Hibernate implementation of AnnotationSetDao.

Nested Class Summary

Nested classes/interfaces inherited from interface AnnotationSetDao

AnnotationSetDao.SummarySort

Field Summary

Fields inherited from class AbstractDao

log

Constructor Summary

Constructors

Constructor	Description
AnnotationSetDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
long	countByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)	Count rows attached to the given investigation matching the role filter (or all roles if null).
Map<AnnotationSetRole, Long>	countByRoleSince(Date since)	Group rows by role, counting per bucket.
long	countDistinctRunIdsSince(Date since, AnnotationSetRole roleFilter)	Number of distinct runIds seen on rows with createdAt >= since (or all-time if null).
long	countSince(Date since, AnnotationSetRole roleFilter)	Count rows with createdAt on or after since (or all rows if since is null).
long	countSummaries(AnnotationSetRole roleFilter, AnnotationSetSource sourceFilter, String createdByFilter, AgentCurationKind kindFilter, String statusFilter, List<Long> investigationIds)	Cross-experiment count.
List<AnnotationSet>	findByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)	All sets attached to the given investigation, newest first.
AnnotationSet	findByInvestigationAndRoleAndRunId(Investigation investigation, AnnotationSetRole role, String runId)	Find an existing row for the (investigation, role, runId) triple, or null.
AnnotationSet	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.
Date	findLatestCreatedAt(AnnotationSetRole roleFilter)
List<AnnotationSetSummaryValueObject>	findSummariesByInvestigation(Investigation investigation, AnnotationSetRole roleFilter)	Thin metadata projection of sets attached to the given investigation, newest first.
List<AnnotationSetSummaryValueObject>	listSummaries(AnnotationSetRole roleFilter, AnnotationSetSource sourceFilter, String createdByFilter, AgentCurationKind kindFilter, String statusFilter, List<Long> investigationIds, int offset, int limit, AnnotationSetDao.SummarySort sort, boolean descending)	Cross-experiment thin metadata projection: every AnnotationSet matching the supplied filter, sliced by offset / limit.
int	rebindInvestigation(Investigation from, Investigation to)	Rebind every row currently attached to from so it points at to.

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

AnnotationSetDaoImpl

@Autowired
public AnnotationSetDaoImpl(SessionFactory sessionFactory)

Method Details

findByInvestigationAndRoleAndRunId

@Nullable
public AnnotationSet findByInvestigationAndRoleAndRunId(Investigation investigation,
 AnnotationSetRole role,
 String runId)

Description copied from interface: AnnotationSetDao

Find an existing row for the (investigation, role, runId) triple, or null. Used by the service to make POST /datasets/{id}/annotation-sets idempotent on retry.

Specified by:

findByInvestigationAndRoleAndRunId in interface AnnotationSetDao

findByInvestigation

public List<AnnotationSet> findByInvestigation(Investigation investigation,
 @Nullable
 AnnotationSetRole roleFilter)

Description copied from interface: AnnotationSetDao

All sets attached to the given investigation, newest first.

Specified by:

findByInvestigation in interface AnnotationSetDao

Parameters:

investigation - target. Required.

roleFilter - optional role filter; null = all roles.

findSummariesByInvestigation

public List<AnnotationSetSummaryValueObject> findSummariesByInvestigation(Investigation investigation,
 @Nullable
 AnnotationSetRole roleFilter)

Description copied from interface: AnnotationSetDao

Thin metadata projection of sets attached to the given investigation, newest first. payloadJson is NOT loaded; the projection emits length(payloadJson) as payloadSize so the UI can decide whether to fetch the full row.

Specified by:

findSummariesByInvestigation in interface AnnotationSetDao

findLatestByInvestigation

@Nullable
public AnnotationSet findLatestByInvestigation(Investigation investigation,
 @Nullable
 AnnotationSetRole roleFilter)

Description copied from interface: AnnotationSetDao

The most recent set attached to the given investigation matching the role filter (or all roles if null), or null. "Most recent" by createdAt, falling back to id when createdAt ties.

Specified by:

findLatestByInvestigation in interface AnnotationSetDao

countByInvestigation

public long countByInvestigation(Investigation investigation,
 @Nullable
 AnnotationSetRole roleFilter)

Description copied from interface: AnnotationSetDao

Count rows attached to the given investigation matching the role filter (or all roles if null).

Specified by:

countByInvestigation in interface AnnotationSetDao

rebindInvestigation

public int rebindInvestigation(Investigation from,
 Investigation to)

Description copied from interface: AnnotationSetDao

Rebind every row currently attached to from so it points at to. Returns the number of rows rebound. Used by the preboarded-promotion flow so the agent's historical proposals follow the EE after the preboarded row is replaced.

Specified by:

rebindInvestigation in interface AnnotationSetDao

listSummaries

public List<AnnotationSetSummaryValueObject> listSummaries(@Nullable
 AnnotationSetRole roleFilter,
 @Nullable
 AnnotationSetSource sourceFilter,
 @Nullable
 String createdByFilter,
 @Nullable
 AgentCurationKind kindFilter,
 @Nullable
 String statusFilter,
 @Nullable
 List<Long> investigationIds,
 int offset,
 int limit,
 @Nullable
 AnnotationSetDao.SummarySort sort,
 boolean descending)

Description copied from interface: AnnotationSetDao

Cross-experiment thin metadata projection: every AnnotationSet matching the supplied filter, sliced by offset / limit.

Specified by:

listSummaries in interface AnnotationSetDao

Parameters:

roleFilter - optional role filter; null = all roles.

sourceFilter - optional source filter; null = all sources.

createdByFilter - optional createdBy filter; null = no filter.

investigationIds - optional restriction to a set of investigation ids; null or empty = no additional filter (ACL enforced upstream).

sort - field to order by; null = AnnotationSetDao.SummarySort.CREATED_AT.

descending - newest / highest first.

countSummaries

public long countSummaries(@Nullable
 AnnotationSetRole roleFilter,
 @Nullable
 AnnotationSetSource sourceFilter,
 @Nullable
 String createdByFilter,
 @Nullable
 AgentCurationKind kindFilter,
 @Nullable
 String statusFilter,
 @Nullable
 List<Long> investigationIds)

Description copied from interface: AnnotationSetDao

Cross-experiment count. Counterpart of AnnotationSetDao.listSummaries(AnnotationSetRole, AnnotationSetSource, String, AgentCurationKind, String, List, int, int, SummarySort, boolean).

Specified by:

countSummaries in interface AnnotationSetDao

countSince

public long countSince(@Nullable
 Date since,
 @Nullable
 AnnotationSetRole roleFilter)

Description copied from interface: AnnotationSetDao

Count rows with createdAt on or after since (or all rows if since is null). Optionally restricted by role.

Specified by:

countSince in interface AnnotationSetDao

countByRoleSince

public Map<AnnotationSetRole, Long> countByRoleSince(@Nullable
 Date since)

Description copied from interface: AnnotationSetDao

Group rows by role, counting per bucket. Rows with createdAt >= since only when since is non-null.

Specified by:

countByRoleSince in interface AnnotationSetDao

countDistinctRunIdsSince

public long countDistinctRunIdsSince(@Nullable
 Date since,
 @Nullable
 AnnotationSetRole roleFilter)

Description copied from interface: AnnotationSetDao

Number of distinct runIds seen on rows with createdAt >= since (or all-time if null). Approximates "how many agent runs have we ingested in the window" when filtered to role=PROPOSAL.

Specified by:

countDistinctRunIdsSince in interface AnnotationSetDao

findLatestCreatedAt

@Nullable
public Date findLatestCreatedAt(@Nullable
 AnnotationSetRole roleFilter)

Specified by:

findLatestCreatedAt in interface AnnotationSetDao

Returns:

the most-recent createdAt across every row matching the role filter, or null if no rows.