Class BibliographicReferenceReadServiceImpl

java.lang.Object

ubic.gemma.persistence.service.common.description.BibliographicReferenceReadServiceImpl

All Implemented Interfaces:

BibliographicReferenceReadService

@Service("bibliographicReferenceReadService")
@ParametersAreNonnullByDefault
public class BibliographicReferenceReadServiceImpl
extends Object
implements BibliographicReferenceReadService

Implementation of BibliographicReferenceReadService.

All public methods are @Transactional(readOnly = true). ACL enforcement is the responsibility of the facade BibliographicReferenceService interface -- this class is unsecured at the AOP boundary on purpose, so intra-gemma-core callers can bypass duplicate ACL checks once authenticated.

See Also:

• BibliographicReferenceService

Constructor Summary

Constructors

Constructor	Description
BibliographicReferenceReadServiceImpl(BibliographicReferenceDao bibliographicReferenceDao, SearchService searchService, ExpressionExperimentService expressionExperimentService)

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)

Methods inherited from class Object

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

Constructor Details

BibliographicReferenceReadServiceImpl

@Autowired
public BibliographicReferenceReadServiceImpl(BibliographicReferenceDao bibliographicReferenceDao,
 SearchService searchService,
 ExpressionExperimentService expressionExperimentService)

Method Details

browse

@Transactional(readOnly=true)
public List<BibliographicReference> browse(int start,
 int limit)

Specified by:

browse in interface BibliographicReferenceReadService

browse

@Transactional(readOnly=true)
public List<BibliographicReference> browse(int start,
 int limit,
 String orderField,
 boolean descending)

Specified by:

browse in interface BibliographicReferenceReadService

findByExternalId

@Transactional(readOnly=true)
public BibliographicReference findByExternalId(DatabaseEntry accession)

Specified by:

findByExternalId in interface BibliographicReferenceReadService

findByExternalId

@Transactional(readOnly=true)
public BibliographicReference findByExternalId(String id)

Description copied from interface: BibliographicReferenceReadService

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

Specified by:

findByExternalId in interface BibliographicReferenceReadService

findByExternalId

@Transactional(readOnly=true)
public BibliographicReference findByExternalId(String id,
 String databaseName)

Description copied from interface: BibliographicReferenceReadService

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

Specified by:

findByExternalId in interface BibliographicReferenceReadService

findAllByExternalId

@Transactional(readOnly=true)
public List<BibliographicReference> findAllByExternalId(String id,
 String databaseName)

Description copied from interface: BibliographicReferenceReadService

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.

Specified by:

findAllByExternalId in interface BibliographicReferenceReadService

findVOByExternalId

@Nullable
@Transactional(readOnly=true)
public BibliographicReferenceValueObject findVOByExternalId(String id)

Description copied from interface: BibliographicReferenceReadService

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

Specified by:

findVOByExternalId in interface BibliographicReferenceReadService

countDistinctWithRelatedExperiments

@Transactional(readOnly=true)
public long countDistinctWithRelatedExperiments()

Specified by:

countDistinctWithRelatedExperiments in interface BibliographicReferenceReadService

countWithRelatedExperiments

@Transactional(readOnly=true)
public long countWithRelatedExperiments()

Specified by:

countWithRelatedExperiments in interface BibliographicReferenceReadService

getRelatedExperiments

@Transactional(readOnly=true)
public Map<BibliographicReference, Set<ExpressionExperimentIdAndShortName>> getRelatedExperiments(int offset,
 int limit)

Specified by:

getRelatedExperiments in interface BibliographicReferenceReadService

getRelatedExperiments

@Transactional(readOnly=true)
public Map<BibliographicReference, Collection<ExpressionExperiment>> getRelatedExperiments(Collection<BibliographicReference> records)

Specified by:

getRelatedExperiments in interface BibliographicReferenceReadService

listAll

@Transactional(readOnly=true)
public Collection<Long> listAll()

Specified by:

listAll in interface BibliographicReferenceReadService

Returns:

all the IDs of bibliographic references in the system.

search

@Transactional(readOnly=true)
public List<BibliographicReferenceValueObject> search(String query,
 boolean searchExperiments,
 boolean searchBibrefs)
                                               throws SearchException

Specified by:

search in interface BibliographicReferenceReadService

Throws:

SearchException

search

@Transactional(readOnly=true)
public List<BibliographicReferenceValueObject> search(String query)
                                               throws SearchException

Specified by:

search in interface BibliographicReferenceReadService

Throws:

SearchException

thaw

@Transactional(readOnly=true)
public BibliographicReference thaw(BibliographicReference bibliographicReference)

Specified by:

thaw in interface BibliographicReferenceReadService

thaw

@Transactional(readOnly=true)
public Collection<BibliographicReference> thaw(Collection<BibliographicReference> bibliographicReferences)

Specified by:

thaw in interface BibliographicReferenceReadService