Class TwoChannelExpressionDataDoubleMatrixTest

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.preprocess.TwoChannelExpressionDataDoubleMatrixTest

@ExtendWith(NetworkAvailableExtension.class)
public class TwoChannelExpressionDataDoubleMatrixTest
extends AbstractGeoServiceTest5

Author:

keshav, pavlidis

Field Summary

Fields inherited from class BaseSpringContextTest5

arrayDesignPersister, externalDatabaseService, log, persisterHelper, taxonService, testHelper

Constructor Summary

Constructors

Constructor	Description
TwoChannelExpressionDataDoubleMatrixTest()

Method Summary

Modifier and Type	Method	Description
void	setUp()
void	tearDown()
void	testConstructExpressionDataDoubleMatrix()	Tests the construction of an ExpressionDataDoubleMatrix
void	testConstructExpressionDataDoubleMatrixWithGeoValues()	This is a self-contained test.
void	testMatrixConversion()

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

TwoChannelExpressionDataDoubleMatrixTest

public TwoChannelExpressionDataDoubleMatrixTest()

Method Details

setUp

@BeforeEach
public void setUp()
           throws Exception

Throws:

Exception

tearDown

@AfterEach
public void tearDown()

testConstructExpressionDataDoubleMatrix

@Test
public void testConstructExpressionDataDoubleMatrix()

Tests the construction of an ExpressionDataDoubleMatrix

testConstructExpressionDataDoubleMatrixWithGeoValues

@Test
public void testConstructExpressionDataDoubleMatrixWithGeoValues()

This is a self-contained test. That is, it does not depend on the setup in onSetUpInTransaction}. It tests creating an ExpressionDataDoubleMatrix using real values from the Gene Expression Omnibus (GEO). That is, we have obtained information from GSE994. The probe sets used are 218120_s_at and 121_at, and the samples used are GSM15697 and GSM15744. Specifically, we the Gemma objects that correspond to the GEO objects are: DesignElement 1 = 218120_s_at, DesignElement 2 = 121_at BioAssay 1 = "Current Smoker 73", BioAssay 2 = "Former Smoker 34" BioMaterial 1 = "GSM15697", BioMaterial 2 = "GSM15744" BioAssayDimension = "GSM15697, GSM15744" (the names of all the biomaterials).

testMatrixConversion

@Test
@Tag("slow")
@NetworkAvailable(url="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi")
public void testMatrixConversion()
                          throws Exception

Throws:

Exception