Interface AnnotationRelationDao

All Superinterfaces:

BaseDao<AnnotationRelation>

All Known Implementing Classes:

AnnotationRelationDaoImpl

public interface AnnotationRelationDao
extends BaseDao<AnnotationRelation>

Reads over AnnotationRelation.

Two read shapes, because there are two questions and conflating them is a design error:

• findRelations(AnnotationRelationDao.RelationQuery) - the ranked, evidenced list. For showing a curator, and for anything that has to choose a term. Ambiguity is fatal here: SURF1 carries three germline disease axioms in MONDO, so a producer asked to emit one annotation has to pick, and picking wrong ships a wrong annotation. That is why the curation rule forbids generating the tag.
• findRelatedTerms(Collection, Collection, AnnotationRelationDao.Direction, Set, Collection, Long, Collection, int, int) - set membership. For query expansion, and for asking "is this proposed tag already implied by what the experiment carries?". Ambiguity is harmless here: all three of SURF1's diseases go into the set, and testing membership against the set gives the right answer whichever one is meant.

Many-to-many kills generation and is irrelevant to suppression. A caller that needs the second and reaches for the first inherits a problem it does not have.

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static enum	AnnotationRelationDao.Direction	Which end of the relation a caller is seeding from.
static class	AnnotationRelationDao.RelationQuery	What to look for.
static class	AnnotationRelationDao.RelationSummary	A relation aggregated over its attesting experiments, for one basis.

Method Summary

Modifier and Type	Method	Description
List<String[]>	findRelatedTerms(Collection<String> seedValueUris, Collection<String> seedValues, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, Collection<String> predicateUris, Long taxonId, Collection<Long> excludedExperimentIds, int maximumObjectBreadth, int maxResults)	Set membership: every term related to any of the seeds, with no counting, no ranking and no ambiguity to resolve.
List<AnnotationRelationDao.RelationSummary>	findRelations(AnnotationRelationDao.RelationQuery query)	The ranked, evidenced read.
int	removeByBasis(AnnotationRelationBasis basis, Long experimentId)	Remove every derived row for a basis, optionally for one experiment.
int	removeByBasis(AnnotationRelationBasis basis, Long experimentId, String source)	The same rebuild delete, narrowed to one source.

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

Method Details

findRelations

List<AnnotationRelationDao.RelationSummary> findRelations(AnnotationRelationDao.RelationQuery query)

The ranked, evidenced read. Empty when the query names neither end of the relation.

Support is counted here, never stored, so the counts are exact for the calling user's ACL.

findRelatedTerms

List<String[]> findRelatedTerms(Collection<String> seedValueUris,
 Collection<String> seedValues,
 AnnotationRelationDao.Direction direction,
 Set<AnnotationRelationBasis> bases,
 Collection<String> predicateUris,
 @Nullable
 Long taxonId,
 Collection<Long> excludedExperimentIds,
 int maximumObjectBreadth,
 int maxResults)

Set membership: every term related to any of the seeds, with no counting, no ranking and no ambiguity to resolve.

This is the primitive behind query expansion and behind "is this tag already implied?". It is one indexed lookup and has to stay cheap enough to sit on an interactive path.

Parameters:

seedValueUris - grounded seeds; may be empty if seedValues is not

seedValues - ungrounded seeds, matched on the value string - ordinary here, since plenty of curated statement objects are free text (aortic banding has none)

Returns:

the related terms, each as [value, valueUri], the URI possibly null

removeByBasis

int removeByBasis(AnnotationRelationBasis basis,
 @Nullable
 Long experimentId)

Remove every derived row for a basis, optionally for one experiment.

Rebuild, not upsert - see AnnotationRelation. An upsert can only correct rows the new query still produces, so a row whose source annotation was deleted would outlive it.

removeByBasis

int removeByBasis(AnnotationRelationBasis basis,
 @Nullable
 Long experimentId,
 @Nullable
 String source)

The same rebuild delete, narrowed to one source.

AnnotationRelationBasis.ONTOLOGY has more than one producer — CLO states which disease a cell line came from, CHEBI which roles a chemical bears — and they are loaded and rebuilt independently. Rebuilding one with the basis-wide delete would silently drop the other's rows and leave the table looking like the other producer had never run.

Parameters:

source - the source to remove, or null for every source under the basis