Class BibliographicReferenceServiceImpl

java.lang.Object

ubic.gemma.persistence.service.AbstractService<BibliographicReference>

ubic.gemma.persistence.service.AbstractVoEnabledService<BibliographicReference, BibliographicReferenceValueObject>

ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceImpl

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, BaseImmutableService<BibliographicReference>, BaseReadOnlyService<BibliographicReference>, BaseService<BibliographicReference>, BaseVoEnabledService<BibliographicReference, BibliographicReferenceValueObject>, BibliographicReferenceService

@Service
@ParametersAreNonnullByDefault
public class BibliographicReferenceServiceImpl
extends AbstractVoEnabledService<BibliographicReference, BibliographicReferenceValueObject>
implements BibliographicReferenceService, org.springframework.beans.factory.InitializingBean

Implementation of BibliographicReferenceService.

As of the Phase 3 strangler-fig decomposition, the read cluster (browse, findByExternalId variants, findVOByExternalId, count*, getRelatedExperiments, listAll, search, thaw) lives on BibliographicReferenceReadService; this facade delegates to that read service. Write-side methods (refresh + the inherited BaseService mutators) stay here.

Note: This is only in Core because it uses SearchService (via the read service), but it could be refactored.

Author:

keshav

See Also:

• BibliographicReferenceService
• BibliographicReferenceReadService

Field Summary

Fields inherited from class AbstractService

log

Constructor Summary

Constructors

Constructor	Description
BibliographicReferenceServiceImpl(BibliographicReferenceDao bibliographicReferenceDao)

Method Summary

Modifier and Type	Method	Description
void	afterPropertiesSet()
List<BibliographicReference>	browse(int start, int limit)
List<BibliographicReference>	browse(int start, int limit, String orderField, boolean descending)
long	countDistinctWithRelatedExperiments()
long	countWithRelatedExperiments()
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)
BibliographicReference	findOrCreate(BibliographicReference ref)	Find an existing BibliographicReference by its pubAccession, or create a new one.
BibliographicReference	findOrCreateByDoi(String doi)	Resolve a DOI to a persistent BibliographicReference, fetching it when necessary.
BibliographicReference	findOrCreateByPubMedId(String pubMedId)	Resolve a PubMed id to a persistent BibliographicReference, fetching it from PubMed and persisting it when it is not already in the system.
BibliographicReferenceValueObject	findVOByExternalId(String id)	Get a reference by the unqualified external id.
Map<BibliographicReference, Set<ExpressionExperimentIdAndShortName>>	getRelatedExperiments(int offset, int limit)	Return all the BibRefs that are linked to ExpressionExperiments.
Map<BibliographicReference, Collection<ExpressionExperiment>>	getRelatedExperiments(Collection<BibliographicReference> records)
Collection<Long>	listAll()
List<BibliographicReferenceValueObject>	loadAllValueObjects()	Loads value objects representing all the entities of specific type.
BibliographicReferenceValueObject	loadValueObject(BibliographicReference entity)
BibliographicReference	refresh(String pubMedId)
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 AbstractVoEnabledService

loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from class AbstractService

countAll, create, create, ensureInSession, ensureInSession, find, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from class Object

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

Methods inherited from interface BaseReadOnlyService

countAll, findOrFail, getElementClass, load, load, loadAll, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, loadOrFail, streamAll, streamAll

Methods inherited from interface BaseVoEnabledService

loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Methods inherited from interface BibliographicReferenceService

create, create, find, remove, remove, save, save, update, update

Constructor Details

BibliographicReferenceServiceImpl

@Autowired
public BibliographicReferenceServiceImpl(BibliographicReferenceDao bibliographicReferenceDao)

Method Details

afterPropertiesSet

public void afterPropertiesSet()
                        throws Exception

Specified by:

afterPropertiesSet in interface org.springframework.beans.factory.InitializingBean

Throws:

Exception

findOrCreate

@Transactional
public BibliographicReference findOrCreate(BibliographicReference ref)

Find an existing BibliographicReference by its pubAccession, or create a new one. The embedded ExternalDatabase on the pubAccession is resolved (find-or-create by name) before delegating to BaseDao.findOrCreate(T) so the caller can pass a transient XDB instance without violating the cascade="none" on DatabaseEntry.externalDatabase.

Phase 3 persister-retirement: replaces persisterHelper.persist(BibRef) (which routed through CommonPersister.persistBibliographicReference).

Specified by:

findOrCreate in interface BaseImmutableService<BibliographicReference>

Specified by:

findOrCreate in interface BibliographicReferenceService

Overrides:

findOrCreate in class AbstractService<BibliographicReference>

See Also:

• BaseDao.findOrCreate(Identifiable)

findOrCreateByPubMedId

@Transactional
public BibliographicReference findOrCreateByPubMedId(String pubMedId)

Description copied from interface: BibliographicReferenceService

Resolve a PubMed id to a persistent BibliographicReference, fetching it from PubMed and persisting it when it is not already in the system.

Encapsulates the find-or-fetch dance that UpdatePubMedCli and the retired gemma-web ExpressionExperimentController.updatePubMed both open-coded: look up by external id first, otherwise retrieve the record over the wire and BibliographicReferenceService.findOrCreate(BibliographicReference) it.

Specified by:

findOrCreateByPubMedId in interface BibliographicReferenceService

Parameters:

pubMedId - a PubMed id (must be non-blank).

Returns:

the persistent reference for pubMedId.

findOrCreateByDoi

@Transactional
public BibliographicReference findOrCreateByDoi(String doi)

Description copied from interface: BibliographicReferenceService

Resolve a DOI to a persistent BibliographicReference, fetching it when necessary.

Resolution order: (1) an existing DOI-keyed reference already in Gemma; (2) PubMed-by-DOI (covers DOIs NCBI indexes — yields the richer PubMed record); (3) CrossRef by DOI (covers the rest, notably bioRxiv / medRxiv preprints PubMed does not carry). This is what lets a preprint be attached to an experiment instead of being noted in a free-text comment.

Specified by:

findOrCreateByDoi in interface BibliographicReferenceService

Parameters:

doi - a DOI in any common form (10.x/…, https://doi.org/…, doi:…); normalized internally.

Returns:

the persistent reference for doi.

loadValueObject

@Transactional(readOnly=true)
public BibliographicReferenceValueObject loadValueObject(BibliographicReference entity)

Specified by:

loadValueObject in interface BaseVoEnabledService<BibliographicReference, BibliographicReferenceValueObject>

Overrides:

loadValueObject in class AbstractVoEnabledService<BibliographicReference, BibliographicReferenceValueObject>

See Also:

• BaseVoEnabledDao.loadValueObject(Identifiable)

loadAllValueObjects

@Transactional(readOnly=true)
public List<BibliographicReferenceValueObject> loadAllValueObjects()

Description copied from interface: BaseVoEnabledService

Loads value objects representing all the entities of specific type.

Specified by:

loadAllValueObjects in interface BaseVoEnabledService<BibliographicReference, BibliographicReferenceValueObject>

Overrides:

loadAllValueObjects in class AbstractVoEnabledService<BibliographicReference, BibliographicReferenceValueObject>

Returns:

a collection of value objects

browse

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

Specified by:

browse in interface BibliographicReferenceService

browse

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

Specified by:

browse in interface BibliographicReferenceService

findByExternalId

public BibliographicReference findByExternalId(DatabaseEntry accession)

Specified by:

findByExternalId in interface BibliographicReferenceService

findByExternalId

public BibliographicReference findByExternalId(String id)

Description copied from interface: BibliographicReferenceService

Get a reference by the unqualified external id.

Specified by:

findByExternalId in interface BibliographicReferenceService

Parameters:

id - id

Returns:

reference

findByExternalId

public BibliographicReference findByExternalId(String id,
 String databaseName)

Description copied from interface: BibliographicReferenceService

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

Specified by:

findByExternalId in interface BibliographicReferenceService

Parameters:

id - id

databaseName - db name

Returns:

reference

findVOByExternalId

public BibliographicReferenceValueObject findVOByExternalId(String id)

Description copied from interface: BibliographicReferenceService

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

Specified by:

findVOByExternalId in interface BibliographicReferenceService

Parameters:

id - id

Returns:

reference VO

countDistinctWithRelatedExperiments

public long countDistinctWithRelatedExperiments()

Specified by:

countDistinctWithRelatedExperiments in interface BibliographicReferenceService

countWithRelatedExperiments

public long countWithRelatedExperiments()

Specified by:

countWithRelatedExperiments in interface BibliographicReferenceService

getRelatedExperiments

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

Description copied from interface: BibliographicReferenceService

Return all the BibRefs that are linked to ExpressionExperiments.

Specified by:

getRelatedExperiments in interface BibliographicReferenceService

Returns:

all references with EEs

getRelatedExperiments

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

Specified by:

getRelatedExperiments in interface BibliographicReferenceService

listAll

public Collection<Long> listAll()

Specified by:

listAll in interface BibliographicReferenceService

Returns:

all the IDs of bibliographic references in the system.

refresh

@Transactional
public BibliographicReference refresh(String pubMedId)

Specified by:

refresh in interface BibliographicReferenceService

search

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

Specified by:

search in interface BibliographicReferenceService

Throws:

SearchException

search

public List<BibliographicReferenceValueObject> search(String query)
                                               throws SearchException

Specified by:

search in interface BibliographicReferenceService

Throws:

SearchException

thaw

public BibliographicReference thaw(BibliographicReference bibliographicReference)

Specified by:

thaw in interface BibliographicReferenceService

thaw

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

Specified by:

thaw in interface BibliographicReferenceService