Class AnnotationRelationServiceImpl

java.lang.Object

ubic.gemma.persistence.service.common.description.AnnotationRelationServiceImpl

All Implemented Interfaces:

AnnotationRelationService

@Service
public class AnnotationRelationServiceImpl
extends Object
implements AnnotationRelationService

Read-only service over AnnotationRelationDao.

No write path, deliberately. Every row in this table is derived, and the only writer is the maintenance rebuild in TableMaintenanceUtil. A service-level write would let a caller assert a relation that no basis supports, which is the one thing the BASIS column exists to make impossible.

Constructor Summary

Constructors

Constructor	Description
AnnotationRelationServiceImpl(AnnotationRelationDao annotationRelationDao)

Method Summary

Modifier and Type	Method	Description
List<String[]>	findRelatedTermsForSearch(Collection<String> seedValueUris, Collection<String> seedValues, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, Long taxonId, Collection<Long> excludedExperimentIds, int maximumObjectBreadth, int maxResults)	Terms related to the seeds, for widening a query or testing membership.
List<AnnotationRelationDao.RelationSummary>	findRelations(AnnotationRelationDao.RelationQuery query)	The ranked, evidenced read.
List<AnnotationRelationDao.RelationSummary>	findRelationsForExperiment(ExpressionExperiment ee, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, int maxResults)	What this experiment's own annotations imply, for display beside them.

Methods inherited from class Object

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

Constructor Details

AnnotationRelationServiceImpl

@Autowired
public AnnotationRelationServiceImpl(AnnotationRelationDao annotationRelationDao)

Method Details

findRelations

@Transactional(readOnly=true)
public List<AnnotationRelationDao.RelationSummary> findRelations(AnnotationRelationDao.RelationQuery query)

Description copied from interface: AnnotationRelationService

The ranked, evidenced read. See AnnotationRelationDao.findRelations(AnnotationRelationDao.RelationQuery).

Specified by:

findRelations in interface AnnotationRelationService

findRelationsForExperiment

@Transactional(readOnly=true)
public List<AnnotationRelationDao.RelationSummary> findRelationsForExperiment(ExpressionExperiment ee,
 AnnotationRelationDao.Direction direction,
 Set<AnnotationRelationBasis> bases,
 int maxResults)

Description copied from interface: AnnotationRelationService

What this experiment's own annotations imply, for display beside them.

Seeds from every annotation the experiment carries and reports what each stands in relation to, with the experiment itself held out of the evidence — a dataset shown its own annotation as support for itself is showing a tautology.

Only forward walks, and no conclusion the experiment already carries: both follow from AnnotationRelationDao.RelationQuery.seedFromExperimentId(Long), which is what makes this an inference rather than a symmetric browse.

Specified by:

findRelationsForExperiment in interface AnnotationRelationService

Parameters:

direction - which way to read: what the experiment's terms stand for, or what stands for them

findRelatedTermsForSearch

@Transactional(readOnly=true)
public List<String[]> findRelatedTermsForSearch(Collection<String> seedValueUris,
 Collection<String> seedValues,
 AnnotationRelationDao.Direction direction,
 Set<AnnotationRelationBasis> bases,
 @Nullable
 Long taxonId,
 Collection<Long> excludedExperimentIds,
 int maximumObjectBreadth,
 int maxResults)

Description copied from interface: AnnotationRelationService

Terms related to the seeds, for widening a query or testing membership.

No ranking and no ambiguity resolution, on purpose: SURF1's three diseases all belong in the set, and a caller testing membership gets the right answer whichever one is meant. A caller that needs to choose one wants AnnotationRelationService.findRelations(AnnotationRelationDao.RelationQuery) and its evidence instead.

Specified by:

findRelatedTermsForSearch in interface AnnotationRelationService