java.lang.Object
- org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests
- - ubic.gemma.core.util.test.BaseTest
  - - ubic.gemma.core.util.test.BaseIntegrationTest
    - - ubic.gemma.core.util.test.BaseSpringContextTest

All Implemented Interfaces:

org.springframework.beans.factory.Aware, org.springframework.context.ApplicationContextAware

Direct Known Subclasses:

AbstractArrayDesignProcessingTest, AbstractGeoServiceTest, AclAdviceTest, AclAuthorizationTest, AclCollectionBeforeTest, AclCriteriaUtilsTest, AclQueryUtilsTest, ArrayDesignMergeServiceTest, ArrayDesignReportServiceTest, ArrayDesignServiceTest, AuditAdviceTest, AuditEventServiceTest, AuditTrailDaoTest, AuditTrailServiceImplTest, BaseSpringWebTest, BibliographicReferenceServiceImplTest, BibliographicReferenceServiceTest, BioAssayServiceTest, BioMaterialServiceTest, BioSequencePersistTest, BlacklistedEntityServiceTest, BlacklistTest, BlatAssociationServiceTest, BlatResultServiceTest, CharacteristicServiceTest, CompositeSequenceServiceTest, CuratableValueObjectTest, DatabaseEntryDaoImplTest, DifferentialExpressionAnalysisServiceTest, ExecutingTaskTest, ExperimentalDesignImportDuplicateValueTest, ExperimentalDesignImporterTest, ExpressionAnalysisResultSetServiceTest, ExpressionExperimentDeleteTest, ExpressionExperimentReportServiceTest, ExpressionExperimentServiceIntegrationTest, ExpressionExperimentSetServiceTest, ExpressionExperimentSetValueObjectHelperTest, ExpressionExperimentSubSetServiceTest, ExternalDatabaseServiceTest, ExternalFileGeneLoaderServiceTest, FactorValueServiceIntegrationTest, FilteringVoEnabledServiceIntegrationTest, Gene2GeneCoexpressionServiceTest, GeneDiffExMetaAnalysisServiceTest, GeneMultifunctionalityPopulationServiceTest, GeneSearchTest, GeneServiceTest, GeneSetServiceTest, GeneSetValueObjectHelperTest, GenomePersisterTest, GeoBrowserServiceTest, GeoConverterTest, LinkAnalysisServiceTest, ManualAuthenticationProcessingTest, NCBIGene2GOAssociationParserTest, NCBIGeneLoadingTest, PersisterTest, PrincipalTest, RetryTest, SampleCoexpressionAnalysisServiceTest, SearchServiceIntegrationTest, SecureValueObjectAuthorizationTest, SecurityServiceTest, SimpleExpressionDataLoaderServiceTest, SplitExperimentTest, StrictBeanDefinitionValidatorTest, TableMaintenanceUtilIntegrationTest, TaxonLoaderTest, TaxonServiceImplTest, TaxonUtilsTest, TwoChannelMissingValuesTest, TwoWayAnovaWithInteractionTest2, UserGroupServiceTest, WhatsNewServiceTest
```
@Deprecated
public abstract class BaseSpringContextTest
extends BaseIntegrationTest
```
Deprecated.
favour the simpler BaseIntegrationTest for new tests

Add a few utilities on top of BaseIntegrationTest.

Author:

pavlidis

Field Summary

Fields
Modifier and Type	Field	Description
`protected ubic.gemma.persistence.service.common.description.ExternalDatabaseService`	`externalDatabaseService`	Deprecated.
`protected org.apache.commons.logging.Log`	`log`	Deprecated.
`protected ubic.gemma.persistence.persister.PersisterHelper`	`persisterHelper`	Deprecated.
`org.mockito.junit.MockitoRule`	`rule`	Deprecated. This allows the usage of `Mock` annotation to create mocks.
`protected ubic.gemma.persistence.service.genome.taxon.TaxonService`	`taxonService`	Deprecated.
`protected PersistentDummyObjectHelper`	`testHelper`	Deprecated.

Fields inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests
applicationContext, logger

Constructor Summary

Constructors
Constructor Description

BaseSpringContextTest()
Deprecated.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`protected Collection<ubic.gemma.model.analysis.Analysis>`	`addTestAnalyses(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)`	Deprecated. Create test `Analysis` for the given expression experiment.
`protected int`	`countRowsInTable(String tableName)`	Deprecated. Count the rows in the given table.
`protected int`	`deleteFromTables(String... names)`	Deprecated. Convenience method for deleting all rows from the specified tables.
`protected org.springframework.jdbc.core.JdbcTemplate`	`getJdbcTemplate()`	Deprecated.
`protected ubic.gemma.model.expression.experiment.ExpressionExperiment`	`getNewTestPersistentCompleteExpressionExperiment()`	Deprecated.
`ubic.gemma.model.genome.Taxon`	`getTaxon(String commonName)`	Deprecated. Obtain a taxon by its common name.
`protected ubic.gemma.model.genome.biosequence.BioSequence`	`getTestNonPersistentBioSequence(ubic.gemma.model.genome.Taxon t)`	Deprecated.
`protected ubic.gemma.model.expression.arrayDesign.ArrayDesign`	`getTestPersistentArrayDesign(int numCompositeSequences, boolean randomNames)`	Deprecated. Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
`protected ubic.gemma.model.expression.arrayDesign.ArrayDesign`	`getTestPersistentArrayDesign(int numCompositeSequences, boolean randomNames, boolean doSequence, boolean readOnly)`	Deprecated. Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
`protected ubic.gemma.model.expression.arrayDesign.ArrayDesign`	`getTestPersistentArrayDesign(List<String> probeNames, ubic.gemma.model.genome.Taxon taxon)`	Deprecated. Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
`protected ubic.gemma.model.expression.experiment.ExpressionExperiment`	`getTestPersistentBasicExpressionExperiment()`	Deprecated.
`protected ubic.gemma.model.expression.experiment.ExpressionExperiment`	`getTestPersistentBasicExpressionExperiment(ubic.gemma.model.expression.arrayDesign.ArrayDesign arrayDesign)`	Deprecated.
`protected ubic.gemma.model.common.description.BibliographicReference`	`getTestPersistentBibliographicReference(String accession)`	Deprecated.
`protected ubic.gemma.model.expression.bioAssay.BioAssay`	`getTestPersistentBioAssay(ubic.gemma.model.expression.arrayDesign.ArrayDesign ad)`	Deprecated. Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
`protected ubic.gemma.model.expression.bioAssay.BioAssay`	`getTestPersistentBioAssay(ubic.gemma.model.expression.arrayDesign.ArrayDesign ad, ubic.gemma.model.expression.biomaterial.BioMaterial bm)`	Deprecated. Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
`protected ubic.gemma.model.expression.biomaterial.BioMaterial`	`getTestPersistentBioMaterial()`	Deprecated.
`protected ubic.gemma.model.expression.biomaterial.BioMaterial`	`getTestPersistentBioMaterial(ubic.gemma.model.genome.Taxon tax)`	Deprecated.
`protected ubic.gemma.model.genome.biosequence.BioSequence`	`getTestPersistentBioSequence()`	Deprecated.
`protected ubic.gemma.model.genome.biosequence.BioSequence`	`getTestPersistentBioSequence(ubic.gemma.model.genome.Taxon t)`	Deprecated.
`Set<ubic.gemma.model.association.BioSequence2GeneProduct>`	`getTestPersistentBioSequence2GeneProducts(ubic.gemma.model.genome.biosequence.BioSequence bioSequence)`	Deprecated.
`protected ubic.gemma.model.genome.sequenceAnalysis.BlatResult`	`getTestPersistentBlatResult(ubic.gemma.model.genome.biosequence.BioSequence querySequence)`	Deprecated.
`protected ubic.gemma.model.genome.sequenceAnalysis.BlatResult`	`getTestPersistentBlatResult(ubic.gemma.model.genome.biosequence.BioSequence querySequence, ubic.gemma.model.genome.Taxon taxon)`	Deprecated.
`protected ubic.gemma.model.expression.experiment.ExpressionExperiment`	`getTestPersistentCompleteExpressionExperiment(boolean readOnly)`	Deprecated. Convenience method to get a (fairly) complete randomly generated persisted expression experiment.
`protected ubic.gemma.model.expression.experiment.ExpressionExperiment`	`getTestPersistentCompleteExpressionExperimentWithSequences()`	Deprecated. Convenience method to get a (fairly) complete randomly generated persisted expression experiment.
`protected ubic.gemma.model.expression.experiment.ExpressionExperiment`	`getTestPersistentCompleteExpressionExperimentWithSequences(ubic.gemma.model.expression.experiment.ExpressionExperiment prototype)`	Deprecated.
`protected ubic.gemma.model.common.auditAndSecurity.Contact`	`getTestPersistentContact()`	Deprecated. Convenience method to provide a Contact that can be used to fill non-nullable associations in test objects.
`protected ubic.gemma.model.common.description.DatabaseEntry`	`getTestPersistentDatabaseEntry()`	Deprecated. Get a database entry from a fictitious database.
`protected ubic.gemma.model.common.description.DatabaseEntry`	`getTestPersistentDatabaseEntry(String ed)`	Deprecated.
`protected ubic.gemma.model.common.description.DatabaseEntry`	`getTestPersistentDatabaseEntry(String accession, String ed)`	Deprecated.
`protected ubic.gemma.model.common.description.DatabaseEntry`	`getTestPersistentDatabaseEntry(String accession, ubic.gemma.model.common.description.ExternalDatabase ed)`	Deprecated. Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
`protected ubic.gemma.model.common.description.DatabaseEntry`	`getTestPersistentDatabaseEntry(ubic.gemma.model.common.description.ExternalDatabase ed)`	Deprecated. Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
`protected ubic.gemma.model.expression.experiment.ExpressionExperiment`	`getTestPersistentExpressionExperiment()`	Deprecated. Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
`protected ubic.gemma.model.expression.experiment.ExpressionExperiment`	`getTestPersistentExpressionExperiment(ubic.gemma.model.genome.Taxon taxon)`	Deprecated. Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
`protected ubic.gemma.model.genome.Gene`	`getTestPersistentGene()`	Deprecated.
`ubic.gemma.model.genome.Gene`	`getTestPersistentGene(ubic.gemma.model.genome.Taxon taxon)`	Deprecated.
`protected ubic.gemma.model.genome.gene.GeneProduct`	`getTestPersistentGeneProduct(ubic.gemma.model.genome.Gene gene)`	Deprecated.
`protected ubic.gemma.model.common.quantitationtype.QuantitationType`	`getTestPersistentQuantitationType()`	Deprecated. Convenience method to provide a QuantitationType that can be used to fill non-nullable associations in test objects.
`String`	`randomName()`	Deprecated. Convenience shortcut for RandomStringUtils.randomAlphabetic( 10 ) (or something similar to that)
`protected void`	`resetTestCollectionSize()`	Deprecated. Restore to default.
`protected void`	`runAsAdmin()`	Deprecated.
`protected void`	`runAsAgent()`	Deprecated.
`protected void`	`runAsAnonymous()`	Deprecated.
`protected void`	`runAsUser(String userName)`	Deprecated.
`protected void`	`runAsUser(String userName, boolean createIfMissing)`	Deprecated.
`protected void`	`setTestCollectionSize(int size)`	Deprecated. Change the number of elements created in collections (basically controls the size of test data sets).

Methods inherited from class ubic.gemma.core.util.test.BaseIntegrationTest
setUpAuthentication, tearDownSecurityContext

Methods inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests
setApplicationContext

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - log
```
protected final org.apache.commons.logging.Log log
```
    Deprecated.
  - rule
```
public org.mockito.junit.MockitoRule rule
```
    Deprecated.
    
    This allows the usage of Mock annotation to create mocks.
  - externalDatabaseService
```
@Autowired
protected ubic.gemma.persistence.service.common.description.ExternalDatabaseService externalDatabaseService
```
    Deprecated.
  - persisterHelper
```
@Autowired
protected ubic.gemma.persistence.persister.PersisterHelper persisterHelper
```
    Deprecated.
  - taxonService
```
@Autowired
protected ubic.gemma.persistence.service.genome.taxon.TaxonService taxonService
```
    Deprecated.
  - testHelper
```
@Autowired
protected PersistentDummyObjectHelper testHelper
```
    Deprecated.
- Constructor Detail
  - BaseSpringContextTest
```
public BaseSpringContextTest()
```
    Deprecated.
- Method Detail
  - getJdbcTemplate
```
protected org.springframework.jdbc.core.JdbcTemplate getJdbcTemplate()
```
    Deprecated.
  - getTaxon
```
public ubic.gemma.model.genome.Taxon getTaxon(String commonName)
```
    Deprecated.
    
    Obtain a taxon by its common name.
    See sql/init-data.sql for a list of available taxa to use in tests.
  - getTestPersistentGene
```
public ubic.gemma.model.genome.Gene getTestPersistentGene(ubic.gemma.model.genome.Taxon taxon)
```
    Deprecated.
  - getTestPersistentBioSequence2GeneProducts
```
public Set<ubic.gemma.model.association.BioSequence2GeneProduct> getTestPersistentBioSequence2GeneProducts(ubic.gemma.model.genome.biosequence.BioSequence bioSequence)
```
    Deprecated.
  - randomName
```
public String randomName()
```
    Deprecated.
    
    Convenience shortcut for RandomStringUtils.randomAlphabetic( 10 ) (or something similar to that)
    
    Returns:
    
    random alphabetic string
  - addTestAnalyses
```
protected Collection<ubic.gemma.model.analysis.Analysis> addTestAnalyses(ubic.gemma.model.expression.experiment.ExpressionExperiment ee)
```
    Deprecated.
    
    Create test Analysis for the given expression experiment.
    
    Parameters:
    
    ee - expression experiment to use for creating test analyses
    
    Returns:
    
    a collection of persisted analyses that were created
  - countRowsInTable
```
protected int countRowsInTable(String tableName)
```
    Deprecated.
    
    Count the rows in the given table.
    
    Parameters:
    
    tableName - table name to count rows in
    
    Returns:
    
    the number of rows in the table
  - deleteFromTables
```
protected int deleteFromTables(String... names)
```
    Deprecated.
    
    Convenience method for deleting all rows from the specified tables. Use with caution outside of a transaction!
    
    Parameters:
    
    names - the names of the tables from which to remove
    
    Returns:
    
    the total number of rows deleted from all specified tables
  - getTestPersistentGene
```
protected ubic.gemma.model.genome.Gene getTestPersistentGene()
```
    Deprecated.
  - getTestPersistentArrayDesign
```
protected ubic.gemma.model.expression.arrayDesign.ArrayDesign getTestPersistentArrayDesign(int numCompositeSequences,
                                                                                           boolean randomNames)
```
    Deprecated.
    
    Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects. The ArrayDesign is provided with some CompositeSequence DesignElements if desired. If composite sequences are created, they are each associated with a single generated Reporter.
    
    Parameters:
    
    numCompositeSequences - The number of CompositeSequences to populate the ArrayDesign with.
    
    randomNames - If true, probe names will be random strings; otherwise they will be 0_at....N_at
    
    Returns:
    
    array design
  - getTestPersistentArrayDesign
```
protected ubic.gemma.model.expression.arrayDesign.ArrayDesign getTestPersistentArrayDesign(int numCompositeSequences,
                                                                                           boolean randomNames,
                                                                                           boolean doSequence,
                                                                                           boolean readOnly)
```
    Deprecated.
    
    Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects. The ArrayDesign is provided with some CompositeSequence DesignElements if desired. If composite sequences are created, they are each associated with a single generated Reporter.
    
    Parameters:
    
    numCompositeSequences - The number of CompositeSequences to populate the ArrayDesign with.
    
    randomNames - If true, probe names will be random strings; otherwise they will be 0_at....N_at
    
    doSequence - add sequences to the array design that is created. Faster to avoid if you can.
    
    readOnly - read only
    
    Returns:
    
    array design
  - getTestPersistentArrayDesign
```
protected ubic.gemma.model.expression.arrayDesign.ArrayDesign getTestPersistentArrayDesign(List<String> probeNames,
                                                                                           ubic.gemma.model.genome.Taxon taxon)
```
    Deprecated.
    
    Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
    
    Parameters:
    
    probeNames - will be assigned to each CompositeSequence in the ArrayDesign
    
    taxon - of the ArrayDesign
    
    Returns:
    
    ArrayDesign with no TechnologyType
  - getTestPersistentBasicExpressionExperiment
```
protected ubic.gemma.model.expression.experiment.ExpressionExperiment getTestPersistentBasicExpressionExperiment()
```
    Deprecated.
    
    Returns:
    
    EE with no data; just bioassays, biomaterials, quantitation types and (minimal) array designs.
  - getTestPersistentBasicExpressionExperiment
```
protected ubic.gemma.model.expression.experiment.ExpressionExperiment getTestPersistentBasicExpressionExperiment(ubic.gemma.model.expression.arrayDesign.ArrayDesign arrayDesign)
```
    Deprecated.
    
    Parameters:
    
    arrayDesign - platform
    
    Returns:
    
    EE with no data; just bioassays, biomaterials, quantitation types and provided arrayDesign
  - getTestPersistentBibliographicReference
```
protected ubic.gemma.model.common.description.BibliographicReference getTestPersistentBibliographicReference(String accession)
```
    Deprecated.
  - getTestPersistentBioAssay
```
protected ubic.gemma.model.expression.bioAssay.BioAssay getTestPersistentBioAssay(ubic.gemma.model.expression.arrayDesign.ArrayDesign ad)
```
    Deprecated.
    
    Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
    
    Parameters:
    
    ad - paltform
    
    Returns:
    
    bio assay
  - getTestPersistentBioAssay
```
protected ubic.gemma.model.expression.bioAssay.BioAssay getTestPersistentBioAssay(ubic.gemma.model.expression.arrayDesign.ArrayDesign ad,
                                                                                  ubic.gemma.model.expression.biomaterial.BioMaterial bm)
```
    Deprecated.
    
    Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
    
    Parameters:
    
    ad - platform
    
    bm - material
    
    Returns:
    
    bio assay
  - getTestPersistentBioMaterial
```
protected ubic.gemma.model.expression.biomaterial.BioMaterial getTestPersistentBioMaterial()
```
    Deprecated.
  - getTestPersistentBioMaterial
```
protected ubic.gemma.model.expression.biomaterial.BioMaterial getTestPersistentBioMaterial(ubic.gemma.model.genome.Taxon tax)
```
    Deprecated.
  - getTestPersistentBioSequence
```
protected ubic.gemma.model.genome.biosequence.BioSequence getTestPersistentBioSequence()
```
    Deprecated.
  - getTestPersistentBioSequence
```
protected ubic.gemma.model.genome.biosequence.BioSequence getTestPersistentBioSequence(ubic.gemma.model.genome.Taxon t)
```
    Deprecated.
  - getTestNonPersistentBioSequence
```
protected ubic.gemma.model.genome.biosequence.BioSequence getTestNonPersistentBioSequence(ubic.gemma.model.genome.Taxon t)
```
    Deprecated.
  - getTestPersistentBlatResult
```
protected ubic.gemma.model.genome.sequenceAnalysis.BlatResult getTestPersistentBlatResult(ubic.gemma.model.genome.biosequence.BioSequence querySequence,
                                                                                          ubic.gemma.model.genome.Taxon taxon)
```
    Deprecated.
  - getTestPersistentBlatResult
```
protected ubic.gemma.model.genome.sequenceAnalysis.BlatResult getTestPersistentBlatResult(ubic.gemma.model.genome.biosequence.BioSequence querySequence)
```
    Deprecated.
  - getTestPersistentCompleteExpressionExperiment
```
protected ubic.gemma.model.expression.experiment.ExpressionExperiment getTestPersistentCompleteExpressionExperiment(boolean readOnly)
```
    Deprecated.
    
    Convenience method to get a (fairly) complete randomly generated persisted expression experiment.
    
    Parameters:
    
    readOnly - If the test only needs to read, a new data set might not be created.
    
    Returns:
    
    EE
  - getTestPersistentCompleteExpressionExperimentWithSequences
```
protected ubic.gemma.model.expression.experiment.ExpressionExperiment getTestPersistentCompleteExpressionExperimentWithSequences()
```
    Deprecated.
    
    Convenience method to get a (fairly) complete randomly generated persisted expression experiment.
    
    Returns:
    
    EE
  - getNewTestPersistentCompleteExpressionExperiment
```
protected ubic.gemma.model.expression.experiment.ExpressionExperiment getNewTestPersistentCompleteExpressionExperiment()
```
    Deprecated.
  - getTestPersistentCompleteExpressionExperimentWithSequences
```
protected ubic.gemma.model.expression.experiment.ExpressionExperiment getTestPersistentCompleteExpressionExperimentWithSequences(ubic.gemma.model.expression.experiment.ExpressionExperiment prototype)
```
    Deprecated.
    
    Parameters:
    
    prototype - used to choose the platform
    
    Returns:
    
    EE
  - getTestPersistentContact
```
protected ubic.gemma.model.common.auditAndSecurity.Contact getTestPersistentContact()
```
    Deprecated.
    
    Convenience method to provide a Contact that can be used to fill non-nullable associations in test objects.
    
    Returns:
    
    Contact
  - getTestPersistentDatabaseEntry
```
protected ubic.gemma.model.common.description.DatabaseEntry getTestPersistentDatabaseEntry()
```
    Deprecated.
    
    Get a database entry from a fictitious database.
    
    Returns:
    
    Db entry
  - getTestPersistentDatabaseEntry
```
protected ubic.gemma.model.common.description.DatabaseEntry getTestPersistentDatabaseEntry(ubic.gemma.model.common.description.ExternalDatabase ed)
```
    Deprecated.
    
    Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects. The accession and ExternalDatabase name are set to random strings.
    
    Parameters:
    
    ed - external Db
    
    Returns:
    
    Db entry
  - getTestPersistentDatabaseEntry
```
protected ubic.gemma.model.common.description.DatabaseEntry getTestPersistentDatabaseEntry(String ed)
```
    Deprecated.
  - getTestPersistentDatabaseEntry
```
protected ubic.gemma.model.common.description.DatabaseEntry getTestPersistentDatabaseEntry(String accession,
                                                                                           ubic.gemma.model.common.description.ExternalDatabase ed)
```
    Deprecated.
    
    Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects. The accession and ExternalDatabase name are set to random strings.
    
    Parameters:
    
    accession - accession
    
    ed - database
    
    Returns:
    
    Db entry
  - getTestPersistentDatabaseEntry
```
protected ubic.gemma.model.common.description.DatabaseEntry getTestPersistentDatabaseEntry(String accession,
                                                                                           String ed)
```
    Deprecated.
  - getTestPersistentExpressionExperiment
```
protected ubic.gemma.model.expression.experiment.ExpressionExperiment getTestPersistentExpressionExperiment()
```
    Deprecated.
    
    Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects. This implementation does NOT fill in associations of the created object.
    
    Returns:
    
    EE
  - getTestPersistentExpressionExperiment
```
protected ubic.gemma.model.expression.experiment.ExpressionExperiment getTestPersistentExpressionExperiment(ubic.gemma.model.genome.Taxon taxon)
```
    Deprecated.
    
    Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects. This implementation does NOT fill in associations of the created object except for the creation of persistent BioMaterials and BioAssays so that database taxon lookups for this experiment will work.
    
    Parameters:
    
    taxon - taxon
    
    Returns:
    
    EE
  - getTestPersistentGeneProduct
```
protected ubic.gemma.model.genome.gene.GeneProduct getTestPersistentGeneProduct(ubic.gemma.model.genome.Gene gene)
```
    Deprecated.
  - getTestPersistentQuantitationType
```
protected ubic.gemma.model.common.quantitationtype.QuantitationType getTestPersistentQuantitationType()
```
    Deprecated.
    
    Convenience method to provide a QuantitationType that can be used to fill non-nullable associations in test objects.
    
    Returns:
    
    QT
  - resetTestCollectionSize
```
protected void resetTestCollectionSize()
```
    Deprecated.
    
    Restore to default.
  - runAsAdmin
```
protected void runAsAdmin()
```
    Deprecated.
    
    See Also:
    
    TestAuthenticationUtils.runAsAdmin()
  - runAsAgent
```
protected void runAsAgent()
```
    Deprecated.
    
    See Also:
    
    TestAuthenticationUtils.runAsAgent()
  - runAsUser
```
protected void runAsUser(String userName)
```
    Deprecated.
    
    See Also:
    
    TestAuthenticationUtils.runAsUser(String, boolean)
  - runAsUser
```
protected void runAsUser(String userName,
                         boolean createIfMissing)
```
    Deprecated.
    
    See Also:
    
    TestAuthenticationUtils.runAsUser(String, boolean)
  - runAsAnonymous
```
protected void runAsAnonymous()
```
    Deprecated.
    
    See Also:
    
    TestAuthenticationUtils.runAsAnonymous()
  - setTestCollectionSize
```
protected void setTestCollectionSize(int size)
```
    Deprecated.
    
    Change the number of elements created in collections (basically controls the size of test data sets). This need not be called unless the test needs larger data sets. Call resetTestCollectionSize after you are done.
    
    Parameters:
    
    size - size

Class BaseSpringContextTest

Field Summary

Fields inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

Constructor Summary

Method Summary

Methods inherited from class ubic.gemma.core.util.test.BaseIntegrationTest

Methods inherited from class org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

Methods inherited from class java.lang.Object

Field Detail

log

rule

externalDatabaseService

persisterHelper

taxonService

testHelper

Constructor Detail

BaseSpringContextTest

Method Detail

getJdbcTemplate

getTaxon

getTestPersistentGene

getTestPersistentBioSequence2GeneProducts

randomName

addTestAnalyses

countRowsInTable

deleteFromTables

getTestPersistentGene

getTestPersistentArrayDesign

getTestPersistentArrayDesign

getTestPersistentArrayDesign

getTestPersistentBasicExpressionExperiment

getTestPersistentBasicExpressionExperiment

getTestPersistentBibliographicReference

getTestPersistentBioAssay

getTestPersistentBioAssay

getTestPersistentBioMaterial

getTestPersistentBioMaterial

getTestPersistentBioSequence

getTestPersistentBioSequence

getTestNonPersistentBioSequence

getTestPersistentBlatResult

getTestPersistentBlatResult

getTestPersistentCompleteExpressionExperiment

getTestPersistentCompleteExpressionExperimentWithSequences

getNewTestPersistentCompleteExpressionExperiment

getTestPersistentCompleteExpressionExperimentWithSequences

getTestPersistentContact

getTestPersistentDatabaseEntry

getTestPersistentDatabaseEntry

getTestPersistentDatabaseEntry

getTestPersistentDatabaseEntry

getTestPersistentDatabaseEntry

getTestPersistentExpressionExperiment

getTestPersistentExpressionExperiment

getTestPersistentGeneProduct

getTestPersistentQuantitationType

resetTestCollectionSize

runAsAdmin

runAsAgent

runAsUser

runAsUser

runAsAnonymous

setTestCollectionSize