Class SampleCoexpressionAnalysisServiceTest

java.lang.Object

ubic.gemma.core.util.test.BaseTest5

ubic.gemma.core.util.test.BaseIntegrationTest5

ubic.gemma.core.util.test.BaseSpringContextTest5

ubic.gemma.core.analysis.preprocess.SampleCoexpressionAnalysisServiceTest

public class SampleCoexpressionAnalysisServiceTest
extends BaseSpringContextTest5

Author:

paul

Field Summary

Fields inherited from class BaseSpringContextTest5

arrayDesignPersister, externalDatabaseService, log, persisterHelper, taxonService, testHelper

Constructor Summary

Constructors

Constructor	Description
SampleCoexpressionAnalysisServiceTest()

Method Summary

Modifier and Type	Method	Description
void	test()
void	testWithAFlaggedOutlier()	A flagged outlier sends prepare down the unmasked rebuild, whose dimension is loaded in a different session from the stored vectors'.

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

SampleCoexpressionAnalysisServiceTest

public SampleCoexpressionAnalysisServiceTest()

Method Details

test

@Test
@Tag("slow")
public void test()
          throws Exception

Throws:

Exception

testWithAFlaggedOutlier

@Test
public void testWithAFlaggedOutlier()
                             throws Exception

A flagged outlier sends prepare down the unmasked rebuild, whose dimension is loaded in a different session from the stored vectors'. compute then sorts that dimension by experimental design, reading each factor value's experimental factor.

Not slow-tagged: it takes seconds, and while test() was the only test here the default run missed a LazyInitializationException on this path that failed corrMat on GSE260875.

Throws:

Exception