Class AnnotationSetDispositionDaoImpl

java.lang.Object

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

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

All Implemented Interfaces:

BaseDao<AnnotationSetDisposition>, AnnotationSetDispositionDao

@Repository
public class AnnotationSetDispositionDaoImpl
extends AbstractDao<AnnotationSetDisposition>
implements AnnotationSetDispositionDao

Hibernate implementation of AnnotationSetDispositionDao.

Field Summary

Fields inherited from class AbstractDao

log

Constructor Summary

Constructors

Constructor	Description
AnnotationSetDispositionDaoImpl(SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
int	deleteBySet(AnnotationSet annotationSet)	Delete every ruling on one set and report how many rows went.
List<AnnotationSetDisposition>	findBySet(AnnotationSet annotationSet)	Every ruling on one set, most recent first — the full log, including rulings that have since been superseded.
List<AnnotationSetDisposition>	findBySetAndTarget(AnnotationSet annotationSet, String targetId)	Every ruling on one finding, most recent first.
List<AnnotationSetDisposition>	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.
Map<Long, List<AnnotationSetDisposition>>	findStandingBySetIds(Collection<Long> annotationSetIds)	Batched AnnotationSetDispositionDao.findStandingBySet(AnnotationSet), for a list view that would otherwise ask once per set.

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

AnnotationSetDispositionDaoImpl

@Autowired
public AnnotationSetDispositionDaoImpl(SessionFactory sessionFactory)

Method Details

findBySet

public List<AnnotationSetDisposition> findBySet(AnnotationSet annotationSet)

Description copied from interface: AnnotationSetDispositionDao

Every ruling on one set, most recent first — the full log, including rulings that have since been superseded.

Specified by:

findBySet in interface AnnotationSetDispositionDao

findBySetAndTarget

public List<AnnotationSetDisposition> findBySetAndTarget(AnnotationSet annotationSet,
 String targetId)

Description copied from interface: AnnotationSetDispositionDao

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

Specified by:

findBySetAndTarget in interface AnnotationSetDispositionDao

findStandingBySet

public List<AnnotationSetDisposition> findStandingBySet(AnnotationSet annotationSet)

Description copied from interface: AnnotationSetDispositionDao

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.

Specified by:

findStandingBySet in interface AnnotationSetDispositionDao

Returns:

the standing rulings, most recent first

findStandingBySetIds

public Map<Long, List<AnnotationSetDisposition>> findStandingBySetIds(Collection<Long> annotationSetIds)

Description copied from interface: AnnotationSetDispositionDao

Batched AnnotationSetDispositionDao.findStandingBySet(AnnotationSet), for a list view that would otherwise ask once per set.

One query for the whole page rather than N: the per-dataset annotation set list routinely returns every set on a dataset, and folding dispositions in one set at a time turns that list into an N+1.

Specified by:

findStandingBySetIds in interface AnnotationSetDispositionDao

Returns:

annotation set id -> its standing rulings. Sets with no rulings are absent from the map.

deleteBySet

public int deleteBySet(AnnotationSet annotationSet)

Description copied from interface: AnnotationSetDispositionDao

Delete every ruling on one set and report how many rows went.

🛑 The one exception to the append-only rule above, and it is not a curator's tool. It exists for a do-over after a fault — a calibration package rebuilt, a wire-schema bug that made the rulings meaningless — where the rows record a mistake rather than a decision, and the superseding-row mechanism would preserve exactly the noise the caller is trying to be rid of. A curator who has changed their mind rules again; that is what rule is for.

Specified by:

deleteBySet in interface AnnotationSetDispositionDao

Returns:

how many rulings were deleted; 0 when there were none