Interface BibliographicReferenceReadService

All Known Implementing Classes:

BibliographicReferenceReadServiceImpl

@ParametersAreNonnullByDefault
public interface BibliographicReferenceReadService

Read-only retrieval service for BibliographicReference.

Phase 3 of the BibliographicReferenceService decomposition (strangler fig). This service houses the read cluster previously implemented directly on the BibliographicReferenceServiceImpl facade: browse, findByExternalId, findVOByExternalId, countDistinctWithRelatedExperiments, countWithRelatedExperiments, getRelatedExperiments, listAll, search, and thaw. Methods delegate to BibliographicReferenceDao (plus SearchService and ExpressionExperimentService where the original facade methods needed them to populate related-experiment VOs).

Write-side methods (create, save, update, remove, refresh, findOrCreate, plus the inherited BaseService mutators) stay on the BibliographicReferenceService facade.

Callers should generally keep using BibliographicReferenceService as the facade -- the facade delegates to this service. Direct injection is appropriate where a class is logically read-only (REST endpoints, CLIs, browser controllers, intra-core readers).

ACL / @Secured annotations live on BibliographicReferenceService (the caller-facing facade interface); enforcement happens at the facade proxy boundary, so this interface is intentionally unsecured.

See Also:

• BibliographicReferenceService

Method Summary

Modifier and Type	Method	Description
List<BibliographicReference>	browse(int start, int limit)
List<BibliographicReference>	browse(int start, int limit, String orderField, boolean descending)
long	countDistinctWithRelatedExperiments()
long	countWithRelatedExperiments()
List<BibliographicReference>	findAllByExternalId(String id, String databaseName)	Retrieve ALL references sharing an identifier (accession + database name), ordered by id ascending.
BibliographicReference	findByExternalId(String id)	Get a reference by the unqualified external id.
BibliographicReference	findByExternalId(String id, String databaseName)	Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').
BibliographicReference	findByExternalId(DatabaseEntry accession)
BibliographicReferenceValueObject	findVOByExternalId(String id)	Get a reference VO by the unqualified external id.
Map<BibliographicReference, Set<ExpressionExperimentIdAndShortName>>	getRelatedExperiments(int offset, int limit)
Map<BibliographicReference, Collection<ExpressionExperiment>>	getRelatedExperiments(Collection<BibliographicReference> records)
Collection<Long>	listAll()
List<BibliographicReferenceValueObject>	search(String query)
List<BibliographicReferenceValueObject>	search(String query, boolean searchExperiments, boolean searchBibrefs)
Collection<BibliographicReference>	thaw(Collection<BibliographicReference> bibliographicReferences)
BibliographicReference	thaw(BibliographicReference bibliographicReference)

Method Details

browse

List<BibliographicReference> browse(int start,
 int limit)

browse

List<BibliographicReference> browse(int start,
 int limit,
 String orderField,
 boolean descending)

findByExternalId

@Nullable
BibliographicReference findByExternalId(DatabaseEntry accession)

findByExternalId

@Nullable
BibliographicReference findByExternalId(String id)

Get a reference by the unqualified external id. Searches for pubmed by default.

findByExternalId

@Nullable
BibliographicReference findByExternalId(String id,
 String databaseName)

Retrieve a reference by identifier, qualified by the database name (such as 'pubmed').

findAllByExternalId

List<BibliographicReference> findAllByExternalId(String id,
 String databaseName)

Retrieve ALL references sharing an identifier (accession + database name), ordered by id ascending. Usually at most one, but prod has duplicate rows for some accessions; this exposes the whole set for de-duplication.

findVOByExternalId

@Nullable
BibliographicReferenceValueObject findVOByExternalId(String id)

Get a reference VO by the unqualified external id. Searches for pubmed by default.

countDistinctWithRelatedExperiments

long countDistinctWithRelatedExperiments()

countWithRelatedExperiments

long countWithRelatedExperiments()

getRelatedExperiments

Map<BibliographicReference, Set<ExpressionExperimentIdAndShortName>> getRelatedExperiments(int offset,
 int limit)

getRelatedExperiments

Map<BibliographicReference, Collection<ExpressionExperiment>> getRelatedExperiments(Collection<BibliographicReference> records)

listAll

Collection<Long> listAll()

Returns:

all the IDs of bibliographic references in the system.

search

List<BibliographicReferenceValueObject> search(String query,
 boolean searchExperiments,
 boolean searchBibrefs)
                                        throws SearchException

Throws:

SearchException

search

List<BibliographicReferenceValueObject> search(String query)
                                        throws SearchException

Throws:

SearchException

thaw

BibliographicReference thaw(BibliographicReference bibliographicReference)

thaw

Collection<BibliographicReference> thaw(Collection<BibliographicReference> bibliographicReferences)