Class BibliographicReferenceServiceTest

java.lang.Object

ubic.gemma.core.util.test.BaseTest5

ubic.gemma.core.util.test.BaseIntegrationTest5

ubic.gemma.core.util.test.BaseSpringContextTest5

ubic.gemma.persistence.service.common.description.BibliographicReferenceServiceTest

public class BibliographicReferenceServiceTest
extends BaseSpringContextTest5

This class tests the bibliographic reference data access object. It is also used to test some of the Hibernate features.

Author:

pavlidis

Field Summary

Fields inherited from class BaseSpringContextTest5

arrayDesignPersister, externalDatabaseService, log, persisterHelper, taxonService, testHelper

Constructor Summary

Constructors

Constructor	Description
BibliographicReferenceServiceTest()

Method Summary

Modifier and Type	Method	Description
void	setUp()
final void	testfind()
final void	testFindByExternalIdentString()
final void	testFindByExternalIdToleratesDuplicates()	Prod has duplicate BibliographicReference rows for the same PubMed accession; the external-id lookups must return one (the lowest-id) rather than throwing NonUniqueResultException (which surfaced as a 500 on PUT /datasets/{id}/publications), and find must too so findOrCreate doesn't add yet another duplicate.
void	testGetRelatedExperiments()

Methods inherited from class BaseSpringContextTest5

addTestAnalyses, countRowsInTable, deleteFromTables, getJdbcTemplate, getNewTestPersistentCompleteExpressionExperiment, getTaxon, getTestNonPersistentBioSequence, getTestPersistentArrayDesign, getTestPersistentArrayDesign, getTestPersistentArrayDesign, getTestPersistentBasicExpressionExperiment, getTestPersistentBasicExpressionExperiment, getTestPersistentBibliographicReference, getTestPersistentBioAssay, getTestPersistentBioAssay, getTestPersistentBioMaterial, getTestPersistentBioMaterial, getTestPersistentBioSequence, getTestPersistentBioSequence, getTestPersistentBioSequence2GeneProducts, getTestPersistentBlatResult, getTestPersistentBlatResult, getTestPersistentCompleteExpressionExperiment, getTestPersistentCompleteExpressionExperimentWithSequences, getTestPersistentCompleteExpressionExperimentWithSequences, getTestPersistentContact, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentDatabaseEntry, getTestPersistentExpressionExperiment, getTestPersistentExpressionExperiment, getTestPersistentGene, getTestPersistentGene, getTestPersistentGeneProduct, getTestPersistentQuantitationType, randomName, resetTestCollectionSize, runAsAdmin, runAsAgent, runAsAnonymous, runAsUser, runAsUser, setTestCollectionSize

Methods inherited from class BaseIntegrationTest5

setUpAuthentication, tearDownSecurityContext

Methods inherited from class Object

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

Constructor Details

BibliographicReferenceServiceTest

public BibliographicReferenceServiceTest()

Method Details

setUp

@BeforeEach
public void setUp()
           throws Exception

Throws:

Exception

testfind

@Test
public final void testfind()

testFindByExternalIdentString

@Test
public final void testFindByExternalIdentString()

testFindByExternalIdToleratesDuplicates

@Test
public final void testFindByExternalIdToleratesDuplicates()

Prod has duplicate BibliographicReference rows for the same PubMed accession; the external-id lookups must return one (the lowest-id) rather than throwing NonUniqueResultException (which surfaced as a 500 on PUT /datasets/{id}/publications), and find must too so findOrCreate doesn't add yet another duplicate.

testGetRelatedExperiments

@Test
public void testGetRelatedExperiments()