Class CompositeSequenceGeneMapperServiceFastTest

java.lang.Object

ubic.gemma.core.util.test.BaseTest5

ubic.gemma.core.util.test.BaseIntegrationTest5

ubic.gemma.core.util.test.BaseSpringContextTest5

ubic.gemma.core.loader.expression.geo.AbstractGeoServiceTest5

ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceFastTest

@ContextConfiguration(classes=ubic.gemma.core.analysis.service.CompositeSequenceGeneMapperServiceFastTest.FastGoldenPathConfig.class,
                      inheritLocations=false)
@Tag("slow")
public class CompositeSequenceGeneMapperServiceFastTest
extends AbstractGeoServiceTest5

Fast mock variant of CompositeSequenceGeneMapperServiceTest.

Mirrors the assertions of the @Tag("goldenPath") truth-source test, but replaces the live UCSC GoldenPath lookup with a Mockito stub backed by a JSON fixture captured from hg19 (see data/loader/genome/goldenpath/gpl96-hg19-fixture.json and GoldenPathFixtureRecorder).

The seam is the GoldenPathSequenceAnalysisFactory bean (commit 317ea9c785). The inner CompositeSequenceGeneMapperServiceFastTest.FastGoldenPathConfig registers a @Primary factory that returns a Mockito-mocked GoldenPathSequenceAnalysis whose findAssociations responses come from the fixture.

Field Summary

Fields inherited from class BaseSpringContextTest5

arrayDesignPersister, externalDatabaseService, log, persisterHelper, taxonService, testHelper

Constructor Summary

Constructors

Constructor	Description
CompositeSequenceGeneMapperServiceFastTest()

Method Summary

Modifier and Type	Method	Description
void	cleanup()
void	setUp()
void	testGetCompositeSequencesByGeneId()
void	testGetGenesForCompositeSequence()

Methods inherited from class AbstractGeoServiceTest5

getTestFileBasePath, getTestFileBasePath

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

CompositeSequenceGeneMapperServiceFastTest

public CompositeSequenceGeneMapperServiceFastTest()

Method Details

cleanup

@AfterEach
public void cleanup()

setUp

@BeforeEach
public void setUp()
           throws Exception

Throws:

Exception

testGetCompositeSequencesByGeneId

@Test
public void testGetCompositeSequencesByGeneId()

testGetGenesForCompositeSequence

@Test
public void testGetGenesForCompositeSequence()